Daily Papers

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery. However, it remains a challenging computational task due to the large modeling space of protein structures. In this study, we propose a latent diffusion model that can reduce the complexity of protein modeling while flexibly capturing the distribution of natural protein structures in a condensed latent space. Specifically, we propose an equivariant protein autoencoder that embeds proteins into a latent space and then uses an equivariant diffusion model to learn the distribution of the latent protein representations. Experimental results demonstrate that our method can effectively generate novel protein backbone structures with high designability and efficiency.

Antibody design is an essential yet challenging task in various domains like therapeutics and biology. There are two major defects in current learning-based methods: 1) tackling only a certain subtask of the whole antibody design pipeline, making them suboptimal or resource-intensive. 2) omitting either the framework regions or side chains, thus incapable of capturing the full-atom geometry. To address these pitfalls, we propose dynamic Multi-channel Equivariant grAph Network (dyMEAN), an end-to-end full-atom model for E(3)-equivariant antibody design given the epitope and the incomplete sequence of the antibody. Specifically, we first explore structural initialization as a knowledgeable guess of the antibody structure and then propose shadow paratope to bridge the epitope-antibody connections. Both 1D sequences and 3D structures are updated via an adaptive multi-channel equivariant encoder that is able to process protein residues of variable sizes when considering full atoms. Finally, the updated antibody is docked to the epitope via the alignment of the shadow paratope. Experiments on epitope-binding CDR-H3 design, complex structure prediction, and affinity optimization demonstrate the superiority of our end-to-end framework and full-atom modeling.

Recent progress has been made towards learning invariant or equivariant representations with self-supervised learning. While invariant methods are evaluated on large scale datasets, equivariant ones are evaluated in smaller, more controlled, settings. We aim at bridging the gap between the two in order to learn more diverse representations that are suitable for a wide range of tasks. We start by introducing a dataset called 3DIEBench, consisting of renderings from 3D models over 55 classes and more than 2.5 million images where we have full control on the transformations applied to the objects. We further introduce a predictor architecture based on hypernetworks to learn equivariant representations with no possible collapse to invariance. We introduce SIE (Split Invariant-Equivariant) which combines the hypernetwork-based predictor with representations split in two parts, one invariant, the other equivariant, to learn richer representations. We demonstrate significant performance gains over existing methods on equivariance related tasks from both a qualitative and quantitative point of view. We further analyze our introduced predictor and show how it steers the learned latent space. We hope that both our introduced dataset and approach will enable learning richer representations without supervision in more complex scenarios. Code and data are available at https://github.com/facebookresearch/SIE.

In state-of-the-art self-supervised learning (SSL) pre-training produces semantically good representations by encouraging them to be invariant under meaningful transformations prescribed from human knowledge. In fact, the property of invariance is a trivial instance of a broader class called equivariance, which can be intuitively understood as the property that representations transform according to the way the inputs transform. Here, we show that rather than using only invariance, pre-training that encourages non-trivial equivariance to some transformations, while maintaining invariance to other transformations, can be used to improve the semantic quality of representations. Specifically, we extend popular SSL methods to a more general framework which we name Equivariant Self-Supervised Learning (E-SSL). In E-SSL, a simple additional pre-training objective encourages equivariance by predicting the transformations applied to the input. We demonstrate E-SSL's effectiveness empirically on several popular computer vision benchmarks, e.g. improving SimCLR to 72.5% linear probe accuracy on ImageNet. Furthermore, we demonstrate usefulness of E-SSL for applications beyond computer vision; in particular, we show its utility on regression problems in photonics science. Our code, datasets and pre-trained models are available at https://github.com/rdangovs/essl to aid further research in E-SSL.

Equivariant networks are specifically designed to ensure consistent behavior with respect to a set of input transformations, leading to higher sample efficiency and more accurate and robust predictions. However, redesigning each component of prevalent deep neural network architectures to achieve chosen equivariance is a difficult problem and can result in a computationally expensive network during both training and inference. A recently proposed alternative towards equivariance that removes the architectural constraints is to use a simple canonicalization network that transforms the input to a canonical form before feeding it to an unconstrained prediction network. We show here that this approach can effectively be used to make a large pretrained network equivariant. However, we observe that the produced canonical orientations can be misaligned with those of the training distribution, hindering performance. Using dataset-dependent priors to inform the canonicalization function, we are able to make large pretrained models equivariant while maintaining their performance. This significantly improves the robustness of these models to deterministic transformations of the data, such as rotations. We believe this equivariant adaptation of large pretrained models can help their domain-specific applications with known symmetry priors.

This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does not require computationally expensive higher-order representations in intermediate layers while it still achieves competitive or better performance. In addition, whereas existing methods are limited to equivariance on 3 dimensional spaces, our model is easily scaled to higher-dimensional spaces. We demonstrate the effectiveness of our method on dynamical systems modelling, representation learning in graph autoencoders and predicting molecular properties.

Latent generative models have emerged as a leading approach for high-quality image synthesis. These models rely on an autoencoder to compress images into a latent space, followed by a generative model to learn the latent distribution. We identify that existing autoencoders lack equivariance to semantic-preserving transformations like scaling and rotation, resulting in complex latent spaces that hinder generative performance. To address this, we propose EQ-VAE, a simple regularization approach that enforces equivariance in the latent space, reducing its complexity without degrading reconstruction quality. By finetuning pre-trained autoencoders with EQ-VAE, we enhance the performance of several state-of-the-art generative models, including DiT, SiT, REPA and MaskGIT, achieving a 7 speedup on DiT-XL/2 with only five epochs of SD-VAE fine-tuning. EQ-VAE is compatible with both continuous and discrete autoencoders, thus offering a versatile enhancement for a wide range of latent generative models. Project page and code: https://eq-vae.github.io/.

In this paper, we propose Multiresolution Equivariant Graph Variational Autoencoders (MGVAE), the first hierarchical generative model to learn and generate graphs in a multiresolution and equivariant manner. At each resolution level, MGVAE employs higher order message passing to encode the graph while learning to partition it into mutually exclusive clusters and coarsening into a lower resolution that eventually creates a hierarchy of latent distributions. MGVAE then constructs a hierarchical generative model to variationally decode into a hierarchy of coarsened graphs. Importantly, our proposed framework is end-to-end permutation equivariant with respect to node ordering. MGVAE achieves competitive results with several generative tasks including general graph generation, molecular generation, unsupervised molecular representation learning to predict molecular properties, link prediction on citation graphs, and graph-based image generation.

Group equivariant neural networks are used as building blocks of group invariant neural networks, which have been shown to improve generalisation performance and data efficiency through principled parameter sharing. Such works have mostly focused on group equivariant convolutions, building on the result that group equivariant linear maps are necessarily convolutions. In this work, we extend the scope of the literature to self-attention, that is emerging as a prominent building block of deep learning models. We propose the LieTransformer, an architecture composed of LieSelfAttention layers that are equivariant to arbitrary Lie groups and their discrete subgroups. We demonstrate the generality of our approach by showing experimental results that are competitive to baseline methods on a wide range of tasks: shape counting on point clouds, molecular property regression and modelling particle trajectories under Hamiltonian dynamics.

Datasets often have their intrinsic symmetries, and particular deep-learning models called equivariant or invariant models have been developed to exploit these symmetries. However, if some or all of these symmetries are only approximate, which frequently happens in practice, these models may be suboptimal due to the architectural restrictions imposed on them. We tackle this issue of approximate symmetries in a setup where symmetries are mixed, i.e., they are symmetries of not single but multiple different types and the degree of approximation varies across these types. Instead of proposing a new architectural restriction as in most of the previous approaches, we present a regularizer-based method for building a model for a dataset with mixed approximate symmetries. The key component of our method is what we call equivariance regularizer for a given type of symmetries, which measures how much a model is equivariant with respect to the symmetries of the type. Our method is trained with these regularizers, one per each symmetry type, and the strength of the regularizers is automatically tuned during training, leading to the discovery of the approximation levels of some candidate symmetry types without explicit supervision. Using synthetic function approximation and motion forecasting tasks, we demonstrate that our method achieves better accuracy than prior approaches while discovering the approximate symmetry levels correctly.

Creating fast and accurate force fields is a long-standing challenge in computational chemistry and materials science. Recently, several equivariant message passing neural networks (MPNNs) have been shown to outperform models built using other approaches in terms of accuracy. However, most MPNNs suffer from high computational cost and poor scalability. We propose that these limitations arise because MPNNs only pass two-body messages leading to a direct relationship between the number of layers and the expressivity of the network. In this work, we introduce MACE, a new equivariant MPNN model that uses higher body order messages. In particular, we show that using four-body messages reduces the required number of message passing iterations to just two, resulting in a fast and highly parallelizable model, reaching or exceeding state-of-the-art accuracy on the rMD17, 3BPA, and AcAc benchmark tasks. We also demonstrate that using higher order messages leads to an improved steepness of the learning curves.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for a comprehensive understanding of proteins, existing methods for protein representation learning have utilized only one or two of these modalities due to the difficulty of capturing the asymmetric interrelationships between them. To account for this asymmetry, we introduce our novel asymmetric multi-modal masked autoencoder (AMMA). AMMA adopts (1) a unified multi-modal encoder to integrate all three modalities into a unified representation space and (2) asymmetric decoders to ensure that sequence latent features reflect structural and functional information. The experiments demonstrate that the proposed AMMA is highly effective in learning protein representations that exhibit well-aligned inter-modal relationships, which in turn makes it effective for various downstream protein-related tasks.

Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion models stand out for their robust mathematical foundations and impressive generative capabilities, offering unique advantages in certain applications such as protein design. In this review, we first give the definition and characteristics of diffusion models and then focus on two strategies: Denoising Diffusion Probabilistic Models and Score-based Generative Models, where DDPM is the discrete form of SGM. Furthermore, we discuss their applications in protein design, peptide generation, drug discovery, and protein-ligand interaction. Finally, we outline the future perspectives of diffusion models to advance autonomous protein design and engineering. The E(3) group consists of all rotations, reflections, and translations in three-dimensions. The equivariance on the E(3) group can keep the physical stability of the frame of each amino acid as much as possible, and we reflect on how to keep the diffusion model E(3) equivariant for protein generation.

How can prior knowledge on the transformation invariances of a domain be incorporated into the architecture of a neural network? We propose Equivariant Transformers (ETs), a family of differentiable image-to-image mappings that improve the robustness of models towards pre-defined continuous transformation groups. Through the use of specially-derived canonical coordinate systems, ETs incorporate functions that are equivariant by construction with respect to these transformations. We show empirically that ETs can be flexibly composed to improve model robustness towards more complicated transformation groups in several parameters. On a real-world image classification task, ETs improve the sample efficiency of ResNet classifiers, achieving relative improvements in error rate of up to 15% in the limited data regime while increasing model parameter count by less than 1%.

Humans can learn incrementally, whereas neural networks forget previously acquired information catastrophically. Continual Learning (CL) approaches seek to bridge this gap by facilitating the transfer of knowledge to both previous tasks (backward transfer) and future ones (forward transfer) during training. Recent research has shown that self-supervision can produce versatile models that can generalize well to diverse downstream tasks. However, contrastive self-supervised learning (CSSL), a popular self-supervision technique, has limited effectiveness in online CL (OCL). OCL only permits one iteration of the input dataset, and CSSL's low sample efficiency hinders its use on the input data-stream. In this work, we propose Continual Learning via Equivariant Regularization (CLER), an OCL approach that leverages equivariant tasks for self-supervision, avoiding CSSL's limitations. Our method represents the first attempt at combining equivariant knowledge with CL and can be easily integrated with existing OCL methods. Extensive ablations shed light on how equivariant pretext tasks affect the network's information flow and its impact on CL dynamics.

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

Equivariant neural networks have shown improved performance, expressiveness and sample complexity on symmetrical domains. But for some specific symmetries, representations, and choice of coordinates, the most common point-wise activations, such as ReLU, are not equivariant, hence they cannot be employed in the design of equivariant neural networks. The theorem we present in this paper describes all possible combinations of finite-dimensional representations, choice of coordinates and point-wise activations to obtain an exactly equivariant layer, generalizing and strengthening existing characterizations. Notable cases of practical relevance are discussed as corollaries. Indeed, we prove that rotation-equivariant networks can only be invariant, as it happens for any network which is equivariant with respect to connected compact groups. Then, we discuss implications of our findings when applied to important instances of exactly equivariant networks. First, we completely characterize permutation equivariant networks such as Invariant Graph Networks with point-wise nonlinearities and their geometric counterparts, highlighting a plethora of models whose expressive power and performance are still unknown. Second, we show that feature spaces of disentangled steerable convolutional neural networks are trivial representations.

Simulation-based inference with conditional neural density estimators is a powerful approach to solving inverse problems in science. However, these methods typically treat the underlying forward model as a black box, with no way to exploit geometric properties such as equivariances. Equivariances are common in scientific models, however integrating them directly into expressive inference networks (such as normalizing flows) is not straightforward. We here describe an alternative method to incorporate equivariances under joint transformations of parameters and data. Our method -- called group equivariant neural posterior estimation (GNPE) -- is based on self-consistently standardizing the "pose" of the data while estimating the posterior over parameters. It is architecture-independent, and applies both to exact and approximate equivariances. As a real-world application, we use GNPE for amortized inference of astrophysical binary black hole systems from gravitational-wave observations. We show that GNPE achieves state-of-the-art accuracy while reducing inference times by three orders of magnitude.

Many machine learning tasks involve learning functions that are known to be invariant or equivariant to certain symmetries of the input data. However, it is often challenging to design neural network architectures that respect these symmetries while being expressive and computationally efficient. For example, Euclidean motion invariant/equivariant graph or point cloud neural networks. We introduce Frame Averaging (FA), a general purpose and systematic framework for adapting known (backbone) architectures to become invariant or equivariant to new symmetry types. Our framework builds on the well known group averaging operator that guarantees invariance or equivariance but is intractable. In contrast, we observe that for many important classes of symmetries, this operator can be replaced with an averaging operator over a small subset of the group elements, called a frame. We show that averaging over a frame guarantees exact invariance or equivariance while often being much simpler to compute than averaging over the entire group. Furthermore, we prove that FA-based models have maximal expressive power in a broad setting and in general preserve the expressive power of their backbone architectures. Using frame averaging, we propose a new class of universal Graph Neural Networks (GNNs), universal Euclidean motion invariant point cloud networks, and Euclidean motion invariant Message Passing (MP) GNNs. We demonstrate the practical effectiveness of FA on several applications including point cloud normal estimation, beyond 2-WL graph separation, and n-body dynamics prediction, achieving state-of-the-art results in all of these benchmarks.

Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying Transformers to the domain of 3D atomistic systems. However, they are still limited to small degrees of equivariant representations due to their computational complexity. In this paper, we investigate whether these architectures can scale well to higher degrees. Starting from Equiformer, we first replace SO(3) convolutions with eSCN convolutions to efficiently incorporate higher-degree tensors. Then, to better leverage the power of higher degrees, we propose three architectural improvements -- attention re-normalization, separable S^2 activation and separable layer normalization. Putting this all together, we propose EquiformerV2, which outperforms previous state-of-the-art methods on the large-scale OC20 dataset by up to 12% on forces, 4% on energies, offers better speed-accuracy trade-offs, and 2times reduction in DFT calculations needed for computing adsorption energies.

Graph neural networks that model 3D data, such as point clouds or atoms, are typically desired to be SO(3) equivariant, i.e., equivariant to 3D rotations. Unfortunately equivariant convolutions, which are a fundamental operation for equivariant networks, increase significantly in computational complexity as higher-order tensors are used. In this paper, we address this issue by reducing the SO(3) convolutions or tensor products to mathematically equivalent convolutions in SO(2) . This is accomplished by aligning the node embeddings' primary axis with the edge vectors, which sparsifies the tensor product and reduces the computational complexity from O(L^6) to O(L^3), where L is the degree of the representation. We demonstrate the potential implications of this improvement by proposing the Equivariant Spherical Channel Network (eSCN), a graph neural network utilizing our novel approach to equivariant convolutions, which achieves state-of-the-art results on the large-scale OC-20 and OC-22 datasets.

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree E(3)-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

Popular representation learning methods encourage feature invariance under transformations applied at the input. However, in 3D perception tasks like object localization and segmentation, outputs are naturally equivariant to some transformations, such as rotation. Using pre-training loss functions that encourage equivariance of features under certain transformations provides a strong self-supervision signal while also retaining information of geometric relationships between transformed feature representations. This can enable improved performance in downstream tasks that are equivariant to such transformations. In this paper, we propose a spatio-temporal equivariant learning framework by considering both spatial and temporal augmentations jointly. Our experiments show that the best performance arises with a pre-training approach that encourages equivariance to translation, scaling, and flip, rotation and scene flow. For spatial augmentations, we find that depending on the transformation, either a contrastive objective or an equivariance-by-classification objective yields best results. To leverage real-world object deformations and motion, we consider sequential LiDAR scene pairs and develop a novel 3D scene flow-based equivariance objective that leads to improved performance overall. We show our pre-training method for 3D object detection which outperforms existing equivariant and invariant approaches in many settings.

The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of sparse autoencoders (SAE) to interpret the internal representations of protein language models, specifically focusing on the ESM-2 8M parameter model. By performing a statistical analysis on each latent component's relevance to distinct protein annotations, we identify potential interpretations linked to various protein characteristics, including transmembrane regions, binding sites, and specialized motifs. We then leverage these insights to guide sequence generation, shortlisting the relevant latent components that can steer the model towards desired targets such as zinc finger domains. This work contributes to the emerging field of mechanistic interpretability in biological sequence models, offering new perspectives on model steering for sequence design.

A challenging problem in many modern machine learning tasks is to process weight-space features, i.e., to transform or extract information from the weights and gradients of a neural network. Recent works have developed promising weight-space models that are equivariant to the permutation symmetries of simple feedforward networks. However, they are not applicable to general architectures, since the permutation symmetries of a weight space can be complicated by recurrence or residual connections. This work proposes an algorithm that automatically constructs permutation equivariant models, which we refer to as universal neural functionals (UNFs), for any weight space. Among other applications, we demonstrate how UNFs can be substituted into existing learned optimizer designs, and find promising improvements over prior methods when optimizing small image classifiers and language models. Our results suggest that learned optimizers can benefit from considering the (symmetry) structure of the weight space they optimize. We open-source our library for constructing UNFs at https://github.com/AllanYangZhou/universal_neural_functional.

This study explores the concept of equivariance in vision-language foundation models (VLMs), focusing specifically on the multimodal similarity function that is not only the major training objective but also the core delivery to support downstream tasks. Unlike the existing image-text similarity objective which only categorizes matched pairs as similar and unmatched pairs as dissimilar, equivariance also requires similarity to vary faithfully according to the semantic changes. This allows VLMs to generalize better to nuanced and unseen multimodal compositions. However, modeling equivariance is challenging as the ground truth of semantic change is difficult to collect. For example, given an image-text pair about a dog, it is unclear to what extent the similarity changes when the pixel is changed from dog to cat? To this end, we propose EqSim, a regularization loss that can be efficiently calculated from any two matched training pairs and easily pluggable into existing image-text retrieval fine-tuning. Meanwhile, to further diagnose the equivariance of VLMs, we present a new challenging benchmark EqBen. Compared to the existing evaluation sets, EqBen is the first to focus on "visual-minimal change". Extensive experiments show the lack of equivariance in current VLMs and validate the effectiveness of EqSim. Code is available at https://github.com/Wangt-CN/EqBen.

Despite the success of equivariant neural networks in scientific applications, they require knowing the symmetry group a priori. However, it may be difficult to know which symmetry to use as an inductive bias in practice. Enforcing the wrong symmetry could even hurt the performance. In this paper, we propose a framework, LieGAN, to automatically discover equivariances from a dataset using a paradigm akin to generative adversarial training. Specifically, a generator learns a group of transformations applied to the data, which preserve the original distribution and fool the discriminator. LieGAN represents symmetry as interpretable Lie algebra basis and can discover various symmetries such as the rotation group SO(n), restricted Lorentz group SO(1,3)^+ in trajectory prediction and top-quark tagging tasks. The learned symmetry can also be readily used in several existing equivariant neural networks to improve accuracy and generalization in prediction.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Latent Diffusion Models (LDMs) are known to have an unstable generation process, where even small perturbations or shifts in the input noise can lead to significantly different outputs. This hinders their applicability in applications requiring consistent results. In this work, we redesign LDMs to enhance consistency by making them shift-equivariant. While introducing anti-aliasing operations can partially improve shift-equivariance, significant aliasing and inconsistency persist due to the unique challenges in LDMs, including 1) aliasing amplification during VAE training and multiple U-Net inferences, and 2) self-attention modules that inherently lack shift-equivariance. To address these issues, we redesign the attention modules to be shift-equivariant and propose an equivariance loss that effectively suppresses the frequency bandwidth of the features in the continuous domain. The resulting alias-free LDM (AF-LDM) achieves strong shift-equivariance and is also robust to irregular warping. Extensive experiments demonstrate that AF-LDM produces significantly more consistent results than vanilla LDM across various applications, including video editing and image-to-image translation. Code is available at: https://github.com/SingleZombie/AFLDM

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

Equivariance to random image transformations is an effective method to learn landmarks of object categories, such as the eyes and the nose in faces, without manual supervision. However, this method does not explicitly guarantee that the learned landmarks are consistent with changes between different instances of the same object, such as different facial identities. In this paper, we develop a new perspective on the equivariance approach by noting that dense landmark detectors can be interpreted as local image descriptors equipped with invariance to intra-category variations. We then propose a direct method to enforce such an invariance in the standard equivariant loss. We do so by exchanging descriptor vectors between images of different object instances prior to matching them geometrically. In this manner, the same vectors must work regardless of the specific object identity considered. We use this approach to learn vectors that can simultaneously be interpreted as local descriptors and dense landmarks, combining the advantages of both. Experiments on standard benchmarks show that this approach can match, and in some cases surpass state-of-the-art performance amongst existing methods that learn landmarks without supervision. Code is available at www.robots.ox.ac.uk/~vgg/research/DVE/.

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

We consider the prediction of the Hamiltonian matrix, which finds use in quantum chemistry and condensed matter physics. Efficiency and equivariance are two important, but conflicting factors. In this work, we propose a SE(3)-equivariant network, named QHNet, that achieves efficiency and equivariance. Our key advance lies at the innovative design of QHNet architecture, which not only obeys the underlying symmetries, but also enables the reduction of number of tensor products by 92\%. In addition, QHNet prevents the exponential growth of channel dimension when more atom types are involved. We perform experiments on MD17 datasets, including four molecular systems. Experimental results show that our QHNet can achieve comparable performance to the state of the art methods at a significantly faster speed. Besides, our QHNet consumes 50\% less memory due to its streamlined architecture. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Shift equivariance is a fundamental principle that governs how we perceive the world - our recognition of an object remains invariant with respect to shifts. Transformers have gained immense popularity due to their effectiveness in both language and vision tasks. While the self-attention operator in vision transformers (ViT) is permutation-equivariant and thus shift-equivariant, patch embedding, positional encoding, and subsampled attention in ViT variants can disrupt this property, resulting in inconsistent predictions even under small shift perturbations. Although there is a growing trend in incorporating the inductive bias of convolutional neural networks (CNNs) into vision transformers, it does not fully address the issue. We propose an adaptive polyphase anchoring algorithm that can be seamlessly integrated into vision transformer models to ensure shift-equivariance in patch embedding and subsampled attention modules, such as window attention and global subsampled attention. Furthermore, we utilize depth-wise convolution to encode positional information. Our algorithms enable ViT, and its variants such as Twins to achieve 100% consistency with respect to input shift, demonstrate robustness to cropping, flipping, and affine transformations, and maintain consistent predictions even when the original models lose 20 percentage points on average when shifted by just a few pixels with Twins' accuracy dropping from 80.57% to 62.40%.

Recent advances in fast sampling methods for diffusion models have demonstrated significant potential to accelerate generation on image modalities. We apply these methods to 3-dimensional molecular conformations by building on the recently introduced GeoLDM equivariant latent diffusion model (Xu et al., 2023). We evaluate trade-offs between speed gains and quality loss, as measured by molecular conformation structural stability. We introduce Equivariant Latent Progressive Distillation, a fast sampling algorithm that preserves geometric equivariance and accelerates generation from latent diffusion models. Our experiments demonstrate up to 7.5x gains in sampling speed with limited degradation in molecular stability. These results suggest this accelerated sampling method has strong potential for high-throughput in silico molecular conformations screening in computational biochemistry, drug discovery, and life sciences applications.

Multi-modality image fusion is a technique that combines information from different sensors or modalities, enabling the fused image to retain complementary features from each modality, such as functional highlights and texture details. However, effective training of such fusion models is challenging due to the scarcity of ground truth fusion data. To tackle this issue, we propose the Equivariant Multi-Modality imAge fusion (EMMA) paradigm for end-to-end self-supervised learning. Our approach is rooted in the prior knowledge that natural imaging responses are equivariant to certain transformations. Consequently, we introduce a novel training paradigm that encompasses a fusion module, a pseudo-sensing module, and an equivariant fusion module. These components enable the net training to follow the principles of the natural sensing-imaging process while satisfying the equivariant imaging prior. Extensive experiments confirm that EMMA yields high-quality fusion results for infrared-visible and medical images, concurrently facilitating downstream multi-modal segmentation and detection tasks. The code is available at https://github.com/Zhaozixiang1228/MMIF-EMMA.

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.

Autoencoders and their variants are among the most widely used models in representation learning and generative modeling. However, autoencoder-based models usually assume that the learned representations are i.i.d. and fail to capture the correlations between the data samples. To address this issue, we propose a novel Sparse Gaussian Process Bayesian Autoencoder (SGPBAE) model in which we impose fully Bayesian sparse Gaussian Process priors on the latent space of a Bayesian Autoencoder. We perform posterior estimation for this model via stochastic gradient Hamiltonian Monte Carlo. We evaluate our approach qualitatively and quantitatively on a wide range of representation learning and generative modeling tasks and show that our approach consistently outperforms multiple alternatives relying on Variational Autoencoders.

Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While machine learning (ML) has produced accurate and efficient CG simulations of proteins, fast and reliable backmapping remains a challenge. Rule-based methods produce poor all-atom geometries, needing computationally costly refinement through additional simulations. Recently proposed ML approaches outperform traditional baselines but are not transferable between proteins and sometimes generate unphysical atom placements with steric clashes and implausible torsion angles. This work addresses both issues to build a fast, transferable, and reliable generative backmapping tool for CG protein representations. We achieve generalization and reliability through a combined set of innovations: representation based on internal coordinates; an equivariant encoder/prior; a custom loss function that helps ensure local structure, global structure, and physical constraints; and expert curation of high-quality out-of-equilibrium protein data for training. Our results pave the way for out-of-the-box backmapping of coarse-grained simulations for arbitrary proteins.

Developing equivariant neural networks for the E(3) group plays an important role in modeling 3D data across real-world applications. Enforcing this equivariance primarily involves the tensor products of irreducible representations (irreps). However, the computational complexity of such operations increases significantly as higher-order tensors are used. In this work, we propose a systematic approach to substantially accelerate the computation of the tensor products of irreps. We mathematically connect the commonly used Clebsch-Gordan coefficients to the Gaunt coefficients, which are integrals of products of three spherical harmonics. Through Gaunt coefficients, the tensor product of irreps becomes equivalent to the multiplication between spherical functions represented by spherical harmonics. This perspective further allows us to change the basis for the equivariant operations from spherical harmonics to a 2D Fourier basis. Consequently, the multiplication between spherical functions represented by a 2D Fourier basis can be efficiently computed via the convolution theorem and Fast Fourier Transforms. This transformation reduces the complexity of full tensor products of irreps from O(L^6) to O(L^3), where L is the max degree of irreps. Leveraging this approach, we introduce the Gaunt Tensor Product, which serves as a new method to construct efficient equivariant operations across different model architectures. Our experiments on the Open Catalyst Project and 3BPA datasets demonstrate both the increased efficiency and improved performance of our approach.

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly operates on both continuous (atom coordinates) and categorical features (atom types). In addition, we provide a probabilistic analysis which admits likelihood computation of molecules using our model. Experimentally, the proposed method significantly outperforms previous 3D molecular generative methods regarding the quality of generated samples and efficiency at training time.

This paper proposes a new type of generative model that is able to quickly learn a latent representation without an encoder. This is achieved using empirical Bayes to calculate the expectation of the posterior, which is implemented by initialising a latent vector with zeros, then using the gradient of the log-likelihood of the data with respect to this zero vector as new latent points. The approach has similar characteristics to autoencoders, but with a simpler architecture, and is demonstrated in a variational autoencoder equivalent that permits sampling. This also allows implicit representation networks to learn a space of implicit functions without requiring a hypernetwork, retaining their representation advantages across datasets. The experiments show that the proposed method converges faster, with significantly lower reconstruction error than autoencoders, while requiring half the parameters.

Integrating a notion of symmetry into point cloud neural networks is a provably effective way to improve their generalization capability. Of particular interest are E(3) equivariant point cloud networks where Euclidean transformations applied to the inputs are preserved in the outputs. Recent efforts aim to extend networks that are E(3) equivariant, to accommodate inputs made of multiple parts, each of which exhibits local E(3) symmetry. In practical settings, however, the partitioning into individually transforming regions is unknown a priori. Errors in the partition prediction would unavoidably map to errors in respecting the true input symmetry. Past works have proposed different ways to predict the partition, which may exhibit uncontrolled errors in their ability to maintain equivariance to the actual partition. To this end, we introduce APEN: a general framework for constructing approximate piecewise-E(3) equivariant point networks. Our primary insight is that functions that are equivariant with respect to a finer partition will also maintain equivariance in relation to the true partition. Leveraging this observation, we propose a design where the equivariance approximation error at each layers can be bounded solely in terms of (i) uncertainty quantification of the partition prediction, and (ii) bounds on the probability of failing to suggest a proper subpartition of the ground truth one. We demonstrate the effectiveness of APEN using two data types exemplifying part-based symmetry: (i) real-world scans of room scenes containing multiple furniture-type objects; and, (ii) human motions, characterized by articulated parts exhibiting rigid movement. Our empirical results demonstrate the advantage of integrating piecewise E(3) symmetry into network design, showing a distinct improvement in generalization compared to prior works for both classification and segmentation tasks.

Neural networks efficiently encode learned information within their parameters. Consequently, many tasks can be unified by treating neural networks themselves as input data. When doing so, recent studies demonstrated the importance of accounting for the symmetries and geometry of parameter spaces. However, those works developed architectures tailored to specific networks such as MLPs and CNNs without normalization layers, and generalizing such architectures to other types of networks can be challenging. In this work, we overcome these challenges by building new metanetworks - neural networks that take weights from other neural networks as input. Put simply, we carefully build graphs representing the input neural networks and process the graphs using graph neural networks. Our approach, Graph Metanetworks (GMNs), generalizes to neural architectures where competing methods struggle, such as multi-head attention layers, normalization layers, convolutional layers, ResNet blocks, and group-equivariant linear layers. We prove that GMNs are expressive and equivariant to parameter permutation symmetries that leave the input neural network functions unchanged. We validate the effectiveness of our method on several metanetwork tasks over diverse neural network architectures.

Invariance and equivariance to geometrical transformations have proven to be very useful inductive biases when training (convolutional) neural network models, especially in the low-data regime. Much work has focused on the case where the symmetry group employed is compact or abelian, or both. Recent work has explored enlarging the class of transformations used to the case of Lie groups, principally through the use of their Lie algebra, as well as the group exponential and logarithm maps. The applicability of such methods to larger transformation groups is limited by the fact that depending on the group of interest G, the exponential map may not be surjective. Further limitations are encountered when G is neither compact nor abelian. Using the structure and geometry of Lie groups and their homogeneous spaces, we present a framework by which it is possible to work with such groups primarily focusing on the Lie groups G = GL^{+}(n, R) and G = SL(n, R), as well as their representation as affine transformations R^{n} rtimes G. Invariant integration as well as a global parametrization is realized by decomposing the `larger` groups into subgroups and submanifolds which can be handled individually. Under this framework, we show how convolution kernels can be parametrized to build models equivariant with respect to affine transformations. We evaluate the robustness and out-of-distribution generalisation capability of our model on the standard affine-invariant benchmark classification task, where we outperform all previous equivariant models as well as all Capsule Network proposals.

Designing machine learning architectures for processing neural networks in their raw weight matrix form is a newly introduced research direction. Unfortunately, the unique symmetry structure of deep weight spaces makes this design very challenging. If successful, such architectures would be capable of performing a wide range of intriguing tasks, from adapting a pre-trained network to a new domain to editing objects represented as functions (INRs or NeRFs). As a first step towards this goal, we present here a novel network architecture for learning in deep weight spaces. It takes as input a concatenation of weights and biases of a pre-trained MLP and processes it using a composition of layers that are equivariant to the natural permutation symmetry of the MLP's weights: Changing the order of neurons in intermediate layers of the MLP does not affect the function it represents. We provide a full characterization of all affine equivariant and invariant layers for these symmetries and show how these layers can be implemented using three basic operations: pooling, broadcasting, and fully connected layers applied to the input in an appropriate manner. We demonstrate the effectiveness of our architecture and its advantages over natural baselines in a variety of learning tasks.

In recent years, exploiting the domain-specific underlying structure of data and its generative factors for representation learning has shown success in various use-case agnostic applications. However, the diversity and complexity of tabular data have made it challenging to represent these structures in a latent space through multi-dimensional vectors. We design an autoencoder-based framework for building general purpose embeddings, we assess the performance of different autoencoder architectures, and show simpler models outperform complex ones in embedding highly complex tabular data. We apply our framework to produce plug-and-play, rich, and anonymized embeddings representing AWS customers for usage in any model, saving up to 45% of development time, and observe significant improvements in downstream models. Moreover, we propose a significant improvement to the calculation of reconstruction loss for multi-layer contractive autoencoders (CAE) by calculating the Jacobian of the entire encoder leading to a 15% improvement in reconstruction quality when compared to a stacked CAE.

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.

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

The autoencoder is an unsupervised learning paradigm that aims to create a compact latent representation of data by minimizing the reconstruction loss. However, it tends to overlook the fact that most data (images) are embedded in a lower-dimensional space, which is crucial for effective data representation. To address this limitation, we propose a novel approach called Low-Rank Autoencoder (LoRAE). In LoRAE, we incorporated a low-rank regularizer to adaptively reconstruct a low-dimensional latent space while preserving the basic objective of an autoencoder. This helps embed the data in a lower-dimensional space while preserving important information. It is a simple autoencoder extension that learns low-rank latent space. Theoretically, we establish a tighter error bound for our model. Empirically, our model's superiority shines through various tasks such as image generation and downstream classification. Both theoretical and practical outcomes highlight the importance of acquiring low-dimensional embeddings.

The variational autoencoder (VAE; Kingma, Welling (2014)) is a recently proposed generative model pairing a top-down generative network with a bottom-up recognition network which approximates posterior inference. It typically makes strong assumptions about posterior inference, for instance that the posterior distribution is approximately factorial, and that its parameters can be approximated with nonlinear regression from the observations. As we show empirically, the VAE objective can lead to overly simplified representations which fail to use the network's entire modeling capacity. We present the importance weighted autoencoder (IWAE), a generative model with the same architecture as the VAE, but which uses a strictly tighter log-likelihood lower bound derived from importance weighting. In the IWAE, the recognition network uses multiple samples to approximate the posterior, giving it increased flexibility to model complex posteriors which do not fit the VAE modeling assumptions. We show empirically that IWAEs learn richer latent space representations than VAEs, leading to improved test log-likelihood on density estimation benchmarks.

Density estimation, compression and data generation are crucial tasks in artificial intelligence. Variational Auto-Encoders (VAEs) constitute a single framework to achieve these goals. Here, we present a novel class of generative models, called self-supervised Variational Auto-Encoder (selfVAE), that utilizes deterministic and discrete variational posteriors. This class of models allows to perform both conditional and unconditional sampling, while simplifying the objective function. First, we use a single self-supervised transformation as a latent variable, where a transformation is either downscaling or edge detection. Next, we consider a hierarchical architecture, i.e., multiple transformations, and we show its benefits compared to the VAE. The flexibility of selfVAE in data reconstruction finds a particularly interesting use case in data compression tasks, where we can trade-off memory for better data quality, and vice-versa. We present performance of our approach on three benchmark image data (Cifar10, Imagenette64, and CelebA).

Representation learning seeks to expose certain aspects of observed data in a learned representation that's amenable to downstream tasks like classification. For instance, a good representation for 2D images might be one that describes only global structure and discards information about detailed texture. In this paper, we present a simple but principled method to learn such global representations by combining Variational Autoencoder (VAE) with neural autoregressive models such as RNN, MADE and PixelRNN/CNN. Our proposed VAE model allows us to have control over what the global latent code can learn and , by designing the architecture accordingly, we can force the global latent code to discard irrelevant information such as texture in 2D images, and hence the VAE only "autoencodes" data in a lossy fashion. In addition, by leveraging autoregressive models as both prior distribution p(z) and decoding distribution p(x|z), we can greatly improve generative modeling performance of VAEs, achieving new state-of-the-art results on MNIST, OMNIGLOT and Caltech-101 Silhouettes density estimation tasks.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.2 billion parameters, trained on over 280 million protein sequences belonging to the UniRef-100 database. Such generative models hold the promise of greatly accelerating protein design. We conduct the first systematic study of how capabilities evolve with model size for autoregressive transformers in the protein domain: we evaluate RITA models in next amino acid prediction, zero-shot fitness, and enzyme function prediction, showing benefits from increased scale. We release the RITA models openly, to the benefit of the research community.

Self-supervised learning converts raw perceptual data such as images to a compact space where simple Euclidean distances measure meaningful variations in data. In this paper, we extend this formulation by adding additional geometric structure to the embedding space by enforcing transformations of input space to correspond to simple (i.e., linear) transformations of embedding space. Specifically, in the contrastive learning setting, we introduce an equivariance objective and theoretically prove that its minima forces augmentations on input space to correspond to rotations on the spherical embedding space. We show that merely combining our equivariant loss with a non-collapse term results in non-trivial representations, without requiring invariance to data augmentations. Optimal performance is achieved by also encouraging approximate invariance, where input augmentations correspond to small rotations. Our method, CARE: Contrastive Augmentation-induced Rotational Equivariance, leads to improved performance on downstream tasks, and ensures sensitivity in embedding space to important variations in data (e.g., color) that standard contrastive methods do not achieve. Code is available at https://github.com/Sharut/CARE.

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.

This paper shows that masked autoencoders (MAE) are scalable self-supervised learners for computer vision. Our MAE approach is simple: we mask random patches of the input image and reconstruct the missing pixels. It is based on two core designs. First, we develop an asymmetric encoder-decoder architecture, with an encoder that operates only on the visible subset of patches (without mask tokens), along with a lightweight decoder that reconstructs the original image from the latent representation and mask tokens. Second, we find that masking a high proportion of the input image, e.g., 75%, yields a nontrivial and meaningful self-supervisory task. Coupling these two designs enables us to train large models efficiently and effectively: we accelerate training (by 3x or more) and improve accuracy. Our scalable approach allows for learning high-capacity models that generalize well: e.g., a vanilla ViT-Huge model achieves the best accuracy (87.8%) among methods that use only ImageNet-1K data. Transfer performance in downstream tasks outperforms supervised pre-training and shows promising scaling behavior.

This is an exploratory study that discovers the current image quantization (vector quantization) do not satisfy translation equivariance in the quantized space due to aliasing. Instead of focusing on anti-aliasing, we propose a simple yet effective way to achieve translation-equivariant image quantization by enforcing orthogonality among the codebook embeddings. To explore the advantages of translation-equivariant image quantization, we conduct three proof-of-concept experiments with a carefully controlled dataset: (1) text-to-image generation, where the quantized image indices are the target to predict, (2) image-to-text generation, where the quantized image indices are given as a condition, (3) using a smaller training set to analyze sample efficiency. From the strictly controlled experiments, we empirically verify that the translation-equivariant image quantizer improves not only sample efficiency but also the accuracy over VQGAN up to +11.9% in text-to-image generation and +3.9% in image-to-text generation.

Recent self-supervised methods for image representation learning are based on maximizing the agreement between embedding vectors from different views of the same image. A trivial solution is obtained when the encoder outputs constant vectors. This collapse problem is often avoided through implicit biases in the learning architecture, that often lack a clear justification or interpretation. In this paper, we introduce VICReg (Variance-Invariance-Covariance Regularization), a method that explicitly avoids the collapse problem with a simple regularization term on the variance of the embeddings along each dimension individually. VICReg combines the variance term with a decorrelation mechanism based on redundancy reduction and covariance regularization, and achieves results on par with the state of the art on several downstream tasks. In addition, we show that incorporating our new variance term into other methods helps stabilize the training and leads to performance improvements.

We present Transformation Invariance and Covariance Contrast (TiCo) for self-supervised visual representation learning. Similar to other recent self-supervised learning methods, our method is based on maximizing the agreement among embeddings of different distorted versions of the same image, which pushes the encoder to produce transformation invariant representations. To avoid the trivial solution where the encoder generates constant vectors, we regularize the covariance matrix of the embeddings from different images by penalizing low rank solutions. By jointly minimizing the transformation invariance loss and covariance contrast loss, we get an encoder that is able to produce useful representations for downstream tasks. We analyze our method and show that it can be viewed as a variant of MoCo with an implicit memory bank of unlimited size at no extra memory cost. This makes our method perform better than alternative methods when using small batch sizes. TiCo can also be seen as a modification of Barlow Twins. By connecting the contrastive and redundancy-reduction methods together, TiCo gives us new insights into how joint embedding methods work.

Attention-based models such as Transformers and recurrent models like state space models (SSMs) have emerged as successful methods for autoregressive sequence modeling. Although both enable parallel training, none enable parallel generation due to their autoregressiveness. We propose the variational SSM (VSSM), a variational autoencoder (VAE) where both the encoder and decoder are SSMs. Since sampling the latent variables and decoding them with the SSM can be parallelized, both training and generation can be conducted in parallel. Moreover, the decoder recurrence allows generation to be resumed without reprocessing the whole sequence. Finally, we propose the autoregressive VSSM that can be conditioned on a partial realization of the sequence, as is common in language generation tasks. Interestingly, the autoregressive VSSM still enables parallel generation. We highlight on toy problems (MNIST, CIFAR) the empirical gains in speed-up and show that it competes with traditional models in terms of generation quality (Transformer, Mamba SSM).

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at https://github.com/bytedance/dplm.

Much of the success of deep learning is drawn from building architectures that properly respect underlying symmetry and structure in the data on which they operate - a set of considerations that have been united under the banner of geometric deep learning. Often problems in the physical sciences deal with relatively small sets of points in two- or three-dimensional space wherein translation, rotation, and permutation equivariance are important or even vital for models to be useful in practice. In this work, we present rotation- and permutation-equivariant architectures for deep learning on these small point clouds, composed of a set of products of terms from the geometric algebra and reductions over those products using an attention mechanism. The geometric algebra provides valuable mathematical structure by which to combine vector, scalar, and other types of geometric inputs in a systematic way to account for rotation invariance or covariance, while attention yields a powerful way to impose permutation equivariance. We demonstrate the usefulness of these architectures by training models to solve sample problems relevant to physics, chemistry, and biology.

Generative autoencoders offer a promising approach for controllable text generation by leveraging their latent sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text manipulations via latent vector operations. Specifically, we demonstrate by example that neural encoders do not necessarily map similar sentences to nearby latent vectors. A theoretical explanation for this phenomenon establishes that high capacity autoencoders can learn an arbitrary mapping between sequences and associated latent representations. To remedy this issue, we augment adversarial autoencoders with a denoising objective where original sentences are reconstructed from perturbed versions (referred to as DAAE). We prove that this simple modification guides the latent space geometry of the resulting model by encouraging the encoder to map similar texts to similar latent representations. In empirical comparisons with various types of autoencoders, our model provides the best trade-off between generation quality and reconstruction capacity. Moreover, the improved geometry of the DAAE latent space enables zero-shot text style transfer via simple latent vector arithmetic.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Sparse autoencoders (SAEs) have lately been used to uncover interpretable latent features in large language models. Here, we explore their potential for decomposing latent representations in complex and high-dimensional biological data, where the underlying variables are often unknown. On simulated data we show that generative hidden variables can be captured in learned representations in the form of superpositions. The degree to which they are learned depends on the completeness of the representations. Superpositions, however, are not identifiable if these generative variables are unknown. SAEs can to some extent recover these variables, yielding interpretable features. Applied to single-cell multi-omics data, we show that an SAE can uncover key biological processes such as carbon dioxide transport and ion homeostasis, which are crucial for red blood cell differentiation and immune function. Our findings highlight how SAEs can be used in advancing interpretability in biological and other scientific domains.

Deep networks for computer vision are not reliable when they encounter adversarial examples. In this paper, we introduce a framework that uses the dense intrinsic constraints in natural images to robustify inference. By introducing constraints at inference time, we can shift the burden of robustness from training to the inference algorithm, thereby allowing the model to adjust dynamically to each individual image's unique and potentially novel characteristics at inference time. Among different constraints, we find that equivariance-based constraints are most effective, because they allow dense constraints in the feature space without overly constraining the representation at a fine-grained level. Our theoretical results validate the importance of having such dense constraints at inference time. Our empirical experiments show that restoring feature equivariance at inference time defends against worst-case adversarial perturbations. The method obtains improved adversarial robustness on four datasets (ImageNet, Cityscapes, PASCAL VOC, and MS-COCO) on image recognition, semantic segmentation, and instance segmentation tasks. Project page is available at equi4robust.cs.columbia.edu.

The development of efficient machine learning models for molecular systems representation is becoming crucial in scientific research. We introduce TensorNet, an innovative O(3)-equivariant message-passing neural network architecture that leverages Cartesian tensor representations. By using Cartesian tensor atomic embeddings, feature mixing is simplified through matrix product operations. Furthermore, the cost-effective decomposition of these tensors into rotation group irreducible representations allows for the separate processing of scalars, vectors, and tensors when necessary. Compared to higher-rank spherical tensor models, TensorNet demonstrates state-of-the-art performance with significantly fewer parameters. For small molecule potential energies, this can be achieved even with a single interaction layer. As a result of all these properties, the model's computational cost is substantially decreased. Moreover, the accurate prediction of vector and tensor molecular quantities on top of potential energies and forces is possible. In summary, TensorNet's framework opens up a new space for the design of state-of-the-art equivariant models.

Learning useful representations without supervision remains a key challenge in machine learning. In this paper, we propose a simple yet powerful generative model that learns such discrete representations. Our model, the Vector Quantised-Variational AutoEncoder (VQ-VAE), differs from VAEs in two key ways: the encoder network outputs discrete, rather than continuous, codes; and the prior is learnt rather than static. In order to learn a discrete latent representation, we incorporate ideas from vector quantisation (VQ). Using the VQ method allows the model to circumvent issues of "posterior collapse" -- where the latents are ignored when they are paired with a powerful autoregressive decoder -- typically observed in the VAE framework. Pairing these representations with an autoregressive prior, the model can generate high quality images, videos, and speech as well as doing high quality speaker conversion and unsupervised learning of phonemes, providing further evidence of the utility of the learnt representations.

We propose a new model for digital pathology segmentation, based on the observation that histopathology images are inherently symmetric under rotation and reflection. Utilizing recent findings on rotation equivariant CNNs, the proposed model leverages these symmetries in a principled manner. We present a visual analysis showing improved stability on predictions, and demonstrate that exploiting rotation equivariance significantly improves tumor detection performance on a challenging lymph node metastases dataset. We further present a novel derived dataset to enable principled comparison of machine learning models, in combination with an initial benchmark. Through this dataset, the task of histopathology diagnosis becomes accessible as a challenging benchmark for fundamental machine learning research.

We introduce the variational graph auto-encoder (VGAE), a framework for unsupervised learning on graph-structured data based on the variational auto-encoder (VAE). This model makes use of latent variables and is capable of learning interpretable latent representations for undirected graphs. We demonstrate this model using a graph convolutional network (GCN) encoder and a simple inner product decoder. Our model achieves competitive results on a link prediction task in citation networks. In contrast to most existing models for unsupervised learning on graph-structured data and link prediction, our model can naturally incorporate node features, which significantly improves predictive performance on a number of benchmark datasets.

Two competing paradigms exist for self-supervised learning of data representations. Joint Embedding Predictive Architecture (JEPA) is a class of architectures in which semantically similar inputs are encoded into representations that are predictive of each other. A recent successful approach that falls under the JEPA framework is self-distillation, where an online encoder is trained to predict the output of the target encoder, sometimes using a lightweight predictor network. This is contrasted with the Masked AutoEncoder (MAE) paradigm, where an encoder and decoder are trained to reconstruct missing parts of the input in the data space rather, than its latent representation. A common motivation for using the JEPA approach over MAE is that the JEPA objective prioritizes abstract features over fine-grained pixel information (which can be unpredictable and uninformative). In this work, we seek to understand the mechanism behind this empirical observation by analyzing the training dynamics of deep linear models. We uncover a surprising mechanism: in a simplified linear setting where both approaches learn similar representations, JEPAs are biased to learn high-influence features, i.e., features characterized by having high regression coefficients. Our results point to a distinct implicit bias of predicting in latent space that may shed light on its success in practice.

Symmetry-based neural networks often constrain the architecture in order to achieve invariance or equivariance to a group of transformations. In this paper, we propose an alternative that avoids this architectural constraint by learning to produce a canonical representation of the data. These canonicalization functions can readily be plugged into non-equivariant backbone architectures. We offer explicit ways to implement them for many groups of interest. We show that this approach enjoys universality while providing interpretable insights. Our main hypothesis is that learning a neural network to perform canonicalization is better than using predefined heuristics. Our results show that learning the canonicalization function indeed leads to better results and that the approach achieves excellent performance in practice.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Variational Autoencoders (VAEs) have become a cornerstone in generative modeling and representation learning within machine learning. This paper explores a nuanced aspect of VAEs, focusing on interpreting the Kullback-Leibler (KL) Divergence, a critical component within the Evidence Lower Bound (ELBO) that governs the trade-off between reconstruction accuracy and regularization. Meanwhile, the KL Divergence enforces alignment between latent variable distributions and a prior imposing a structure on the overall latent space but leaves individual variable distributions unconstrained. The proposed method redefines the ELBO with a mixture of Gaussians for the posterior probability, introduces a regularization term to prevent variance collapse, and employs a PatchGAN discriminator to enhance texture realism. Implementation details involve ResNetV2 architectures for both the Encoder and Decoder. The experiments demonstrate the ability to generate realistic faces, offering a promising solution for enhancing VAE-based generative models.

Learning a robust video Variational Autoencoder (VAE) is essential for reducing video redundancy and facilitating efficient video generation. Directly applying image VAEs to individual frames in isolation can result in temporal inconsistencies and suboptimal compression rates due to a lack of temporal compression. Existing Video VAEs have begun to address temporal compression; however, they often suffer from inadequate reconstruction performance. In this paper, we present a novel and powerful video autoencoder capable of high-fidelity video encoding. First, we observe that entangling spatial and temporal compression by merely extending the image VAE to a 3D VAE can introduce motion blur and detail distortion artifacts. Thus, we propose temporal-aware spatial compression to better encode and decode the spatial information. Additionally, we integrate a lightweight motion compression model for further temporal compression. Second, we propose to leverage the textual information inherent in text-to-video datasets and incorporate text guidance into our model. This significantly enhances reconstruction quality, particularly in terms of detail preservation and temporal stability. Third, we further improve the versatility of our model through joint training on both images and videos, which not only enhances reconstruction quality but also enables the model to perform both image and video autoencoding. Extensive evaluations against strong recent baselines demonstrate the superior performance of our method. The project website can be found at~https://yzxing87.github.io/vae/{https://yzxing87.github.io/vae/}.

We present a novel method for constructing Variational Autoencoder (VAE). Instead of using pixel-by-pixel loss, we enforce deep feature consistency between the input and the output of a VAE, which ensures the VAE's output to preserve the spatial correlation characteristics of the input, thus leading the output to have a more natural visual appearance and better perceptual quality. Based on recent deep learning works such as style transfer, we employ a pre-trained deep convolutional neural network (CNN) and use its hidden features to define a feature perceptual loss for VAE training. Evaluated on the CelebA face dataset, we show that our model produces better results than other methods in the literature. We also show that our method can produce latent vectors that can capture the semantic information of face expressions and can be used to achieve state-of-the-art performance in facial attribute prediction.

Autoencoder networks are unsupervised approaches aiming at combining generative and representational properties by learning simultaneously an encoder-generator map. Although studied extensively, the issues of whether they have the same generative power of GANs, or learn disentangled representations, have not been fully addressed. We introduce an autoencoder that tackles these issues jointly, which we call Adversarial Latent Autoencoder (ALAE). It is a general architecture that can leverage recent improvements on GAN training procedures. We designed two autoencoders: one based on a MLP encoder, and another based on a StyleGAN generator, which we call StyleALAE. We verify the disentanglement properties of both architectures. We show that StyleALAE can not only generate 1024x1024 face images with comparable quality of StyleGAN, but at the same resolution can also produce face reconstructions and manipulations based on real images. This makes ALAE the first autoencoder able to compare with, and go beyond the capabilities of a generator-only type of architecture.

Vision Transformers (ViT), when paired with large-scale pretraining, have shown remarkable performance across various computer vision tasks, primarily due to their weak inductive bias. However, while such weak inductive bias aids in pretraining scalability, this may hinder the effective adaptation of ViTs for visuo-motor control tasks as a result of the absence of control-centric inductive biases. Such absent inductive biases include spatial locality and translation equivariance bias which convolutions naturally offer. To this end, we introduce Convolution Injector (CoIn), an add-on module that injects convolutions which are rich in locality and equivariance biases into a pretrained ViT for effective adaptation in visuo-motor control. We evaluate CoIn with three distinct types of pretrained ViTs (CLIP, MVP, VC-1) across 12 varied control tasks within three separate domains (Adroit, MetaWorld, DMC), and demonstrate that CoIn consistently enhances control task performance across all experimented environments and models, validating the effectiveness of providing pretrained ViTs with control-centric biases.

We develop a novel method for carrying out model selection for Bayesian autoencoders (BAEs) by means of prior hyper-parameter optimization. Inspired by the common practice of type-II maximum likelihood optimization and its equivalence to Kullback-Leibler divergence minimization, we propose to optimize the distributional sliced-Wasserstein distance (DSWD) between the output of the autoencoder and the empirical data distribution. The advantages of this formulation are that we can estimate the DSWD based on samples and handle high-dimensional problems. We carry out posterior estimation of the BAE parameters via stochastic gradient Hamiltonian Monte Carlo and turn our BAE into a generative model by fitting a flexible Dirichlet mixture model in the latent space. Consequently, we obtain a powerful alternative to variational autoencoders, which are the preferred choice in modern applications of autoencoders for representation learning with uncertainty. We evaluate our approach qualitatively and quantitatively using a vast experimental campaign on a number of unsupervised learning tasks and show that, in small-data regimes where priors matter, our approach provides state-of-the-art results, outperforming multiple competitive baselines.

Self-supervised learning excels in learning representations from large amounts of unlabeled data, demonstrating success across multiple data modalities. Yet, extending self-supervised learning to new modalities is non-trivial because the specifics of existing methods are tailored to each domain, such as domain-specific augmentations which reflect the invariances in the target task. While masked modeling is promising as a domain-agnostic framework for self-supervised learning because it does not rely on input augmentations, its mask sampling procedure remains domain-specific. We present Self-guided Masked Autoencoders (SMA), a fully domain-agnostic masked modeling method. SMA trains an attention based model using a masked modeling objective, by learning masks to sample without any domain-specific assumptions. We evaluate SMA on three self-supervised learning benchmarks in protein biology, chemical property prediction, and particle physics. We find SMA is capable of learning representations without domain-specific knowledge and achieves state-of-the-art performance on these three benchmarks.

We study the problem of learning equivariant neural networks via gradient descent. The incorporation of known symmetries ("equivariance") into neural nets has empirically improved the performance of learning pipelines, in domains ranging from biology to computer vision. However, a rich yet separate line of learning theoretic research has demonstrated that actually learning shallow, fully-connected (i.e. non-symmetric) networks has exponential complexity in the correlational statistical query (CSQ) model, a framework encompassing gradient descent. In this work, we ask: are known problem symmetries sufficient to alleviate the fundamental hardness of learning neural nets with gradient descent? We answer this question in the negative. In particular, we give lower bounds for shallow graph neural networks, convolutional networks, invariant polynomials, and frame-averaged networks for permutation subgroups, which all scale either superpolynomially or exponentially in the relevant input dimension. Therefore, in spite of the significant inductive bias imparted via symmetry, actually learning the complete classes of functions represented by equivariant neural networks via gradient descent remains hard.

We propose Equiangular Basis Vectors (EBVs) for classification tasks. In deep neural networks, models usually end with a k-way fully connected layer with softmax to handle different classification tasks. The learning objective of these methods can be summarized as mapping the learned feature representations to the samples' label space. While in metric learning approaches, the main objective is to learn a transformation function that maps training data points from the original space to a new space where similar points are closer while dissimilar points become farther apart. Different from previous methods, our EBVs generate normalized vector embeddings as "predefined classifiers" which are required to not only be with the equal status between each other, but also be as orthogonal as possible. By minimizing the spherical distance of the embedding of an input between its categorical EBV in training, the predictions can be obtained by identifying the categorical EBV with the smallest distance during inference. Various experiments on the ImageNet-1K dataset and other downstream tasks demonstrate that our method outperforms the general fully connected classifier while it does not introduce huge additional computation compared with classical metric learning methods. Our EBVs won the first place in the 2022 DIGIX Global AI Challenge, and our code is open-source and available at https://github.com/NJUST-VIPGroup/Equiangular-Basis-Vectors.

We present a framework for the unsupervised learning of neurosymbolic encoders, which are encoders obtained by composing neural networks with symbolic programs from a domain-specific language. Our framework naturally incorporates symbolic expert knowledge into the learning process, which leads to more interpretable and factorized latent representations compared to fully neural encoders. We integrate modern program synthesis techniques with the variational autoencoding (VAE) framework, in order to learn a neurosymbolic encoder in conjunction with a standard decoder. The programmatic descriptions from our encoders can benefit many analysis workflows, such as in behavior modeling where interpreting agent actions and movements is important. We evaluate our method on learning latent representations for real-world trajectory data from animal biology and sports analytics. We show that our approach offers significantly better separation of meaningful categories than standard VAEs and leads to practical gains on downstream analysis tasks, such as for behavior classification.

We introduce a novel method for pre-training of large-scale vision encoders. Building on recent advancements in autoregressive pre-training of vision models, we extend this framework to a multimodal setting, i.e., images and text. In this paper, we present AIMV2, a family of generalist vision encoders characterized by a straightforward pre-training process, scalability, and remarkable performance across a range of downstream tasks. This is achieved by pairing the vision encoder with a multimodal decoder that autoregressively generates raw image patches and text tokens. Our encoders excel not only in multimodal evaluations but also in vision benchmarks such as localization, grounding, and classification. Notably, our AIMV2-3B encoder achieves 89.5% accuracy on ImageNet-1k with a frozen trunk. Furthermore, AIMV2 consistently outperforms state-of-the-art contrastive models (e.g., CLIP, SigLIP) in multimodal image understanding across diverse settings.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Variational Auto-Encoder (VAE) has become the de-facto learning paradigm in achieving representation learning and generation for natural language at the same time. Nevertheless, existing VAE-based language models either employ elementary RNNs, which is not powerful to handle complex works in the multi-task situation, or fine-tunes two pre-trained language models (PLMs) for any downstream task, which is a huge drain on resources. In this paper, we propose the first VAE framework empowered with adaptive GPT-2s (AdaVAE). Different from existing systems, we unify both the encoder\&decoder of the VAE model using GPT-2s with adaptive parameter-efficient components, and further introduce Latent Attention operation to better construct latent space from transformer models. Experiments from multiple dimensions validate that AdaVAE is competent to effectively organize language in three related tasks (language modeling, representation modeling and guided text generation) even with less than 15% activated parameters in training. Our code is available at https://github.com/ImKeTT/AdaVAE.

This paper studies a conceptually simple extension of Masked Autoencoders (MAE) to spatiotemporal representation learning from videos. We randomly mask out spacetime patches in videos and learn an autoencoder to reconstruct them in pixels. Interestingly, we show that our MAE method can learn strong representations with almost no inductive bias on spacetime (only except for patch and positional embeddings), and spacetime-agnostic random masking performs the best. We observe that the optimal masking ratio is as high as 90% (vs. 75% on images), supporting the hypothesis that this ratio is related to information redundancy of the data. A high masking ratio leads to a large speedup, e.g., > 4x in wall-clock time or even more. We report competitive results on several challenging video datasets using vanilla Vision Transformers. We observe that MAE can outperform supervised pre-training by large margins. We further report encouraging results of training on real-world, uncurated Instagram data. Our study suggests that the general framework of masked autoencoding (BERT, MAE, etc.) can be a unified methodology for representation learning with minimal domain knowledge.

Sparse autoencoders provide a promising unsupervised approach for extracting interpretable features from a language model by reconstructing activations from a sparse bottleneck layer. Since language models learn many concepts, autoencoders need to be very large to recover all relevant features. However, studying the properties of autoencoder scaling is difficult due to the need to balance reconstruction and sparsity objectives and the presence of dead latents. We propose using k-sparse autoencoders [Makhzani and Frey, 2013] to directly control sparsity, simplifying tuning and improving the reconstruction-sparsity frontier. Additionally, we find modifications that result in few dead latents, even at the largest scales we tried. Using these techniques, we find clean scaling laws with respect to autoencoder size and sparsity. We also introduce several new metrics for evaluating feature quality based on the recovery of hypothesized features, the explainability of activation patterns, and the sparsity of downstream effects. These metrics all generally improve with autoencoder size. To demonstrate the scalability of our approach, we train a 16 million latent autoencoder on GPT-4 activations for 40 billion tokens. We release training code and autoencoders for open-source models, as well as a visualizer.

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable (latent) Diffusion models, we propose a novel and principled method for 3D molecule generation named Geometric Latent Diffusion Models (GeoLDM). GeoLDM is the first latent DM model for the molecular geometry domain, composed of autoencoders encoding structures into continuous latent codes and DMs operating in the latent space. Our key innovation is that for modeling the 3D molecular geometries, we capture its critical roto-translational equivariance constraints by building a point-structured latent space with both invariant scalars and equivariant tensors. Extensive experiments demonstrate that GeoLDM can consistently achieve better performance on multiple molecule generation benchmarks, with up to 7\% improvement for the valid percentage of large biomolecules. Results also demonstrate GeoLDM's higher capacity for controllable generation thanks to the latent modeling. Code is provided at https://github.com/MinkaiXu/GeoLDM.

Masked Autoencoders (MAE) have been popular paradigms for large-scale vision representation pre-training. However, MAE solely reconstructs the low-level RGB signals after the decoder and lacks supervision upon high-level semantics for the encoder, thus suffering from sub-optimal learned representations and long pre-training epochs. To alleviate this, previous methods simply replace the pixel reconstruction targets of 75% masked tokens by encoded features from pre-trained image-image (DINO) or image-language (CLIP) contrastive learning. Different from those efforts, we propose to Mimic before Reconstruct for Masked Autoencoders, named as MR-MAE, which jointly learns high-level and low-level representations without interference during pre-training. For high-level semantics, MR-MAE employs a mimic loss over 25% visible tokens from the encoder to capture the pre-trained patterns encoded in CLIP and DINO. For low-level structures, we inherit the reconstruction loss in MAE to predict RGB pixel values for 75% masked tokens after the decoder. As MR-MAE applies high-level and low-level targets respectively at different partitions, the learning conflicts between them can be naturally overcome and contribute to superior visual representations for various downstream tasks. On ImageNet-1K, the MR-MAE base pre-trained for only 400 epochs achieves 85.8% top-1 accuracy after fine-tuning, surpassing the 1600-epoch MAE base by +2.2% and the previous state-of-the-art BEiT V2 base by +0.3%. Code and pre-trained models will be released at https://github.com/Alpha-VL/ConvMAE.

A key requirement for graph neural networks is that they must process a graph in a way that does not depend on how the graph is described. Traditionally this has been taken to mean that a graph network must be equivariant to node permutations. Here we show that instead of equivariance, the more general concept of naturality is sufficient for a graph network to be well-defined, opening up a larger class of graph networks. We define global and local natural graph networks, the latter of which are as scalable as conventional message passing graph neural networks while being more flexible. We give one practical instantiation of a natural network on graphs which uses an equivariant message network parameterization, yielding good performance on several benchmarks.

The variational autoencoder (VAE) framework is a popular option for training unsupervised generative models, featuring ease of training and latent representation of data. The objective function of VAE does not guarantee to achieve the latter, however, and failure to do so leads to a frequent failure mode called posterior collapse. Even in successful cases, VAEs often result in low-precision reconstructions and generated samples. The introduction of the KL-divergence weight beta can help steer the model clear of posterior collapse, but its tuning is often a trial-and-error process with no guiding metrics. Here we test the idea of using the total VAE loss of generated samples (generated loss) as the proxy metric for generation quality, the related hypothesis that VAE reconstruction from the mean latent vector tends to be a more typical example of its class than the original, and the idea of exploiting this property by augmenting training data with generated variants (augmented training). The results are mixed, but repeated encoding and decoding indeed result in qualitatively and quantitatively more typical examples from both convolutional and fully-connected MNIST VAEs, suggesting that it may be an inherent property of the VAE framework.

In this paper, a novel self-supervised learning (SSL) method is proposed, which learns not only representations but also representations uncertainties by considering SSL in terms of variational inference. SSL is a method of learning representation without labels by maximizing the similarity between image representations of different augmented views of the same image. Variational autoencoder (VAE) is an unsupervised representation learning method that trains a probabilistic generative model with variational inference. VAE and SSL can learn representations without labels, but the relationship between VAE and SSL has not been revealed. In this paper, the theoretical relationship between SSL and variational inference is clarified. In addition, variational inference SimSiam (VI-SimSiam) is proposed, which can predict the representation uncertainty by interpreting SimSiam with variational inference and defining the latent space distribution. The experiment qualitatively showed that VISimSiam could learn uncertainty by comparing input images and predicted uncertainties. We also revealed a relationship between estimated uncertainty and classification accuracy.

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.

This paper studies how to synthesize face images of non-existent persons, to create a dataset that allows effective training of face recognition (FR) models. Two important goals are (1) the ability to generate a large number of distinct identities (inter-class separation) with (2) a wide variation in appearance of each identity (intra-class variation). However, existing works 1) are typically limited in how many well-separated identities can be generated and 2) either neglect or use a separate editing model for attribute augmentation. We propose Vec2Face, a holistic model that uses only a sampled vector as input and can flexibly generate and control face images and their attributes. Composed of a feature masked autoencoder and a decoder, Vec2Face is supervised by face image reconstruction and can be conveniently used in inference. Using vectors with low similarity among themselves as inputs, Vec2Face generates well-separated identities. Randomly perturbing an input identity vector within a small range allows Vec2Face to generate faces of the same identity with robust variation in face attributes. It is also possible to generate images with designated attributes by adjusting vector values with a gradient descent method. Vec2Face has efficiently synthesized as many as 300K identities with 15 million total images, whereas 60K is the largest number of identities created in the previous works. FR models trained with the generated HSFace datasets, from 10k to 300k identities, achieve state-of-the-art accuracy, from 92% to 93.52%, on five real-world test sets. For the first time, our model created using a synthetic training set achieves higher accuracy than the model created using a same-scale training set of real face images (on the CALFW test set).

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

We present a novel masked image modeling (MIM) approach, context autoencoder (CAE), for self-supervised representation pretraining. We pretrain an encoder by making predictions in the encoded representation space. The pretraining tasks include two tasks: masked representation prediction - predict the representations for the masked patches, and masked patch reconstruction - reconstruct the masked patches. The network is an encoder-regressor-decoder architecture: the encoder takes the visible patches as input; the regressor predicts the representations of the masked patches, which are expected to be aligned with the representations computed from the encoder, using the representations of visible patches and the positions of visible and masked patches; the decoder reconstructs the masked patches from the predicted encoded representations. The CAE design encourages the separation of learning the encoder (representation) from completing the pertaining tasks: masked representation prediction and masked patch reconstruction tasks, and making predictions in the encoded representation space empirically shows the benefit to representation learning. We demonstrate the effectiveness of our CAE through superior transfer performance in downstream tasks: semantic segmentation, object detection and instance segmentation, and classification. The code will be available at https://github.com/Atten4Vis/CAE.

We tackle the problem disentangling the latent space of an autoencoder in order to separate labelled attribute information from other characteristic information. This then allows us to change selected attributes while preserving other information. Our method, matrix subspace projection, is much simpler than previous approaches to latent space factorisation, for example not requiring multiple discriminators or a careful weighting among their loss functions. Furthermore our new model can be applied to autoencoders as a plugin, and works across diverse domains such as images or text. We demonstrate the utility of our method for attribute manipulation in autoencoders trained across varied domains, using both human evaluation and automated methods. The quality of generation of our new model (e.g. reconstruction, conditional generation) is highly competitive to a number of strong baselines.

Sequence-to-sequence (seq2seq) learning is a popular fashion for large-scale pretraining language models. However, the prior seq2seq pretraining models generally focus on reconstructive objectives on the decoder side and neglect the effect of encoder-side supervision, which we argue may lead to sub-optimal performance. To verify our hypothesis, we first empirically study the functionalities of the encoder and decoder in seq2seq pretrained language models, and find that the encoder takes an important but under-exploitation role than the decoder regarding the downstream performance and neuron activation. Therefore, we propose an encoding-enhanced seq2seq pretraining strategy, namely E2S2, which improves the seq2seq models via integrating more efficient self-supervised information into the encoders. Specifically, E2S2 adopts two self-supervised objectives on the encoder side from two aspects: 1) locally denoising the corrupted sentence (denoising objective); and 2) globally learning better sentence representations (contrastive objective). With the help of both objectives, the encoder can effectively distinguish the noise tokens and capture high-level (i.e. syntactic and semantic) knowledge, thus strengthening the ability of seq2seq model to accurately achieve the conditional generation. On a large diversity of downstream natural language understanding and generation tasks, E2S2 dominantly improves the performance of its powerful backbone models, e.g. BART and T5. For example, upon BART backbone, we achieve +1.1% averaged gain on the general language understanding evaluation (GLUE) benchmark and +1.75% F_0.5 score improvement on CoNLL2014 dataset. We also provide in-depth analyses to show the improvement stems from better linguistic representation. We hope that our work will foster future self-supervision research on seq2seq language model pretraining.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Latent variable models (LVMs) with discrete compositional latents are an important but challenging setting due to a combinatorially large number of possible configurations of the latents. A key tradeoff in modeling the posteriors over latents is between expressivity and tractable optimization. For algorithms based on expectation-maximization (EM), the E-step is often intractable without restrictive approximations to the posterior. We propose the use of GFlowNets, algorithms for sampling from an unnormalized density by learning a stochastic policy for sequential construction of samples, for this intractable E-step. By training GFlowNets to sample from the posterior over latents, we take advantage of their strengths as amortized variational inference algorithms for complex distributions over discrete structures. Our approach, GFlowNet-EM, enables the training of expressive LVMs with discrete compositional latents, as shown by experiments on non-context-free grammar induction and on images using discrete variational autoencoders (VAEs) without conditional independence enforced in the encoder.

This work addresses the problem of generating 3D holistic body motions from human speech. Given a speech recording, we synthesize sequences of 3D body poses, hand gestures, and facial expressions that are realistic and diverse. To achieve this, we first build a high-quality dataset of 3D holistic body meshes with synchronous speech. We then define a novel speech-to-motion generation framework in which the face, body, and hands are modeled separately. The separated modeling stems from the fact that face articulation strongly correlates with human speech, while body poses and hand gestures are less correlated. Specifically, we employ an autoencoder for face motions, and a compositional vector-quantized variational autoencoder (VQ-VAE) for the body and hand motions. The compositional VQ-VAE is key to generating diverse results. Additionally, we propose a cross-conditional autoregressive model that generates body poses and hand gestures, leading to coherent and realistic motions. Extensive experiments and user studies demonstrate that our proposed approach achieves state-of-the-art performance both qualitatively and quantitatively. Our novel dataset and code will be released for research purposes at https://talkshow.is.tue.mpg.de.

We present a new approach for understanding the periodicity structure and semantics of motion datasets, independently of the morphology and skeletal structure of characters. Unlike existing methods using an overly sparse high-dimensional latent, we propose a phase manifold consisting of multiple closed curves, each corresponding to a latent amplitude. With our proposed vector quantized periodic autoencoder, we learn a shared phase manifold for multiple characters, such as a human and a dog, without any supervision. This is achieved by exploiting the discrete structure and a shallow network as bottlenecks, such that semantically similar motions are clustered into the same curve of the manifold, and the motions within the same component are aligned temporally by the phase variable. In combination with an improved motion matching framework, we demonstrate the manifold's capability of timing and semantics alignment in several applications, including motion retrieval, transfer and stylization. Code and pre-trained models for this paper are available at https://peizhuoli.github.io/walkthedog.

We present a general framework for symmetrizing an arbitrary neural-network architecture and making it equivariant with respect to a given group. We build upon the proposals of Kim et al. (2023); Kaba et al. (2023) for symmetrization, and improve them by replacing their conversion of neural features into group representations, with an optimization whose loss intuitively measures the distance between group orbits. This change makes our approach applicable to a broader range of matrix groups, such as the Lorentz group O(1, 3), than these two proposals. We experimentally show our method's competitiveness on the SO(2) image classification task, and also its increased generality on the task with O(1, 3). Our implementation will be made accessible at https://github.com/tiendatnguyen-vision/Orbit-symmetrize.

Neural sequence-to-sequence models are currently the dominant approach in several natural language processing tasks, but require large parallel corpora. We present a sequence-to-sequence-to-sequence autoencoder (SEQ^3), consisting of two chained encoder-decoder pairs, with words used as a sequence of discrete latent variables. We apply the proposed model to unsupervised abstractive sentence compression, where the first and last sequences are the input and reconstructed sentences, respectively, while the middle sequence is the compressed sentence. Constraining the length of the latent word sequences forces the model to distill important information from the input. A pretrained language model, acting as a prior over the latent sequences, encourages the compressed sentences to be human-readable. Continuous relaxations enable us to sample from categorical distributions, allowing gradient-based optimization, unlike alternatives that rely on reinforcement learning. The proposed model does not require parallel text-summary pairs, achieving promising results in unsupervised sentence compression on benchmark datasets.

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.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

What do auto-encoders learn about the underlying data generating distribution? Recent work suggests that some auto-encoder variants do a good job of capturing the local manifold structure of data. This paper clarifies some of these previous observations by showing that minimizing a particular form of regularized reconstruction error yields a reconstruction function that locally characterizes the shape of the data generating density. We show that the auto-encoder captures the score (derivative of the log-density with respect to the input). It contradicts previous interpretations of reconstruction error as an energy function. Unlike previous results, the theorems provided here are completely generic and do not depend on the parametrization of the auto-encoder: they show what the auto-encoder would tend to if given enough capacity and examples. These results are for a contractive training criterion we show to be similar to the denoising auto-encoder training criterion with small corruption noise, but with contraction applied on the whole reconstruction function rather than just encoder. Similarly to score matching, one can consider the proposed training criterion as a convenient alternative to maximum likelihood because it does not involve a partition function. Finally, we show how an approximate Metropolis-Hastings MCMC can be setup to recover samples from the estimated distribution, and this is confirmed in sampling experiments.

We introduce a novel method for representation learning that uses an artificial supervision signal based on counting visual primitives. This supervision signal is obtained from an equivariance relation, which does not require any manual annotation. We relate transformations of images to transformations of the representations. More specifically, we look for the representation that satisfies such relation rather than the transformations that match a given representation. In this paper, we use two image transformations in the context of counting: scaling and tiling. The first transformation exploits the fact that the number of visual primitives should be invariant to scale. The second transformation allows us to equate the total number of visual primitives in each tile to that in the whole image. These two transformations are combined in one constraint and used to train a neural network with a contrastive loss. The proposed task produces representations that perform on par or exceed the state of the art in transfer learning benchmarks.

For any graph G having n vertices and its automorphism group Aut(G), we provide a full characterisation of all of the possible Aut(G)-equivariant neural networks whose layers are some tensor power of R^{n}. In particular, we find a spanning set of matrices for the learnable, linear, Aut(G)-equivariant layer functions between such tensor power spaces in the standard basis of R^{n}.

We present Deep Compression Autoencoder (DC-AE), a new family of autoencoder models for accelerating high-resolution diffusion models. Existing autoencoder models have demonstrated impressive results at a moderate spatial compression ratio (e.g., 8x), but fail to maintain satisfactory reconstruction accuracy for high spatial compression ratios (e.g., 64x). We address this challenge by introducing two key techniques: (1) Residual Autoencoding, where we design our models to learn residuals based on the space-to-channel transformed features to alleviate the optimization difficulty of high spatial-compression autoencoders; (2) Decoupled High-Resolution Adaptation, an efficient decoupled three-phases training strategy for mitigating the generalization penalty of high spatial-compression autoencoders. With these designs, we improve the autoencoder's spatial compression ratio up to 128 while maintaining the reconstruction quality. Applying our DC-AE to latent diffusion models, we achieve significant speedup without accuracy drop. For example, on ImageNet 512x512, our DC-AE provides 19.1x inference speedup and 17.9x training speedup on H100 GPU for UViT-H while achieving a better FID, compared with the widely used SD-VAE-f8 autoencoder. Our code is available at https://github.com/mit-han-lab/efficientvit.

Structured variational autoencoders (SVAEs) combine probabilistic graphical model priors on latent variables, deep neural networks to link latent variables to observed data, and structure-exploiting algorithms for approximate posterior inference. These models are particularly appealing for sequential data, where the prior can capture temporal dependencies. However, despite their conceptual elegance, SVAEs have proven difficult to implement, and more general approaches have been favored in practice. Here, we revisit SVAEs using modern machine learning tools and demonstrate their advantages over more general alternatives in terms of both accuracy and efficiency. First, we develop a modern implementation for hardware acceleration, parallelization, and automatic differentiation of the message passing algorithms at the core of the SVAE. Second, we show that by exploiting structure in the prior, the SVAE learns more accurate models and posterior distributions, which translate into improved performance on prediction tasks. Third, we show how the SVAE can naturally handle missing data, and we leverage this ability to develop a novel, self-supervised training approach. Altogether, these results show that the time is ripe to revisit structured variational autoencoders.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and learns the inverse map using an E(n)-Equivariant Graph Neural Network (EGNN). The induced point cloud-structured latent space is well-suited to apply existing 3D molecular generative models. This approach simplifies the graph generation problem - without relying on molecular fragments nor autoregressive decoding - into a point cloud generation problem followed by node and edge classification tasks. Further, we propose a novel similarity-constrained optimization scheme for 3D diffusion models based on inpainting and guidance. As a concrete implementation of our framework, we develop EDM-SyCo based on the E(3) Equivariant Diffusion Model (EDM). EDM-SyCo achieves state-of-the-art performance in distribution learning of molecular graphs, outperforming the best non-autoregressive methods by more than 30% on ZINC250K and 16% on the large-scale GuacaMol dataset while improving conditional generation by up to 3.9 times.

Graph Neural Networks (GNNs) with equivariant properties have emerged as powerful tools for modeling complex dynamics of multi-object physical systems. However, their generalization ability is limited by the inadequate consideration of physical inductive biases: (1) Existing studies overlook the continuity of transitions among system states, opting to employ several discrete transformation layers to learn the direct mapping between two adjacent states; (2) Most models only account for first-order velocity information, despite the fact that many physical systems are governed by second-order motion laws. To incorporate these inductive biases, we propose the Second-order Equivariant Graph Neural Ordinary Differential Equation (SEGNO). Specifically, we show how the second-order continuity can be incorporated into GNNs while maintaining the equivariant property. Furthermore, we offer theoretical insights into SEGNO, highlighting that it can learn a unique trajectory between adjacent states, which is crucial for model generalization. Additionally, we prove that the discrepancy between this learned trajectory of SEGNO and the true trajectory is bounded. Extensive experiments on complex dynamical systems including molecular dynamics and motion capture demonstrate that our model yields a significant improvement over the state-of-the-art baselines.

In quantised autoencoders, images are usually split into local patches, each encoded by one token. This representation is redundant in the sense that the same number of tokens is spend per region, regardless of the visual information content in that region. Adaptive discretisation schemes like quadtrees are applied to allocate tokens for patches with varying sizes, but this just varies the region of influence for a token which nevertheless remains a local descriptor. Modern architectures add an attention mechanism to the autoencoder which infuses some degree of global information into the local tokens. Despite the global context, tokens are still associated with a local image region. In contrast, our method is inspired by spectral decompositions which transform an input signal into a superposition of global frequencies. Taking the data-driven perspective, we learn custom basis functions corresponding to the codebook entries in our VQ-VAE setup. Furthermore, a decoder combines these basis functions in a non-linear fashion, going beyond the simple linear superposition of spectral decompositions. We can achieve this global description with an efficient transpose operation between features and channels and demonstrate our performance on compression.

Deep ensembles (DE) have been successful in improving model performance by learning diverse members via the stochasticity of random initialization. While recent works have attempted to promote further diversity in DE via hyperparameters or regularizing loss functions, these methods primarily still rely on a stochastic approach to explore the hypothesis space. In this work, we present Multi-Symmetry Ensembles (MSE), a framework for constructing diverse ensembles by capturing the multiplicity of hypotheses along symmetry axes, which explore the hypothesis space beyond stochastic perturbations of model weights and hyperparameters. We leverage recent advances in contrastive representation learning to create models that separately capture opposing hypotheses of invariant and equivariant functional classes and present a simple ensembling approach to efficiently combine appropriate hypotheses for a given task. We show that MSE effectively captures the multiplicity of conflicting hypotheses that is often required in large, diverse datasets like ImageNet. As a result of their inherent diversity, MSE improves classification performance, uncertainty quantification, and generalization across a series of transfer tasks.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

This work contributes to breast cancer sub-type classification using histopathological images. We utilize masked autoencoders (MAEs) to learn a self-supervised embedding tailored for computer vision tasks in this domain. This embedding captures informative representations of histopathological data, facilitating feature learning without extensive labeled datasets. During pre-training, we investigate employing a random crop technique to generate a large dataset from WSIs automatically. Additionally, we assess the performance of linear probes for multi-class classification tasks of cancer sub-types using the representations learnt by the MAE. Our approach aims to achieve strong performance on downstream tasks by leveraging the complementary strengths of ViTs and autoencoders. We evaluate our model's performance on the BRACS dataset and compare it with existing benchmarks.

Dense retrieval requires high-quality text sequence embeddings to support effective search in the representation space. Autoencoder-based language models are appealing in dense retrieval as they train the encoder to output high-quality embedding that can reconstruct the input texts. However, in this paper, we provide theoretical analyses and show empirically that an autoencoder language model with a low reconstruction loss may not provide good sequence representations because the decoder may take shortcuts by exploiting language patterns. To address this, we propose a new self-learning method that pre-trains the autoencoder using a weak decoder, with restricted capacity and attention flexibility to push the encoder to provide better text representations. Our experiments on web search, news recommendation, and open domain question answering show that our pre-trained model significantly boosts the effectiveness and few-shot ability of dense retrieval models. Our code is available at https://github.com/microsoft/SEED-Encoder/.

Masked Autoencoder (MAE) has demonstrated superior performance on various vision tasks via randomly masking image patches and reconstruction. However, effective data augmentation strategies for MAE still remain open questions, different from those in contrastive learning that serve as the most important part. This paper studies the prevailing mixing augmentation for MAE. We first demonstrate that naive mixing will in contrast degenerate model performance due to the increase of mutual information (MI). To address, we propose homologous recognition, an auxiliary pretext task, not only to alleviate the MI increasement by explicitly requiring each patch to recognize homologous patches, but also to perform object-aware self-supervised pre-training for better downstream dense perception performance. With extensive experiments, we demonstrate that our proposed Mixed Autoencoder (MixedAE) achieves the state-of-the-art transfer results among masked image modeling (MIM) augmentations on different downstream tasks with significant efficiency. Specifically, our MixedAE outperforms MAE by +0.3% accuracy, +1.7 mIoU and +0.9 AP on ImageNet-1K, ADE20K and COCO respectively with a standard ViT-Base. Moreover, MixedAE surpasses iBOT, a strong MIM method combined with instance discrimination, while accelerating training by 2x. To our best knowledge, this is the very first work to consider mixing for MIM from the perspective of pretext task design. Code will be made available.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Latent variable generative models have emerged as powerful tools for generative tasks including image and video synthesis. These models are enabled by pretrained autoencoders that map high resolution data into a compressed lower dimensional latent space, where the generative models can subsequently be developed while requiring fewer computational resources. Despite their effectiveness, the direct application of latent variable models to higher dimensional domains such as videos continues to pose challenges for efficient training and inference. In this paper, we propose an autoencoder that projects volumetric data onto a four-plane factorized latent space that grows sublinearly with the input size, making it ideal for higher dimensional data like videos. The design of our factorized model supports straightforward adoption in a number of conditional generation tasks with latent diffusion models (LDMs), such as class-conditional generation, frame prediction, and video interpolation. Our results show that the proposed four-plane latent space retains a rich representation needed for high-fidelity reconstructions despite the heavy compression, while simultaneously enabling LDMs to operate with significant improvements in speed and memory.

Diffusion probabilistic models have been shown to generate state-of-the-art results on several competitive image synthesis benchmarks but lack a low-dimensional, interpretable latent space, and are slow at generation. On the other hand, standard Variational Autoencoders (VAEs) typically have access to a low-dimensional latent space but exhibit poor sample quality. We present DiffuseVAE, a novel generative framework that integrates VAE within a diffusion model framework, and leverage this to design novel conditional parameterizations for diffusion models. We show that the resulting model equips diffusion models with a low-dimensional VAE inferred latent code which can be used for downstream tasks like controllable synthesis. The proposed method also improves upon the speed vs quality tradeoff exhibited in standard unconditional DDPM/DDIM models (for instance, FID of 16.47 vs 34.36 using a standard DDIM on the CelebA-HQ-128 benchmark using T=10 reverse process steps) without having explicitly trained for such an objective. Furthermore, the proposed model exhibits synthesis quality comparable to state-of-the-art models on standard image synthesis benchmarks like CIFAR-10 and CelebA-64 while outperforming most existing VAE-based methods. Lastly, we show that the proposed method exhibits inherent generalization to different types of noise in the conditioning signal. For reproducibility, our source code is publicly available at https://github.com/kpandey008/DiffuseVAE.

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

Transformers rely on both content-based and position-based addressing mechanisms to make predictions, but existing positional encoding techniques often diminish the effectiveness of position-based addressing. Many current methods enforce rigid patterns in attention maps, limiting the ability to model long-range dependencies and adapt to diverse tasks. Additionally, most positional encodings are learned as general biases, lacking the specialization required for different instances within a dataset. To address this, we propose conTextualized equivariAnt Position Embedding (TAPE), a novel framework that enhances positional embeddings by incorporating sequence content across layers. TAPE introduces dynamic, context-aware positional encodings, overcoming the constraints of traditional fixed patterns. By enforcing permutation and orthogonal equivariance, TAPE ensures the stability of positional encodings during updates, improving robustness and adaptability. Our method can be easily integrated into pre-trained transformers, offering parameter-efficient fine-tuning with minimal overhead. Extensive experiments shows that TAPE achieves superior performance in language modeling, arithmetic reasoning, and long-context retrieval tasks compared to existing positional embedding techniques.

A key advance in learning generative models is the use of amortized inference distributions that are jointly trained with the models. We find that existing training objectives for variational autoencoders can lead to inaccurate amortized inference distributions and, in some cases, improving the objective provably degrades the inference quality. In addition, it has been observed that variational autoencoders tend to ignore the latent variables when combined with a decoding distribution that is too flexible. We again identify the cause in existing training criteria and propose a new class of objectives (InfoVAE) that mitigate these problems. We show that our model can significantly improve the quality of the variational posterior and can make effective use of the latent features regardless of the flexibility of the decoding distribution. Through extensive qualitative and quantitative analyses, we demonstrate that our models outperform competing approaches on multiple performance metrics.

Vector Quantized Variational AutoEncoders (VQ-VAEs) are designed to compress a continuous input to a discrete latent space and reconstruct it with minimal distortion. They operate by maintaining a set of vectors -- often referred to as the codebook -- and quantizing each encoder output to the nearest vector in the codebook. However, as vector quantization is non-differentiable, the gradient to the encoder flows around the vector quantization layer rather than through it in a straight-through approximation. This approximation may be undesirable as all information from the vector quantization operation is lost. In this work, we propose a way to propagate gradients through the vector quantization layer of VQ-VAEs. We smoothly transform each encoder output into its corresponding codebook vector via a rotation and rescaling linear transformation that is treated as a constant during backpropagation. As a result, the relative magnitude and angle between encoder output and codebook vector becomes encoded into the gradient as it propagates through the vector quantization layer and back to the encoder. Across 11 different VQ-VAE training paradigms, we find this restructuring improves reconstruction metrics, codebook utilization, and quantization error. Our code is available at https://github.com/cfifty/rotation_trick.

The trade-off between robustness and accuracy has been widely studied in the adversarial literature. Although still controversial, the prevailing view is that this trade-off is inherent, either empirically or theoretically. Thus, we dig for the origin of this trade-off in adversarial training and find that it may stem from the improperly defined robust error, which imposes an inductive bias of local invariance -- an overcorrection towards smoothness. Given this, we advocate employing local equivariance to describe the ideal behavior of a robust model, leading to a self-consistent robust error named SCORE. By definition, SCORE facilitates the reconciliation between robustness and accuracy, while still handling the worst-case uncertainty via robust optimization. By simply substituting KL divergence with variants of distance metrics, SCORE can be efficiently minimized. Empirically, our models achieve top-rank performance on RobustBench under AutoAttack. Besides, SCORE provides instructive insights for explaining the overfitting phenomenon and semantic input gradients observed on robust models. Code is available at https://github.com/P2333/SCORE.

Semantic image synthesis enables control over unconditional image generation by allowing guidance on what is being generated. We conditionally synthesize the latent space from a vector quantized model (VQ-model) pre-trained to autoencode images. Instead of training an autoregressive Transformer on separately learned conditioning latents and image latents, we find that jointly learning the conditioning and image latents significantly improves the modeling capabilities of the Transformer model. While our jointly trained VQ-model achieves a similar reconstruction performance to a vanilla VQ-model for both semantic and image latents, tying the two modalities at the autoencoding stage proves to be an important ingredient to improve autoregressive modeling performance. We show that our model improves semantic image synthesis using autoregressive models on popular semantic image datasets ADE20k, Cityscapes and COCO-Stuff.

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However, existing approaches either overlook the inherent permutation symmetry in the neural network or rely on intricate weight-sharing patterns to achieve equivariance, while ignoring the impact of the network architecture itself. In this work, we propose to represent neural networks as computational graphs of parameters, which allows us to harness powerful graph neural networks and transformers that preserve permutation symmetry. Consequently, our approach enables a single model to encode neural computational graphs with diverse architectures. We showcase the effectiveness of our method on a wide range of tasks, including classification and editing of implicit neural representations, predicting generalization performance, and learning to optimize, while consistently outperforming state-of-the-art methods. The source code is open-sourced at https://github.com/mkofinas/neural-graphs.

Recent advancements in subject-driven image generation have led to zero-shot generation, yet precise selection and focus on crucial subject representations remain challenging. Addressing this, we introduce the SSR-Encoder, a novel architecture designed for selectively capturing any subject from single or multiple reference images. It responds to various query modalities including text and masks, without necessitating test-time fine-tuning. The SSR-Encoder combines a Token-to-Patch Aligner that aligns query inputs with image patches and a Detail-Preserving Subject Encoder for extracting and preserving fine features of the subjects, thereby generating subject embeddings. These embeddings, used in conjunction with original text embeddings, condition the generation process. Characterized by its model generalizability and efficiency, the SSR-Encoder adapts to a range of custom models and control modules. Enhanced by the Embedding Consistency Regularization Loss for improved training, our extensive experiments demonstrate its effectiveness in versatile and high-quality image generation, indicating its broad applicability. Project page: https://ssr-encoder.github.io

Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.

Autoregressive next-token prediction is a standard pretraining method for large-scale language models, but its application to vision tasks is hindered by the non-sequential nature of image data, leading to cumulative errors. Most vision models employ masked autoencoder (MAE) based pretraining, which faces scalability issues. To address these challenges, we introduce TokenUnify, a novel pretraining method that integrates random token prediction, next-token prediction, and next-all token prediction. We provide theoretical evidence demonstrating that TokenUnify mitigates cumulative errors in visual autoregression. Cooperated with TokenUnify, we have assembled a large-scale electron microscopy (EM) image dataset with ultra-high resolution, ideal for creating spatially correlated long sequences. This dataset includes over 120 million annotated voxels, making it the largest neuron segmentation dataset to date and providing a unified benchmark for experimental validation. Leveraging the Mamba network inherently suited for long-sequence modeling on this dataset, TokenUnify not only reduces the computational complexity but also leads to a significant 45\% improvement in segmentation performance on downstream EM neuron segmentation tasks compared to existing methods. Furthermore, TokenUnify demonstrates superior scalability over MAE and traditional autoregressive methods, effectively bridging the gap between pretraining strategies for language and vision models. Code is available at https://github.com/ydchen0806/TokenUnify.

Self-supervised learning (SSL) is rapidly closing the gap with supervised methods on large computer vision benchmarks. A successful approach to SSL is to learn embeddings which are invariant to distortions of the input sample. However, a recurring issue with this approach is the existence of trivial constant solutions. Most current methods avoid such solutions by careful implementation details. We propose an objective function that naturally avoids collapse by measuring the cross-correlation matrix between the outputs of two identical networks fed with distorted versions of a sample, and making it as close to the identity matrix as possible. This causes the embedding vectors of distorted versions of a sample to be similar, while minimizing the redundancy between the components of these vectors. The method is called Barlow Twins, owing to neuroscientist H. Barlow's redundancy-reduction principle applied to a pair of identical networks. Barlow Twins does not require large batches nor asymmetry between the network twins such as a predictor network, gradient stopping, or a moving average on the weight updates. Intriguingly it benefits from very high-dimensional output vectors. Barlow Twins outperforms previous methods on ImageNet for semi-supervised classification in the low-data regime, and is on par with current state of the art for ImageNet classification with a linear classifier head, and for transfer tasks of classification and object detection.

The premise of identifiable and causal representation learning is to improve the current representation learning paradigm in terms of generalizability or robustness. Despite recent progress in questions of identifiability, more theoretical results demonstrating concrete advantages of these methods for downstream tasks are needed. In this paper, we consider the task of intervention extrapolation: predicting how interventions affect an outcome, even when those interventions are not observed at training time, and show that identifiable representations can provide an effective solution to this task even if the interventions affect the outcome non-linearly. Our setup includes an outcome Y, observed features X, which are generated as a non-linear transformation of latent features Z, and exogenous action variables A, which influence Z. The objective of intervention extrapolation is to predict how interventions on A that lie outside the training support of A affect Y. Here, extrapolation becomes possible if the effect of A on Z is linear and the residual when regressing Z on A has full support. As Z is latent, we combine the task of intervention extrapolation with identifiable representation learning, which we call Rep4Ex: we aim to map the observed features X into a subspace that allows for non-linear extrapolation in A. We show that the hidden representation is identifiable up to an affine transformation in Z-space, which is sufficient for intervention extrapolation. The identifiability is characterized by a novel constraint describing the linearity assumption of A on Z. Based on this insight, we propose a method that enforces the linear invariance constraint and can be combined with any type of autoencoder. We validate our theoretical findings through synthetic experiments and show that our approach succeeds in predicting the effects of unseen interventions.

The Variational Autoencoder (VAE) is a seminal approach in deep generative modeling with latent variables. Interpreting its reconstruction process as a nonlinear transformation of samples from the latent posterior distribution, we apply the Unscented Transform (UT) -- a well-known distribution approximation used in the Unscented Kalman Filter (UKF) from the field of filtering. A finite set of statistics called sigma points, sampled deterministically, provides a more informative and lower-variance posterior representation than the ubiquitous noise-scaling of the reparameterization trick, while ensuring higher-quality reconstruction. We further boost the performance by replacing the Kullback-Leibler (KL) divergence with the Wasserstein distribution metric that allows for a sharper posterior. Inspired by the two components, we derive a novel, deterministic-sampling flavor of the VAE, the Unscented Autoencoder (UAE), trained purely with regularization-like terms on the per-sample posterior. We empirically show competitive performance in Fr\'echet Inception Distance (FID) scores over closely-related models, in addition to a lower training variance than the VAE.

A large part of the literature on learning disentangled representations focuses on variational autoencoders (VAE). Recent developments demonstrate that disentanglement cannot be obtained in a fully unsupervised setting without inductive biases on models and data. However, Khemakhem et al., AISTATS, 2020 suggest that employing a particular form of factorized prior, conditionally dependent on auxiliary variables complementing input observations, can be one such bias, resulting in an identifiable model with guarantees on disentanglement. Working along this line, we propose a novel VAE-based generative model with theoretical guarantees on identifiability. We obtain our conditional prior over the latents by learning an optimal representation, which imposes an additional strength on their regularization. We also extend our method to semi-supervised settings. Experimental results indicate superior performance with respect to state-of-the-art approaches, according to several established metrics proposed in the literature on disentanglement.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

Learning visual representations with self-supervised learning has become popular in computer vision. The idea is to design auxiliary tasks where labels are free to obtain. Most of these tasks end up providing data to learn specific kinds of invariance useful for recognition. In this paper, we propose to exploit different self-supervised approaches to learn representations invariant to (i) inter-instance variations (two objects in the same class should have similar features) and (ii) intra-instance variations (viewpoint, pose, deformations, illumination, etc). Instead of combining two approaches with multi-task learning, we argue to organize and reason the data with multiple variations. Specifically, we propose to generate a graph with millions of objects mined from hundreds of thousands of videos. The objects are connected by two types of edges which correspond to two types of invariance: "different instances but a similar viewpoint and category" and "different viewpoints of the same instance". By applying simple transitivity on the graph with these edges, we can obtain pairs of images exhibiting richer visual invariance. We use this data to train a Triplet-Siamese network with VGG16 as the base architecture and apply the learned representations to different recognition tasks. For object detection, we achieve 63.2% mAP on PASCAL VOC 2007 using Fast R-CNN (compare to 67.3% with ImageNet pre-training). For the challenging COCO dataset, our method is surprisingly close (23.5%) to the ImageNet-supervised counterpart (24.4%) using the Faster R-CNN framework. We also show that our network can perform significantly better than the ImageNet network in the surface normal estimation task.

We present new intuitions and theoretical assessments of the emergence of disentangled representation in variational autoencoders. Taking a rate-distortion theory perspective, we show the circumstances under which representations aligned with the underlying generative factors of variation of data emerge when optimising the modified ELBO bound in beta-VAE, as training progresses. From these insights, we propose a modification to the training regime of beta-VAE, that progressively increases the information capacity of the latent code during training. This modification facilitates the robust learning of disentangled representations in beta-VAE, without the previous trade-off in reconstruction accuracy.

In disentangled representation learning, a model is asked to tease apart a dataset's underlying sources of variation and represent them independently of one another. Since the model is provided with no ground truth information about these sources, inductive biases take a paramount role in enabling disentanglement. In this work, we construct an inductive bias towards encoding to and decoding from an organized latent space. Concretely, we do this by (i) quantizing the latent space into discrete code vectors with a separate learnable scalar codebook per dimension and (ii) applying strong model regularization via an unusually high weight decay. Intuitively, the latent space design forces the encoder to combinatorially construct codes from a small number of distinct scalar values, which in turn enables the decoder to assign a consistent meaning to each value. Regularization then serves to drive the model towards this parsimonious strategy. We demonstrate the broad applicability of this approach by adding it to both basic data-reconstructing (vanilla autoencoder) and latent-reconstructing (InfoGAN) generative models. For reliable evaluation, we also propose InfoMEC, a new set of metrics for disentanglement that is cohesively grounded in information theory and fixes well-established shortcomings in previous metrics. Together with regularization, latent quantization dramatically improves the modularity and explicitness of learned representations on a representative suite of benchmark datasets. In particular, our quantized-latent autoencoder (QLAE) consistently outperforms strong methods from prior work in these key disentanglement properties without compromising data reconstruction.

Video representation learning is an increasingly important topic in machine learning research. We present Video JEPA with Variance-Covariance Regularization (VJ-VCR): a joint-embedding predictive architecture for self-supervised video representation learning that employs variance and covariance regularization to avoid representation collapse. We show that hidden representations from our VJ-VCR contain abstract, high-level information about the input data. Specifically, they outperform representations obtained from a generative baseline on downstream tasks that require understanding of the underlying dynamics of moving objects in the videos. Additionally, we explore different ways to incorporate latent variables into the VJ-VCR framework that capture information about uncertainty in the future in non-deterministic settings.

Vision Transformers (ViTs) have attracted a lot of popularity in recent years, due to their exceptional capabilities in modeling long-range spatial dependencies and scalability for large scale training. Although the training parallelism of self-attention mechanism plays an important role in retaining great performance, its quadratic complexity baffles the application of ViTs in many scenarios which demand fast inference. This effect is even more pronounced in applications in which autoregressive modeling of input features is required. In Natural Language Processing (NLP), a new stream of efforts have proposed parallelizable models with recurrent formulation that allows for efficient inference in generative applications. Inspired by this trend, we propose a new class of computer vision models, dubbed Vision Retention Networks (ViR), with dual parallel and recurrent formulations, which strike an optimal balance between fast inference and parallel training with competitive performance. In particular, ViR scales favorably for image throughput and memory consumption in tasks that require higher-resolution images due to its flexible formulation in processing large sequence lengths. The ViR is the first attempt to realize dual parallel and recurrent equivalency in a general vision backbone for recognition tasks. We have validated the effectiveness of ViR through extensive experiments with different dataset sizes and various image resolutions and achieved competitive performance. Our code and pretrained models will be made publicly available.

Variational Autoencoders (VAEs) have been a pioneering force in the realm of deep generative models. Amongst its legions of progenies, Wasserstein Autoencoders (WAEs) stand out in particular due to the dual offering of heightened generative quality and a strong theoretical backbone. WAEs consist of an encoding and a decoding network forming a bottleneck with the prime objective of generating new samples resembling the ones it was catered to. In the process, they aim to achieve a target latent representation of the encoded data. Our work is an attempt to offer a theoretical understanding of the machinery behind WAEs. From a statistical viewpoint, we pose the problem as concurrent density estimation tasks based on neural network-induced transformations. This allows us to establish deterministic upper bounds on the realized errors WAEs commit. We also analyze the propagation of these stochastic errors in the presence of adversaries. As a result, both the large sample properties of the reconstructed distribution and the resilience of WAE models are explored.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

In this work, we re-examine inter-patch dependencies in the decoding mechanism of masked autoencoders (MAE). We decompose this decoding mechanism for masked patch reconstruction in MAE into self-attention and cross-attention. Our investigations suggest that self-attention between mask patches is not essential for learning good representations. To this end, we propose a novel pretraining framework: Cross-Attention Masked Autoencoders (CrossMAE). CrossMAE's decoder leverages only cross-attention between masked and visible tokens, with no degradation in downstream performance. This design also enables decoding only a small subset of mask tokens, boosting efficiency. Furthermore, each decoder block can now leverage different encoder features, resulting in improved representation learning. CrossMAE matches MAE in performance with 2.5 to 3.7times less decoding compute. It also surpasses MAE on ImageNet classification and COCO instance segmentation under the same compute. Code and models: https://crossmae.github.io

Visual environments are structured, consisting of distinct objects or entities. These entities have properties -- both visible and latent -- that determine the manner in which they interact with one another. To partition images into entities, deep-learning researchers have proposed structural inductive biases such as slot-based architectures. To model interactions among entities, equivariant graph neural nets (GNNs) are used, but these are not particularly well suited to the task for two reasons. First, GNNs do not predispose interactions to be sparse, as relationships among independent entities are likely to be. Second, GNNs do not factorize knowledge about interactions in an entity-conditional manner. As an alternative, we take inspiration from cognitive science and resurrect a classic approach, production systems, which consist of a set of rule templates that are applied by binding placeholder variables in the rules to specific entities. Rules are scored on their match to entities, and the best fitting rules are applied to update entity properties. In a series of experiments, we demonstrate that this architecture achieves a flexible, dynamic flow of control and serves to factorize entity-specific and rule-based information. This disentangling of knowledge achieves robust future-state prediction in rich visual environments, outperforming state-of-the-art methods using GNNs, and allows for the extrapolation from simple (few object) environments to more complex environments.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this hierarchy has propelled significant advances in GNN analysis and architecture developments, it suffers from several significant limitations. These include a complex definition that lacks direct guidance for model improvement and a WL hierarchy that is too coarse to study current GNNs. This paper introduces an alternative expressive power hierarchy based on the ability of GNNs to calculate equivariant polynomials of a certain degree. As a first step, we provide a full characterization of all equivariant graph polynomials by introducing a concrete basis, significantly generalizing previous results. Each basis element corresponds to a specific multi-graph, and its computation over some graph data input corresponds to a tensor contraction problem. Second, we propose algorithmic tools for evaluating the expressiveness of GNNs using tensor contraction sequences, and calculate the expressive power of popular GNNs. Finally, we enhance the expressivity of common GNN architectures by adding polynomial features or additional operations / aggregations inspired by our theory. These enhanced GNNs demonstrate state-of-the-art results in experiments across multiple graph learning benchmarks.

Unsupervised learning with functional data is an emerging paradigm of machine learning research with applications to computer vision, climate modeling and physical systems. A natural way of modeling functional data is by learning operators between infinite dimensional spaces, leading to discretization invariant representations that scale independently of the sample grid resolution. Here we present Variational Autoencoding Neural Operators (VANO), a general strategy for making a large class of operator learning architectures act as variational autoencoders. For this purpose, we provide a novel rigorous mathematical formulation of the variational objective in function spaces for training. VANO first maps an input function to a distribution over a latent space using a parametric encoder and then decodes a sample from the latent distribution to reconstruct the input, as in classic variational autoencoders. We test VANO with different model set-ups and architecture choices for a variety of benchmarks. We start from a simple Gaussian random field where we can analytically track what the model learns and progressively transition to more challenging benchmarks including modeling phase separation in Cahn-Hilliard systems and real world satellite data for measuring Earth surface deformation.

Breast cancer is a significant health concern affecting millions of women worldwide. Accurate survival risk stratification plays a crucial role in guiding personalised treatment decisions and improving patient outcomes. Here we present BioFusionNet, a deep learning framework that fuses image-derived features with genetic and clinical data to achieve a holistic patient profile and perform survival risk stratification of ER+ breast cancer patients. We employ multiple self-supervised feature extractors, namely DINO and MoCoV3, pretrained on histopathology patches to capture detailed histopathological image features. We then utilise a variational autoencoder (VAE) to fuse these features, and harness the latent space of the VAE to feed into a self-attention network, generating patient-level features. Next, we develop a co-dual-cross-attention mechanism to combine the histopathological features with genetic data, enabling the model to capture the interplay between them. Additionally, clinical data is incorporated using a feed-forward network (FFN), further enhancing predictive performance and achieving comprehensive multimodal feature integration. Furthermore, we introduce a weighted Cox loss function, specifically designed to handle imbalanced survival data, which is a common challenge in the field. The proposed model achieves a mean concordance index (C-index) of 0.77 and a time-dependent area under the curve (AUC) of 0.84, outperforming state-of-the-art methods. It predicts risk (high versus low) with prognostic significance for overall survival (OS) in univariate analysis (HR=2.99, 95% CI: 1.88--4.78, p<0.005), and maintains independent significance in multivariate analysis incorporating standard clinicopathological variables (HR=2.91, 95% CI: 1.80--4.68, p<0.005). The proposed method not only improves model performance but also addresses a critical gap in handling imbalanced data.

We introduce a new method for learning a generative model of articulated 3D animal motions from raw, unlabeled online videos. Unlike existing approaches for 3D motion synthesis, our model requires no pose annotations or parametric shape models for training; it learns purely from a collection of unlabeled web video clips, leveraging semantic correspondences distilled from self-supervised image features. At the core of our method is a video Photo-Geometric Auto-Encoding framework that decomposes each training video clip into a set of explicit geometric and photometric representations, including a rest-pose 3D shape, an articulated pose sequence, and texture, with the objective of re-rendering the input video via a differentiable renderer. This decomposition allows us to learn a generative model over the underlying articulated pose sequences akin to a Variational Auto-Encoding (VAE) formulation, but without requiring any external pose annotations. At inference time, we can generate new motion sequences by sampling from the learned motion VAE, and create plausible 4D animations of an animal automatically within seconds given a single input image.

We provide a full characterisation of all of the possible alternating group (A_n) equivariant neural networks whose layers are some tensor power of R^{n}. In particular, we find a basis of matrices for the learnable, linear, A_n-equivariant layer functions between such tensor power spaces in the standard basis of R^{n}. We also describe how our approach generalises to the construction of neural networks that are equivariant to local symmetries.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

Variational auto-encoders are powerful probabilistic models in generative tasks but suffer from generating low-quality samples which are caused by the holes in the prior. We propose the Coupled Variational Auto-Encoder (C-VAE), which formulates the VAE problem as one of Optimal Transport (OT) between the prior and data distributions. The C-VAE allows greater flexibility in priors and natural resolution of the prior hole problem by enforcing coupling between the prior and the data distribution and enables flexible optimization through the primal, dual, and semi-dual formulations of entropic OT. Simulations on synthetic and real data show that the C-VAE outperforms alternatives including VAE, WAE, and InfoVAE in fidelity to the data, quality of the latent representation, and in quality of generated samples.

Accurately modeling protein 3D structure is essential for the design of functional proteins. An important sub-task of structure modeling is protein side-chain packing: predicting the conformation of side-chains (rotamers) given the protein's backbone structure and amino-acid sequence. Conventional approaches for this task rely on expensive sampling procedures over hand-crafted energy functions and rotamer libraries. Recently, several deep learning methods have been developed to tackle the problem in a data-driven way, albeit with vastly different formulations (from image-to-image translation to directly predicting atomic coordinates). Here, we frame the problem as a joint regression over the side-chains' true degrees of freedom: the dihedral chi angles. We carefully study possible objective functions for this task, while accounting for the underlying symmetries of the task. We propose Holographic Packer (H-Packer), a novel two-stage algorithm for side-chain packing built on top of two light-weight rotationally equivariant neural networks. We evaluate our method on CASP13 and CASP14 targets. H-Packer is computationally efficient and shows favorable performance against conventional physics-based algorithms and is competitive against alternative deep learning solutions.

We propose the Wasserstein Auto-Encoder (WAE)---a new algorithm for building a generative model of the data distribution. WAE minimizes a penalized form of the Wasserstein distance between the model distribution and the target distribution, which leads to a different regularizer than the one used by the Variational Auto-Encoder (VAE). This regularizer encourages the encoded training distribution to match the prior. We compare our algorithm with several other techniques and show that it is a generalization of adversarial auto-encoders (AAE). Our experiments show that WAE shares many of the properties of VAEs (stable training, encoder-decoder architecture, nice latent manifold structure) while generating samples of better quality, as measured by the FID score.

Learning deep discrete latent presentations offers a promise of better symbolic and summarized abstractions that are more useful to subsequent downstream tasks. Inspired by the seminal Vector Quantized Variational Auto-Encoder (VQ-VAE), most of work in learning deep discrete representations has mainly focused on improving the original VQ-VAE form and none of them has studied learning deep discrete representations from the generative viewpoint. In this work, we study learning deep discrete representations from the generative viewpoint. Specifically, we endow discrete distributions over sequences of codewords and learn a deterministic decoder that transports the distribution over the sequences of codewords to the data distribution via minimizing a WS distance between them. We develop further theories to connect it with the clustering viewpoint of WS distance, allowing us to have a better and more controllable clustering solution. Finally, we empirically evaluate our method on several well-known benchmarks, where it achieves better qualitative and quantitative performances than the other VQ-VAE variants in terms of the codebook utilization and image reconstruction/generation.

We decompose the evidence lower bound to show the existence of a term measuring the total correlation between latent variables. We use this to motivate our beta-TCVAE (Total Correlation Variational Autoencoder), a refinement of the state-of-the-art beta-VAE objective for learning disentangled representations, requiring no additional hyperparameters during training. We further propose a principled classifier-free measure of disentanglement called the mutual information gap (MIG). We perform extensive quantitative and qualitative experiments, in both restricted and non-restricted settings, and show a strong relation between total correlation and disentanglement, when the latent variables model is trained using our framework.

Self-supervised learning (SSL) has recently achieved promising performance for 3D medical image analysis tasks. Most current methods follow existing SSL paradigm originally designed for photographic or natural images, which cannot explicitly and thoroughly exploit the intrinsic similar anatomical structures across varying medical images. This may in fact degrade the quality of learned deep representations by maximizing the similarity among features containing spatial misalignment information and different anatomical semantics. In this work, we propose a new self-supervised learning framework, namely Alice, that explicitly fulfills Anatomical invariance modeling and semantic alignment via elaborately combining discriminative and generative objectives. Alice introduces a new contrastive learning strategy which encourages the similarity between views that are diversely mined but with consistent high-level semantics, in order to learn invariant anatomical features. Moreover, we design a conditional anatomical feature alignment module to complement corrupted embeddings with globally matched semantics and inter-patch topology information, conditioned by the distribution of local image content, which permits to create better contrastive pairs. Our extensive quantitative experiments on three 3D medical image analysis tasks demonstrate and validate the performance superiority of Alice, surpassing the previous best SSL counterpart methods and showing promising ability for united representation learning. Codes are available at https://github.com/alibaba-damo-academy/alice.

Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. Equivariant graph neural networks are used for the diffusion model to respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.

Understanding how features evolve across layers in deep neural networks is a fundamental challenge in mechanistic interpretability, particularly due to polysemanticity and feature superposition. While Sparse Autoencoders (SAEs) have been used to extract interpretable features from individual layers, aligning these features across layers has remained an open problem. In this paper, we introduce SAE Match, a novel, data-free method for aligning SAE features across different layers of a neural network. Our approach involves matching features by minimizing the mean squared error between the folded parameters of SAEs, a technique that incorporates activation thresholds into the encoder and decoder weights to account for differences in feature scales. Through extensive experiments on the Gemma 2 language model, we demonstrate that our method effectively captures feature evolution across layers, improving feature matching quality. We also show that features persist over several layers and that our approach can approximate hidden states across layers. Our work advances the understanding of feature dynamics in neural networks and provides a new tool for mechanistic interpretability studies.