Daily Papers

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

Several recent advances in AI systems (e.g., Tree-of-Thoughts and Program-Aided Language Models) solve problems by providing a "scaffolding" program that structures multiple calls to language models to generate better outputs. A scaffolding program is written in a programming language such as Python. In this work, we use a language-model-infused scaffolding program to improve itself. We start with a seed "improver" that improves an input program according to a given utility function by querying a language model several times and returning the best solution. We then run this seed improver to improve itself. Across a small set of downstream tasks, the resulting improved improver generates programs with significantly better performance than its seed improver. Afterward, we analyze the variety of self-improvement strategies proposed by the language model, including beam search, genetic algorithms, and simulated annealing. Since the language models themselves are not altered, this is not full recursive self-improvement. Nonetheless, it demonstrates that a modern language model, GPT-4 in our proof-of-concept experiments, is capable of writing code that can call itself to improve itself. We critically consider concerns around the development of self-improving technologies and evaluate the frequency with which the generated code bypasses a sandbox.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Training multiple tasks jointly in one deep network yields reduced latency during inference and better performance over the single-task counterpart by sharing certain layers of a network. However, over-sharing a network could erroneously enforce over-generalization, causing negative knowledge transfer across tasks. Prior works rely on human intuition or pre-computed task relatedness scores for ad hoc branching structures. They provide sub-optimal end results and often require huge efforts for the trial-and-error process. In this work, we present an automated multi-task learning algorithm that learns where to share or branch within a network, designing an effective network topology that is directly optimized for multiple objectives across tasks. Specifically, we propose a novel tree-structured design space that casts a tree branching operation as a gumbel-softmax sampling procedure. This enables differentiable network splitting that is end-to-end trainable. We validate the proposed method on controlled synthetic data, CelebA, and Taskonomy.

We introduce Tree D-fusion, featuring the first collection of 600,000 environmentally aware, 3D simulation-ready tree models generated through Diffusion priors. Each reconstructed 3D tree model corresponds to an image from Google's Auto Arborist Dataset, comprising street view images and associated genus labels of trees across North America. Our method distills the scores of two tree-adapted diffusion models by utilizing text prompts to specify a tree genus, thus facilitating shape reconstruction. This process involves reconstructing a 3D tree envelope filled with point markers, which are subsequently utilized to estimate the tree's branching structure using the space colonization algorithm conditioned on a specified genus.

Given the generational gap in available hardware between lay practitioners and the most endowed institutions, LLMs are becoming increasingly inaccessible as they grow in size. Whilst many approaches have been proposed to compress LLMs to make their resource consumption manageable, these methods themselves tend to be resource intensive, putting them out of the reach of the very user groups they target. In this work, we explore the problem of structured pruning of LLMs using only forward passes. We seek to empower practitioners to prune models so large that their available hardware has just enough memory to run inference. We develop Bonsai, a gradient-free, perturbative pruning method capable of delivering small, fast, and accurate pruned models. We observe that Bonsai outputs pruned models that (i) outperform those generated by more expensive gradient-based structured pruning methods, and (ii) are twice as fast (with comparable accuracy) as those generated by semi-structured pruning methods requiring comparable resources as Bonsai. We also leverage Bonsai to produce a new sub-2B model using a single A6000 that yields state-of-the-art performance on 4/6 tasks on the Huggingface Open LLM leaderboard.

In this paper, we highlight a critical yet often overlooked factor in most 3D human tasks, namely modeling humans with complex garments. It is known that the parameterized formulation of SMPL is able to fit human skin; while complex garments, e.g., hand-held objects and loose-fitting garments, are difficult to get modeled within the unified framework, since their movements are usually decoupled with the human body. To enhance the capability of SMPL skeleton in response to this situation, we propose a modular growth strategy that enables the joint tree of the skeleton to expand adaptively. Specifically, our method, called ToMiE, consists of parent joints localization and external joints optimization. For parent joints localization, we employ a gradient-based approach guided by both LBS blending weights and motion kernels. Once the external joints are obtained, we proceed to optimize their transformations in SE(3) across different frames, enabling rendering and explicit animation. ToMiE manages to outperform other methods across various cases with garments, not only in rendering quality but also by offering free animation of grown joints, thereby enhancing the expressive ability of SMPL skeleton for a broader range of applications.

2D keypoints are commonly used as an additional cue to refine estimated 3D human meshes. Current methods optimize the pose and shape parameters with a reprojection loss on the provided 2D keypoints. Such an approach, while simple and intuitive, has limited effectiveness because the optimal solution is hard to find in ambiguous parameter space and may sacrifice depth. Additionally, divergent gradients from distal joints complicate and deviate the refinement of proximal joints in the kinematic chain. To address these, we introduce Kinematic-Tree Rotation (KITRO), a novel mesh refinement strategy that explicitly models depth and human kinematic-tree structure. KITRO treats refinement from a bone-wise perspective. Unlike previous methods which perform gradient-based optimizations, our method calculates bone directions in closed form. By accounting for the 2D pose, bone length, and parent joint's depth, the calculation results in two possible directions for each child joint. We then use a decision tree to trace binary choices for all bones along the human skeleton's kinematic-tree to select the most probable hypothesis. Our experiments across various datasets and baseline models demonstrate that KITRO significantly improves 3D joint estimation accuracy and achieves an ideal 2D fit simultaneously. Our code available at: https://github.com/MartaYang/KITRO.

Effective instruction tuning is indispensable for optimizing code LLMs, aligning model behavior with user expectations and enhancing model performance in real-world applications. However, most existing methods focus on code snippets, which are limited to specific functionalities and rigid structures, restricting the complexity and diversity of the synthesized data. To address these limitations, we introduce a novel feature tree-based synthesis framework inspired by Abstract Syntax Trees (AST). Unlike AST, which captures syntactic structure of code, our framework models semantic relationships between code elements, enabling the generation of more nuanced and diverse data. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features. This process enables the identification of more complex patterns and relationships within the code. By sampling subtrees with controlled depth and breadth, our framework allows precise adjustments to the complexity of the generated code, supporting a wide range of tasks from simple function-level operations to intricate multi-file scenarios. We fine-tuned widely-used base models to create the EpiCoder series, achieving state-of-the-art performance at both the function and file levels across multiple benchmarks. Notably, empirical evidence indicates that our approach shows significant potential in synthesizing highly complex repository-level code data. Further analysis elucidates the merits of this approach by rigorously assessing data complexity and diversity through software engineering principles and LLM-as-a-judge method.

The development of deep learning software libraries enabled significant progress in the field by allowing users to focus on modeling, while letting the library to take care of the tedious and time-consuming task of optimizing execution for modern hardware accelerators. However, this has benefited only particular types of deep learning models, such as Transformers, whose primitives map easily to the vectorized computation. The models that explicitly account for structured objects, such as trees and segmentations, did not benefit equally because they require custom algorithms that are difficult to implement in a vectorized form. SynJax directly addresses this problem by providing an efficient vectorized implementation of inference algorithms for structured distributions covering alignment, tagging, segmentation, constituency trees and spanning trees. With SynJax we can build large-scale differentiable models that explicitly model structure in the data. The code is available at https://github.com/deepmind/synjax.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

3D characters are essential to modern creative industries, but making them animatable often demands extensive manual work in tasks like rigging and skinning. Existing automatic rigging tools face several limitations, including the necessity for manual annotations, rigid skeleton topologies, and limited generalization across diverse shapes and poses. An alternative approach is to generate animatable avatars pre-bound to a rigged template mesh. However, this method often lacks flexibility and is typically limited to realistic human shapes. To address these issues, we present Make-It-Animatable, a novel data-driven method to make any 3D humanoid model ready for character animation in less than one second, regardless of its shapes and poses. Our unified framework generates high-quality blend weights, bones, and pose transformations. By incorporating a particle-based shape autoencoder, our approach supports various 3D representations, including meshes and 3D Gaussian splats. Additionally, we employ a coarse-to-fine representation and a structure-aware modeling strategy to ensure both accuracy and robustness, even for characters with non-standard skeleton structures. We conducted extensive experiments to validate our framework's effectiveness. Compared to existing methods, our approach demonstrates significant improvements in both quality and speed.

Autonomous wire harness assembly requires robots to manipulate complex branched cables with high precision and reliability. A key challenge in automating this process is predicting how these flexible and branched structures behave under manipulation. Without accurate predictions, it is difficult for robots to reliably plan or execute assembly operations. While existing research has made progress in modeling single-threaded Deformable Linear Objects (DLOs), extending these approaches to Branched Deformable Linear Objects (BDLOs) presents fundamental challenges. The junction points in BDLOs create complex force interactions and strain propagation patterns that cannot be adequately captured by simply connecting multiple single-DLO models. To address these challenges, this paper presents Differentiable discrete branched Elastic rods for modeling Furcated DLOs in real-Time (DEFT), a novel framework that combines a differentiable physics-based model with a learning framework to: 1) accurately model BDLO dynamics, including dynamic propagation at junction points and grasping in the middle of a BDLO, 2) achieve efficient computation for real-time inference, and 3) enable planning to demonstrate dexterous BDLO manipulation. A comprehensive series of real-world experiments demonstrates DEFT's efficacy in terms of accuracy, computational speed, and generalizability compared to state-of-the-art alternatives. Project page:https://roahmlab.github.io/DEFT/.

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

Hyperbolic embeddings offer excellent quality with few dimensions when embedding hierarchical data structures like synonym or type hierarchies. Given a tree, we give a combinatorial construction that embeds the tree in hyperbolic space with arbitrarily low distortion without using optimization. On WordNet, our combinatorial embedding obtains a mean-average-precision of 0.989 with only two dimensions, while Nickel et al.'s recent construction obtains 0.87 using 200 dimensions. We provide upper and lower bounds that allow us to characterize the precision-dimensionality tradeoff inherent in any hyperbolic embedding. To embed general metric spaces, we propose a hyperbolic generalization of multidimensional scaling (h-MDS). We show how to perform exact recovery of hyperbolic points from distances, provide a perturbation analysis, and give a recovery result that allows us to reduce dimensionality. The h-MDS approach offers consistently low distortion even with few dimensions across several datasets. Finally, we extract lessons from the algorithms and theory above to design a PyTorch-based implementation that can handle incomplete information and is scalable.

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular low displacement rank) for integrating tensor fields defined on weighted trees. Several applications of the resulting fast tree-field integrators (FTFIs) are presented, including (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) Topological Transformers (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as three extra learnable parameters per Transformer layer, leading to 1.0-1.5%+ accuracy gains. Importantly, most of FTFIs are exact methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide 5.7-13x speedups. We also provide an extensive theoretical analysis of our methods.

Neural network pruning serves as a critical technique for enhancing the efficiency of deep learning models. Unlike unstructured pruning, which only sets specific parameters to zero, structured pruning eliminates entire channels, thus yielding direct computational and storage benefits. However, the diverse patterns for coupling parameters, such as residual connections and group convolutions, the diverse deep learning frameworks, and the various time stages at which pruning can be performed make existing pruning methods less adaptable to different architectures, frameworks, and pruning criteria. To address this, we introduce Structurally Prune Anything (SPA), a versatile structured pruning framework that can prune neural networks with any architecture, from any framework, and at any stage of training. SPA leverages a standardized computational graph and ONNX representation to prune diverse neural network architectures without the need for manual intervention. SPA employs a group-level importance estimation method, which groups dependent computational operators, estimates their importance, and prunes unimportant coupled channels. This enables the transfer of various existing pruning criteria into a structured group style. As a result, SPA supports pruning at any time, either before training, after training with fine-tuning, or after training without fine-tuning. In the context of the latter, we introduce Optimal Brain SPA (OBSPA), an algorithm that achieves state-of-the-art pruning results needing neither fine-tuning nor calibration data. In extensive experiments, SPA shows competitive to state-of-the-art pruning performance across various architectures, from popular frameworks, at different pruning times.

Prototype-based methods use interpretable representations to address the black-box nature of deep learning models, in contrast to post-hoc explanation methods that only approximate such models. We propose the Neural Prototype Tree (ProtoTree), an intrinsically interpretable deep learning method for fine-grained image recognition. ProtoTree combines prototype learning with decision trees, and thus results in a globally interpretable model by design. Additionally, ProtoTree can locally explain a single prediction by outlining a decision path through the tree. Each node in our binary tree contains a trainable prototypical part. The presence or absence of this learned prototype in an image determines the routing through a node. Decision making is therefore similar to human reasoning: Does the bird have a red throat? And an elongated beak? Then it's a hummingbird! We tune the accuracy-interpretability trade-off using ensemble methods, pruning and binarizing. We apply pruning without sacrificing accuracy, resulting in a small tree with only 8 learned prototypes along a path to classify a bird from 200 species. An ensemble of 5 ProtoTrees achieves competitive accuracy on the CUB-200- 2011 and Stanford Cars data sets. Code is available at https://github.com/M-Nauta/ProtoTree

We study inferring a tree-structured representation from a single image for object shading. Prior work typically uses the parametric or measured representation to model shading, which is neither interpretable nor easily editable. We propose using the shade tree representation, which combines basic shading nodes and compositing methods to factorize object surface shading. The shade tree representation enables novice users who are unfamiliar with the physical shading process to edit object shading in an efficient and intuitive manner. A main challenge in inferring the shade tree is that the inference problem involves both the discrete tree structure and the continuous parameters of the tree nodes. We propose a hybrid approach to address this issue. We introduce an auto-regressive inference model to generate a rough estimation of the tree structure and node parameters, and then we fine-tune the inferred shade tree through an optimization algorithm. We show experiments on synthetic images, captured reflectance, real images, and non-realistic vector drawings, allowing downstream applications such as material editing, vectorized shading, and relighting. Project website: https://chen-geng.com/inv-shade-trees

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

In deep learning, performance is strongly affected by the choice of architecture and hyperparameters. While there has been extensive work on automatic hyperparameter optimization for simple spaces, complex spaces such as the space of deep architectures remain largely unexplored. As a result, the choice of architecture is done manually by the human expert through a slow trial and error process guided mainly by intuition. In this paper we describe a framework for automatically designing and training deep models. We propose an extensible and modular language that allows the human expert to compactly represent complex search spaces over architectures and their hyperparameters. The resulting search spaces are tree-structured and therefore easy to traverse. Models can be automatically compiled to computational graphs once values for all hyperparameters have been chosen. We can leverage the structure of the search space to introduce different model search algorithms, such as random search, Monte Carlo tree search (MCTS), and sequential model-based optimization (SMBO). We present experiments comparing the different algorithms on CIFAR-10 and show that MCTS and SMBO outperform random search. In addition, these experiments show that our framework can be used effectively for model discovery, as it is possible to describe expressive search spaces and discover competitive models without much effort from the human expert. Code for our framework and experiments has been made publicly available.

The popularity of LLaMA (Touvron et al., 2023a;b) and other recently emerged moderate-sized large language models (LLMs) highlights the potential of building smaller yet powerful LLMs. Regardless, the cost of training such models from scratch on trillions of tokens remains high. In this work, we study structured pruning as an effective means to develop smaller LLMs from pre-trained, larger models. Our approach employs two key techniques: (1) targeted structured pruning, which prunes a larger model to a specified target shape by removing layers, heads, and intermediate and hidden dimensions in an end-to-end manner, and (2) dynamic batch loading, which dynamically updates the composition of sampled data in each training batch based on varying losses across different domains. We demonstrate the efficacy of our approach by presenting the Sheared-LLaMA series, pruning the LLaMA2-7B model down to 1.3B and 2.7B parameters. Sheared-LLaMA models outperform state-of-the-art open-source models of equivalent sizes, such as Pythia, INCITE, and OpenLLaMA models, on a wide range of downstream and instruction tuning evaluations, while requiring only 3% of compute compared to training such models from scratch. This work provides compelling evidence that leveraging existing LLMs with structured pruning is a far more cost-effective approach for building smaller LLMs.

We present a method for estimating neural scenes representations of objects given only a single image. The core of our method is the estimation of a geometric scaffold for the object and its use as a guide for the reconstruction of the underlying radiance field. Our formulation is based on a generative process that first maps a latent code to a voxelized shape, and then renders it to an image, with the object appearance being controlled by a second latent code. During inference, we optimize both the latent codes and the networks to fit a test image of a new object. The explicit disentanglement of shape and appearance allows our model to be fine-tuned given a single image. We can then render new views in a geometrically consistent manner and they represent faithfully the input object. Additionally, our method is able to generalize to images outside of the training domain (more realistic renderings and even real photographs). Finally, the inferred geometric scaffold is itself an accurate estimate of the object's 3D shape. We demonstrate in several experiments the effectiveness of our approach in both synthetic and real images.

Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.

Computer-aided design (CAD) tools are utilized in the manufacturing industry for modeling everything from cups to spacecraft. These programs are complex to use and typically require years of training and experience to master. Structured and well-constrained 2D sketches and 3D constructions are crucial components of CAD modeling. A well-executed CAD model can be seamlessly integrated into the manufacturing process, thereby enhancing production efficiency. Deep generative models of 3D shapes and 3D object reconstruction models have garnered significant research interest. However, most of these models produce discrete forms of 3D objects that are not editable. Moreover, the few models based on CAD operations often have substantial input restrictions. In this work, we fine-tuned pre-trained models to create OpenECAD models (0.55B, 0.89B, 2.4B and 3.1B), leveraging the visual, logical, coding, and general capabilities of visual language models. OpenECAD models can process images of 3D designs as input and generate highly structured 2D sketches and 3D construction commands, ensuring that the designs are editable. These outputs can be directly used with existing CAD tools' APIs to generate project files. To train our network, we created a series of OpenECAD datasets. These datasets are derived from existing public CAD datasets, adjusted and augmented to meet the specific requirements of vision language model (VLM) training. Additionally, we have introduced an approach that utilizes dependency relationships to define and generate sketches, further enriching the content and functionality of the datasets.

Articulated 3D object generation is fundamental for creating realistic, functional, and interactable virtual assets which are not simply static. We introduce MeshArt, a hierarchical transformer-based approach to generate articulated 3D meshes with clean, compact geometry, reminiscent of human-crafted 3D models. We approach articulated mesh generation in a part-by-part fashion across two stages. First, we generate a high-level articulation-aware object structure; then, based on this structural information, we synthesize each part's mesh faces. Key to our approach is modeling both articulation structures and part meshes as sequences of quantized triangle embeddings, leading to a unified hierarchical framework with transformers for autoregressive generation. Object part structures are first generated as their bounding primitives and articulation modes; a second transformer, guided by these articulation structures, then generates each part's mesh triangles. To ensure coherency among generated parts, we introduce structure-guided conditioning that also incorporates local part mesh connectivity. MeshArt shows significant improvements over state of the art, with 57.1% improvement in structure coverage and a 209-point improvement in mesh generation FID.

Federated learning has emerged as a promising distributed learning paradigm that facilitates collaborative learning among multiple parties without transferring raw data. However, most existing federated learning studies focus on either horizontal or vertical data settings, where the data of different parties are assumed to be from the same feature or sample space. In practice, a common scenario is the hybrid data setting, where data from different parties may differ both in the features and samples. To address this, we propose HybridTree, a novel federated learning approach that enables federated tree learning on hybrid data. We observe the existence of consistent split rules in trees. With the help of these split rules, we theoretically show that the knowledge of parties can be incorporated into the lower layers of a tree. Based on our theoretical analysis, we propose a layer-level solution that does not need frequent communication traffic to train a tree. Our experiments demonstrate that HybridTree can achieve comparable accuracy to the centralized setting with low computational and communication overhead. HybridTree can achieve up to 8 times speedup compared with the other baselines.

Novel machine learning methods for tabular data generation are often developed on small datasets which do not match the scale required for scientific applications. We investigate a recent proposal to use XGBoost as the function approximator in diffusion and flow-matching models on tabular data, which proved to be extremely memory intensive, even on tiny datasets. In this work, we conduct a critical analysis of the existing implementation from an engineering perspective, and show that these limitations are not fundamental to the method; with better implementation it can be scaled to datasets 370x larger than previously used. Our efficient implementation also unlocks scaling models to much larger sizes which we show directly leads to improved performance on benchmark tasks. We also propose algorithmic improvements that can further benefit resource usage and model performance, including multi-output trees which are well-suited to generative modeling. Finally, we present results on large-scale scientific datasets derived from experimental particle physics as part of the Fast Calorimeter Simulation Challenge. Code is available at https://github.com/layer6ai-labs/calo-forest.

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

Advancements in LLMs have recently unveiled challenges tied to computational efficiency and continual scalability due to their requirements of huge parameters, making the applications and evolution of these models on devices with limited computation resources and scenarios requiring various abilities increasingly cumbersome. Inspired by modularity within the human brain, there is a growing tendency to decompose LLMs into numerous functional modules, allowing for inference with part of modules and dynamic assembly of modules to tackle complex tasks, such as mixture-of-experts. To highlight the inherent efficiency and composability of the modular approach, we coin the term brick to represent each functional module, designating the modularized structure as configurable foundation models. In this paper, we offer a comprehensive overview and investigation of the construction, utilization, and limitation of configurable foundation models. We first formalize modules into emergent bricks - functional neuron partitions that emerge during the pre-training phase, and customized bricks - bricks constructed via additional post-training to improve the capabilities and knowledge of LLMs. Based on diverse functional bricks, we further present four brick-oriented operations: retrieval and routing, merging, updating, and growing. These operations allow for dynamic configuration of LLMs based on instructions to handle complex tasks. To verify our perspective, we conduct an empirical analysis on widely-used LLMs. We find that the FFN layers follow modular patterns with functional specialization of neurons and functional neuron partitions. Finally, we highlight several open issues and directions for future research. Overall, this paper aims to offer a fresh modular perspective on existing LLM research and inspire the future creation of more efficient and scalable foundational models.

Diatoms have been described as nanometer-born lithographers because of their ability to create sophisticated three-dimensional amorphous silica exoskeletons. The hierarchical architecture of these structures provides diatoms with mechanical protection and the ability to filter, float, and manipulate light. Therefore, they emerge as an extraordinary model of multifunctional materials from which to draw inspiration. In this paper, we use numerical simulations, analytical models, and experimental tests to unveil the structural and fluid dynamic efficiency of the Coscinodiscus species diatom. Then we propose a novel 3D printable multifunctional biomimetic material for applications such as porous filters, heat exchangers, drug delivery systems, lightweight structures, and robotics. Our results demonstrate the role of Nature as a material designer for efficient and tunable systems and highlight the potential of diatoms for engineering materials innovation. Additionally, the results reported in this paper lay the foundation to extend the structure-property characterization of diatoms.

We present Image Sculpting, a new framework for editing 2D images by incorporating tools from 3D geometry and graphics. This approach differs markedly from existing methods, which are confined to 2D spaces and typically rely on textual instructions, leading to ambiguity and limited control. Image Sculpting converts 2D objects into 3D, enabling direct interaction with their 3D geometry. Post-editing, these objects are re-rendered into 2D, merging into the original image to produce high-fidelity results through a coarse-to-fine enhancement process. The framework supports precise, quantifiable, and physically-plausible editing options such as pose editing, rotation, translation, 3D composition, carving, and serial addition. It marks an initial step towards combining the creative freedom of generative models with the precision of graphics pipelines.

We introduce a new function-preserving transformation for efficient neural architecture search. This network transformation allows reusing previously trained networks and existing successful architectures that improves sample efficiency. We aim to address the limitation of current network transformation operations that can only perform layer-level architecture modifications, such as adding (pruning) filters or inserting (removing) a layer, which fails to change the topology of connection paths. Our proposed path-level transformation operations enable the meta-controller to modify the path topology of the given network while keeping the merits of reusing weights, and thus allow efficiently designing effective structures with complex path topologies like Inception models. We further propose a bidirectional tree-structured reinforcement learning meta-controller to explore a simple yet highly expressive tree-structured architecture space that can be viewed as a generalization of multi-branch architectures. We experimented on the image classification datasets with limited computational resources (about 200 GPU-hours), where we observed improved parameter efficiency and better test results (97.70% test accuracy on CIFAR-10 with 14.3M parameters and 74.6% top-1 accuracy on ImageNet in the mobile setting), demonstrating the effectiveness and transferability of our designed architectures.

The rapid advancement of AI technology has led to widespread applications of agent systems across various domains. However, the need for detailed architecture design poses significant challenges in designing and operating these systems. This paper introduces a taxonomy focused on the architectures of foundation-model-based agents, addressing critical aspects such as functional capabilities and non-functional qualities. We also discuss the operations involved in both design-time and run-time phases, providing a comprehensive view of architectural design and operational characteristics. By unifying and detailing these classifications, our taxonomy aims to improve the design of foundation-model-based agents. Additionally, the paper establishes a decision model that guides critical design and runtime decisions, offering a structured approach to enhance the development of foundation-model-based agents. Our contributions include providing a structured architecture design option and guiding the development process of foundation-model-based agents, thereby addressing current fragmentation in the field.

With the explosive growth of 3D content creation, there is an increasing demand for automatically converting static 3D models into articulation-ready versions that support realistic animation. Traditional approaches rely heavily on manual annotation, which is both time-consuming and labor-intensive. Moreover, the lack of large-scale benchmarks has hindered the development of learning-based solutions. In this work, we present MagicArticulate, an effective framework that automatically transforms static 3D models into articulation-ready assets. Our key contributions are threefold. First, we introduce Articulation-XL, a large-scale benchmark containing over 33k 3D models with high-quality articulation annotations, carefully curated from Objaverse-XL. Second, we propose a novel skeleton generation method that formulates the task as a sequence modeling problem, leveraging an auto-regressive transformer to naturally handle varying numbers of bones or joints within skeletons and their inherent dependencies across different 3D models. Third, we predict skinning weights using a functional diffusion process that incorporates volumetric geodesic distance priors between vertices and joints. Extensive experiments demonstrate that MagicArticulate significantly outperforms existing methods across diverse object categories, achieving high-quality articulation that enables realistic animation. Project page: https://chaoyuesong.github.io/MagicArticulate.

In this paper, we propose Img2CAD, the first approach to our knowledge that uses 2D image inputs to generate CAD models with editable parameters. Unlike existing AI methods for 3D model generation using text or image inputs often rely on mesh-based representations, which are incompatible with CAD tools and lack editability and fine control, Img2CAD enables seamless integration between AI-based 3D reconstruction and CAD software. We have identified an innovative intermediate representation called Structured Visual Geometry (SVG), characterized by vectorized wireframes extracted from objects. This representation significantly enhances the performance of generating conditioned CAD models. Additionally, we introduce two new datasets to further support research in this area: ABC-mono, the largest known dataset comprising over 200,000 3D CAD models with rendered images, and KOCAD, the first dataset featuring real-world captured objects alongside their ground truth CAD models, supporting further research in conditioned CAD model generation.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

This paper studies close-loop task planning, which refers to the process of generating a sequence of skills (a plan) to accomplish a specific goal while adapting the plan based on real-time observations. Recently, prompting Large Language Models (LLMs) to generate actions iteratively has become a prevalent paradigm due to its superior performance and user-friendliness. However, this paradigm is plagued by two inefficiencies: high token consumption and redundant error correction, both of which hinder its scalability for large-scale testing and applications. To address these issues, we propose Tree-Planner, which reframes task planning with LLMs into three distinct phases: plan sampling, action tree construction, and grounded deciding. Tree-Planner starts by using an LLM to sample a set of potential plans before execution, followed by the aggregation of them to form an action tree. Finally, the LLM performs a top-down decision-making process on the tree, taking into account real-time environmental information. Experiments show that Tree-Planner achieves state-of-the-art performance while maintaining high efficiency. By decomposing LLM queries into a single plan-sampling call and multiple grounded-deciding calls, a considerable part of the prompt are less likely to be repeatedly consumed. As a result, token consumption is reduced by 92.2% compared to the previously best-performing model. Additionally, by enabling backtracking on the action tree as needed, the correction process becomes more flexible, leading to a 40.5% decrease in error corrections. Project page: https://tree-planner.github.io/

Large Language Models (LLMs) have achieved significant success across various NLP tasks. However, their massive computational costs limit their widespread use, particularly in real-time applications. Structured pruning offers an effective solution by compressing models and directly providing end-to-end speed improvements, regardless of the hardware environment. Meanwhile, different components of the model exhibit varying sensitivities towards pruning, calling for non-uniform model compression. However, a pruning method should not only identify a capable substructure, but also account for post-compression training. To this end, we propose \sysname, a method for training-aware structured pruning. \sysname builds upon an evolutionary search process, generating multiple offspring models in each generation through mutation, and selecting the fittest for survival. To assess the effect of post-training, we incorporate a lightweight, multistep training process within the offspring population, progressively increasing the number of tokens and eliminating poorly performing models in each selection stage. We validate our method through extensive experiments on Llama-2-7B, Llama-3.1-8B and Qwen-2.5-14B-Instruct, achieving state-of-the-art performance for structured pruning. For instance, \sysname surpasses ShearedLlama while requiring 5times less training data during post-compression training.

While LLMs can effectively help prototype single ML functionalities, many real-world applications involve complex tasks that cannot be easily handled via a single run of an LLM. Recent work has found that chaining multiple LLM runs together (with the output of one step being the input to the next) can help users accomplish these more complex tasks, and in a way that is perceived to be more transparent and controllable. However, it remains unknown what users need when authoring their own LLM chains -- a key step for lowering the barriers for non-AI-experts to prototype AI-infused applications. In this work, we explore the LLM chain authoring process. We conclude from pilot studies find that chaining requires careful scaffolding for transforming intermediate node outputs, as well as debugging the chain at multiple granularities; to help with these needs, we designed PromptChainer, an interactive interface for visually programming chains. Through case studies with four people, we show that PromptChainer supports building prototypes for a range of applications, and conclude with open questions on scaling chains to complex tasks, and supporting low-fi chain prototyping.

We propose Beam Tree Recursive Cell (BT-Cell) - a backpropagation-friendly framework to extend Recursive Neural Networks (RvNNs) with beam search for latent structure induction. We further extend this framework by proposing a relaxation of the hard top-k operators in beam search for better propagation of gradient signals. We evaluate our proposed models in different out-of-distribution splits in both synthetic and realistic data. Our experiments show that BTCell achieves near-perfect performance on several challenging structure-sensitive synthetic tasks like ListOps and logical inference while maintaining comparable performance in realistic data against other RvNN-based models. Additionally, we identify a previously unknown failure case for neural models in generalization to unseen number of arguments in ListOps. The code is available at: https://github.com/JRC1995/BeamTreeRecursiveCells.

Dense linear layers are the dominant computational bottleneck in foundation models. Identifying more efficient alternatives to dense matrices has enormous potential for building more compute-efficient models, as exemplified by the success of convolutional networks in the image domain. In this work, we systematically explore structured matrices as replacements for dense matrices. We show that different structures often require drastically different initialization scales and learning rates, which are crucial to performance, especially as models scale. Using insights from the Maximal Update Parameterization, we determine the optimal scaling for initialization and learning rates of these unconventional layers. Finally, we measure the scaling laws of different structures to compare how quickly their performance improves with compute. We propose a novel matrix family containing Monarch matrices, the Block Tensor-Train (BTT), which we show performs better than dense matrices for the same compute on multiple tasks. On CIFAR-10/100 with augmentation, BTT achieves exponentially lower training loss than dense when training MLPs and ViTs. BTT matches dense ViT-S/32 performance on ImageNet-1k with 3.8 times less compute and is more efficient than dense for training small GPT-2 language models.

We study the set of networks, which consist of sources, sinks and neutral points, bijective to the permutations. The set of directed edges, which characterizes a network, is constructed from a polyomino or a Rothe diagram of a permutation through a Dyck tiling on a ribbon. We introduce a new combinatorial object similar to a tree-like tableau, which we call a forest. A forest is shown to give a permutation, and be bijective to a network corresponding to the inverse of the permutation. We show that the poset of networks is a finite graded lattice and admits an EL-labeling. By use of this EL-labeling, we show the lattice is supersolvable and compute the M\"obius function of an interval of the poset.

A spanning tree T of graph G is a rho-approximate universal Steiner tree (UST) for root vertex r if, for any subset of vertices S containing r, the cost of the minimal subgraph of T connecting S is within a rho factor of the minimum cost tree connecting S in G. Busch et al. (FOCS 2012) showed that every graph admits 2^{O(log n)}-approximate USTs by showing that USTs are equivalent to strong sparse partition hierarchies (up to poly-logs). Further, they posed poly-logarithmic USTs and strong sparse partition hierarchies as open questions. We settle these open questions by giving polynomial-time algorithms for computing both O(log ^ 7 n)-approximate USTs and poly-logarithmic strong sparse partition hierarchies. For graphs with constant doubling dimension or constant pathwidth we improve this to O(log n)-approximate USTs and O(1) strong sparse partition hierarchies. Our doubling dimension result is tight up to second order terms. We reduce the existence of these objects to the previously studied cluster aggregation problem and what we call dangling nets.

We present a novel generative 3D modeling system, coined CraftsMan, which can generate high-fidelity 3D geometries with highly varied shapes, regular mesh topologies, and detailed surfaces, and, notably, allows for refining the geometry in an interactive manner. Despite the significant advancements in 3D generation, existing methods still struggle with lengthy optimization processes, irregular mesh topologies, noisy surfaces, and difficulties in accommodating user edits, consequently impeding their widespread adoption and implementation in 3D modeling software. Our work is inspired by the craftsman, who usually roughs out the holistic figure of the work first and elaborates the surface details subsequently. Specifically, we employ a 3D native diffusion model, which operates on latent space learned from latent set-based 3D representations, to generate coarse geometries with regular mesh topology in seconds. In particular, this process takes as input a text prompt or a reference image and leverages a powerful multi-view (MV) diffusion model to generate multiple views of the coarse geometry, which are fed into our MV-conditioned 3D diffusion model for generating the 3D geometry, significantly improving robustness and generalizability. Following that, a normal-based geometry refiner is used to significantly enhance the surface details. This refinement can be performed automatically, or interactively with user-supplied edits. Extensive experiments demonstrate that our method achieves high efficacy in producing superior-quality 3D assets compared to existing methods. HomePage: https://craftsman3d.github.io/, Code: https://github.com/wyysf-98/CraftsMan

Scaffolding Large Language Models (LLMs) into multi-agent systems often improves performance on complex tasks, but the safety impact of such scaffolds has not been as thoroughly explored. In this paper, we introduce AGENTBREEDER a framework for multi-objective evolutionary search over scaffolds. Our REDAGENTBREEDER evolves scaffolds towards jailbreaking the base LLM while achieving high task success, while BLUEAGENTBREEDER instead aims to combine safety with task reward. We evaluate the systems discovered by the different instances of AGENTBREEDER and popular baselines using widely recognized reasoning, mathematics, and safety benchmarks. Our work highlights and mitigates the safety risks due to multi-agent scaffolding.

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

Current language models tailored for code tasks often adopt the pre-training-then-fine-tuning paradigm from natural language processing, modeling source code as plain text. This approach, however, overlooks the unambiguous structures inherent in programming languages. In this work, we explore data-efficient adaptation of pre-trained code models by further pre-training and fine-tuning them with program structures. Specifically, we represent programs as parse trees -- also known as concrete syntax trees (CSTs) -- and adapt pre-trained models on serialized CSTs. Although the models that we adapt have been pre-trained only on the surface form of programs, we find that a small amount of continual pre-training and fine-tuning on CSTs without changing the model architecture yields improvements over the baseline approach across various code tasks. The improvements are found to be particularly significant when there are limited training examples, demonstrating the effectiveness of integrating program structures with plain-text representation even when working with backbone models that have not been pre-trained with structures.

Modeling and designing urban building layouts is of significant interest in computer vision, computer graphics, and urban applications. A building layout consists of a set of buildings in city blocks defined by a network of roads. We observe that building layouts are discrete structures, consisting of multiple rows of buildings of various shapes, and are amenable to skeletonization for mapping arbitrary city block shapes to a canonical form. Hence, we propose a fully automatic approach to building layout generation using graph attention networks. Our method generates realistic urban layouts given arbitrary road networks, and enables conditional generation based on learned priors. Our results, including user study, demonstrate superior performance as compared to prior layout generation networks, support arbitrary city block and varying building shapes as demonstrated by generating layouts for 28 large cities.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Structured pruning is a commonly used technique in deploying deep neural networks (DNNs) onto resource-constrained devices. However, the existing pruning methods are usually heuristic, task-specified, and require an extra fine-tuning procedure. To overcome these limitations, we propose a framework that compresses DNNs into slimmer architectures with competitive performances and significant FLOPs reductions by Only-Train-Once (OTO). OTO contains two keys: (i) we partition the parameters of DNNs into zero-invariant groups, enabling us to prune zero groups without affecting the output; and (ii) to promote zero groups, we then formulate a structured-sparsity optimization problem and propose a novel optimization algorithm, Half-Space Stochastic Projected Gradient (HSPG), to solve it, which outperforms the standard proximal methods on group sparsity exploration and maintains comparable convergence. To demonstrate the effectiveness of OTO, we train and compress full models simultaneously from scratch without fine-tuning for inference speedup and parameter reduction, and achieve state-of-the-art results on VGG16 for CIFAR10, ResNet50 for CIFAR10 and Bert for SQuAD and competitive result on ResNet50 for ImageNet. The source code is available at https://github.com/tianyic/only_train_once.

Large, pre-trained models are problematic to use in resource constrained applications. Fortunately, task-aware structured pruning methods offer a solution. These approaches reduce model size by dropping structural units like layers and attention heads in a manner that takes into account the end-task. However, these pruning algorithms require more task-specific data than is typically available. We propose a framework which combines structured pruning with transfer learning to reduce the need for task-specific data. Our empirical results answer questions such as: How should the two tasks be coupled? What parameters should be transferred? And, when during training should transfer learning be introduced? Leveraging these insights, we demonstrate that our framework results in pruned models with improved generalization over strong baselines.

We study how to train personalized models for different tasks on decentralized devices with limited local data. We propose "Structured Cooperative Learning (SCooL)", in which a cooperation graph across devices is generated by a graphical model prior to automatically coordinate mutual learning between devices. By choosing graphical models enforcing different structures, we can derive a rich class of existing and novel decentralized learning algorithms via variational inference. In particular, we show three instantiations of SCooL that adopt Dirac distribution, stochastic block model (SBM), and attention as the prior generating cooperation graphs. These EM-type algorithms alternate between updating the cooperation graph and cooperative learning of local models. They can automatically capture the cross-task correlations among devices by only monitoring their model updating in order to optimize the cooperation graph. We evaluate SCooL and compare it with existing decentralized learning methods on an extensive set of benchmarks, on which SCooL always achieves the highest accuracy of personalized models and significantly outperforms other baselines on communication efficiency. Our code is available at https://github.com/ShuangtongLi/SCooL.

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.

Recent research suggests that tree search algorithms (e.g. Monte Carlo Tree Search) can dramatically boost LLM performance on complex mathematical reasoning tasks. However, they often require more than 10 times the computational resources of greedy decoding due to wasteful search strategies, making them difficult to be deployed in practical applications. This study introduces a novel guided tree search algorithm with dynamic node selection and node-level exploration budget (maximum number of children) calculation to tackle this issue. By considering the search progress towards the final answer (history) and the guidance from a value network (future) trained without any step-wise annotations, our algorithm iteratively selects the most promising tree node before expanding it within the boundaries of the allocated computational budget. Experiments conducted on the GSM8K and TabMWP datasets demonstrate that our approach not only offers competitive performance but also enjoys significantly lower computational costs compared to baseline methods.

Foundation models for interactive segmentation in 2D natural images and videos have sparked significant interest in building 3D foundation models for medical imaging. However, the domain gaps and clinical use cases for 3D medical imaging require a dedicated model that diverges from existing 2D solutions. Specifically, such foundation models should support a full workflow that can actually reduce human effort. Treating 3D medical images as sequences of 2D slices and reusing interactive 2D foundation models seems straightforward, but 2D annotation is too time-consuming for 3D tasks. Moreover, for large cohort analysis, it's the highly accurate automatic segmentation models that reduce the most human effort. However, these models lack support for interactive corrections and lack zero-shot ability for novel structures, which is a key feature of "foundation". While reusing pre-trained 2D backbones in 3D enhances zero-shot potential, their performance on complex 3D structures still lags behind leading 3D models. To address these issues, we present VISTA3D, Versatile Imaging SegmenTation and Annotation model, that targets to solve all these challenges and requirements with one unified foundation model. VISTA3D is built on top of the well-established 3D segmentation pipeline, and it is the first model to achieve state-of-the-art performance in both 3D automatic (supporting 127 classes) and 3D interactive segmentation, even when compared with top 3D expert models on large and diverse benchmarks. Additionally, VISTA3D's 3D interactive design allows efficient human correction, and a novel 3D supervoxel method that distills 2D pretrained backbones grants VISTA3D top 3D zero-shot performance. We believe the model, recipe, and insights represent a promising step towards a clinically useful 3D foundation model. Code and weights are publicly available at https://github.com/Project-MONAI/VISTA.

Neural networks (NN) achieve remarkable results in various tasks, but lack key characteristics: interpretability, support for categorical features, and lightweight implementations suitable for edge devices. While ongoing efforts aim to address these challenges, Gradient Boosting Trees (GBT) inherently meet these requirements. As a result, GBTs have become the go-to method for supervised learning tasks in many real-world applications and competitions. However, their application in online learning scenarios, notably in reinforcement learning (RL), has been limited. In this work, we bridge this gap by introducing Gradient-Boosting RL (GBRL), a framework that extends the advantages of GBT to the RL domain. Using the GBRL framework, we implement various actor-critic algorithms and compare their performance with their NN counterparts. Inspired by shared backbones in NN we introduce a tree-sharing approach for policy and value functions with distinct learning rates, enhancing learning efficiency over millions of interactions. GBRL achieves competitive performance across a diverse array of tasks, excelling in domains with structured or categorical features. Additionally, we present a high-performance, GPU-accelerated implementation that integrates seamlessly with widely-used RL libraries (available at https://github.com/NVlabs/gbrl). GBRL expands the toolkit for RL practitioners, demonstrating the viability and promise of GBT within the RL paradigm, particularly in domains characterized by structured or categorical features.

Automated assembly of 3D fractures is essential in orthopedics, archaeology, and our daily life. This paper presents Jigsaw, a novel framework for assembling physically broken 3D objects from multiple pieces. Our approach leverages hierarchical features of global and local geometry to match and align the fracture surfaces. Our framework consists of four components: (1) front-end point feature extractor with attention layers, (2) surface segmentation to separate fracture and original parts, (3) multi-parts matching to find correspondences among fracture surface points, and (4) robust global alignment to recover the global poses of the pieces. We show how to jointly learn segmentation and matching and seamlessly integrate feature matching and rigidity constraints. We evaluate Jigsaw on the Breaking Bad dataset and achieve superior performance compared to state-of-the-art methods. Our method also generalizes well to diverse fracture modes, objects, and unseen instances. To the best of our knowledge, this is the first learning-based method designed specifically for 3D fracture assembly over multiple pieces. Our code is available at https://jiaxin-lu.github.io/Jigsaw/.

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, we propose a gating strategy that uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations of adaptations are established to solve specific tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model (LLM) without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics and design. The impact of this work include access to readily expandable, adaptable and changeable models with strong domain knowledge and the capability to integrate across areas of knowledge. With the X-LoRA model featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, and protein mechanics we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, and adversarial agentic modeling including ontological knowledge graphs. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins, but also reasons over the results and correctly predicts likely mechanisms that explain distinct molecular behaviors.

The skeleton of a digital image is a compact representation of its topology, geometry, and scale. It has utility in many computer vision applications, such as image description, segmentation, and registration. However, skeletonization has only seen limited use in contemporary deep learning solutions. Most existing skeletonization algorithms are not differentiable, making it impossible to integrate them with gradient-based optimization. Compatible algorithms based on morphological operations and neural networks have been proposed, but their results often deviate from the geometry and topology of the true medial axis. This work introduces the first three-dimensional skeletonization algorithm that is both compatible with gradient-based optimization and preserves an object's topology. Our method is exclusively based on matrix additions and multiplications, convolutional operations, basic non-linear functions, and sampling from a uniform probability distribution, allowing it to be easily implemented in any major deep learning library. In benchmarking experiments, we prove the advantages of our skeletonization algorithm compared to non-differentiable, morphological, and neural-network-based baselines. Finally, we demonstrate the utility of our algorithm by integrating it with two medical image processing applications that use gradient-based optimization: deep-learning-based blood vessel segmentation, and multimodal registration of the mandible in computed tomography and magnetic resonance images.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Adapting pre-trained foundation models for various downstream tasks has been prevalent in artificial intelligence. Due to the vast number of tasks and high costs, adjusting all parameters becomes unfeasible. To mitigate this, several fine-tuning techniques have been developed to update the pre-trained model weights in a more resource-efficient manner, such as through low-rank adjustments. Yet, almost all of these methods focus on linear weights, neglecting the intricacies of parameter spaces in higher dimensions like 4D. Alternatively, some methods can be adapted for high-dimensional parameter space by compressing changes in the original space into two dimensions and then employing low-rank matrix decomposition. However, these approaches destructs the structural integrity of the involved high-dimensional spaces. To tackle the diversity of dimensional spaces across different foundation models and provide a more precise representation of the changes within these spaces, this paper introduces a generalized parameter-efficient fine-tuning framework, FLoRA, designed for various dimensional parameter space. Specifically, utilizing Tucker decomposition, FLoRA asserts that changes in each dimensional parameter space are based on a low-rank core space which maintains the consistent topological structure with the original space. It then models the changes through this core space alongside corresponding weights to reconstruct alterations in the original space. FLoRA effectively preserves the structural integrity of the change of original N-dimensional parameter space, meanwhile decomposes it via low-rank tensor decomposition. Extensive experiments on computer vision, natural language processing and multi-modal tasks validate FLoRA's effectiveness. Codes are available at https://github.com/SJTU-DeepVisionLab/FLoRA.

Animating various character drawings is an engaging visual content creation task. Given a single character drawing, existing animation methods are limited to flat 2D motions and thus lack 3D effects. An alternative solution is to reconstruct a 3D model from a character drawing as a proxy and then retarget 3D motion data onto it. However, the existing image-to-3D methods could not work well for amateur character drawings in terms of appearance and geometry. We observe the contour lines, commonly existing in character drawings, would introduce significant ambiguity in texture synthesis due to their view-dependence. Additionally, thin regions represented by single-line contours are difficult to reconstruct (e.g., slim limbs of a stick figure) due to their delicate structures. To address these issues, we propose a novel system, DrawingSpinUp, to produce plausible 3D animations and breathe life into character drawings, allowing them to freely spin up, leap, and even perform a hip-hop dance. For appearance improvement, we adopt a removal-then-restoration strategy to first remove the view-dependent contour lines and then render them back after retargeting the reconstructed character. For geometry refinement, we develop a skeleton-based thinning deformation algorithm to refine the slim structures represented by the single-line contours. The experimental evaluations and a perceptual user study show that our proposed method outperforms the existing 2D and 3D animation methods and generates high-quality 3D animations from a single character drawing. Please refer to our project page (https://lordliang.github.io/DrawingSpinUp) for the code and generated animations.

Polygonal meshes are ubiquitous, but have only played a relatively minor role in the deep learning revolution. State-of-the-art neural generative models for 3D shapes learn implicit functions and generate meshes via expensive iso-surfacing. We overcome these challenges by employing a classical spatial data structure from computer graphics, Binary Space Partitioning (BSP), to facilitate 3D learning. The core operation of BSP involves recursive subdivision of 3D space to obtain convex sets. By exploiting this property, we devise BSP-Net, a network that learns to represent a 3D shape via convex decomposition without supervision. The network is trained to reconstruct a shape using a set of convexes obtained from a BSP-tree built over a set of planes, where the planes and convexes are both defined by learned network weights. BSP-Net directly outputs polygonal meshes from the inferred convexes. The generated meshes are watertight, compact (i.e., low-poly), and well suited to represent sharp geometry. We show that the reconstruction quality by BSP-Net is competitive with those from state-of-the-art methods while using much fewer primitives. We also explore variations to BSP-Net including using a more generic decoder for reconstruction, more general primitives than planes, as well as training a generative model with variational auto-encoders. Code is available at https://github.com/czq142857/BSP-NET-original.

JSON Schema is an important, evolving standard schema language for families of JSON documents. It is based on a complex combination of structural and Boolean assertions, and features negation and recursion. The static analysis of JSON Schema documents comprises practically relevant problems, including schema satisfiability, inclusion, and equivalence. These three problems can be reduced to witness generation: given a schema, generate an element of the schema, if it exists, and report failure otherwise. Schema satisfiability, inclusion, and equivalence have been shown to be decidable, by reduction to reachability in alternating tree automata. However, no witness generation algorithm has yet been formally described. We contribute a first, direct algorithm for JSON Schema witness generation. We study its effectiveness and efficiency, in experiments over several schema collections, including thousands of real-world schemas. Our focus is on the completeness of the language, where we only exclude the uniqueItems operator, and on the ability of the algorithm to run in a reasonable time on a large set of real-world examples, despite the exponential complexity of the underlying problem.

Pre-trained on massive amounts of code and text data, large language models (LLMs) have demonstrated remarkable achievements in performing code generation tasks. With additional execution-based feedback, these models can act as agents with capabilities to self-refine and improve generated code autonomously. However, on challenging coding tasks with extremely large search space, current agentic approaches still struggle with multi-stage planning, generating, and debugging. To address this problem, we propose CodeTree, a framework for LLM agents to efficiently explore the search space in different stages of the code generation process. Specifically, we adopted a unified tree structure to explicitly explore different coding strategies, generate corresponding coding solutions, and subsequently refine the solutions. In each stage, critical decision-making (ranking, termination, expanding) of the exploration process is guided by both the environmental execution-based feedback and LLM-agent-generated feedback. We comprehensively evaluated CodeTree on 7 code generation benchmarks and demonstrated the significant performance gains of CodeTree against strong baselines. Using GPT-4o as the base model, we consistently achieved top results of 95.1 on HumanEval, 98.7 on MBPP, and 43.0 on CodeContests. On the challenging SWEBench benchmark, our approach led to significant performance gains.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Open source code: https://github.com/chaitjo/geometric-rna-design

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

The inference of topological principles is a key problem in structured reconstruction. We observe that wrongly predicted topological relationships are often incurred by the lack of holistic geometry clues in low-level features. Inspired by the fact that massive signals can be compactly described with frequency analysis, we experimentally explore the efficiency and tendency of learning structure geometry in the frequency domain. Accordingly, we propose a frequency-domain feature learning strategy (F-Learn) to fuse scattered geometric fragments holistically for topology-intact structure reasoning. Benefiting from the parsimonious design, the F-Learn strategy can be easily deployed into a deep reconstructor with a lightweight model modification. Experiments demonstrate that the F-Learn strategy can effectively introduce structure awareness into geometric primitive detection and topology inference, bringing significant performance improvement to final structured reconstruction. Code and pre-trained models are available at https://github.com/Geo-Tell/F-Learn.

For a full-stack web or app development, it requires a software firm or more specifically a team of experienced developers to contribute a large portion of their time and resources to design the website and then convert it to code. As a result, the efficiency of the development team is significantly reduced when it comes to converting UI wireframes and database schemas into an actual working system. It would save valuable resources and fasten the overall workflow if the clients or developers can automate this process of converting the pre-made full-stack website design to get a partially working if not fully working code. In this paper, we present a novel approach of generating the skeleton code from sketched images using Deep Learning and Computer Vision approaches. The dataset for training are first-hand sketched images of low fidelity wireframes, database schemas and class diagrams. The approach consists of three parts. First, the front-end or UI elements detection and extraction from custom-made UI wireframes. Second, individual database table creation from schema designs and lastly, creating a class file from class diagrams.

The remarkable performance of deep Convolutional neural networks (CNNs) is generally attributed to their deeper and wider architectures, which can come with significant computational costs. Pruning neural networks has thus gained interest since it effectively lowers storage and computational costs. In contrast to weight pruning, which results in unstructured models, structured pruning provides the benefit of realistic acceleration by producing models that are friendly to hardware implementation. The special requirements of structured pruning have led to the discovery of numerous new challenges and the development of innovative solutions. This article surveys the recent progress towards structured pruning of deep CNNs. We summarize and compare the state-of-the-art structured pruning techniques with respect to filter ranking methods, regularization methods, dynamic execution, neural architecture search, the lottery ticket hypothesis, and the applications of pruning. While discussing structured pruning algorithms, we briefly introduce the unstructured pruning counterpart to emphasize their differences. Furthermore, we provide insights into potential research opportunities in the field of structured pruning. A curated list of neural network pruning papers can be found at https://github.com/he-y/Awesome-Pruning

Network pruning is widely used for reducing the heavy inference cost of deep models in low-resource settings. A typical pruning algorithm is a three-stage pipeline, i.e., training (a large model), pruning and fine-tuning. During pruning, according to a certain criterion, redundant weights are pruned and important weights are kept to best preserve the accuracy. In this work, we make several surprising observations which contradict common beliefs. For all state-of-the-art structured pruning algorithms we examined, fine-tuning a pruned model only gives comparable or worse performance than training that model with randomly initialized weights. For pruning algorithms which assume a predefined target network architecture, one can get rid of the full pipeline and directly train the target network from scratch. Our observations are consistent for multiple network architectures, datasets, and tasks, which imply that: 1) training a large, over-parameterized model is often not necessary to obtain an efficient final model, 2) learned "important" weights of the large model are typically not useful for the small pruned model, 3) the pruned architecture itself, rather than a set of inherited "important" weights, is more crucial to the efficiency in the final model, which suggests that in some cases pruning can be useful as an architecture search paradigm. Our results suggest the need for more careful baseline evaluations in future research on structured pruning methods. We also compare with the "Lottery Ticket Hypothesis" (Frankle & Carbin 2019), and find that with optimal learning rate, the "winning ticket" initialization as used in Frankle & Carbin (2019) does not bring improvement over random initialization.

Competition-level code generation tasks pose significant challenges for current state-of-the-art large language models (LLMs). For example, on the LiveCodeBench-Hard dataset, models such as O1-Mini and O1-Preview achieve pass@1 rates of only 0.366 and 0.143, respectively. While tree search techniques have proven effective in domains like mathematics and general coding, their potential in competition-level code generation remains under-explored. In this work, we propose a novel token-level tree search method specifically designed for code generation. Leveraging Qwen2.5-Coder-32B-Instruct, our approach achieves a pass rate of 0.305 on LiveCodeBench-Hard, surpassing the pass@100 performance of GPT4o-0513 (0.245). Furthermore, by integrating Chain-of-Thought (CoT) prompting, we improve our method's performance to 0.351, approaching O1-Mini's pass@1 rate. To ensure reproducibility, we report the average number of generations required per problem by our tree search method on the test set. Our findings underscore the potential of tree search to significantly enhance performance on competition-level code generation tasks. This opens up new possibilities for large-scale synthesis of challenging code problems supervised fine-tuning (SFT) data, advancing competition-level code generation tasks.

Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as their size or depth. We are not aware of such research for tree ensembles and aim to contribute to this area. Mainly, we provide two novel algorithms and corresponding lower bounds. First, we are able to carry over and substantially improve on tractability results for decision trees, obtaining a (6delta D S)^S cdot poly-time algorithm, where S is the number of cuts in the tree ensemble, D the largest domain size, and delta is the largest number of features in which two examples differ. To achieve this, we introduce the witness-tree technique which also seems promising for practice. Second, we show that dynamic programming, which has been successful for decision trees, may also be viable for tree ensembles, providing an ell^n cdot poly-time algorithm, where ell is the number of trees and n the number of examples. Finally, we compare the number of cuts necessary to classify training data sets for decision trees and tree ensembles, showing that ensembles may need exponentially fewer cuts for increasing number of trees.

We present a computational framework that transforms single images into 3D physical objects. The visual geometry of a physical object in an image is determined by three orthogonal attributes: mechanical properties, external forces, and rest-shape geometry. Existing single-view 3D reconstruction methods often overlook this underlying composition, presuming rigidity or neglecting external forces. Consequently, the reconstructed objects fail to withstand real-world physical forces, resulting in instability or undesirable deformation -- diverging from their intended designs as depicted in the image. Our optimization framework addresses this by embedding physical compatibility into the reconstruction process. We explicitly decompose the three physical attributes and link them through static equilibrium, which serves as a hard constraint, ensuring that the optimized physical shapes exhibit desired physical behaviors. Evaluations on a dataset collected from Objaverse demonstrate that our framework consistently enhances the physical realism of 3D models over existing methods. The utility of our framework extends to practical applications in dynamic simulations and 3D printing, where adherence to physical compatibility is paramount.

Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.

We propose an intuitive LLM prompting framework (AgentKit) for multifunctional agents. AgentKit offers a unified framework for explicitly constructing a complex "thought process" from simple natural language prompts. The basic building block in AgentKit is a node, containing a natural language prompt for a specific subtask. The user then puts together chains of nodes, like stacking LEGO pieces. The chains of nodes can be designed to explicitly enforce a naturally structured "thought process". For example, for the task of writing a paper, one may start with the thought process of 1) identify a core message, 2) identify prior research gaps, etc. The nodes in AgentKit can be designed and combined in different ways to implement multiple advanced capabilities including on-the-fly hierarchical planning, reflection, and learning from interactions. In addition, due to the modular nature and the intuitive design to simulate explicit human thought process, a basic agent could be implemented as simple as a list of prompts for the subtasks and therefore could be designed and tuned by someone without any programming experience. Quantitatively, we show that agents designed through AgentKit achieve SOTA performance on WebShop and Crafter. These advances underscore AgentKit's potential in making LLM agents effective and accessible for a wider range of applications. https://github.com/holmeswww/AgentKit

Materials synthesis is vital for innovations such as energy storage, catalysis, electronics, and biomedical devices. Yet, the process relies heavily on empirical, trial-and-error methods guided by expert intuition. Our work aims to support the materials science community by providing a practical, data-driven resource. We have curated a comprehensive dataset of 17K expert-verified synthesis recipes from open-access literature, which forms the basis of our newly developed benchmark, AlchemyBench. AlchemyBench offers an end-to-end framework that supports research in large language models applied to synthesis prediction. It encompasses key tasks, including raw materials and equipment prediction, synthesis procedure generation, and characterization outcome forecasting. We propose an LLM-as-a-Judge framework that leverages large language models for automated evaluation, demonstrating strong statistical agreement with expert assessments. Overall, our contributions offer a supportive foundation for exploring the capabilities of LLMs in predicting and guiding materials synthesis, ultimately paving the way for more efficient experimental design and accelerated innovation in materials science.

In this paper, we present DendroMap, a novel approach to interactively exploring large-scale image datasets for machine learning (ML). ML practitioners often explore image datasets by generating a grid of images or projecting high-dimensional representations of images into 2-D using dimensionality reduction techniques (e.g., t-SNE). However, neither approach effectively scales to large datasets because images are ineffectively organized and interactions are insufficiently supported. To address these challenges, we develop DendroMap by adapting Treemaps, a well-known visualization technique. DendroMap effectively organizes images by extracting hierarchical cluster structures from high-dimensional representations of images. It enables users to make sense of the overall distributions of datasets and interactively zoom into specific areas of interests at multiple levels of abstraction. Our case studies with widely-used image datasets for deep learning demonstrate that users can discover insights about datasets and trained models by examining the diversity of images, identifying underperforming subgroups, and analyzing classification errors. We conducted a user study that evaluates the effectiveness of DendroMap in grouping and searching tasks by comparing it with a gridified version of t-SNE and found that participants preferred DendroMap. DendroMap is available at https://div-lab.github.io/dendromap/.

Humans are good at recomposing novel objects, i.e. they can identify commonalities between unknown objects from general structure to finer detail, an ability difficult to replicate by machines. We propose a framework, ISCO, to recompose an object using 3D superquadrics as semantic parts directly from 2D views without training a model that uses 3D supervision. To achieve this, we optimize the superquadric parameters that compose a specific instance of the object, comparing its rendered 3D view and 2D image silhouette. Our ISCO framework iteratively adds new superquadrics wherever the reconstruction error is high, abstracting first coarse regions and then finer details of the target object. With this simple coarse-to-fine inductive bias, ISCO provides consistent superquadrics for related object parts, despite not having any semantic supervision. Since ISCO does not train any neural network, it is also inherently robust to out-of-distribution objects. Experiments show that, compared to recent single instance superquadrics reconstruction approaches, ISCO provides consistently more accurate 3D reconstructions, even from images in the wild. Code available at https://github.com/ExplainableML/ISCO .

This paper introduces a public dataset of 1.4 million procedurally-generated bicycle designs represented parametrically, as JSON files, and as rasterized images. The dataset is created through the use of a rendering engine which harnesses the BikeCAD software to generate vector graphics from parametric designs. This rendering engine is discussed in the paper and also released publicly alongside the dataset. Though this dataset has numerous applications, a principal motivation is the need to train cross-modal predictive models between parametric and image-based design representations. For example, we demonstrate that a predictive model can be trained to accurately estimate Contrastive Language-Image Pretraining (CLIP) embeddings from a parametric representation directly. This allows similarity relations to be established between parametric bicycle designs and text strings or reference images. Trained predictive models are also made public. The dataset joins the BIKED dataset family which includes thousands of mixed-representation human-designed bicycle models and several datasets quantifying design performance. The code and dataset can be found at: https://github.com/Lyleregenwetter/BIKED_multimodal/tree/main

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

The caliber and configuration of retinal blood vessels serve as important biomarkers for various diseases and medical conditions. A thorough analysis of the retinal vasculature requires the segmentation of the blood vessels and their classification into arteries and veins, typically performed on color fundus images obtained by retinography. However, manually performing these tasks is labor-intensive and prone to human error. While several automated methods have been proposed to address this task, the current state of art faces challenges due to manifest classification errors affecting the topological consistency of segmentation maps. In this work, we introduce RRWNet, a novel end-to-end deep learning framework that addresses this limitation. The framework consists of a fully convolutional neural network that recursively refines semantic segmentation maps, correcting manifest classification errors and thus improving topological consistency. In particular, RRWNet is composed of two specialized subnetworks: a Base subnetwork that generates base segmentation maps from the input images, and a Recursive Refinement subnetwork that iteratively and recursively improves these maps. Evaluation on three different public datasets demonstrates the state-of-the-art performance of the proposed method, yielding more topologically consistent segmentation maps with fewer manifest classification errors than existing approaches. In addition, the Recursive Refinement module within RRWNet proves effective in post-processing segmentation maps from other methods, further demonstrating its potential. The model code, weights, and predictions will be publicly available at https://github.com/j-morano/rrwnet.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

We address 2D floorplan reconstruction from 3D scans. Existing approaches typically employ heuristically designed multi-stage pipelines. Instead, we formulate floorplan reconstruction as a single-stage structured prediction task: find a variable-size set of polygons, which in turn are variable-length sequences of ordered vertices. To solve it we develop a novel Transformer architecture that generates polygons of multiple rooms in parallel, in a holistic manner without hand-crafted intermediate stages. The model features two-level queries for polygons and corners, and includes polygon matching to make the network end-to-end trainable. Our method achieves a new state-of-the-art for two challenging datasets, Structured3D and SceneCAD, along with significantly faster inference than previous methods. Moreover, it can readily be extended to predict additional information, i.e., semantic room types and architectural elements like doors and windows. Our code and models are available at: https://github.com/ywyue/RoomFormer.

Parse graphs of the human body can be obtained in the human brain to help humans complete the human pose estimation (HPE). It contains a hierarchical structure, like a tree structure, and context relations among nodes. Many researchers pre-design the parse graph of body structure, and then design framework for HPE. However, these frameworks are difficulty adapting when encountering situations that differ from the preset human structure. Different from them, we regard the feature map as a whole, similarly to human body, so the feature map can be optimized based on parse graphs and each node feature is learned implicitly instead of explicitly, which means it can flexibly respond to different human body structure. In this paper, we design the Refinement Module based on the Parse Graph of feature map (RMPG), which includes two stages: top-down decomposition and bottom-up combination. In the top-down decomposition stage, the feature map is decomposed into multiple sub-feature maps along the channel and their context relations are calculated to obtain their respective context information. In the bottom-up combination stage, the sub-feature maps and their context information are combined to obtain refined sub-feature maps, and then these refined sub-feature maps are concatenated to obtain the refined feature map. Additionally ,we design a top-down framework by using multiple RMPG modules for HPE, some of which are supervised to obtain context relations among body parts. Our framework achieves excellent results on the COCO keypoint detection, CrowdPose and MPII human pose datasets. More importantly, our experiments also demonstrate the effectiveness of RMPG on different methods, including SimpleBaselines, Hourglass, and ViTPose.

Autoregressive language models demonstrate excellent performance in various scenarios. However, the inference efficiency is limited by its one-step-one-word generation mode, which has become a pressing problem recently as the models become increasingly larger. Speculative decoding employs a "draft and then verify" mechanism to allow multiple tokens to be generated in one step, realizing lossless acceleration. Existing methods mainly adopt fixed heuristic draft structures, which fail to adapt to different situations to maximize the acceptance length during verification. To alleviate this dilemma, we proposed OPT-Tree, an algorithm to construct adaptive and scalable draft trees. It searches the optimal tree structure that maximizes the mathematical expectation of the acceptance length in each decoding step. Experimental results reveal that OPT-Tree outperforms the existing draft structures and achieves a speed-up ratio of up to 3.2 compared with autoregressive decoding. If the draft model is powerful enough and the node budget is sufficient, it can generate more than ten tokens in a single step. Our code is available at https://github.com/Jikai0Wang/OPT-Tree.

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

Recent advancements in implicit 3D representations and generative models have markedly propelled the field of 3D object generation forward. However, it remains a significant challenge to accurately model geometries with defined sharp features under parametric controls, which is crucial in fields like industrial design and manufacturing. To bridge this gap, we introduce a framework that employs Large Language Models (LLMs) to generate text-driven 3D shapes, manipulating 3D software via program synthesis. We present 3D-PreMise, a dataset specifically tailored for 3D parametric modeling of industrial shapes, designed to explore state-of-the-art LLMs within our proposed pipeline. Our work reveals effective generation strategies and delves into the self-correction capabilities of LLMs using a visual interface. Our work highlights both the potential and limitations of LLMs in 3D parametric modeling for industrial applications.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches rely on various local heuristics for enforcing the acyclicity constraint. In this paper, we introduce a fundamentally different strategy: We formulate the structure learning problem as a purely continuous optimization problem over real matrices that avoids this combinatorial constraint entirely. This is achieved by a novel characterization of acyclicity that is not only smooth but also exact. The resulting problem can be efficiently solved by standard numerical algorithms, which also makes implementation effortless. The proposed method outperforms existing ones, without imposing any structural assumptions on the graph such as bounded treewidth or in-degree. Code implementing the proposed algorithm is open-source and publicly available at https://github.com/xunzheng/notears.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

Graph neural networks (GNNs) emerged recently as a standard toolkit for learning from data on graphs. Current GNN designing works depend on immense human expertise to explore different message-passing mechanisms, and require manual enumeration to determine the proper message-passing depth. Inspired by the strong searching capability of neural architecture search (NAS) in CNN, this paper proposes Graph Neural Architecture Search (GNAS) with novel-designed search space. The GNAS can automatically learn better architecture with the optimal depth of message passing on the graph. Specifically, we design Graph Neural Architecture Paradigm (GAP) with tree-topology computation procedure and two types of fine-grained atomic operations (feature filtering and neighbor aggregation) from message-passing mechanism to construct powerful graph network search space. Feature filtering performs adaptive feature selection, and neighbor aggregation captures structural information and calculates neighbors' statistics. Experiments show that our GNAS can search for better GNNs with multiple message-passing mechanisms and optimal message-passing depth. The searched network achieves remarkable improvement over state-of-the-art manual designed and search-based GNNs on five large-scale datasets at three classical graph tasks. Codes can be found at https://github.com/phython96/GNAS-MP.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

This paper introduces YOLOv8-TO, a novel approach for reverse engineering of topology-optimized structures into interpretable geometric parameters using the YOLOv8 instance segmentation model. Density-based topology optimization methods require post-processing to convert the optimal density distribution into a parametric representation for design exploration and integration with CAD tools. Traditional methods such as skeletonization struggle with complex geometries and require manual intervention. YOLOv8-TO addresses these challenges by training a custom YOLOv8 model to automatically detect and reconstruct structural components from binary density distributions. The model is trained on a diverse dataset of both optimized and random structures generated using the Moving Morphable Components method. A custom reconstruction loss function based on the dice coefficient of the predicted geometry is used to train the new regression head of the model via self-supervised learning. The method is evaluated on test sets generated from different topology optimization methods, including out-of-distribution samples, and compared against a skeletonization approach. Results show that YOLOv8-TO significantly outperforms skeletonization in reconstructing visually and structurally similar designs. The method showcases an average improvement of 13.84% in the Dice coefficient, with peak enhancements reaching 20.78%. The method demonstrates good generalization to complex geometries and fast inference times, making it suitable for integration into design workflows using regular workstations. Limitations include the sensitivity to non-max suppression thresholds. YOLOv8-TO represents a significant advancement in topology optimization post-processing, enabling efficient and accurate reverse engineering of optimized structures for design exploration and manufacturing.

We introduce a novel 3D generation method for versatile and high-quality 3D asset creation. The cornerstone is a unified Structured LATent (SLAT) representation which allows decoding to different output formats, such as Radiance Fields, 3D Gaussians, and meshes. This is achieved by integrating a sparsely-populated 3D grid with dense multiview visual features extracted from a powerful vision foundation model, comprehensively capturing both structural (geometry) and textural (appearance) information while maintaining flexibility during decoding. We employ rectified flow transformers tailored for SLAT as our 3D generation models and train models with up to 2 billion parameters on a large 3D asset dataset of 500K diverse objects. Our model generates high-quality results with text or image conditions, significantly surpassing existing methods, including recent ones at similar scales. We showcase flexible output format selection and local 3D editing capabilities which were not offered by previous models. Code, model, and data will be released.

The multi-modal nature of many vision problems calls for neural network architectures that can perform multiple tasks concurrently. Typically, such architectures have been handcrafted in the literature. However, given the size and complexity of the problem, this manual architecture exploration likely exceeds human design abilities. In this paper, we propose a principled approach, rooted in differentiable neural architecture search, to automatically define branching (tree-like) structures in the encoding stage of a multi-task neural network. To allow flexibility within resource-constrained environments, we introduce a proxyless, resource-aware loss that dynamically controls the model size. Evaluations across a variety of dense prediction tasks show that our approach consistently finds high-performing branching structures within limited resource budgets.

Learning effective representations of source code is critical for any Machine Learning for Software Engineering (ML4SE) system. Inspired by natural language processing, large language models (LLMs) like Codex and CodeGen treat code as generic sequences of text and are trained on huge corpora of code data, achieving state of the art performance on several software engineering (SE) tasks. However, valid source code, unlike natural language, follows a strict structure and pattern governed by the underlying grammar of the programming language. Current LLMs do not exploit this property of the source code as they treat code like a sequence of tokens and overlook key structural and semantic properties of code that can be extracted from code-views like the Control Flow Graph (CFG), Data Flow Graph (DFG), Abstract Syntax Tree (AST), etc. Unfortunately, the process of generating and integrating code-views for every programming language is cumbersome and time consuming. To overcome this barrier, we propose our tool COMEX - a framework that allows researchers and developers to create and combine multiple code-views which can be used by machine learning (ML) models for various SE tasks. Some salient features of our tool are: (i) it works directly on source code (which need not be compilable), (ii) it currently supports Java and C#, (iii) it can analyze both method-level snippets and program-level snippets by using both intra-procedural and inter-procedural analysis, and (iv) it is easily extendable to other languages as it is built on tree-sitter - a widely used incremental parser that supports over 40 languages. We believe this easy-to-use code-view generation and customization tool will give impetus to research in source code representation learning methods and ML4SE. Tool: https://pypi.org/project/comex - GitHub: https://github.com/IBM/tree-sitter-codeviews - Demo: https://youtu.be/GER6U87FVbU

The capabilities and adoption of deep neural networks (DNNs) grow at an exhilarating pace: Vision models accurately classify human actions in videos and identify cancerous tissue in medical scans as precisely than human experts; large language models answer wide-ranging questions, generate code, and write prose, becoming the topic of everyday dinner-table conversations. Even though their uses are exhilarating, the continually increasing model sizes and computational complexities have a dark side. The economic cost and negative environmental externalities of training and serving models is in evident disharmony with financial viability and climate action goals. Instead of pursuing yet another increase in predictive performance, this dissertation is dedicated to the improvement of neural network efficiency. Specifically, a core contribution addresses the efficiency aspects during online inference. Here, the concept of Continual Inference Networks (CINs) is proposed and explored across four publications. CINs extend prior state-of-the-art methods developed for offline processing of spatio-temporal data and reuse their pre-trained weights, improving their online processing efficiency by an order of magnitude. These advances are attained through a bottom-up computational reorganization and judicious architectural modifications. The benefit to online inference is demonstrated by reformulating several widely used network architectures into CINs, including 3D CNNs, ST-GCNs, and Transformer Encoders. An orthogonal contribution tackles the concurrent adaptation and computational acceleration of a large source model into multiple lightweight derived models. Drawing on fusible adapter networks and structured pruning, Structured Pruning Adapters achieve superior predictive accuracy under aggressive pruning using significantly fewer learned weights compared to fine-tuning with pruning.

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the guidance from the domain expert in the form of high-level instructions can be essential for an automated system to output candidate crystals that are viable for downstream research. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives of directly using language models to generate structures both in satisfying user request and in generating low-energy structures. We confirm that GenMS is able to generate common crystal structures such as double perovskites, or spinels, solely from natural language input, and hence can form the foundation for more complex structure generation in near future.

Hierarchical clustering of networks consists in finding a tree of communities, such that lower levels of the hierarchy reveal finer-grained community structures. There are two main classes of algorithms tackling this problem. Divisive (top-down) algorithms recursively partition the nodes into two communities, until a stopping rule indicates that no further split is needed. In contrast, agglomerative (bottom-up) algorithms first identify the smallest community structure and then repeatedly merge the communities using a linkage method. In this article, we establish theoretical guarantees for the recovery of the hierarchical tree and community structure of a Hierarchical Stochastic Block Model by a bottom-up algorithm. We also establish that this bottom-up algorithm attains the information-theoretic threshold for exact recovery at intermediate levels of the hierarchy. Notably, these recovery conditions are less restrictive compared to those existing for top-down algorithms. This shows that bottom-up algorithms extend the feasible region for achieving exact recovery at intermediate levels. Numerical experiments on both synthetic and real data sets confirm the superiority of bottom-up algorithms over top-down algorithms. We also observe that top-down algorithms can produce dendrograms with inversions. These findings contribute to a better understanding of hierarchical clustering techniques and their applications in network analysis.

Recently, there has been growing interest in developing learning-based methods to detect and utilize salient semi-global or global structures, such as junctions, lines, planes, cuboids, smooth surfaces, and all types of symmetries, for 3D scene modeling and understanding. However, the ground truth annotations are often obtained via human labor, which is particularly challenging and inefficient for such tasks due to the large number of 3D structure instances (e.g., line segments) and other factors such as viewpoints and occlusions. In this paper, we present a new synthetic dataset, Structured3D, with the aim of providing large-scale photo-realistic images with rich 3D structure annotations for a wide spectrum of structured 3D modeling tasks. We take advantage of the availability of professional interior designs and automatically extract 3D structures from them. We generate high-quality images with an industry-leading rendering engine. We use our synthetic dataset in combination with real images to train deep networks for room layout estimation and demonstrate improved performance on benchmark datasets.

Knowledge of tree species distribution is fundamental to managing forests. New deep learning approaches promise significant accuracy gains for forest mapping, and are becoming a critical tool for mapping multiple tree species at scale. To advance the field, deep learning researchers need large benchmark datasets with high-quality annotations. To this end, we present the PureForest dataset: a large-scale, open, multimodal dataset designed for tree species classification from both Aerial Lidar Scanning (ALS) point clouds and Very High Resolution (VHR) aerial images. Most current public Lidar datasets for tree species classification have low diversity as they only span a small area of a few dozen annotated hectares at most. In contrast, PureForest has 18 tree species grouped into 13 semantic classes, and spans 339 km^2 across 449 distinct monospecific forests, and is to date the largest and most comprehensive Lidar dataset for the identification of tree species. By making PureForest publicly available, we hope to provide a challenging benchmark dataset to support the development of deep learning approaches for tree species identification from Lidar and/or aerial imagery. In this data paper, we describe the annotation workflow, the dataset, the recommended evaluation methodology, and establish a baseline performance from both 3D and 2D modalities.

Generalizable articulated object manipulation is essential for home-assistant robots. Recent efforts focus on imitation learning from demonstrations or reinforcement learning in simulation, however, due to the prohibitive costs of real-world data collection and precise object simulation, it still remains challenging for these works to achieve broad adaptability across diverse articulated objects. Recently, many works have tried to utilize the strong in-context learning ability of Large Language Models (LLMs) to achieve generalizable robotic manipulation, but most of these researches focus on high-level task planning, sidelining low-level robotic control. In this work, building on the idea that the kinematic structure of the object determines how we can manipulate it, we propose a kinematic-aware prompting framework that prompts LLMs with kinematic knowledge of objects to generate low-level motion trajectory waypoints, supporting various object manipulation. To effectively prompt LLMs with the kinematic structure of different objects, we design a unified kinematic knowledge parser, which represents various articulated objects as a unified textual description containing kinematic joints and contact location. Building upon this unified description, a kinematic-aware planner model is proposed to generate precise 3D manipulation waypoints via a designed kinematic-aware chain-of-thoughts prompting method. Our evaluation spanned 48 instances across 16 distinct categories, revealing that our framework not only outperforms traditional methods on 8 seen categories but also shows a powerful zero-shot capability for 8 unseen articulated object categories. Moreover, the real-world experiments on 7 different object categories prove our framework's adaptability in practical scenarios. Code is released at https://github.com/GeWu-Lab/LLM_articulated_object_manipulation/tree/main.

The rapid development of AI systems has been greatly influenced by the emergence of foundation models. A common approach for targeted problems involves fine-tuning these pre-trained foundation models for specific target tasks, resulting in a rapid spread of models fine-tuned across a diverse array of tasks. This work focuses on the problem of merging multiple fine-tunings of the same foundation model derived from a spectrum of auxiliary tasks. We introduce a new simple method, Model Breadcrumbs, which consists of a sparsely defined set of weights that carve out a trajectory within the weight space of a pre-trained model, enhancing task performance when traversed. These breadcrumbs are constructed by subtracting the weights from a pre-trained model before and after fine-tuning, followed by a sparsification process that eliminates weight outliers and negligible perturbations. Our experiments demonstrate the effectiveness of Model Breadcrumbs to simultaneously improve performance across multiple tasks. This contribution aligns with the evolving paradigm of updatable machine learning, reminiscent of the collaborative principles underlying open-source software development, fostering a community-driven effort to reliably update machine learning models. Our method is shown to be more efficient and unlike previous proposals does not require hyperparameter tuning for each new task added. Through extensive experimentation involving various models, tasks, and modalities we establish that integrating Model Breadcrumbs offers a simple, efficient, and highly effective approach for constructing multi-task models and facilitating updates to foundation models.

Articulated 3D reconstruction has valuable applications in various domains, yet it remains costly and demands intensive work from domain experts. Recent advancements in template-free learning methods show promising results with monocular videos. Nevertheless, these approaches necessitate a comprehensive coverage of all viewpoints of the subject in the input video, thus limiting their applicability to casually captured videos from online sources. In this work, we study articulated 3D shape reconstruction from a single and casually captured internet video, where the subject's view coverage is incomplete. We propose DreaMo that jointly performs shape reconstruction while solving the challenging low-coverage regions with view-conditioned diffusion prior and several tailored regularizations. In addition, we introduce a skeleton generation strategy to create human-interpretable skeletons from the learned neural bones and skinning weights. We conduct our study on a self-collected internet video collection characterized by incomplete view coverage. DreaMo shows promising quality in novel-view rendering, detailed articulated shape reconstruction, and skeleton generation. Extensive qualitative and quantitative studies validate the efficacy of each proposed component, and show existing methods are unable to solve correct geometry due to the incomplete view coverage.

We present DreamCraft3D, a hierarchical 3D content generation method that produces high-fidelity and coherent 3D objects. We tackle the problem by leveraging a 2D reference image to guide the stages of geometry sculpting and texture boosting. A central focus of this work is to address the consistency issue that existing works encounter. To sculpt geometries that render coherently, we perform score distillation sampling via a view-dependent diffusion model. This 3D prior, alongside several training strategies, prioritizes the geometry consistency but compromises the texture fidelity. We further propose Bootstrapped Score Distillation to specifically boost the texture. We train a personalized diffusion model, Dreambooth, on the augmented renderings of the scene, imbuing it with 3D knowledge of the scene being optimized. The score distillation from this 3D-aware diffusion prior provides view-consistent guidance for the scene. Notably, through an alternating optimization of the diffusion prior and 3D scene representation, we achieve mutually reinforcing improvements: the optimized 3D scene aids in training the scene-specific diffusion model, which offers increasingly view-consistent guidance for 3D optimization. The optimization is thus bootstrapped and leads to substantial texture boosting. With tailored 3D priors throughout the hierarchical generation, DreamCraft3D generates coherent 3D objects with photorealistic renderings, advancing the state-of-the-art in 3D content generation. Code available at https://github.com/deepseek-ai/DreamCraft3D.

3D Reconstruction of moving articulated objects without additional information about object structure is a challenging problem. Current methods overcome such challenges by employing category-specific skeletal models. Consequently, they do not generalize well to articulated objects in the wild. We treat an articulated object as an unknown, semi-rigid skeletal structure surrounded by nonrigid material (e.g., skin). Our method simultaneously estimates the visible (explicit) representation (3D shapes, colors, camera parameters) and the implicit skeletal representation, from motion cues in the object video without 3D supervision. Our implicit representation consists of four parts. (1) Skeleton, which specifies how semi-rigid parts are connected. (2) black{Skinning Weights}, which associates each surface vertex with semi-rigid parts with probability. (3) Rigidity Coefficients, specifying the articulation of the local surface. (4) Time-Varying Transformations, which specify the skeletal motion and surface deformation parameters. We introduce an algorithm that uses physical constraints as regularization terms and iteratively estimates both implicit and explicit representations. Our method is category-agnostic, thus eliminating the need for category-specific skeletons, we show that our method outperforms state-of-the-art across standard video datasets.

Business Intelligence (BI) is crucial in modern enterprises and billion-dollar business. Traditionally, technical experts like database administrators would manually prepare BI-models (e.g., in star or snowflake schemas) that join tables in data warehouses, before less-technical business users can run analytics using end-user dashboarding tools. However, the popularity of self-service BI (e.g., Tableau and Power-BI) in recent years creates a strong demand for less technical end-users to build BI-models themselves. We develop an Auto-BI system that can accurately predict BI models given a set of input tables, using a principled graph-based optimization problem we propose called k-Min-Cost-Arborescence (k-MCA), which holistically considers both local join prediction and global schema-graph structures, leveraging a graph-theoretical structure called arborescence. While we prove k-MCA is intractable and inapproximate in general, we develop novel algorithms that can solve k-MCA optimally, which is shown to be efficient in practice with sub-second latency and can scale to the largest BI-models we encounter (with close to 100 tables). Auto-BI is rigorously evaluated on a unique dataset with over 100K real BI models we harvested, as well as on 4 popular TPC benchmarks. It is shown to be both efficient and accurate, achieving over 0.9 F1-score on both real and synthetic benchmarks.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

Several approaches are proposed to deal with the problem of the Automatic Schema Matching (ASM). The challenges and difficulties caused by the complexity and uncertainty characterizing both the process and the outcome of Schema Matching motivated us to investigate how bio-inspired emerging paradigm can help with understanding, managing, and ultimately overcoming those challenges. In this paper, we explain how we approached Automatic Schema Matching as a systemic and Complex Adaptive System (CAS) and how we modeled it using the approach of Agent-Based Modeling and Simulation (ABMS). This effort gives birth to a tool (prototype) for schema matching called Reflex-SMAS. A set of experiments demonstrates the viability of our approach on two main aspects: (i) effectiveness (increasing the quality of the found matchings) and (ii) efficiency (reducing the effort required for this efficiency). Our approach represents a significant paradigm-shift, in the field of Automatic Schema Matching.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Given thousands of equally accurate machine learning (ML) models, how can users choose among them? A recent ML technique enables domain experts and data scientists to generate a complete Rashomon set for sparse decision trees--a huge set of almost-optimal interpretable ML models. To help ML practitioners identify models with desirable properties from this Rashomon set, we develop TimberTrek, the first interactive visualization system that summarizes thousands of sparse decision trees at scale. Two usage scenarios highlight how TimberTrek can empower users to easily explore, compare, and curate models that align with their domain knowledge and values. Our open-source tool runs directly in users' computational notebooks and web browsers, lowering the barrier to creating more responsible ML models. TimberTrek is available at the following public demo link: https://poloclub.github.io/timbertrek.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

In this paper, we push the boundaries of fine-grained 3D generation into truly creative territory. Current methods either lack intricate details or simply mimic existing objects -- we enable both. By lifting 2D fine-grained understanding into 3D through multi-view diffusion and modeling part latents as continuous distributions, we unlock the ability to generate entirely new, yet plausible parts through interpolation and sampling. A self-supervised feature consistency loss further ensures stable generation of these unseen parts. The result is the first system capable of creating novel 3D objects with species-specific details that transcend existing examples. While we demonstrate our approach on birds, the underlying framework extends beyond things that can chirp! Code will be released at https://github.com/kamwoh/chirpy3d.

Low-precision formats such as float8 have been introduced in machine learning accelerated hardware to improve computational efficiency for large language models training and inference. Nevertheless, adoption by the ML community has been slowed down by the complex, and sometimes brittle, techniques required to match higher precision training accuracy. In this work, we present Scalify, a end-to-end scale propagation paradigm for computational graphs, generalizing and formalizing existing tensor scaling methods. Experiment results show that Scalify supports out-of-the-box float8 matrix multiplication and gradients representation, as well as float16 optimizer state storage. Our JAX implementation of Scalify is open-sourced at https://github.com/graphcore-research/jax-scalify

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

Timber represents an increasingly valuable and versatile resource. However, forestry operations such as harvesting, handling and measuring logs still require substantial human labor in remote environments posing significant safety risks. Progressively automating these tasks has the potential of increasing their efficiency as well as safety, but requires an accurate detection of individual logs as well as live trees and their context. Although initial approaches have been proposed for this challenging application domain, specialized data and algorithms are still too scarce to develop robust solutions. To mitigate this gap, we introduce the TimberVision dataset, consisting of more than 2k annotated RGB images containing a total of 51k trunk components including cut and lateral surfaces, thereby surpassing any existing dataset in this domain in terms of both quantity and detail by a large margin. Based on this data, we conduct a series of ablation experiments for oriented object detection and instance segmentation and evaluate the influence of multiple scene parameters on model performance. We introduce a generic framework to fuse the components detected by our models for both tasks into unified trunk representations. Furthermore, we automatically derive geometric properties and apply multi-object tracking to further enhance robustness. Our detection and tracking approach provides highly descriptive and accurate trunk representations solely from RGB image data, even under challenging environmental conditions. Our solution is suitable for a wide range of application scenarios and can be readily combined with other sensor modalities.

Large language models (LLMs) have demonstrated remarkable potential in solving complex tasks across diverse domains, typically by employing agentic workflows that follow detailed instructions and operational sequences. However, constructing these workflows requires significant human effort, limiting scalability and generalizability. Recent research has sought to automate the generation and optimization of these workflows, but existing methods still rely on initial manual setup and fall short of achieving fully automated and effective workflow generation. To address this challenge, we reformulate workflow optimization as a search problem over code-represented workflows, where LLM-invoking nodes are connected by edges. We introduce AFlow, an automated framework that efficiently explores this space using Monte Carlo Tree Search, iteratively refining workflows through code modification, tree-structured experience, and execution feedback. Empirical evaluations across six benchmark datasets demonstrate AFlow's efficacy, yielding a 5.7% average improvement over state-of-the-art baselines. Furthermore, AFlow enables smaller models to outperform GPT-4o on specific tasks at 4.55% of its inference cost in dollars. The code will be available at https://github.com/geekan/MetaGPT.

Despite much progress in large 3D datasets there are currently few interactive 3D object datasets, and their scale is limited due to the manual effort required in their construction. We introduce the static to openable (S2O) task which creates interactive articulated 3D objects from static counterparts through openable part detection, motion prediction, and interior geometry completion. We formulate a unified framework to tackle this task, and curate a challenging dataset of openable 3D objects that serves as a test bed for systematic evaluation. Our experiments benchmark methods from prior work and simple yet effective heuristics for the S2O task. We find that turning static 3D objects into interactively openable counterparts is possible but that all methods struggle to generalize to realistic settings of the task, and we highlight promising future work directions.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Automated code generation with large language models has gained significant traction, but there remains no guarantee on the correctness of generated code. We aim to use formal verification to provide mathematical guarantees that the generated code is correct. However, generating formally verified code with LLMs is hindered by the scarcity of training data and the complexity of formal proofs. To tackle this challenge, we introduce AlphaVerus, a self-improving framework that bootstraps formally verified code generation by iteratively translating programs from a higher-resource language and leveraging feedback from a verifier. AlphaVerus operates in three phases: exploration of candidate translations, Treefinement -- a novel tree search algorithm for program refinement using verifier feedback, and filtering misaligned specifications and programs to prevent reward hacking. Through this iterative process, AlphaVerus enables a LLaMA-3.1-70B model to generate verified code without human intervention or model finetuning. AlphaVerus shows an ability to generate formally verified solutions for HumanEval and MBPP, laying the groundwork for truly trustworthy code-generation agents.

Computer-Aided Design (CAD) model reconstruction from point clouds is an important problem at the intersection of computer vision, graphics, and machine learning; it saves the designer significant time when iterating on in-the-wild objects. Recent advancements in this direction achieve relatively reliable semantic segmentation but still struggle to produce an adequate topology of the CAD model. In this work, we analyze the current state of the art for that ill-posed task and identify shortcomings of existing methods. We propose a hybrid analytic-neural reconstruction scheme that bridges the gap between segmented point clouds and structured CAD models and can be readily combined with different segmentation backbones. Moreover, to power the surface fitting stage, we propose a novel implicit neural representation of freeform surfaces, driving up the performance of our overall CAD reconstruction scheme. We extensively evaluate our method on the popular ABC benchmark of CAD models and set a new state-of-the-art for that dataset. Project page: https://www.obukhov.ai/point2cad}{https://www.obukhov.ai/point2cad.

Recent works on text-to-3d generation show that using only 2D diffusion supervision for 3D generation tends to produce results with inconsistent appearances (e.g., faces on the back view) and inaccurate shapes (e.g., animals with extra legs). Existing methods mainly address this issue by retraining diffusion models with images rendered from 3D data to ensure multi-view consistency while struggling to balance 2D generation quality with 3D consistency. In this paper, we present a new framework Sculpt3D that equips the current pipeline with explicit injection of 3D priors from retrieved reference objects without re-training the 2D diffusion model. Specifically, we demonstrate that high-quality and diverse 3D geometry can be guaranteed by keypoints supervision through a sparse ray sampling approach. Moreover, to ensure accurate appearances of different views, we further modulate the output of the 2D diffusion model to the correct patterns of the template views without altering the generated object's style. These two decoupled designs effectively harness 3D information from reference objects to generate 3D objects while preserving the generation quality of the 2D diffusion model. Extensive experiments show our method can largely improve the multi-view consistency while retaining fidelity and diversity. Our project page is available at: https://stellarcheng.github.io/Sculpt3D/.

We introduce HunyuanProver, an language model finetuned from the Hunyuan 7B for interactive automatic theorem proving with LEAN4. To alleviate the data sparsity issue, we design a scalable framework to iterative synthesize data with low cost. Besides, guided tree search algorithms are designed to enable effective ``system 2 thinking`` of the prover. HunyuanProver achieves state-of-the-art (SOTA) performances on major benchmarks. Specifically, it achieves a pass of 68.4% on the miniF2F-test compared to 65.9%, the current SOTA results. It proves 4 IMO statements (imo_1960_p2, imo_1962_p2}, imo_1964_p2 and imo_1983_p6) in miniF2F-test. To benefit the community, we will open-source a dataset of 30k synthesized instances, where each instance contains the original question in natural language, the converted statement by autoformalization, and the proof by HunyuanProver.

Precise reconstruction and manipulation of the crumpled cloths is challenging due to the high dimensionality of cloth models, as well as the limited observation at self-occluded regions. We leverage the recent progress in the field of single-view human reconstruction to template-based reconstruct crumpled cloths from their top-view depth observations only, with our proposed sim-real registration protocols. In contrast to previous implicit cloth representations, our reconstruction mesh explicitly describes the positions and visibilities of the entire cloth mesh vertices, enabling more efficient dual-arm and single-arm target-oriented manipulations. Experiments demonstrate that our TRTM system can be applied to daily cloths that have similar topologies as our template mesh, but with different shapes, sizes, patterns, and physical properties. Videos, datasets, pre-trained models, and code can be downloaded from our project website: https://wenbwa.github.io/TRTM/ .

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

Creating large-scale interactive 3D environments is essential for the development of Robotics and Embodied AI research. Current methods, including manual design, procedural generation, diffusion-based scene generation, and large language model (LLM) guided scene design, are hindered by limitations such as excessive human effort, reliance on predefined rules or training datasets, and limited 3D spatial reasoning ability. Since pre-trained 2D image generative models better capture scene and object configuration than LLMs, we address these challenges by introducing Architect, a generative framework that creates complex and realistic 3D embodied environments leveraging diffusion-based 2D image inpainting. In detail, we utilize foundation visual perception models to obtain each generated object from the image and leverage pre-trained depth estimation models to lift the generated 2D image to 3D space. Our pipeline is further extended to a hierarchical and iterative inpainting process to continuously generate placement of large furniture and small objects to enrich the scene. This iterative structure brings the flexibility for our method to generate or refine scenes from various starting points, such as text, floor plans, or pre-arranged environments.

The K-core of a graph is the unique maximum subgraph within which each vertex connects to at least K other vertices. The K-core optimal attack problem asks to construct a minimum-sized set of vertices whose removal results in the complete collapse of the K-core. In this paper, we construct a hierarchical cycle-tree packing model which converts a long-range correlated K-core pruning process into static patterns and analyze this model through the replica-symmetric (RS) cavity method of statistical physics. The cycle-tree guided attack (CTGA) message-passing algorithm exhibits superior performance on random regular and Erdos-Renyi graphs. It provides new upper bounds on the minimal cardinality of the K-core attack set. The model of this work may be extended to construct optimal initial conditions for other irreversible dynamical processes.

Motion synthesis for diverse object categories holds great potential for 3D content creation but remains underexplored due to two key challenges: (1) the lack of comprehensive motion datasets that include a wide range of high-quality motions and annotations, and (2) the absence of methods capable of handling heterogeneous skeletal templates from diverse objects. To address these challenges, we contribute the following: First, we augment the Truebones Zoo dataset, a high-quality animal motion dataset covering over 70 species, by annotating it with detailed text descriptions, making it suitable for text-based motion synthesis. Second, we introduce rig augmentation techniques that generate diverse motion data while preserving consistent dynamics, enabling models to adapt to various skeletal configurations. Finally, we redesign existing motion diffusion models to dynamically adapt to arbitrary skeletal templates, enabling motion synthesis for a diverse range of objects with varying structures. Experiments show that our method learns to generate high-fidelity motions from textual descriptions for diverse and even unseen objects, setting a strong foundation for motion synthesis across diverse object categories and skeletal templates. Qualitative results are available on this link: t2m4lvo.github.io

Global vegetation structure mapping is critical for understanding the global carbon cycle and maximizing the efficacy of nature-based carbon sequestration initiatives. Moreover, vegetation structure mapping can help reduce the impacts of climate change by, for example, guiding actions to improve water security, increase biodiversity and reduce flood risk. Global satellite measurements provide an important set of observations for monitoring and managing deforestation and degradation of existing forests, natural forest regeneration, reforestation, biodiversity restoration, and the implementation of sustainable agricultural practices. In this paper, we explore the effectiveness of fine-tuning of a geospatial foundation model to estimate above-ground biomass (AGB) using space-borne data collected across different eco-regions in Brazil. The fine-tuned model architecture consisted of a Swin-B transformer as the encoder (i.e., backbone) and a single convolutional layer for the decoder head. All results were compared to a U-Net which was trained as the baseline model Experimental results of this sparse-label prediction task demonstrate that the fine-tuned geospatial foundation model with a frozen encoder has comparable performance to a U-Net trained from scratch. This is despite the fine-tuned model having 13 times less parameters requiring optimization, which saves both time and compute resources. Further, we explore the transfer-learning capabilities of the geospatial foundation models by fine-tuning on satellite imagery with sparse labels from different eco-regions in Brazil.

Domain adaptation aims to mitigate distribution shifts among different domains. However, traditional formulations are mostly limited to categorical domains, greatly simplifying nuanced domain relationships in the real world. In this work, we tackle a generalization with taxonomy-structured domains, which formalizes domains with nested, hierarchical similarity structures such as animal species and product catalogs. We build on the classic adversarial framework and introduce a novel taxonomist, which competes with the adversarial discriminator to preserve the taxonomy information. The equilibrium recovers the classic adversarial domain adaptation's solution if given a non-informative domain taxonomy (e.g., a flat taxonomy where all leaf nodes connect to the root node) while yielding non-trivial results with other taxonomies. Empirically, our method achieves state-of-the-art performance on both synthetic and real-world datasets with successful adaptation. Code is available at https://github.com/Wang-ML-Lab/TSDA.

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

sec:abstract Large Language Models (LLMs) have shown promise in assisting scientific discovery. However, such applications are currently limited by LLMs' deficiencies in understanding intricate scientific concepts, deriving symbolic equations, and solving advanced numerical calculations. To bridge these gaps, we introduce SciGLM, a suite of scientific language models able to conduct college-level scientific reasoning. Central to our approach is a novel self-reflective instruction annotation framework to address the data scarcity challenge in the science domain. This framework leverages existing LLMs to generate step-by-step reasoning for unlabelled scientific questions, followed by a process of self-reflective critic-and-revise. Applying this framework, we curated SciInstruct, a diverse and high-quality dataset encompassing mathematics, physics, chemistry, and formal proofs. We fine-tuned the ChatGLM family of language models with SciInstruct, enhancing their capabilities in scientific and mathematical reasoning. Remarkably, SciGLM consistently improves both the base model (ChatGLM3-6B-Base) and larger-scale models (12B and 32B), without sacrificing the language understanding capabilities of the base model. This makes SciGLM a suitable foundational model to facilitate diverse scientific discovery tasks. For the benefit of the wider research community, we release SciInstruct, SciGLM, alongside a self-reflective framework and fine-tuning code at https://github.com/THUDM/SciGLM.

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

This paper presents a novel generative model for Computer Aided Design (CAD) that 1) represents high-level design concepts of a CAD model as a three-level hierarchical tree of neural codes, from global part arrangement down to local curve geometry; and 2) controls the generation or completion of CAD models by specifying the target design using a code tree. Concretely, a novel variant of a vector quantized VAE with "masked skip connection" extracts design variations as neural codebooks at three levels. Two-stage cascaded auto-regressive transformers learn to generate code trees from incomplete CAD models and then complete CAD models following the intended design. Extensive experiments demonstrate superior performance on conventional tasks such as random generation while enabling novel interaction capabilities on conditional generation tasks. The code is available at https://github.com/samxuxiang/hnc-cad.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

We study the problem of few-shot physically-aware articulated mesh generation. By observing an articulated object dataset containing only a few examples, we wish to learn a model that can generate diverse meshes with high visual fidelity and physical validity. Previous mesh generative models either have difficulties in depicting a diverse data space from only a few examples or fail to ensure physical validity of their samples. Regarding the above challenges, we propose two key innovations, including 1) a hierarchical mesh deformation-based generative model based upon the divide-and-conquer philosophy to alleviate the few-shot challenge by borrowing transferrable deformation patterns from large scale rigid meshes and 2) a physics-aware deformation correction scheme to encourage physically plausible generations. We conduct extensive experiments on 6 articulated categories to demonstrate the superiority of our method in generating articulated meshes with better diversity, higher visual fidelity, and better physical validity over previous methods in the few-shot setting. Further, we validate solid contributions of our two innovations in the ablation study. Project page with code is available at https://meowuu7.github.io/few-arti-obj-gen.

Significant progress has been made in training large generative models for natural language and images. Yet, the advancement of 3D generative models is hindered by their substantial resource demands for training, along with inefficient, non-compact, and less expressive representations. This paper introduces Make-A-Shape, a new 3D generative model designed for efficient training on a vast scale, capable of utilizing 10 millions publicly-available shapes. Technical-wise, we first innovate a wavelet-tree representation to compactly encode shapes by formulating the subband coefficient filtering scheme to efficiently exploit coefficient relations. We then make the representation generatable by a diffusion model by devising the subband coefficients packing scheme to layout the representation in a low-resolution grid. Further, we derive the subband adaptive training strategy to train our model to effectively learn to generate coarse and detail wavelet coefficients. Last, we extend our framework to be controlled by additional input conditions to enable it to generate shapes from assorted modalities, e.g., single/multi-view images, point clouds, and low-resolution voxels. In our extensive set of experiments, we demonstrate various applications, such as unconditional generation, shape completion, and conditional generation on a wide range of modalities. Our approach not only surpasses the state of the art in delivering high-quality results but also efficiently generates shapes within a few seconds, often achieving this in just 2 seconds for most conditions.

Generative machine learning models are increasingly being used to design novel proteins for therapeutic and biotechnological applications. However, the current methods mostly focus on the design of proteins with a fixed backbone structure, which leads to their limited ability to account for protein flexibility, one of the crucial properties for protein function. Learning to engineer protein flexibility is problematic because the available data are scarce, heterogeneous, and costly to obtain using computational as well as experimental methods. Our contributions to address this problem are three-fold. First, we comprehensively compare methods for quantifying protein flexibility and identify data relevant to learning. Second, we design and train flexibility predictors utilizing sequential or both sequential and structural information on the input. We overcome the data scarcity issue by leveraging a pre-trained protein language model. Third, we introduce a method for fine-tuning a protein inverse folding model to steer it toward desired flexibility in specified regions. We demonstrate that our method Flexpert-Design enables guidance of inverse folding models toward increased flexibility. This opens up new possibilities for protein flexibility engineering and the development of proteins with enhanced biological activities.

Hyperbolic geometry is gaining traction in machine learning for its effectiveness at capturing hierarchical structures in real-world data. Hyperbolic spaces, where neighborhoods grow exponentially, offer substantial advantages and consistently deliver state-of-the-art results across diverse applications. However, hyperbolic classifiers often grapple with computational challenges. Methods reliant on Riemannian optimization frequently exhibit sluggishness, stemming from the increased computational demands of operations on Riemannian manifolds. In response to these challenges, we present hyperDT, a novel extension of decision tree algorithms into hyperbolic space. Crucially, hyperDT eliminates the need for computationally intensive Riemannian optimization, numerically unstable exponential and logarithmic maps, or pairwise comparisons between points by leveraging inner products to adapt Euclidean decision tree algorithms to hyperbolic space. Our approach is conceptually straightforward and maintains constant-time decision complexity while mitigating the scalability issues inherent in high-dimensional Euclidean spaces. Building upon hyperDT we introduce hyperRF, a hyperbolic random forest model. Extensive benchmarking across diverse datasets underscores the superior performance of these models, providing a swift, precise, accurate, and user-friendly toolkit for hyperbolic data analysis.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

Triggered by limitations of graph-based deep learning methods in terms of computational expressivity and model flexibility, recent years have seen a surge of interest in computational models that operate on higher-order topological domains such as hypergraphs and simplicial complexes. While the increased expressivity of these models can indeed lead to a better classification performance and a more faithful representation of the underlying system, the computational cost of these higher-order models can increase dramatically. To this end, we here explore a simplicial complex neural network learning architecture based on random walks and fast 1D convolutions (SCRaWl), in which we can adjust the increase in computational cost by varying the length and number of random walks considered while accounting for higher-order relationships. Importantly, due to the random walk-based design, the expressivity of the proposed architecture is provably incomparable to that of existing message-passing simplicial neural networks. We empirically evaluate SCRaWl on real-world datasets and show that it outperforms other simplicial neural networks.

The rapid development of AR/VR brings tremendous demands for 3D content. While the widely-used Computer-Aided Design (CAD) method requires a time-consuming and labor-intensive modeling process, sketch-based 3D modeling offers a potential solution as a natural form of computer-human interaction. However, the sparsity and ambiguity of sketches make it challenging to generate high-fidelity content reflecting creators' ideas. Precise drawing from multiple views or strategic step-by-step drawings is often required to tackle the challenge but is not friendly to novice users. In this work, we introduce a novel end-to-end approach, Deep3DSketch+, which performs 3D modeling using only a single free-hand sketch without inputting multiple sketches or view information. Specifically, we introduce a lightweight generation network for efficient inference in real-time and a structural-aware adversarial training approach with a Stroke Enhancement Module (SEM) to capture the structural information to facilitate learning of the realistic and fine-detailed shape structures for high-fidelity performance. Extensive experiments demonstrated the effectiveness of our approach with the state-of-the-art (SOTA) performance on both synthetic and real datasets.

We present two new classes of algorithms for efficient field integration on graphs encoding point clouds. The first class, SeparatorFactorization(SF), leverages the bounded genus of point cloud mesh graphs, while the second class, RFDiffusion(RFD), uses popular epsilon-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g., shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (particularly for mesh-dynamics modeling), Wasserstein distance computations for point clouds, and the Gromov-Wasserstein variant.

There are few known exponential speedups for quantum algorithms and these tend to fall into even fewer families. One speedup that has mostly resisted generalization is the use of quantum walks to traverse the welded-tree graph, due to Childs, Cleve, Deotto, Farhi, Gutmann, and Spielman. We show how to generalize this to a large class of hierarchical graphs in which the vertices are grouped into "supervertices" which are arranged according to a d-dimensional lattice. Supervertices can have different sizes, and edges between supervertices correspond to random connections between their constituent vertices. The hitting times of quantum walks on these graphs are related to the localization properties of zero modes in certain disordered tight binding Hamiltonians. The speedups range from superpolynomial to exponential, depending on the underlying dimension and the random graph model. We also provide concrete realizations of these hierarchical graphs, and introduce a general method for constructing graphs with efficient quantum traversal times using graph sparsification.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

The lifting of 3D structure and camera from 2D landmarks is at the cornerstone of the entire discipline of computer vision. Traditional methods have been confined to specific rigid objects, such as those in Perspective-n-Point (PnP) problems, but deep learning has expanded our capability to reconstruct a wide range of object classes (e.g. C3PDO and PAUL) with resilience to noise, occlusions, and perspective distortions. All these techniques, however, have been limited by the fundamental need to establish correspondences across the 3D training data -- significantly limiting their utility to applications where one has an abundance of "in-correspondence" 3D data. Our approach harnesses the inherent permutation equivariance of transformers to manage varying number of points per 3D data instance, withstands occlusions, and generalizes to unseen categories. We demonstrate state of the art performance across 2D-3D lifting task benchmarks. Since our approach can be trained across such a broad class of structures we refer to it simply as a 3D Lifting Foundation Model (3D-LFM) -- the first of its kind.

Existing single image-to-3D creation methods typically involve a two-stage process, first generating multi-view images, and then using these images for 3D reconstruction. However, training these two stages separately leads to significant data bias in the inference phase, thus affecting the quality of reconstructed results. We introduce a unified 3D generation framework, named Ouroboros3D, which integrates diffusion-based multi-view image generation and 3D reconstruction into a recursive diffusion process. In our framework, these two modules are jointly trained through a self-conditioning mechanism, allowing them to adapt to each other's characteristics for robust inference. During the multi-view denoising process, the multi-view diffusion model uses the 3D-aware maps rendered by the reconstruction module at the previous timestep as additional conditions. The recursive diffusion framework with 3D-aware feedback unites the entire process and improves geometric consistency.Experiments show that our framework outperforms separation of these two stages and existing methods that combine them at the inference phase. Project page: https://costwen.github.io/Ouroboros3D/

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

In 3D modeling, designers often use an existing 3D model as a reference to create new ones. This practice has inspired the development of Phidias, a novel generative model that uses diffusion for reference-augmented 3D generation. Given an image, our method leverages a retrieved or user-provided 3D reference model to guide the generation process, thereby enhancing the generation quality, generalization ability, and controllability. Our model integrates three key components: 1) meta-ControlNet that dynamically modulates the conditioning strength, 2) dynamic reference routing that mitigates misalignment between the input image and 3D reference, and 3) self-reference augmentations that enable self-supervised training with a progressive curriculum. Collectively, these designs result in a clear improvement over existing methods. Phidias establishes a unified framework for 3D generation using text, image, and 3D conditions with versatile applications.

Recent advances in synthetic methods enable designing subunits that self-assemble into structures with well-defined sizes and architectures, but yields are frequently suppressed by the formation of off-target metastable structures. Increasing the complexity (number of distinct inter-subunit interaction types) can inhibit off-target structures, but leads to slower kinetics and higher synthesis costs. Here, we use icosahedral shells formed of programmable triangular subunits as a model system, and identify design principles that produce the highest target yield at the lowest complexity. We use a symmetry-based construction to create a range of design complexities, starting from the maximal symmetry Caspar-Klug assembly up to the fully addressable, zero-symmetry assembly. Kinetic Monte Carlo simulations reveal that the most prominent defects leading to off-target assemblies are a class of disclinations. We derive symmetry-based rules for identifying the optimal (lowest-complexity, highest-symmetry) design that inhibits these disclinations, leading to robust, high-fidelity assembly of targets with arbitrarily large sizes. Optimal complexity varies non-monotonically with target size, with `magic' sizes appearing for high-symmetry designs in which symmetry axes do not intersect vertices of the triangular net. The optimal designs at magic sizes require 12 times fewer inequivalent interaction-types than the (minimal symmetry) fully addressable construction.

In this paper, we address the challenge of reconstructing general articulated 3D objects from a single video. Existing works employing dynamic neural radiance fields have advanced the modeling of articulated objects like humans and animals from videos, but face challenges with piece-wise rigid general articulated objects due to limitations in their deformation models. To tackle this, we propose Quasi-Rigid Blend Skinning, a novel deformation model that enhances the rigidity of each part while maintaining flexible deformation of the joints. Our primary insight combines three distinct approaches: 1) an enhanced bone rigging system for improved component modeling, 2) the use of quasi-sparse skinning weights to boost part rigidity and reconstruction fidelity, and 3) the application of geodesic point assignment for precise motion and seamless deformation. Our method outperforms previous works in producing higher-fidelity 3D reconstructions of general articulated objects, as demonstrated on both real and synthetic datasets. Project page: https://chaoyuesong.github.io/REACTO.

Compressing a predefined deep neural network (DNN) into a compact sub-network with competitive performance is crucial in the efficient machine learning realm. This topic spans various techniques, from structured pruning to neural architecture search, encompassing both pruning and erasing operators perspectives. Despite advancements, existing methods suffers from complex, multi-stage processes that demand substantial engineering and domain knowledge, limiting their broader applications. We introduce the third-generation Only-Train-Once (OTOv3), which first automatically trains and compresses a general DNN through pruning and erasing operations, creating a compact and competitive sub-network without the need of fine-tuning. OTOv3 simplifies and automates the training and compression process, minimizes the engineering efforts required from users. It offers key technological advancements: (i) automatic search space construction for general DNNs based on dependency graph analysis; (ii) Dual Half-Space Projected Gradient (DHSPG) and its enhanced version with hierarchical search (H2SPG) to reliably solve (hierarchical) structured sparsity problems and ensure sub-network validity; and (iii) automated sub-network construction using solutions from DHSPG/H2SPG and dependency graphs. Our empirical results demonstrate the efficacy of OTOv3 across various benchmarks in structured pruning and neural architecture search. OTOv3 produces sub-networks that match or exceed the state-of-the-arts. The source code will be available at https://github.com/tianyic/only_train_once.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Toward infinite-scale 3D city synthesis, we propose a novel framework, InfiniCity, which constructs and renders an unconstrainedly large and 3D-grounded environment from random noises. InfiniCity decomposes the seemingly impractical task into three feasible modules, taking advantage of both 2D and 3D data. First, an infinite-pixel image synthesis module generates arbitrary-scale 2D maps from the bird's-eye view. Next, an octree-based voxel completion module lifts the generated 2D map to 3D octrees. Finally, a voxel-based neural rendering module texturizes the voxels and renders 2D images. InfiniCity can thus synthesize arbitrary-scale and traversable 3D city environments, and allow flexible and interactive editing from users. We quantitatively and qualitatively demonstrate the efficacy of the proposed framework. Project page: https://hubert0527.github.io/infinicity/

Often we wish to predict a large number of variables that depend on each other as well as on other observed variables. Structured prediction methods are essentially a combination of classification and graphical modeling, combining the ability of graphical models to compactly model multivariate data with the ability of classification methods to perform prediction using large sets of input features. This tutorial describes conditional random fields, a popular probabilistic method for structured prediction. CRFs have seen wide application in natural language processing, computer vision, and bioinformatics. We describe methods for inference and parameter estimation for CRFs, including practical issues for implementing large scale CRFs. We do not assume previous knowledge of graphical modeling, so this tutorial is intended to be useful to practitioners in a wide variety of fields.

We introduce a new approach for generating realistic 3D models with UV maps through a representation termed "Object Images." This approach encapsulates surface geometry, appearance, and patch structures within a 64x64 pixel image, effectively converting complex 3D shapes into a more manageable 2D format. By doing so, we address the challenges of both geometric and semantic irregularity inherent in polygonal meshes. This method allows us to use image generation models, such as Diffusion Transformers, directly for 3D shape generation. Evaluated on the ABO dataset, our generated shapes with patch structures achieve point cloud FID comparable to recent 3D generative models, while naturally supporting PBR material generation.

Large foundation models, including large language models (LLMs), vision transformers (ViTs), diffusion, and LLM-based multimodal models, are revolutionizing the entire machine learning lifecycle, from training to deployment. However, the substantial advancements in versatility and performance these models offer come at a significant cost in terms of hardware resources. To support the growth of these large models in a scalable and environmentally sustainable way, there has been a considerable focus on developing resource-efficient strategies. This survey delves into the critical importance of such research, examining both algorithmic and systemic aspects. It offers a comprehensive analysis and valuable insights gleaned from existing literature, encompassing a broad array of topics from cutting-edge model architectures and training/serving algorithms to practical system designs and implementations. The goal of this survey is to provide an overarching understanding of how current approaches are tackling the resource challenges posed by large foundation models and to potentially inspire future breakthroughs in this field.

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

Vector Symbolic Architectures (VSAs) give a way to represent a complex object as a single fixed-length vector, so that similar objects have similar vector representations. These vector representations then become easy to use for machine learning or nearest-neighbor search. We review a previously proposed VSA method, MBAT (Matrix Binding of Additive Terms), which uses multiplication by random matrices for binding related terms. However, multiplying by such matrices introduces instabilities which can harm performance. Making the random matrices be orthogonal matrices provably fixes this problem. With respect to larger scale applications, we see how to apply MBAT vector representations for any data expressed in JSON. JSON is used in numerous programming languages to express complex data, but its native format appears highly unsuited for machine learning. Expressing JSON as a fixed-length vector makes it readily usable for machine learning and nearest-neighbor search. Creating such JSON vectors also shows that a VSA needs to employ binding operations that are non-commutative. VSAs are now ready to try with full-scale practical applications, including healthcare, pharmaceuticals, and genomics. Keywords: MBAT (Matrix Binding of Additive Terms), VSA (Vector Symbolic Architecture), HDC (Hyperdimensional Computing), Distributed Representations, Binding, Orthogonal Matrices, Recurrent Connections, Machine Learning, Search, JSON, VSA Applications

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

3D shape modeling is labor-intensive, time-consuming, and requires years of expertise. To facilitate 3D shape modeling, we propose a 3D shape generation network that takes a 3D VR sketch as a condition. We assume that sketches are created by novices without art training and aim to reconstruct geometrically realistic 3D shapes of a given category. To handle potential sketch ambiguity, our method creates multiple 3D shapes that align with the original sketch's structure. We carefully design our method, training the model step-by-step and leveraging multi-modal 3D shape representation to support training with limited training data. To guarantee the realism of generated 3D shapes we leverage the normalizing flow that models the distribution of the latent space of 3D shapes. To encourage the fidelity of the generated 3D shapes to an input sketch, we propose a dedicated loss that we deploy at different stages of the training process. The code is available at https://github.com/Rowl1ng/3Dsketch2shape.

Image-based 3D reconstruction has increasingly stunning results over the past few years with the latest improvements in computer vision and graphics. Geometry and topology are two fundamental concepts when dealing with 3D mesh structures. But the latest often remains a side issue in the 3D mesh-based reconstruction literature. Indeed, performing per-vertex elementary displacements over a 3D sphere mesh only impacts its geometry and leaves the topological structure unchanged and fixed. Whereas few attempts propose to update the geometry and the topology, all need to lean on costly 3D ground-truth to determine the faces/edges to prune. We present in this work a method that aims to refine the topology of any 3D mesh through a face-pruning strategy that extensively relies upon 2D alpha masks and camera pose information. Our solution leverages a differentiable renderer that renders each face as a 2D soft map. Its pixel intensity reflects the probability of being covered during the rendering process by such a face. Based on the 2D soft-masks available, our method is thus able to quickly highlight all the incorrectly rendered faces for a given viewpoint. Because our module is agnostic to the network that produces the 3D mesh, it can be easily plugged into any self-supervised image-based (either synthetic or natural) 3D reconstruction pipeline to get complex meshes with a non-spherical topology.

Large language models (LLMs) are often augmented with tools to solve complex tasks. By generating code snippets and executing them through task-specific Application Programming Interfaces (APIs), they can offload certain functions to dedicated external modules, such as image encoding and performing calculations. However, most existing approaches to augment LLMs with tools are constrained by general-purpose APIs and lack the flexibility for tailoring them to specific tasks. In this work, we present CRAFT, a general tool creation and retrieval framework for LLMs. It creates toolsets specifically curated for the tasks and equips LLMs with a component that retrieves tools from these sets to enhance their capability to solve complex tasks. For each task, we collect specific code solutions by prompting GPT-4 to solve the training examples. Following a validation step ensuring the correctness, these solutions are abstracted into code snippets to enhance reusability, and deduplicated for higher quality. At inference time, the language model retrieves snippets from the toolsets and then executes them or generates the output conditioning on the retrieved snippets. Our method is designed to be flexible and offers a plug-and-play approach to adapt off-the-shelf LLMs to unseen domains and modalities, without any finetuning. Experiments on vision-language, tabular processing, and mathematical reasoning tasks show that our approach achieves substantial improvements compared to strong baselines. In addition, our in-depth analysis reveals that: (1) consistent performance improvement can be achieved by scaling up the number of tools and the capability of the backbone models; (2) each component of our approach contributes to the performance gains; (3) the created tools are well-structured and reliable with low complexity and atomicity. The code is available at https://github.com/lifan-yuan/CRAFT.

Generating 3D models lies at the core of computer graphics and has been the focus of decades of research. With the emergence of advanced neural representations and generative models, the field of 3D content generation is developing rapidly, enabling the creation of increasingly high-quality and diverse 3D models. The rapid growth of this field makes it difficult to stay abreast of all recent developments. In this survey, we aim to introduce the fundamental methodologies of 3D generation methods and establish a structured roadmap, encompassing 3D representation, generation methods, datasets, and corresponding applications. Specifically, we introduce the 3D representations that serve as the backbone for 3D generation. Furthermore, we provide a comprehensive overview of the rapidly growing literature on generation methods, categorized by the type of algorithmic paradigms, including feedforward generation, optimization-based generation, procedural generation, and generative novel view synthesis. Lastly, we discuss available datasets, applications, and open challenges. We hope this survey will help readers explore this exciting topic and foster further advancements in the field of 3D content generation.

Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a complete hierarchy of SWL with strictly growing expressivity. Concretely, we prove that any node-based subgraph GNN falls into one of the six SWL equivalence classes, among which SSWL achieves the maximal expressive power. We also study how these equivalence classes differ in terms of their practical expressiveness such as encoding graph distance and biconnectivity. Furthermore, we give a tight expressivity upper bound of all SWL algorithms by establishing a close relation with localized versions of WL and Folklore WL (FWL) tests. Our results provide insights into the power of existing subgraph GNNs, guide the design of new architectures, and point out their limitations by revealing an inherent gap with the 2-FWL test. Finally, experiments demonstrate that SSWL-inspired subgraph GNNs can significantly outperform prior architectures on multiple benchmarks despite great simplicity.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

3D object generation has undergone significant advancements, yielding high-quality results. However, fall short of achieving precise user control, often yielding results that do not align with user expectations, thus limiting their applicability. User-envisioning 3D object generation faces significant challenges in realizing its concepts using current generative models due to limited interaction capabilities. Existing methods mainly offer two approaches: (i) interpreting textual instructions with constrained controllability, or (ii) reconstructing 3D objects from 2D images. Both of them limit customization to the confines of the 2D reference and potentially introduce undesirable artifacts during the 3D lifting process, restricting the scope for direct and versatile 3D modifications. In this work, we introduce Interactive3D, an innovative framework for interactive 3D generation that grants users precise control over the generative process through extensive 3D interaction capabilities. Interactive3D is constructed in two cascading stages, utilizing distinct 3D representations. The first stage employs Gaussian Splatting for direct user interaction, allowing modifications and guidance of the generative direction at any intermediate step through (i) Adding and Removing components, (ii) Deformable and Rigid Dragging, (iii) Geometric Transformations, and (iv) Semantic Editing. Subsequently, the Gaussian splats are transformed into InstantNGP. We introduce a novel (v) Interactive Hash Refinement module to further add details and extract the geometry in the second stage. Our experiments demonstrate that Interactive3D markedly improves the controllability and quality of 3D generation. Our project webpage is available at https://interactive-3d.github.io/.

We show how to "compile" human-readable programs into standard decoder-only transformer models. Our compiler, Tracr, generates models with known structure. This structure can be used to design experiments. For example, we use it to study "superposition" in transformers that execute multi-step algorithms. Additionally, the known structure of Tracr-compiled models can serve as ground-truth for evaluating interpretability methods. Commonly, because the "programs" learned by transformers are unknown it is unclear whether an interpretation succeeded. We demonstrate our approach by implementing and examining programs including computing token frequencies, sorting, and parenthesis checking. We provide an open-source implementation of Tracr at https://github.com/google-deepmind/tracr.

Structured knowledge bases (KBs) are the backbone of many know\-ledge-intensive applications, and their automated construction has received considerable attention. In particular, open information extraction (OpenIE) is often used to induce structure from a text. However, although it allows high recall, the extracted knowledge tends to inherit noise from the sources and the OpenIE algorithm. Besides, OpenIE tuples contain an open-ended, non-canonicalized set of relations, making the extracted knowledge's downstream exploitation harder. In this paper, we study the problem of mapping an open KB into the fixed schema of an existing KB, specifically for the case of commonsense knowledge. We propose approaching the problem by generative translation, i.e., by training a language model to generate fixed-schema assertions from open ones. Experiments show that this approach occupies a sweet spot between traditional manual, rule-based, or classification-based canonicalization and purely generative KB construction like COMET. Moreover, it produces higher mapping accuracy than the former while avoiding the association-based noise of the latter.

The notion of shortcut partition, introduced recently by Chang, Conroy, Le, Milenkovi\'c, Solomon, and Than [CCLMST23], is a new type of graph partition into low-diameter clusters. Roughly speaking, the shortcut partition guarantees that for every two vertices u and v in the graph, there exists a path between u and v that intersects only a few clusters. They proved that any planar graph admits a shortcut partition and gave several applications, including a construction of tree cover for arbitrary planar graphs with stretch 1+varepsilon and O(1) many trees for any fixed varepsilon in (0,1). However, the construction heavily exploits planarity in multiple steps, and is thus inherently limited to planar graphs. In this work, we breach the "planarity barrier" to construct a shortcut partition for K_r-minor-free graphs for any r. To this end, we take a completely different approach -- our key contribution is a novel deterministic variant of the cop decomposition in minor-free graphs [And86, AGG14]. Our shortcut partition for K_r-minor-free graphs yields several direct applications. Most notably, we construct the first optimal distance oracle for K_r-minor-free graphs, with 1+varepsilon stretch, linear space, and constant query time for any fixed varepsilon in (0,1). The previous best distance oracle [AG06] uses O(nlog n) space and O(log n) query time, and its construction relies on Robertson-Seymour structural theorem and other sophisticated tools. We also obtain the first tree cover of O(1) size for minor-free graphs with stretch 1+varepsilon, while the previous best (1+varepsilon)-tree cover has size O(log^2 n) [BFN19].

We present SkexGen, a novel autoregressive generative model for computer-aided design (CAD) construction sequences containing sketch-and-extrude modeling operations. Our model utilizes distinct Transformer architectures to encode topological, geometric, and extrusion variations of construction sequences into disentangled codebooks. Autoregressive Transformer decoders generate CAD construction sequences sharing certain properties specified by the codebook vectors. Extensive experiments demonstrate that our disentangled codebook representation generates diverse and high-quality CAD models, enhances user control, and enables efficient exploration of the design space. The code is available at https://samxuxiang.github.io/skexgen.

We present APT, an advanced Large Language Model (LLM)-driven framework that enables autonomous agents to construct complex and creative structures within the Minecraft environment. Unlike previous approaches that primarily concentrate on skill-based open-world tasks or rely on image-based diffusion models for generating voxel-based structures, our method leverages the intrinsic spatial reasoning capabilities of LLMs. By employing chain-of-thought decomposition along with multimodal inputs, the framework generates detailed architectural layouts and blueprints that the agent can execute under zero-shot or few-shot learning scenarios. Our agent incorporates both memory and reflection modules to facilitate lifelong learning, adaptive refinement, and error correction throughout the building process. To rigorously evaluate the agent's performance in this emerging research area, we introduce a comprehensive benchmark consisting of diverse construction tasks designed to test creativity, spatial reasoning, adherence to in-game rules, and the effective integration of multimodal instructions. Experimental results using various GPT-based LLM backends and agent configurations demonstrate the agent's capacity to accurately interpret extensive instructions involving numerous items, their positions, and orientations. The agent successfully produces complex structures complete with internal functionalities such as Redstone-powered systems. A/B testing indicates that the inclusion of a memory module leads to a significant increase in performance, emphasizing its role in enabling continuous learning and the reuse of accumulated experience. Additionally, the agent's unexpected emergence of scaffolding behavior highlights the potential of future LLM-driven agents to utilize subroutine planning and leverage the emergence ability of LLMs to autonomously develop human-like problem-solving techniques.

We present Generalized LoRA (GLoRA), an advanced approach for universal parameter-efficient fine-tuning tasks. Enhancing Low-Rank Adaptation (LoRA), GLoRA employs a generalized prompt module to optimize pre-trained model weights and adjust intermediate activations, providing more flexibility and capability across diverse tasks and datasets. Moreover, GLoRA facilitates efficient parameter adaptation by employing a scalable, modular, layer-wise structure search that learns individual adapter of each layer. Originating from a unified mathematical formulation, GLoRA exhibits strong transfer learning, few-shot learning and domain generalization abilities, as it adjusts to new tasks through additional dimensions on weights and activations. Comprehensive experiments demonstrate that GLoRA outperforms all previous methods in natural, specialized, and structured benchmarks, achieving superior accuracy with fewer parameters and computations on various datasets. Furthermore, our structural re-parameterization design ensures that GLoRA incurs no extra inference cost, rendering it a practical solution for resource-limited applications. Code is available at: https://github.com/Arnav0400/ViT-Slim/tree/master/GLoRA.

In the field of graphic design, automating the integration of design elements into a cohesive multi-layered artwork not only boosts productivity but also paves the way for the democratization of graphic design. One existing practice is Graphic Layout Generation (GLG), which aims to layout sequential design elements. It has been constrained by the necessity for a predefined correct sequence of layers, thus limiting creative potential and increasing user workload. In this paper, we present Hierarchical Layout Generation (HLG) as a more flexible and pragmatic setup, which creates graphic composition from unordered sets of design elements. To tackle the HLG task, we introduce Graphist, the first layout generation model based on large multimodal models. Graphist efficiently reframes the HLG as a sequence generation problem, utilizing RGB-A images as input, outputs a JSON draft protocol, indicating the coordinates, size, and order of each element. We develop new evaluation metrics for HLG. Graphist outperforms prior arts and establishes a strong baseline for this field. Project homepage: https://github.com/graphic-design-ai/graphist

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present SLICE-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). SLICE-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

The ability of large language models (LLMs) to follow instructions is crucial to real-world applications. Despite recent advances, several studies have highlighted that LLMs struggle when faced with challenging instructions, especially those that include complex constraints, hindering their effectiveness in various tasks. To address this challenge, we introduce Conifer, a novel instruction tuning dataset, designed to enhance LLMs to follow multi-level instructions with complex constraints. Utilizing GPT-4, we curate the dataset by a series of LLM-driven refinement processes to ensure high quality. We also propose a progressive learning scheme that emphasizes an easy-to-hard progression, and learning from process feedback. Models trained with Conifer exhibit remarkable improvements in instruction-following abilities, especially for instructions with complex constraints. On several instruction-following benchmarks, our 7B model outperforms the state-of-the-art open-source 7B models, even exceeds the performance of models 10 times larger on certain metrics. All the code and Conifer dataset are available at https://www.github.com/ConiferLM/Conifer.

Ensuring that Software Requirements Specifications (SRS) align with higher-level organizational or national requirements is vital, particularly in regulated environments such as finance and aerospace. In these domains, maintaining consistency, adhering to regulatory frameworks, minimizing errors, and meeting critical expectations are essential for the reliable functioning of systems. The widespread adoption of large language models (LLMs) highlights their immense potential, yet there remains considerable scope for improvement in retrieving relevant information and enhancing reasoning capabilities. This study demonstrates that integrating a robust Graph-RAG framework with advanced prompt engineering techniques, such as Chain of Thought and Tree of Thought, can significantly enhance performance. Compared to baseline RAG methods and simple prompting strategies, this approach delivers more accurate and context-aware results. While this method demonstrates significant improvements in performance, it comes with challenges. It is both costly and more complex to implement across diverse contexts, requiring careful adaptation to specific scenarios. Additionally, its effectiveness heavily relies on having complete and accurate input data, which may not always be readily available, posing further limitations to its scalability and practicality.

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these approaches encode, as well as performance trade-offs between them. However, the question of which structural properties yield the most effective encoding remains open. In this paper, we investigate this question from a geometric perspective. We propose a novel structural encoding based on discrete Ricci curvature (Local Curvature Profiles, short LCP) and show that it significantly outperforms existing encoding approaches. We further show that combining local structural encodings, such as LCP, with global positional encodings improves downstream performance, suggesting that they capture complementary geometric information. Finally, we compare different encoding types with (curvature-based) rewiring techniques. Rewiring has recently received a surge of interest due to its ability to improve the performance of Graph Neural Networks by mitigating over-smoothing and over-squashing effects. Our results suggest that utilizing curvature information for structural encodings delivers significantly larger performance increases than rewiring.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Advances in foundation modeling have reshaped computational pathology. However, the increasing number of available models and lack of standardized benchmarks make it increasingly complex to assess their strengths, limitations, and potential for further development. To address these challenges, we introduce a new suite of software tools for whole-slide image processing, foundation model benchmarking, and curated publicly available tasks. We anticipate that these resources will promote transparency, reproducibility, and continued progress in the field.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro*, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro*, and from 5.63 to 4.78 for RetroGraph).

The colossal parameters and computational overhead of Large Language Models (LLMs) challenge their real-world applications. Network pruning, which targets unstructured or structured sparsity by removing redundant parameters, has recently been explored for LLM acceleration. Existing LLM pruning works focus on unstructured pruning, which typically requires special hardware support for a practical speed-up. In contrast, structured pruning can reduce latency on general devices. However, it remains a challenge to perform structured pruning efficiently and maintain performance, especially at high sparsity ratios. To this end, we introduce an efficient structured pruning framework named CFSP, which leverages both Coarse (interblock) and Fine-grained (intrablock) activation information as an importance criterion to guide pruning. The pruning is highly efficient, as it only requires one forward pass to compute feature activations. Specifically, we first allocate the sparsity budget across blocks based on their importance and then retain important weights within each block. In addition, we introduce a recovery fine-tuning strategy that adaptively allocates training overhead based on coarse-grained importance to further improve performance. Experimental results demonstrate that CFSP outperforms existing methods on diverse models across various sparsity budgets. Our code will be available at https://github.com/wyxscir/CFSP.

Recent advances in text-guided 3D avatar generation have made substantial progress by distilling knowledge from diffusion models. Despite the plausible generated appearance, existing methods cannot achieve fine-grained disentanglement or high-fidelity modeling between inner body and outfit. In this paper, we propose Barbie, a novel framework for generating 3D avatars that can be dressed in diverse and high-quality Barbie-like garments and accessories. Instead of relying on a holistic model, Barbie achieves fine-grained disentanglement on avatars by semantic-aligned separated models for human body and outfits. These disentangled 3D representations are then optimized by different expert models to guarantee the domain-specific fidelity. To balance geometry diversity and reasonableness, we propose a series of losses for template-preserving and human-prior evolving. The final avatar is enhanced by unified texture refinement for superior texture consistency. Extensive experiments demonstrate that Barbie outperforms existing methods in both dressed human and outfit generation, supporting flexible apparel combination and animation. The code will be released for research purposes. Our project page is: https://xiaokunsun.github.io/Barbie.github.io/.

In this study, we aim to initiate the development of Radiology Foundation Model, termed as RadFM.We consider the construction of foundational models from the perspectives of data, model design, and evaluation thoroughly. Our contribution can be concluded as follows: (i), we construct a large-scale Medical Multi-modal Dataset, MedMD, consisting of 16M 2D and 3D medical scans. To the best of our knowledge, this is the first multi-modal dataset containing 3D medical scans. (ii), We propose an architecture that enables visually conditioned generative pre-training, allowing for the integration of text input interleaved with 2D or 3D medical scans to generate response for diverse radiologic tasks. The model was initially pre-trained on MedMD and subsequently domain-specific fine-tuned on RadMD, a radiologic cleaned version of MedMD, containing 3M radiologic visual-language pairs. (iii), we propose a new evaluation benchmark that comprises five tasks, aiming to comprehensively assess the capability of foundation models in handling practical clinical problems. Our experimental results confirm that RadFM significantly outperforms existing multi-modal foundation models. The codes, data, and model checkpoint will all be made publicly available to promote further research and development in the field.

Conditional graphic layout generation, which automatically maps user constraints to high-quality layouts, has attracted widespread attention today. Although recent works have achieved promising performance, the lack of versatility and data efficiency hinders their practical applications. In this work, we propose LayoutPrompter, which leverages large language models (LLMs) to address the above problems through in-context learning. LayoutPrompter is made up of three key components, namely input-output serialization, dynamic exemplar selection and layout ranking. Specifically, the input-output serialization component meticulously designs the input and output formats for each layout generation task. Dynamic exemplar selection is responsible for selecting the most helpful prompting exemplars for a given input. And a layout ranker is used to pick the highest quality layout from multiple outputs of LLMs. We conduct experiments on all existing layout generation tasks using four public datasets. Despite the simplicity of our approach, experimental results show that LayoutPrompter can compete with or even outperform state-of-the-art approaches on these tasks without any model training or fine-tuning. This demonstrates the effectiveness of this versatile and training-free approach. In addition, the ablation studies show that LayoutPrompter is significantly superior to the training-based baseline in a low-data regime, further indicating the data efficiency of LayoutPrompter. Our project is available at https://github.com/microsoft/LayoutGeneration/tree/main/LayoutPrompter.

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds millions voxels) of the pore space can be extracted, from grey level 3D CT scanner images, by means of simple image processing tools. Classical methods for numerical simulation of biological dynamics using mesh of voxels, such as Lattice Boltzmann Model (LBM), are too much time consuming. Thus, the use of more compact and reliable geometrical representations of pore space can drastically decrease the computational cost of the simulations. Several recent works propose basic analytic volume primitives (e.g. spheres, generalized cylinders, ellipsoids) to define a piece-wise approximation of pore space for numerical simulation of draining, diffusion and microbial decomposition. Such approaches work well but the drawback is that it generates approximation errors. In the present work, we study another alternative where pore space is described by means of geometrically relevant connected subsets of voxels (regions) computed from the curvilinear skeleton. Indeed, many works use the curvilinear skeleton (3D medial axis) for analyzing and partitioning 3D shapes within various domains (medicine, material sciences, petroleum engineering, etc.) but only a few ones in soil sciences. Within the context of soil sciences, most studies dealing with 3D medial axis focus on the determination of pore throats. Here, we segment pore space using curvilinear skeleton in order to achieve numerical simulation of microbial decomposition (including diffusion processes). We validate simulation outputs by comparison with other methods using different pore space geometrical representations (balls, voxels).

We introduce TADA, a simple-yet-effective approach that takes textual descriptions and produces expressive 3D avatars with high-quality geometry and lifelike textures, that can be animated and rendered with traditional graphics pipelines. Existing text-based character generation methods are limited in terms of geometry and texture quality, and cannot be realistically animated due to inconsistent alignment between the geometry and the texture, particularly in the face region. To overcome these limitations, TADA leverages the synergy of a 2D diffusion model and an animatable parametric body model. Specifically, we derive an optimizable high-resolution body model from SMPL-X with 3D displacements and a texture map, and use hierarchical rendering with score distillation sampling (SDS) to create high-quality, detailed, holistic 3D avatars from text. To ensure alignment between the geometry and texture, we render normals and RGB images of the generated character and exploit their latent embeddings in the SDS training process. We further introduce various expression parameters to deform the generated character during training, ensuring that the semantics of our generated character remain consistent with the original SMPL-X model, resulting in an animatable character. Comprehensive evaluations demonstrate that TADA significantly surpasses existing approaches on both qualitative and quantitative measures. TADA enables creation of large-scale digital character assets that are ready for animation and rendering, while also being easily editable through natural language. The code will be public for research purposes.

Artificial Intelligence (AI) has made incredible progress recently. On the one hand, advanced foundation models like ChatGPT can offer powerful conversation, in-context learning and code generation abilities on a broad range of open-domain tasks. They can also generate high-level solution outlines for domain-specific tasks based on the common sense knowledge they have acquired. However, they still face difficulties with some specialized tasks because they lack enough domain-specific data during pre-training or they often have errors in their neural network computations on those tasks that need accurate executions. On the other hand, there are also many existing models and systems (symbolic-based or neural-based) that can do some domain-specific tasks very well. However, due to the different implementation or working mechanisms, they are not easily accessible or compatible with foundation models. Therefore, there is a clear and pressing need for a mechanism that can leverage foundation models to propose task solution outlines and then automatically match some of the sub-tasks in the outlines to the off-the-shelf models and systems with special functionalities to complete them. Inspired by this, we introduce TaskMatrix.AI as a new AI ecosystem that connects foundation models with millions of APIs for task completion. Unlike most previous work that aimed to improve a single AI model, TaskMatrix.AI focuses more on using existing foundation models (as a brain-like central system) and APIs of other AI models and systems (as sub-task solvers) to achieve diversified tasks in both digital and physical domains. As a position paper, we will present our vision of how to build such an ecosystem, explain each key component, and use study cases to illustrate both the feasibility of this vision and the main challenges we need to address next.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Deep learning approaches have provided state-of-the-art performance in many applications by relying on large and overparameterized neural networks. However, such networks have been shown to be very brittle and are difficult to deploy on resource-limited platforms. Model pruning, i.e., reducing the size of the network, is a widely adopted strategy that can lead to a more robust and compact model. Many heuristics exist for model pruning, but empirical studies show that some heuristics improve performance whereas others can make models more brittle or have other side effects. This work aims to shed light on how different pruning methods alter the network's internal feature representation and the corresponding impact on model performance. To facilitate a comprehensive comparison and characterization of the high-dimensional model feature space, we introduce a visual geometric analysis of feature representations. We decomposed and evaluated a set of critical geometric concepts from the common adopted classification loss, and used them to design a visualization system to compare and highlight the impact of pruning on model performance and feature representation. The proposed tool provides an environment for in-depth comparison of pruning methods and a comprehensive understanding of how model response to common data corruption. By leveraging the proposed visualization, machine learning researchers can reveal the similarities between pruning methods and redundant in robustness evaluation benchmarks, obtain geometric insights about the differences between pruned models that achieve superior robustness performance, and identify samples that are robust or fragile to model pruning and common data corruption to model pruning and data corruption but also obtain insights and explanations on how some pruned models achieve superior robustness performance.

In bipartite networks, community structures are restricted to being disassortative, in that nodes of one type are grouped according to common patterns of connection with nodes of the other type. This makes the stochastic block model (SBM), a highly flexible generative model for networks with block structure, an intuitive choice for bipartite community detection. However, typical formulations of the SBM do not make use of the special structure of bipartite networks. Here we introduce a Bayesian nonparametric formulation of the SBM and a corresponding algorithm to efficiently find communities in bipartite networks which parsimoniously chooses the number of communities. The biSBM improves community detection results over general SBMs when data are noisy, improves the model resolution limit by a factor of 2, and expands our understanding of the complicated optimization landscape associated with community detection tasks. A direct comparison of certain terms of the prior distributions in the biSBM and a related high-resolution hierarchical SBM also reveals a counterintuitive regime of community detection problems, populated by smaller and sparser networks, where nonhierarchical models outperform their more flexible counterpart.

We present a design framework called Conversational Learning with Analytical Step-by-Step Strategies (CLASS) for developing high-performance Intelligent Tutoring Systems (ITS). The CLASS framework aims to empower ITS with with two critical capabilities: imparting tutor-like step-by-step guidance and enabling tutor-like conversations in natural language to effectively engage learners. To empower ITS with the aforementioned capabilities, the CLASS framework employs two carefully curated synthetic datasets. The first scaffolding dataset encompasses a variety of elements, including problems, their corresponding subproblems, hints, incorrect solutions, and tailored feedback. This dataset provides ITS with essential problem-solving strategies necessary for guiding students through each step of the conversation. The second conversational dataset contains simulated student-tutor conversations that involve the application of problem-solving strategies learned from the first dataset. In the second dataset, the tutoring system adheres to a pre-defined response template, which helps to maintain consistency and structure in ITS's responses during its interactions. This structured methodology facilitates seamless integration of user feedback and yields valuable insights into ITS's internal decision-making process, allowing for continuous refinement and improvement of the system. We also present a proof-of-concept ITS, referred to as SPOCK, trained using the CLASS framework with a focus on college level introductory biology content. A carefully constructed protocol was developed for SPOCK's preliminary evaluation, examining aspects such as the factual accuracy and relevance of its responses. Experts in the field of biology offered favorable remarks, particularly highlighting SPOCK's capability to break down questions into manageable subproblems and provide step-by-step guidance to students.

Graph neural networks (GNNs), in general, are built on the assumption of a static set of features characterizing each node in a graph. This assumption is often violated in practice. Existing methods partly address this issue through feature imputation. However, these techniques (i) assume uniformity of feature set across nodes, (ii) are transductive by nature, and (iii) fail to work when features are added or removed over time. In this work, we address these limitations through a novel GNN framework called GRAFENNE. GRAFENNE performs a novel allotropic transformation on the original graph, wherein the nodes and features are decoupled through a bipartite encoding. Through a carefully chosen message passing framework on the allotropic transformation, we make the model parameter size independent of the number of features and thereby inductive to both unseen nodes and features. We prove that GRAFENNE is at least as expressive as any of the existing message-passing GNNs in terms of Weisfeiler-Leman tests, and therefore, the additional inductivity to unseen features does not come at the cost of expressivity. In addition, as demonstrated over four real-world graphs, GRAFENNE empowers the underlying GNN with high empirical efficacy and the ability to learn in continual fashion over streaming feature sets.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Foundation model development attracts a rapidly expanding body of contributors, scientists, and applications. To help shape responsible development practices, we introduce the Foundation Model Development Cheatsheet: a growing collection of 250+ tools and resources spanning text, vision, and speech modalities. We draw on a large body of prior work to survey resources (e.g. software, documentation, frameworks, guides, and practical tools) that support informed data selection, processing, and understanding, precise and limitation-aware artifact documentation, efficient model training, advance awareness of the environmental impact from training, careful model evaluation of capabilities, risks, and claims, as well as responsible model release, licensing and deployment practices. We hope this curated collection of resources helps guide more responsible development. The process of curating this list, enabled us to review the AI development ecosystem, revealing what tools are critically missing, misused, or over-used in existing practices. We find that (i) tools for data sourcing, model evaluation, and monitoring are critically under-serving ethical and real-world needs, (ii) evaluations for model safety, capabilities, and environmental impact all lack reproducibility and transparency, (iii) text and particularly English-centric analyses continue to dominate over multilingual and multi-modal analyses, and (iv) evaluation of systems, rather than just models, is needed so that capabilities and impact are assessed in context.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

The research fields of parametric face models and 3D face reconstruction have been extensively studied. However, a critical question remains unanswered: how to tailor the face model for specific reconstruction settings. We argue that reconstruction with multi-view uncalibrated images demands a new model with stronger capacity. Our study shifts attention from data-dependent 3D Morphable Models (3DMM) to an understudied human-designed skinning model. We propose Adaptive Skinning Model (ASM), which redefines the skinning model with more compact and fully tunable parameters. With extensive experiments, we demonstrate that ASM achieves significantly improved capacity than 3DMM, with the additional advantage of model size and easy implementation for new topology. We achieve state-of-the-art performance with ASM for multi-view reconstruction on the Florence MICC Coop benchmark. Our quantitative analysis demonstrates the importance of a high-capacity model for fully exploiting abundant information from multi-view input in reconstruction. Furthermore, our model with physical-semantic parameters can be directly utilized for real-world applications, such as in-game avatar creation. As a result, our work opens up new research directions for the parametric face models and facilitates future research on multi-view reconstruction.