论文检索

Deep Learning · Robustness

Bhaskar Mukhoty, Hilal AlQuabeh, Giulia De Masi, Huan Xiong, Bin Gu

The spiking neural networks are inspired by the biological neurons that employ binary spikes to propagate information in the neural network. It has garnered considerable attention as the next-generation neural network, as the spiking activity simplifies the computation burden of the network to a large extent and is known for its low energy deployment enabled by specialized neuromorphic hardware. One popular technique to feed a static image to such a network is rate encoding, where each pixel is encoded into random binary spikes, following a Bernoulli distribution that uses the pixel intensity as bias. By establishing a novel connection between rate-encoding and randomized smoothing, we give the first provable robustness guarantee for spiking neural networks against adversarial perturbation of inputs bounded under $l_1$-norm. We introduce novel adversarial training algorithms for rate-encoded models that significantly improve the state-of-the-art empirical robust accuracy result. Experimental validation of the method is performed across various static image datasets, including CIFAR-10, CIFAR-100 and ImageNet-100. The code is available at \url{https://github.com/BhaskarMukhoty/CertifiedSNN}.

Applications · Genetics, Cell Biology, etc

Zhihan Zhou, Yanrong Ji, Weijian Li, Pratik Dutta, Ramana Davuluri, Han Liu

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization.Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates $36$ distinct datasets across $9$ tasks, with input lengths ranging from $70$ to $10000$. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with $21 \times$ fewer parameters and approximately $92 \times$ less GPU time in pre-training. Compared to DNABERT, while being $3 \times$ more efficient, DNABERT-2 outperforms it on $23$ out of $28$ datasets, with an average improvement of $6$ absolute scores on GUE.The code, data, and pre-trained model are available at \url{https://github.com/MAGICS-LAB/DNABERT_2}.

Applications · Computer Vision

Zahra Babaiee, Peyman Kiasari, Daniela Rus, Radu Grosu

Recent advances in depthwise-separable convolutional neural networks (DS-CNNs) have led to novel architectures, that surpass the performance of classical CNNs, by a considerable scalability and accuracy margin. This paper reveals another striking property of DS-CNN architectures: discernible and explainable patterns emerge in their trained depthwise convolutional kernels in all layers. Through an extensive analysis of millions of trained filters, with different sizes and from various models, we employed unsupervised clustering with autoencoders, to categorize these filters. Astonishingly, the patterns converged into a few main clusters, each resembling the difference of Gaussian (DoG) functions, and their first and second-order derivatives. Notably, we classify over 95\% and 90\% of the filters from state-of-the-art ConvNeXtV2 and ConvNeXt models, respectively. This finding is not merely a technological curiosity; it echoes the foundational models neuroscientists have long proposed for the vision systems of mammals. Our results thus deepen our understanding of the emergent properties of trained DS-CNNs and provide a bridge between artificial and biological visual processing systems. More broadly, they pave the way for more interpretable and biologically-inspired neural network designs in the future.

Deep Learning · Algorithms

Yaoyu Zhu, Jianhao Ding, Tiejun Huang, Xiaodong Xie, Zhaofei Yu

Spiking neural networks (SNNs), attributed to the binary, event-driven nature of spikes, possess heightened biological plausibility and enhanced energy efficiency on neuromorphic hardware compared to analog neural networks (ANNs). Mainstream SNN training schemes apply backpropagation-through-time (BPTT) with surrogate gradients to replace the non-differentiable spike emitting process during backpropagation. While achieving competitive performance, the requirement for storing intermediate information at all time-steps incurs higher memory consumption and fails to fulfill the online property crucial to biological brains. Our work focuses on online training techniques, aiming for memory efficiency while preserving biological plausibility. The limitation of not having access to future information in early time steps in online training has constrained previous efforts to incorporate advantageous modules such as batch normalization. To address this problem, we propose Online Spiking Renormalization (OSR) to ensure consistent parameters between testing and training, and Online Threshold Stabilizer (OTS) to stabilize neuron firing rates across time steps. Furthermore, we design a novel online approach to compute the sample mean and variance over time for OSR. Experiments conducted on various datasets demonstrate the proposed method's superior performance among SNN online training algorithms.Our code is available at https://github.com/zhuyaoyu/SNN-online-normalization.

Wenjie Wei, Malu Zhang, Hong Qu, Ammar Belatreche, Jian Zhang, Hong Chen

Spiking Neural Networks (SNNs) offer a highly promising computing paradigm due to their biological plausibility, exceptional spatiotemporal information processing capability and low power consumption. As a temporal encoding scheme for SNNs, Time-To-First-Spike (TTFS) encodes information using the timing of a single spike, which allows spiking neurons to transmit information through sparse spike trains and results in lower power consumption and higher computational efficiency compared to traditional rate-based encoding counterparts. However, despite the advantages of the TTFS encoding scheme, the effective and efficient training of TTFS-based deep SNNs remains a significant and open research problem. In this work, we first examine the factors underlying the limitations of applying existing TTFS-based learning algorithms to deep SNNs. Specifically, we investigate issues related to over-sparsity of spikes and the complexity of finding the `causal set'. We then propose a simple yet efficient dynamic firing threshold (DFT) mechanism for spiking neurons to address these issues. Building upon the proposed DFT mechanism, we further introduce a novel direct training algorithm for TTFS-based deep SNNs, called DTA-TTFS. This method utilizes event-driven processing and spike timing to enable efficient learning of deep SNNs. The proposed training method was validated on the image classification task and experimental results clearly demonstrate that our proposed method achieves state-of-the-art accuracy in comparison to existing TTFS-based learning algorithms, while maintaining high levels of sparsity and energy efficiency on neuromorphic inference accelerator.

Dong Won Lee, Chaitanya Ahuja, Paul Pu Liang, Sanika Natu, Louis-Philippe Morency

Many educational videos use slide presentations, a sequence of visual pages that contain text and figures accompanied by spoken language, which are constructed and presented carefully in order to optimally transfer knowledge to students. Previous studies in multimedia and psychology attribute the effectiveness of lecture presentations to their multimodal nature. As a step toward developing vision-language models to aid in student learning as intelligent teacher assistants, we introduce the Lecture Presentations Multimodal (LPM) Dataset as a large-scale benchmark testing the capabilities of vision-and-language models in multimodal understanding of educational videos. Our dataset contains aligned slides and spoken language, for 180+ hours of video and 9000+ slides, with 10 lecturers from various subjects (e.g., computer science, dentistry, biology). We introduce three research tasks, (1) figure-to-text retrieval, (2) text-to-figure retrieval, and (3) generation of slide explanations, which are grounded in multimedia learning and psychology principles to test a vision-language model's understanding of multimodal content. We provide manual annotations to help implement these tasks and establish baselines on them. Comparing baselines and human student performances, we find that state-of-the-art vision-language models (zero-shot and fine-tuned) struggle in (1) weak crossmodal alignment between slides and spoken text, (2) learning novel visual mediums, (3) technical language, and (4) long-range sequences. We introduce PolyViLT, a novel multimodal transformer trained with a multi-instance learning loss that is more effective than current approaches for retrieval. We conclude by shedding light on the challenges and opportunities in multimodal understanding of educational presentation videos.

Zhiyu Jin, Hanyang Yu, Chen Haul, Linxiang Wang, Zuobin Zhu, Qiu Shen, Xun Cao

Currently, multimedia systems and computer vision algorithms are increasingly playing a crucial role in biological research. However, due to the significant difference between macro and micro scenarios, it is impractical to directly transfer existing computer vision methods to the images captured by microscopes. Taking social behavior analysis of worm for example, it heavily depends on accurate and efficient Multi-object tracking (MOT) methods. Meanwhile, it faces great challenges due to the unique physical characteristics of worm, such as small size, highly uniform appearance, rapid deformation and overlapping movement. This paper studies on the challenges and existing solutions for MOT in worm crowds by building a well-designed dataset ("WormTrack") and a tracking-by-detection benchmark. We observed that the state-of-the-art MOT methods suffers from considerable performance drop on the new dataset. Therefore, we propose a customized MOT method for worm crowds by deeply understanding the physical characteristics of worms and scenes. The method is composed by an instance segmentation based detector, a multiple model fused Kalman filter based tracker and a multi-constraint based trajectory repairer. The experimental results demonstrate that our method can accurately track over 100 worms with almost identical appearance for a long period, which is exceptional compared to existing methods. We hope our work will attract further researches to explore more in this new field, and promote the crossing field researches with biology and medicine. Our code and data is available at https://github.com/Jeerrzy/wormstudio.

V.S.D.S.Mahesh Akavarapu, Arnab Bhattacharya

Phonological reconstruction is one of the central problems in historical linguistics where a proto-word of an ancestral language is determined from the observed cognate words of daughter languages. Computational approaches to historical linguistics attempt to automate the task by learning models on available linguistic data. Several ideas and techniques drawn from computational biology have been successfully applied in this area of computational historical linguistics. Following these lines, we adapt MSA Transformer, a protein language model, to the problem of automated phonological reconstruction. MSA Transformer trains on multiple sequence alignments as input and is, thus, apt for application on aligned cognate words. We, hence, name our model as Cognate Transformer. We also apply the model on another associated task, namely, cognate reflex prediction where a reflex word in a daughter language is predicted based on cognate words from other daughter languages. We show that our model outperforms the existing models on both the tasks, especially when it is pre-trained on masked word prediction task.

Deep Learning/Graph Neural Networks

Tingting Dan, Jiaqi Ding, Ziquan Wei, Shahar Kovalsky, Minjeong Kim, Won Hwa Kim, Guorong Wu

Graphs are ubiquitous in various domains, such as social networks and biological systems. Despite the great successes of graph neural networks (GNNs) in modeling and analyzing complex graph data, the inductive bias of locality assumption, which involves exchanging information only within neighboring connected nodes, restricts GNNs in capturing long-range dependencies and global patterns in graphs. Inspired by the classic Brachistochrone problem, we seek how to devise a new inductive bias for cutting-edge graph application and present a general framework through the lens of variational analysis. The backbone of our framework is a two-way mapping between the discrete GNN model and continuous diffusion functional, which allows us to design application-specific objective function in the continuous domain and engineer discrete deep model with mathematical guarantees. First, we address over-smoothing in current GNNs. Specifically, our inference reveals that the existing layer-by-layer models of graph embedding learning are equivalent to a ${\ell _2}$-norm integral functional of graph gradients, which is the underlying cause of the over-smoothing problem. Similar to edge-preserving filters in image denoising, we introduce the total variation (TV) to promote alignment of the graph diffusion pattern with the global information present in community topologies. On top of this, we devise a new selective mechanism for inductive bias that can be easily integrated into existing GNNs and effectively address the trade-off between model depth and over-smoothing. Second, we devise a novel generative adversarial network (GAN) to predict the spreading flows in the graph through a neural transport equation. To avoid the potential issue of vanishing flows, we tailor the objective function to minimize the transportation within each community while maximizing the inter-community flows. Our new GNN models achieve state-of-the-art (SOTA) performance on graph learning benchmarks such as Cora, Citeseer, and Pubmed.

Applications/Neuroscience, Cognitive Science

Arthur Pellegrino, N Alex Cayco Gajic, Angus Chadwick

Learning relies on coordinated synaptic changes in recurrently connected populations of neurons. Therefore, understanding the collective evolution of synaptic connectivity over learning is a key challenge in neuroscience and machine learning. In particular, recent work has shown that the weight matrices of task-trained RNNs are typically low rank, but how this low rank structure unfolds over learning is unknown. To address this, we investigate the rank of the 3-tensor formed by the weight matrices throughout learning. By fitting RNNs of varying rank to large-scale neural recordings during a motor learning task, we find that the inferred weights are low-tensor-rank and therefore evolve over a fixed low-dimensional subspace throughout the entire course of learning. We next validate the observation of low-tensor-rank learning on an RNN trained to solve the same task. Finally, we present a set of mathematical results bounding the matrix and tensor ranks of gradient descent learning dynamics which show that low-tensor-rank weights emerge naturally in RNNs trained to solve low-dimensional tasks. Taken together, our findings provide insight on the evolution of population connectivity over learning in both biological and artificial neural networks, and enable reverse engineering of learning-induced changes in recurrent dynamics from large-scale neural recordings.

Applications/Neuroscience, Cognitive Science

Lyndon Duong, Eero Simoncelli, Dmitri Chklovskii, David Lipshutz

Neurons in early sensory areas rapidly adapt to changing sensory statistics, both by normalizing the variance of their individual responses and by reducing correlations between their responses. Together, these transformations may be viewed as an adaptive form of statistical whitening. Existing mechanistic models of adaptive whitening exclusively use either synaptic plasticity or gain modulation as the biological substrate for adaptation; however, on their own, each of these models has significant limitations. In this work, we unify these approaches in a normative multi-timescale mechanistic model that adaptively whitens its responses with complementary computational roles for synaptic plasticity and gain modulation. Gains are modified on a fast timescale to adapt to the current statistical context, whereas synapses are modified on a slow timescale to match structural properties of the input statistics that are invariant across contexts. Our model is derived from a novel multi-timescale whitening objective that factorizes the inverse whitening matrix into basis vectors, which correspond to synaptic weights, and a diagonal matrix, which corresponds to neuronal gains. We test our model on synthetic and natural datasets and find that the synapses learn optimal configurations over long timescales that enable adaptive whitening on short timescales using gain modulation.

Applications/Chemistry and Drug Discovery

Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang

Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is important in protein engineering, including therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a novel representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on the generation of protein backbone structures.

Applications/Genetics, Cell Biology, etc

Pascal Notin, Ruben Weitzman, Debora Marks, Yarin Gal

Protein design holds immense potential for optimizing naturally occurring proteins, with broad applications in drug discovery, material design, and sustainability. However, computational methods for protein engineering are confronted with significant challenges, such as an expansive design space, sparse functional regions, and a scarcity of available labels. These issues are further exacerbated in practice by the fact most real-life design scenarios necessitate the simultaneous optimization of multiple properties. In this work, we introduce ProteinNPT, a non-parametric transformer variant tailored to protein sequences and particularly suited to label-scarce and multi-task learning settings. We first focus on the supervised fitness prediction setting and develop several cross-validation schemes which support robust performance assessment. We subsequently reimplement prior top-performing baselines, introduce several extensions of these baselines by integrating diverse branches of the protein engineering literature, and demonstrate that ProteinNPT consistently outperforms all of them across a diverse set of protein property prediction tasks. Finally, we demonstrate the value of our approach for iterative protein design across extensive in silico Bayesian optimization and conditional sampling experiments.

Probabilistic Methods/Everything Else

Paweł Czyż, Frederic Grabowski, Julia Vogt, Niko Beerenwinkel, Alexander Marx

Mutual information is a general statistical dependency measure which has found applications in representation learning, causality, domain generalization and computational biology. However, mutual information estimators are typically evaluated on simple families of probability distributions, namely multivariate normal distribution and selected distributions with one-dimensional random variables. In this paper, we show how to construct a diverse family of distributions with known ground-truth mutual information and propose a language-independent benchmarking platform for mutual information estimators. We discuss the general applicability and limitations of classical and neural estimators in settings involving high dimensions, sparse interactions, long-tailed distributions, and high mutual information. Finally, we provide guidelines for practitioners on how to select appropriate estimator adapted to the difficulty of problem considered and issues one needs to consider when applying an estimator to a new data set.

Applications/Genetics, Cell Biology, etc

Zeyu Zhang, Robert Pless, Nadia Shakoor, Austin Carnahan, Abby Stylianou

Large scale field-phenotyping approaches have the potential to solve important questions about the relationship of plant genotype to plant phenotype. Computational approaches to measuring the phenotype (the observable plant features) are required to address the problem at a large scale, but machine learning approaches to extract phenotypes from sensor data have been hampered by limited access to (a) sufficiently large, organized multi-sensor datasets, (b) field trials that have a large scale and significant number of genotypes, (c) full genetic sequencing of those phenotypes, and (d) datasets sufficiently organized so that algorithm centered researchers can directly address the real biological problems. To address this, we present SGxP, a novel benchmark dataset from a large-scale field trial consisting of the complete genotype of over 300 sorghum varieties, and time sequences of imagery from several field plots growing each variety, taken with RGB and laser 3D scanner imaging. To lower the barrier to entry and facilitate further developments, we provide a set of well organized, multi-sensor imagery and corresponding genomic data. We implement baseline deep learning based phenotyping approaches to create baseline results for individual sensors and multi-sensor fusion for detecting genetic mutations with known impacts. We also provide and support an open-ended challenge by identifying thousands of genetic mutations whose phenotypic impacts are currently unknown. A web interface for machine learning researchers and practitioners to share approaches, visualizations and hypotheses supports engagement with plant biologists to further the understanding of the sorghum genotype x phenotype relationship. The full dataset, leaderboard (including baseline results) and discussion forums can be found at http://sorghumsnpbenchmark.com.

Applications/Genetics, Cell Biology, etc

Wei Zheng, Cheng Peng, Zeyuan Hou, Boyu Lyu, Mengfan Wang, Xuelong Mi, Shuoxuan Qiao, Yinan Wan, Guoqiang Yu

3D segmentation of nuclei images is a fundamental task for many biological studies. Despite the rapid advances of large-volume 3D imaging acquisition methods and the emergence of sophisticated algorithms to segment the nuclei in recent years, a benchmark with all cells completely annotated is still missing, making it hard to accurately assess and further improve the performance of the algorithms. The existing nuclei segmentation benchmarks either worked on 2D only or annotated a small number of 3D cells, perhaps due to the high cost of 3D annotation for large-scale data. To fulfill the critical need, we constructed NIS3D, a 3D, high cell density, large-volume, and completely annotated Nuclei Image Segmentation benchmark, assisted by our newly designed semi-automatic annotation software. NIS3D provides more than 22,000 cells across multiple most-used species in this area. Each cell is labeled by three independent annotators, so we can measure the variability of each annotation. A confidence score is computed for each cell, allowing more nuanced testing and performance comparison. A comprehensive review on the methods of segmenting 3D dense nuclei was conducted. The benchmark was used to evaluate the performance of several selected state-of-the-art segmentation algorithms. The best of current methods is still far away from human-level accuracy, corroborating the necessity of generating such a benchmark. The testing results also demonstrated the strength and weakness of each method and pointed out the directions of further methodological development. The dataset can be downloaded here: https://github.com/yu-lab-vt/NIS3D.

Shengchao Liu, weitao Du, Yanjing Li, Zhuoxinran Li, Zhiling Zheng, Chenru Duan, Zhi-Ming Ma, Omar Yaghi, Animashree Anandkumar, Christian Borgs 等

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science ({\eg}, physics, chemistry, \& biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 52 diverse tasks, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications. The source code is available on \href{https://github.com/chao1224/Geom3D}{the GitHub repository}.

Applications/Computer Vision

Zahra Gharaee, ZeMing Gong, Nicholas Pellegrino, Iuliia Zarubiieva, Joakim Bruslund Haurum, Scott Lowe, Jaclyn McKeown, Chris Ho, Joschka McLeod, Yi-Yun Wei 等

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-1M Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetic-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier. The code repository of the BIOSCAN-1M-Insect dataset is available at https://github.com/zahrag/BIOSCAN-1M

Applications/Neuroscience, Cognitive Science

Yaoyu Zhu, Wei Fang, Xiaodong Xie, Tiejun Huang, Zhaofei Yu

Spiking Neural Networks (SNNs) are considered promising brain-inspired energy-efficient models due to their event-driven computing paradigm.The spatiotemporal spike patterns used to convey information in SNNs consist of both rate coding and temporal coding, where the temporal coding is crucial to biological-plausible learning rules such as spike-timing-dependent-plasticity.The time-based training strategy is proposed to better utilize the temporal information in SNNs and learn in an asynchronous fashion.However, some recent works train SNNs by the time-based scheme with rate-coding-dominated loss functions.In this paper, we first map rate-based loss functions to time-based counterparts and explain why they are also applicable to the time-based training scheme.After that, we infer that loss functions providing adequate positive overall gradients help training by theoretical analysis.Based on this, we propose the enhanced counting loss to replace the commonly used mean square counting loss.In addition, we transfer the training of scale factor in weight standardization into thresholds.Experiments show that our approach outperforms previous time-based training methods in most datasets. Our work provides insights for training SNNs with time-based schemes and offers a fresh perspective on the correlation between rate coding and temporal coding.Our code is available at https://github.com/zhuyaoyu/SNN-temporal-training-losses.

Applications/Everything Else

Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Dan Berenberg, Ian Fisk, Andrew Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.