Publications

GFlowNet-EM for Learning Compositional Latent Variable Models
Edward J. Hu
Nikolay Malkin
Moksh Jain
Katie Everett
Alexandros Graikos
Yoshua Bengio
Latent variable models (LVMs) with discrete compositional latents are an important but challenging setting due to a combinatorially large nu… (voir plus)mber 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.
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining
Shengchao Liu
Weitao Du
Zhiming Ma
Hongyu Guo
Jian Tang
Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be re… (voir plus)presented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
Guided-topic modelling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
Lakshmipuram Seshadri Swapna
Michael Huang
Yuemei Li
Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infe… (voir plus)r cell-type-specific gene topic distributions from single-cell RNA-seq data for deconvolving bulk transcriptomes. GTM-decon performs competitively on deconvolving simulated and real bulk data compared with the state-of-the-art methods. Moreover, as demonstrated in deconvolving disease transcriptomes, GTM-decon can infer multiple cell-type-specific gene topic distributions per cell type, which captures sub-cell-type variations. GTM-decon can also use phenotype labels from single-cell or bulk data as a guide to infer phenotype-specific gene distributions. In a nested-guided design, GTM-decon identified cell-type-specific differentially expressed genes from bulk breast cancer transcriptomes.
2023-07-02
bioRxiv (prépublication)
doi.org
Hidden Symmetries of ReLU Networks
J. Elisenda Grigsby
J. Elisenda Grigsby
Kathryn Lindsey
David Rolnick
The parameter space for any fixed architecture of feedforward ReLU neural networks serves as a proxy during training for the associated clas… (voir plus)s of functions - but how faithful is this representation? It is known that many different parameter settings can determine the same function. Moreover, the degree of this redundancy is inhomogeneous: for some networks, the only symmetries are permutation of neurons in a layer and positive scaling of parameters at a neuron, while other networks admit additional hidden symmetries. In this work, we prove that, for any network architecture where no layer is narrower than the input, there exist parameter settings with no hidden symmetries. We also describe a number of mechanisms through which hidden symmetries can arise, and empirically approximate the functional dimension of different network architectures at initialization. These experiments indicate that the probability that a network has no hidden symmetries decreases towards 0 as depth increases, while increasing towards 1 as width and input dimension increase.
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
High-Probability Bounds for Stochastic Optimization and Variational Inequalities: the Case of Unbounded Variance
Abdurakhmon Sadiev
Marina Danilova
Eduard Gorbunov
Samuel Horváth
Gauthier Gidel
Pavel Dvurechensky
Alexander Gasnikov
Peter Richtárik
During the recent years the interest of optimization and machine learning communities in high-probability convergence of stochastic optimiza… (voir plus)tion methods has been growing. One of the main reasons for this is that high-probability complexity bounds are more accurate and less studied than in-expectation ones. However, SOTA high-probability non-asymptotic convergence results are derived under strong assumptions such as boundedness of the gradient noise variance or of the objective’s gradient itself. In this paper, we propose several algorithms with high-probability convergence results under less restrictive assumptions. In particular, we derive new high-probability convergence results under the assumption that the gradient/operator noise has bounded central
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
Maximal Initial Learning Rates in Deep ReLU Networks
Gaurav Iyer
Boris Hanin
David Rolnick
Training a neural network requires choosing a suitable learning rate, which involves a trade-off between speed and effectiveness of converge… (voir plus)nce. While there has been considerable theoretical and empirical analysis of how large the learning rate can be, most prior work focuses only on late-stage training. In this work, we introduce the maximal initial learning rate
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
Mechanistic Mode Connectivity
Ekdeep Singh Lubana
Eric J Bigelow
Robert P. Dick
David M. Krueger
Hidenori Tanaka
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
Multi-Objective GFlowNets
Moksh Jain
Sharath Chandra Raparthy
Alex Hernández-García
Jarrid Rector-Brooks
Yoshua Bengio
Santiago Miret
Emmanuel Bengio
We study the problem of generating diverse candidates in the context of Multi-Objective Optimization. In many applications of machine learni… (voir plus)ng such as drug discovery and material design, the goal is to generate candidates which simultaneously optimize a set of potentially conflicting objectives. Moreover, these objectives are often imperfect evaluations of some underlying property of interest, making it important to generate diverse candidates to have multiple options for expensive downstream evaluations. We propose Multi-Objective GFlowNets (MOGFNs), a novel method for generating diverse Pareto optimal solutions, based on GFlowNets. We introduce two variants of MOGFNs: MOGFN-PC, which models a family of independent sub-problems defined by a scalarization function, with reward-conditional GFlowNets, and MOGFN-AL, which solves a sequence of sub-problems defined by an acquisition function in an active learning loop. Our experiments on wide variety of synthetic and benchmark tasks demonstrate advantages of the proposed methods in terms of the Pareto performance and importantly, improved candidate diversity, which is the main contribution of this work.
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
Neural FIM for learning Fisher information metrics from point cloud data
Oluwadamilola Fasina
Guillaume Huguet
Alexander Tong
Yanlei Zhang
Guy Wolf
Maximilian Nickel
Ian Adelstein
Smita Krishnaswamy
Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the under… (voir plus)lying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
PAC-Bayesian Generalization Bounds for Adversarial Generative Models
Sokhna Diarra Mbacke
Florence Clerc
Pascal Germain
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press
Privacy-Aware Compression for Federated Learning Through Numerical Mechanism Design
Chuan Guo
Kamalika Chaudhuri
Pierre Stock
Michael G. Rabbat
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
proceedings.mlr.press
proceedings.mlr.press
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts
Minghao Xu
Xinyu Yuan
Santiago Miret
Jian Tang
Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary… (voir plus) 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.
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (publié)
doi.org
proceedings.mlr.press