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SubscribeA Text-guided Protein Design Framework
Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level properties. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP that aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that generates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We empirically verify the effectiveness of ProteinDT from three aspects: (1) consistently superior performance on four out of six protein property prediction benchmarks; (2) over 90% accuracy for text-guided protein generation; and (3) promising results for zero-shot text-guided protein editing.
MIDI-DDSP: Detailed Control of Musical Performance via Hierarchical Modeling
Musical expression requires control of both what notes are played, and how they are performed. Conventional audio synthesizers provide detailed expressive controls, but at the cost of realism. Black-box neural audio synthesis and concatenative samplers can produce realistic audio, but have few mechanisms for control. In this work, we introduce MIDI-DDSP a hierarchical model of musical instruments that enables both realistic neural audio synthesis and detailed user control. Starting from interpretable Differentiable Digital Signal Processing (DDSP) synthesis parameters, we infer musical notes and high-level properties of their expressive performance (such as timbre, vibrato, dynamics, and articulation). This creates a 3-level hierarchy (notes, performance, synthesis) that affords individuals the option to intervene at each level, or utilize trained priors (performance given notes, synthesis given performance) for creative assistance. Through quantitative experiments and listening tests, we demonstrate that this hierarchy can reconstruct high-fidelity audio, accurately predict performance attributes for a note sequence, independently manipulate the attributes of a given performance, and as a complete system, generate realistic audio from a novel note sequence. By utilizing an interpretable hierarchy, with multiple levels of granularity, MIDI-DDSP opens the door to assistive tools to empower individuals across a diverse range of musical experience.
What Makes a Face Look like a Hat: Decoupling Low-level and High-level Visual Properties with Image Triplets
In visual decision making, high-level features, such as object categories, have a strong influence on choice. However, the impact of low-level features on behavior is less understood partly due to the high correlation between high- and low-level features in the stimuli presented (e.g., objects of the same category are more likely to share low-level features). To disentangle these effects, we propose a method that de-correlates low- and high-level visual properties in a novel set of stimuli. Our method uses two Convolutional Neural Networks (CNNs) as candidate models of the ventral visual stream: the CORnet-S that has high neural predictivity in high-level, IT-like responses and the VGG-16 that has high neural predictivity in low-level responses. Triplets (root, image1, image2) of stimuli are parametrized by the level of low- and high-level similarity of images extracted from the different layers. These stimuli are then used in a decision-making task where participants are tasked to choose the most similar-to-the-root image. We found that different networks show differing abilities to predict the effects of low-versus-high-level similarity: while CORnet-S outperforms VGG-16 in explaining human choices based on high-level similarity, VGG-16 outperforms CORnet-S in explaining human choices based on low-level similarity. Using Brain-Score, we observed that the behavioral prediction abilities of different layers of these networks qualitatively corresponded to their ability to explain neural activity at different levels of the visual hierarchy. In summary, our algorithm for stimulus set generation enables the study of how different representations in the visual stream affect high-level cognitive behaviors.
Learning high-level visual representations from a child's perspective without strong inductive biases
Young children develop sophisticated internal models of the world based on their visual experience. Can such models be learned from a child's visual experience without strong inductive biases? To investigate this, we train state-of-the-art neural networks on a realistic proxy of a child's visual experience without any explicit supervision or domain-specific inductive biases. Specifically, we train both embedding models and generative models on 200 hours of headcam video from a single child collected over two years and comprehensively evaluate their performance in downstream tasks using various reference models as yardsticks. On average, the best embedding models perform at a respectable 70% of a high-performance ImageNet-trained model, despite substantial differences in training data. They also learn broad semantic categories and object localization capabilities without explicit supervision, but they are less object-centric than models trained on all of ImageNet. Generative models trained with the same data successfully extrapolate simple properties of partially masked objects, like their rough outline, texture, color, or orientation, but struggle with finer object details. We replicate our experiments with two other children and find remarkably consistent results. Broadly useful high-level visual representations are thus robustly learnable from a representative sample of a child's visual experience without strong inductive biases.
GAIA-1: A Generative World Model for Autonomous Driving
Autonomous driving promises transformative improvements to transportation, but building systems capable of safely navigating the unstructured complexity of real-world scenarios remains challenging. A critical problem lies in effectively predicting the various potential outcomes that may emerge in response to the vehicle's actions as the world evolves. To address this challenge, we introduce GAIA-1 ('Generative AI for Autonomy'), a generative world model that leverages video, text, and action inputs to generate realistic driving scenarios while offering fine-grained control over ego-vehicle behavior and scene features. Our approach casts world modeling as an unsupervised sequence modeling problem by mapping the inputs to discrete tokens, and predicting the next token in the sequence. Emerging properties from our model include learning high-level structures and scene dynamics, contextual awareness, generalization, and understanding of geometry. The power of GAIA-1's learned representation that captures expectations of future events, combined with its ability to generate realistic samples, provides new possibilities for innovation in the field of autonomy, enabling enhanced and accelerated training of autonomous driving technology.
DepthCues: Evaluating Monocular Depth Perception in Large Vision Models
Large-scale pre-trained vision models are becoming increasingly prevalent, offering expressive and generalizable visual representations that benefit various downstream tasks. Recent studies on the emergent properties of these models have revealed their high-level geometric understanding, in particular in the context of depth perception. However, it remains unclear how depth perception arises in these models without explicit depth supervision provided during pre-training. To investigate this, we examine whether the monocular depth cues, similar to those used by the human visual system, emerge in these models. We introduce a new benchmark, DepthCues, designed to evaluate depth cue understanding, and present findings across 20 diverse and representative pre-trained vision models. Our analysis shows that human-like depth cues emerge in more recent larger models. We also explore enhancing depth perception in large vision models by fine-tuning on DepthCues, and find that even without dense depth supervision, this improves depth estimation. To support further research, our benchmark and evaluation code will be made publicly available for studying depth perception in vision models.
Semantic Image Segmentation with Deep Convolutional Nets and Fully Connected CRFs
Deep Convolutional Neural Networks (DCNNs) have recently shown state of the art performance in high level vision tasks, such as image classification and object detection. This work brings together methods from DCNNs and probabilistic graphical models for addressing the task of pixel-level classification (also called "semantic image segmentation"). We show that responses at the final layer of DCNNs are not sufficiently localized for accurate object segmentation. This is due to the very invariance properties that make DCNNs good for high level tasks. We overcome this poor localization property of deep networks by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF). Qualitatively, our "DeepLab" system is able to localize segment boundaries at a level of accuracy which is beyond previous methods. Quantitatively, our method sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 71.6% IOU accuracy in the test set. We show how these results can be obtained efficiently: Careful network re-purposing and a novel application of the 'hole' algorithm from the wavelet community allow dense computation of neural net responses at 8 frames per second on a modern GPU.
PAVLM: Advancing Point Cloud based Affordance Understanding Via Vision-Language Model
Affordance understanding, the task of identifying actionable regions on 3D objects, plays a vital role in allowing robotic systems to engage with and operate within the physical world. Although Visual Language Models (VLMs) have excelled in high-level reasoning and long-horizon planning for robotic manipulation, they still fall short in grasping the nuanced physical properties required for effective human-robot interaction. In this paper, we introduce PAVLM (Point cloud Affordance Vision-Language Model), an innovative framework that utilizes the extensive multimodal knowledge embedded in pre-trained language models to enhance 3D affordance understanding of point cloud. PAVLM integrates a geometric-guided propagation module with hidden embeddings from large language models (LLMs) to enrich visual semantics. On the language side, we prompt Llama-3.1 models to generate refined context-aware text, augmenting the instructional input with deeper semantic cues. Experimental results on the 3D-AffordanceNet benchmark demonstrate that PAVLM outperforms baseline methods for both full and partial point clouds, particularly excelling in its generalization to novel open-world affordance tasks of 3D objects. For more information, visit our project site: pavlm-source.github.io.
CLIPasso: Semantically-Aware Object Sketching
Abstraction is at the heart of sketching due to the simple and minimal nature of line drawings. Abstraction entails identifying the essential visual properties of an object or scene, which requires semantic understanding and prior knowledge of high-level concepts. Abstract depictions are therefore challenging for artists, and even more so for machines. We present CLIPasso, an object sketching method that can achieve different levels of abstraction, guided by geometric and semantic simplifications. While sketch generation methods often rely on explicit sketch datasets for training, we utilize the remarkable ability of CLIP (Contrastive-Language-Image-Pretraining) to distill semantic concepts from sketches and images alike. We define a sketch as a set of B\'ezier curves and use a differentiable rasterizer to optimize the parameters of the curves directly with respect to a CLIP-based perceptual loss. The abstraction degree is controlled by varying the number of strokes. The generated sketches demonstrate multiple levels of abstraction while maintaining recognizability, underlying structure, and essential visual components of the subject drawn.
Private Machine Learning in TensorFlow using Secure Computation
We present a framework for experimenting with secure multi-party computation directly in TensorFlow. By doing so we benefit from several properties valuable to both researchers and practitioners, including tight integration with ordinary machine learning processes, existing optimizations for distributed computation in TensorFlow, high-level abstractions for expressing complex algorithms and protocols, and an expanded set of familiar tooling. We give an open source implementation of a state-of-the-art protocol and report on concrete benchmarks using typical models from private machine learning.
Do Pedestrians Pay Attention? Eye Contact Detection in the Wild
In urban or crowded environments, humans rely on eye contact for fast and efficient communication with nearby people. Autonomous agents also need to detect eye contact to interact with pedestrians and safely navigate around them. In this paper, we focus on eye contact detection in the wild, i.e., real-world scenarios for autonomous vehicles with no control over the environment or the distance of pedestrians. We introduce a model that leverages semantic keypoints to detect eye contact and show that this high-level representation (i) achieves state-of-the-art results on the publicly-available dataset JAAD, and (ii) conveys better generalization properties than leveraging raw images in an end-to-end network. To study domain adaptation, we create LOOK: a large-scale dataset for eye contact detection in the wild, which focuses on diverse and unconstrained scenarios for real-world generalization. The source code and the LOOK dataset are publicly shared towards an open science mission.
Lemur: Integrating Large Language Models in Automated Program Verification
The demonstrated code-understanding capability of LLMs raises the question of whether they can be used for automated program verification, a task that often demands high-level abstract reasoning about program properties, which is challenging for verification tools. We propose a general methodology to combine the power of LLMs and automated reasoners for automated program verification. We formally describe this methodology as a set of derivation rules and prove its soundness. We instantiate the calculus as a sound automated verification procedure, which led to practical improvements on a set of synthetic and competition benchmarks.
Isomer: Isomerous Transformer for Zero-shot Video Object Segmentation
Recent leading zero-shot video object segmentation (ZVOS) works devote to integrating appearance and motion information by elaborately designing feature fusion modules and identically applying them in multiple feature stages. Our preliminary experiments show that with the strong long-range dependency modeling capacity of Transformer, simply concatenating the two modality features and feeding them to vanilla Transformers for feature fusion can distinctly benefit the performance but at a cost of heavy computation. Through further empirical analysis, we find that attention dependencies learned in Transformer in different stages exhibit completely different properties: global query-independent dependency in the low-level stages and semantic-specific dependency in the high-level stages. Motivated by the observations, we propose two Transformer variants: i) Context-Sharing Transformer (CST) that learns the global-shared contextual information within image frames with a lightweight computation. ii) Semantic Gathering-Scattering Transformer (SGST) that models the semantic correlation separately for the foreground and background and reduces the computation cost with a soft token merging mechanism. We apply CST and SGST for low-level and high-level feature fusions, respectively, formulating a level-isomerous Transformer framework for ZVOS task. Compared with the baseline that uses vanilla Transformers for multi-stage fusion, ours significantly increase the speed by 13 times and achieves new state-of-the-art ZVOS performance. Code is available at https://github.com/DLUT-yyc/Isomer.
Generalized Mean Absolute Directional Loss as a Solution to Overfitting and High Transaction Costs in Machine Learning Models Used in High-Frequency Algorithmic Investment Strategies
Regardless of the selected asset class and the level of model complexity (Transformer versus LSTM versus Perceptron/RNN), the GMADL loss function produces superior results than standard MSE-type loss functions and has better numerical properties in the context of optimization than MADL. Better results mean the possibility of achieving a higher risk-weighted return based on buy and sell signals built on forecasts generated by a given theoretical model estimated using the GMADL versus MSE or MADL function. In practice, GMADL solves the problem of selecting the most preferable feature in both classification and regression problems, improving the performance of each estimation. What is important is that, through additional parameterization, GMADL also solves the problem of optimizing investment systems on high-frequency data in such a way that they focus on strategy variants that contain fewer transactions so that transaction costs do not reduce the effectiveness of a given strategy to zero. Moreover, the implementation leverages state-of-the-art machine learning tools, including frameworks for hyperparameter tuning, architecture testing, and walk-forward optimization, ensuring robust and scalable solutions for real-world algorithmic trading.
Urban Radiance Field Representation with Deformable Neural Mesh Primitives
Neural Radiance Fields (NeRFs) have achieved great success in the past few years. However, most current methods still require intensive resources due to ray marching-based rendering. To construct urban-level radiance fields efficiently, we design Deformable Neural Mesh Primitive~(DNMP), and propose to parameterize the entire scene with such primitives. The DNMP is a flexible and compact neural variant of classic mesh representation, which enjoys both the efficiency of rasterization-based rendering and the powerful neural representation capability for photo-realistic image synthesis. Specifically, a DNMP consists of a set of connected deformable mesh vertices with paired vertex features to parameterize the geometry and radiance information of a local area. To constrain the degree of freedom for optimization and lower the storage budgets, we enforce the shape of each primitive to be decoded from a relatively low-dimensional latent space. The rendering colors are decoded from the vertex features (interpolated with rasterization) by a view-dependent MLP. The DNMP provides a new paradigm for urban-level scene representation with appealing properties: (1) High-quality rendering. Our method achieves leading performance for novel view synthesis in urban scenarios. (2) Low computational costs. Our representation enables fast rendering (2.07ms/1k pixels) and low peak memory usage (110MB/1k pixels). We also present a lightweight version that can run 33times faster than vanilla NeRFs, and comparable to the highly-optimized Instant-NGP (0.61 vs 0.71ms/1k pixels). Project page: https://dnmp.github.io/{https://dnmp.github.io/}.
Intriguing Properties of Quantization at Scale
Emergent properties have been widely adopted as a term to describe behavior not present in smaller models but observed in larger models. Recent work suggests that the trade-off incurred by quantization is also an emergent property, with sharp drops in performance in models over 6B parameters. In this work, we ask "are quantization cliffs in performance solely a factor of scale?" Against a backdrop of increased research focus on why certain emergent properties surface at scale, this work provides a useful counter-example. We posit that it is possible to optimize for a quantization friendly training recipe that suppresses large activation magnitude outliers. Here, we find that outlier dimensions are not an inherent product of scale, but rather sensitive to the optimization conditions present during pre-training. This both opens up directions for more efficient quantization, and poses the question of whether other emergent properties are inherent or can be altered and conditioned by optimization and architecture design choices. We successfully quantize models ranging in size from 410M to 52B with minimal degradation in performance.
BUSTLE: Bottom-Up Program Synthesis Through Learning-Guided Exploration
Program synthesis is challenging largely because of the difficulty of search in a large space of programs. Human programmers routinely tackle the task of writing complex programs by writing sub-programs and then analyzing their intermediate results to compose them in appropriate ways. Motivated by this intuition, we present a new synthesis approach that leverages learning to guide a bottom-up search over programs. In particular, we train a model to prioritize compositions of intermediate values during search conditioned on a given set of input-output examples. This is a powerful combination because of several emergent properties. First, in bottom-up search, intermediate programs can be executed, providing semantic information to the neural network. Second, given the concrete values from those executions, we can exploit rich features based on recent work on property signatures. Finally, bottom-up search allows the system substantial flexibility in what order to generate the solution, allowing the synthesizer to build up a program from multiple smaller sub-programs. Overall, our empirical evaluation finds that the combination of learning and bottom-up search is remarkably effective, even with simple supervised learning approaches. We demonstrate the effectiveness of our technique on two datasets, one from the SyGuS competition and one of our own creation.
Toward Formal Data Set Verification for Building Effective Machine Learning Models
In order to properly train a machine learning model, data must be properly collected. To guarantee a proper data collection, verifying that the collected data set holds certain properties is a possible solution. For example, guaranteeing that the data set contains samples across the whole input space, or that the data set is balanced w.r.t. different classes. We present a formal approach for verifying a set of arbitrarily stated properties over a data set. The proposed approach relies on the transformation of the data set into a first order logic formula, which can be later verified w.r.t. the different properties also stated in the same logic. A prototype tool, which uses the z3 solver, has been developed; the prototype can take as an input a set of properties stated in a formal language and formally verify a given data set w.r.t. to the given set of properties. Preliminary experimental results show the feasibility and performance of the proposed approach, and furthermore the flexibility for expressing properties of interest.
GLM-130B: An Open Bilingual Pre-trained Model
We introduce GLM-130B, a bilingual (English and Chinese) pre-trained language model with 130 billion parameters. It is an attempt to open-source a 100B-scale model at least as good as GPT-3 and unveil how models of such a scale can be successfully pre-trained. Over the course of this effort, we face numerous unexpected technical and engineering challenges, particularly on loss spikes and disconvergence. In this paper, we introduce the training process of GLM-130B including its design choices, training strategies for both efficiency and stability, and engineering efforts. The resultant GLM-130B model offers significant outperformance over GPT-3 175B on a wide range of popular English benchmarks while the performance advantage is not observed in OPT-175B and BLOOM-176B. It also consistently and significantly outperforms ERNIE TITAN 3.0 260B -- the largest Chinese language model -- across related benchmarks. Finally, we leverage a unique scaling property of GLM-130B to reach INT4 quantization, without quantization aware training and with almost no performance loss, making it the first among 100B-scale models. More importantly, the property allows its effective inference on 4timesRTX 3090 (24G) or 8timesRTX 2080 Ti (11G) GPUs, the most ever affordable GPUs required for using 100B-scale models. The GLM-130B model weights are publicly accessible and its code, training logs, related toolkit, and lessons learned are open-sourced at https://github.com/THUDM/GLM-130B .
Intensional Inheritance Between Concepts: An Information-Theoretic Interpretation
This paper addresses the problem of formalizing and quantifying the concept of "intensional inheritance" between two concepts. We begin by conceiving the intensional inheritance of W from F as the amount of information the proposition "x is F " provides about the proposition "x is W. To flesh this out, we consider concepts F and W defined by sets of properties left{F_{1}, F_{2}, ldots, F_{n}right} and left{W_{1}, W_{2}, ldots, W_{m}right} with associated degrees left{d_{1}, d_{2}, ldots, d_{n}right} and left{e_{1}, e_{2}, ldots, e_{m}right}, respectively, where the properties may overlap. We then derive formulas for the intensional inheritance using both Shannon information theory and algorithmic information theory, incorporating interaction information among properties. We examine a special case where all properties are mutually exclusive and calculate the intensional inheritance in this case in both frameworks. We also derive expressions for P(W mid F) based on the mutual information formula. Finally we consider the relationship between intensional inheritance and conventional set-theoretic "extensional" inheritance, concluding that in our information-theoretic framework, extensional inheritance emerges as a special case of intensional inheritance.
MatterGen: a generative model for inorganic materials design
The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.
VNE: An Effective Method for Improving Deep Representation by Manipulating Eigenvalue Distribution
Since the introduction of deep learning, a wide scope of representation properties, such as decorrelation, whitening, disentanglement, rank, isotropy, and mutual information, have been studied to improve the quality of representation. However, manipulating such properties can be challenging in terms of implementational effectiveness and general applicability. To address these limitations, we propose to regularize von Neumann entropy~(VNE) of representation. First, we demonstrate that the mathematical formulation of VNE is superior in effectively manipulating the eigenvalues of the representation autocorrelation matrix. Then, we demonstrate that it is widely applicable in improving state-of-the-art algorithms or popular benchmark algorithms by investigating domain-generalization, meta-learning, self-supervised learning, and generative models. In addition, we formally establish theoretical connections with rank, disentanglement, and isotropy of representation. Finally, we provide discussions on the dimension control of VNE and the relationship with Shannon entropy. Code is available at: https://github.com/jaeill/CVPR23-VNE.
Neural networks behave as hash encoders: An empirical study
The input space of a neural network with ReLU-like activations is partitioned into multiple linear regions, each corresponding to a specific activation pattern of the included ReLU-like activations. We demonstrate that this partition exhibits the following encoding properties across a variety of deep learning models: (1) {\it determinism}: almost every linear region contains at most one training example. We can therefore represent almost every training example by a unique activation pattern, which is parameterized by a {\it neural code}; and (2) {\it categorization}: according to the neural code, simple algorithms, such as K-Means, K-NN, and logistic regression, can achieve fairly good performance on both training and test data. These encoding properties surprisingly suggest that {\it normal neural networks well-trained for classification behave as hash encoders without any extra efforts.} In addition, the encoding properties exhibit variability in different scenarios. {Further experiments demonstrate that {\it model size}, {\it training time}, {\it training sample size}, {\it regularization}, and {\it label noise} contribute in shaping the encoding properties, while the impacts of the first three are dominant.} We then define an {\it activation hash phase chart} to represent the space expanded by {model size}, training time, training sample size, and the encoding properties, which is divided into three canonical regions: {\it under-expressive regime}, {\it critically-expressive regime}, and {\it sufficiently-expressive regime}. The source code package is available at https://github.com/LeavesLei/activation-code.
Toward Accurate Interpretable Predictions of Materials Properties within Transformer Language Models
Property prediction accuracy has long been a key parameter of machine learning in materials informatics. Accordingly, advanced models showing state-of-the-art performance turn into highly parameterized black boxes missing interpretability. Here, we present an elegant way to make their reasoning transparent. Human-readable text-based descriptions automatically generated within a suite of open-source tools are proposed as materials representation. Transformer language models pretrained on 2 million peer-reviewed articles take as input well-known terms, e.g., chemical composition, crystal symmetry, and site geometry. Our approach outperforms crystal graph networks by classifying four out of five analyzed properties if one considers all available reference data. Moreover, fine-tuned text-based models show high accuracy in the ultra-small data limit. Explanations of their internal machinery are produced using local interpretability techniques and are faithful and consistent with domain expert rationales. This language-centric framework makes accurate property predictions accessible to people without artificial-intelligence expertise.
From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction
Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.
Intellectual Property Protection for Deep Learning Model and Dataset Intelligence
With the growing applications of Deep Learning (DL), especially recent spectacular achievements of Large Language Models (LLMs) such as ChatGPT and LLaMA, the commercial significance of these remarkable models has soared. However, acquiring well-trained models is costly and resource-intensive. It requires a considerable high-quality dataset, substantial investment in dedicated architecture design, expensive computational resources, and efforts to develop technical expertise. Consequently, safeguarding the Intellectual Property (IP) of well-trained models is attracting increasing attention. In contrast to existing surveys overwhelmingly focusing on model IPP mainly, this survey not only encompasses the protection on model level intelligence but also valuable dataset intelligence. Firstly, according to the requirements for effective IPP design, this work systematically summarizes the general and scheme-specific performance evaluation metrics. Secondly, from proactive IP infringement prevention and reactive IP ownership verification perspectives, it comprehensively investigates and analyzes the existing IPP methods for both dataset and model intelligence. Additionally, from the standpoint of training settings, it delves into the unique challenges that distributed settings pose to IPP compared to centralized settings. Furthermore, this work examines various attacks faced by deep IPP techniques. Finally, we outline prospects for promising future directions that may act as a guide for innovative research.
MatterGPT: A Generative Transformer for Multi-Property Inverse Design of Solid-State Materials
Inverse design of solid-state materials with desired properties represents a formidable challenge in materials science. Although recent generative models have demonstrated potential, their adoption has been hindered by limitations such as inefficiency, architectural constraints and restricted open-source availability. The representation of crystal structures using the SLICES (Simplified Line-Input Crystal-Encoding System) notation as a string of characters enables the use of state-of-the-art natural language processing models, such as Transformers, for crystal design. Drawing inspiration from the success of GPT models in generating coherent text, we trained a generative Transformer on the next-token prediction task to generate solid-state materials with targeted properties. We demonstrate MatterGPT's capability to generate de novo crystal structures with targeted single properties, including both lattice-insensitive (formation energy) and lattice-sensitive (band gap) properties. Furthermore, we extend MatterGPT to simultaneously target multiple properties, addressing the complex challenge of multi-objective inverse design of crystals. Our approach showcases high validity, uniqueness, and novelty in generated structures, as well as the ability to generate materials with properties beyond the training data distribution. This work represents a significant step forward in computational materials discovery, offering a powerful and open tool for designing materials with tailored properties for various applications in energy, electronics, and beyond.
Towards Efficient Fine-tuning of Pre-trained Code Models: An Experimental Study and Beyond
Recently, fine-tuning pre-trained code models such as CodeBERT on downstream tasks has achieved great success in many software testing and analysis tasks. While effective and prevalent, fine-tuning the pre-trained parameters incurs a large computational cost. In this paper, we conduct an extensive experimental study to explore what happens to layer-wise pre-trained representations and their encoded code knowledge during fine-tuning. We then propose efficient alternatives to fine-tune the large pre-trained code model based on the above findings. Our experimental study shows that (1) lexical, syntactic and structural properties of source code are encoded in the lower, intermediate, and higher layers, respectively, while the semantic property spans across the entire model. (2) The process of fine-tuning preserves most of the code properties. Specifically, the basic code properties captured by lower and intermediate layers are still preserved during fine-tuning. Furthermore, we find that only the representations of the top two layers change most during fine-tuning for various downstream tasks. (3) Based on the above findings, we propose Telly to efficiently fine-tune pre-trained code models via layer freezing. The extensive experimental results on five various downstream tasks demonstrate that training parameters and the corresponding time cost are greatly reduced, while performances are similar or better. Replication package including source code, datasets, and online Appendix is available at: https://github.com/DeepSoftwareAnalytics/Telly.
M^{3}-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery
This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.
Haldane Bundles: A Dataset for Learning to Predict the Chern Number of Line Bundles on the Torus
Characteristic classes, which are abstract topological invariants associated with vector bundles, have become an important notion in modern physics with surprising real-world consequences. As a representative example, the incredible properties of topological insulators, which are insulators in their bulk but conductors on their surface, can be completely characterized by a specific characteristic class associated with their electronic band structure, the first Chern class. Given their importance to next generation computing and the computational challenge of calculating them using first-principles approaches, there is a need to develop machine learning approaches to predict the characteristic classes associated with a material system. To aid in this program we introduce the {Haldane bundle dataset}, which consists of synthetically generated complex line bundles on the 2-torus. We envision this dataset, which is not as challenging as noisy and sparsely measured real-world datasets but (as we show) still difficult for off-the-shelf architectures, to be a testing ground for architectures that incorporate the rich topological and geometric priors underlying characteristic classes.
Visualizing Large-scale and High-dimensional Data
We study the problem of visualizing large-scale and high-dimensional data in a low-dimensional (typically 2D or 3D) space. Much success has been reported recently by techniques that first compute a similarity structure of the data points and then project them into a low-dimensional space with the structure preserved. These two steps suffer from considerable computational costs, preventing the state-of-the-art methods such as the t-SNE from scaling to large-scale and high-dimensional data (e.g., millions of data points and hundreds of dimensions). We propose the LargeVis, a technique that first constructs an accurately approximated K-nearest neighbor graph from the data and then layouts the graph in the low-dimensional space. Comparing to t-SNE, LargeVis significantly reduces the computational cost of the graph construction step and employs a principled probabilistic model for the visualization step, the objective of which can be effectively optimized through asynchronous stochastic gradient descent with a linear time complexity. The whole procedure thus easily scales to millions of high-dimensional data points. Experimental results on real-world data sets demonstrate that the LargeVis outperforms the state-of-the-art methods in both efficiency and effectiveness. The hyper-parameters of LargeVis are also much more stable over different data sets.
Generative Discovery of Novel Chemical Designs using Diffusion Modeling and Transformer Deep Neural Networks with Application to Deep Eutectic Solvents
We report a series of deep learning models to solve complex forward and inverse design problems in molecular modeling and design. Using both diffusion models inspired by nonequilibrium thermodynamics and attention-based transformer architectures, we demonstrate a flexible framework to capture complex chemical structures. First trained on the QM9 dataset and a series of quantum mechanical properties (e.g. homo, lumo, free energy, heat capacity, etc.), we then generalize the model to study and design key properties of deep eutectic solvents. In addition to separate forward and inverse models, we also report an integrated fully prompt-based multi-task generative pretrained transformer model that solves multiple forward, inverse design, and prediction tasks, flexibly and within one model. We show that the multi-task generative model has the overall best performance and allows for flexible integration of multiple objectives, within one model, and for distinct chemistries, suggesting that synergies emerge during training of this large language model. Trained jointly in tasks related to the QM9 dataset and deep eutectic solvents (DESs), the model can predict various quantum mechanical properties and critical properties to achieve deep eutectic solvent behavior. Several novel combinations of DESs are proposed based on this framework.
ZeroQuant-FP: A Leap Forward in LLMs Post-Training W4A8 Quantization Using Floating-Point Formats
In the complex domain of large language models (LLMs), striking a balance between computational efficiency and maintaining model quality is a formidable challenge. Navigating the inherent limitations of uniform quantization, particularly when dealing with outliers, and motivated by the launch of NVIDIA's H100 hardware, this study delves into the viability of floating-point (FP) quantization, particularly focusing on FP8 and FP4, as a potential solution. Our comprehensive investigation reveals that for LLMs, FP8 activation consistently outshines its integer (INT8) equivalent, with the performance edge becoming more noticeable in models possessing parameters beyond one billion. For weight quantization, our findings indicate that FP4 exhibits comparable, if not superior, performance to INT4, simplifying deployment on FP-supported hardware like H100. To mitigate the overhead from precision alignment caused by the disparity between weights and activations, we propose two scaling constraints for weight quantization that negligibly impact the performance compared to the standard W4A8 model. We additionally enhance our quantization methods by integrating the Low Rank Compensation (LoRC) strategy, yielding improvements especially in smaller models. The results of our investigation emphasize the immense potential of FP quantization for LLMs, paving the way for high-efficiency deployment in resource-limited settings.
Towards Data-Efficient Pretraining for Atomic Property Prediction
This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.
Research on Optimizing Real-Time Data Processing in High-Frequency Trading Algorithms using Machine Learning
High-frequency trading (HFT) represents a pivotal and intensely competitive domain within the financial markets. The velocity and accuracy of data processing exert a direct influence on profitability, underscoring the significance of this field. The objective of this work is to optimise the real-time processing of data in high-frequency trading algorithms. The dynamic feature selection mechanism is responsible for monitoring and analysing market data in real time through clustering and feature weight analysis, with the objective of automatically selecting the most relevant features. This process employs an adaptive feature extraction method, which enables the system to respond and adjust its feature set in a timely manner when the data input changes, thus ensuring the efficient utilisation of data. The lightweight neural networks are designed in a modular fashion, comprising fast convolutional layers and pruning techniques that facilitate the expeditious completion of data processing and output prediction. In contrast to conventional deep learning models, the neural network architecture has been specifically designed to minimise the number of parameters and computational complexity, thereby markedly reducing the inference time. The experimental results demonstrate that the model is capable of maintaining consistent performance in the context of varying market conditions, thereby illustrating its advantages in terms of processing speed and revenue enhancement.
Finding Neurons in a Haystack: Case Studies with Sparse Probing
Despite rapid adoption and deployment of large language models (LLMs), the internal computations of these models remain opaque and poorly understood. In this work, we seek to understand how high-level human-interpretable features are represented within the internal neuron activations of LLMs. We train k-sparse linear classifiers (probes) on these internal activations to predict the presence of features in the input; by varying the value of k we study the sparsity of learned representations and how this varies with model scale. With k=1, we localize individual neurons which are highly relevant for a particular feature, and perform a number of case studies to illustrate general properties of LLMs. In particular, we show that early layers make use of sparse combinations of neurons to represent many features in superposition, that middle layers have seemingly dedicated neurons to represent higher-level contextual features, and that increasing scale causes representational sparsity to increase on average, but there are multiple types of scaling dynamics. In all, we probe for over 100 unique features comprising 10 different categories in 7 different models spanning 70 million to 6.9 billion parameters.
MHG-GNN: Combination of Molecular Hypergraph Grammar with Graph Neural Network
Property prediction plays an important role in material discovery. As an initial step to eventually develop a foundation model for material science, we introduce a new autoencoder called the MHG-GNN, which combines graph neural network (GNN) with Molecular Hypergraph Grammar (MHG). Results on a variety of property prediction tasks with diverse materials show that MHG-GNN is promising.
Fine-Tuned Language Models Generate Stable Inorganic Materials as Text
We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.
DeepArchitect: Automatically Designing and Training Deep Architectures
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.
CoCoNUT: Structural Code Understanding does not fall out of a tree
Large Language Models (LLMs) have shown impressive performance across a wide array of tasks involving both structured and unstructured textual data. Recent results on various benchmarks for code generation, repair, or completion suggest that certain models have programming abilities comparable to or even surpass humans. In this work, we demonstrate that high performance on such benchmarks does not correlate to humans' innate ability to understand structural control flow in code. To this end, we extract solutions from the HumanEval benchmark, which the relevant models perform strongly on, and trace their execution path using function calls sampled from the respective test set. Using this dataset, we investigate the ability of seven state-of-the-art LLMs to match the execution trace and find that, despite their ability to generate semantically identical code, they possess limited ability to trace execution paths, especially for longer traces and specific control structures. We find that even the top-performing model, Gemini, can fully and correctly generate only 47% of HumanEval task traces. Additionally, we introduce a subset for three key structures not contained in HumanEval: Recursion, Parallel Processing, and Object-Oriented Programming, including concepts like Inheritance and Polymorphism. Besides OOP, we show that none of the investigated models achieve an accuracy over 5% on the relevant traces. Aggregating these specialized parts with HumanEval tasks, we present Benchmark CoCoNUT: Code Control Flow for Navigation Understanding and Testing, which measures a model's ability to trace execution of code upon relevant calls, including advanced structural components. We conclude that current LLMs need significant improvement to enhance code reasoning abilities. We hope our dataset helps researchers bridge this gap.