Yoshua Bengio

Scaling in the Service of Reasoning & Model-Based ML

April 4, 2023

Yoshua Bengio

Edward J. Hu

A collaboration between Mila and Relation Therapeutics to discover novel synergistic combinations of drugs in vitro

March 23, 2022

Paul Bertin

Jake P. Taylor-King

Yoshua Bengio

March 15, 2022

Generative Flow Networks

Yoshua Bengio

Publications

Diffusion Generative Flow Samplers: Improving Learning Signals Through Partial Trajectory Optimization

Dinghuai Zhang

Ricky T. Q. Chen

Cheng-Hao Liu

Aaron Courville

We tackle the problem of sampling from intractable high-dimensional density functions, a fundamental task that often appears in machine lear… (see more)ning and statistics. We extend recent sampling-based approaches that leverage controlled stochastic processes to model approximate samples from these target densities. The main drawback of these approaches is that the training objective requires full trajectories to compute, resulting in sluggish credit assignment issues due to use of entire trajectories and a learning signal present only at the terminal time. In this work, we present Diffusion Generative Flow Samplers (DGFS), a sampling-based framework where the learning process can be tractably broken down into short partial trajectory segments, via parameterizing an additional "flow function". Our method takes inspiration from the theory developed for generative flow networks (GFlowNets), allowing us to make use of intermediate learning signals. Through various challenging experiments, we demonstrate that DGFS achieves more accurate estimates of the normalization constant than closely-related prior methods.

2024-01-15

ICLR.cc/2024/Conference (poster)

Expected Flow Networks in Stochastic Environments and Two-Player Zero-Sum Games

Bilun Sun

Generative flow networks (GFlowNets) are sequential sampling models trained to match a given distribution. GFlowNets have been successfully … (see more)applied to various structured object generation tasks, sampling a diverse set of high-reward objects quickly. We propose expected flow networks (EFlowNets), which extend GFlowNets to stochastic environments. We show that EFlowNets outperform other GFlowNet formulations in stochastic tasks such as protein design. We then extend the concept of EFlowNets to adversarial environments, proposing adversarial flow networks (AFlowNets) for two-player zero-sum games. We show that AFlowNets learn to find above 80% of optimal moves in Connect-4 via self-play and outperform AlphaZero in tournaments.

2024-01-15

ICLR.cc/2024/Conference (poster)

Object-Centric Architectures Enable Efficient Causal Representation Learning

Amin Mansouri

Jason Hartford

Yan Zhang

Causal representation learning has showed a variety of settings in which we can disentangle latent variables with identifiability guarantees… (see more) (up to some reasonable equivalence class). Common to all of these approaches is the assumption that (1) the latent variables are represented as

2024-01-15

ICLR.cc/2024/Conference (poster)

PhyloGFN: Phylogenetic Inference with Generative Flow Networks

Mingyang Zhou

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

2024-01-15

ICLR.cc/2024/Conference (poster)

Pre-Training and Fine-Tuning Generative Flow Networks

Generative Flow Networks (GFlowNets) are amortized samplers that learn stochastic policies to sequentially generate compositional objects fr… (see more)om a given unnormalized reward distribution. They can generate diverse sets of high-reward objects, which is an important consideration in scientific discovery tasks. However, as they are typically trained from a given extrinsic reward function, it remains an important open challenge about how to leverage the power of pre-training and train GFlowNets in an unsupervised fashion for efficient adaptation to downstream tasks. Inspired by recent successes of unsupervised pre-training in various domains, we introduce a novel approach for reward-free pre-training of GFlowNets. By framing the training as a self-supervised problem, we propose an outcome-conditioned GFlowNet (OC-GFN) that learns to explore the candidate space. Specifically, OC-GFN learns to reach any targeted outcomes, akin to goal-conditioned policies in reinforcement learning. We show that the pre-trained OC-GFN model can allow for a direct extraction of a policy capable of sampling from any new reward functions in downstream tasks. Nonetheless, adapting OC-GFN on a downstream task-specific reward involves an intractable marginalization over possible outcomes. We propose a novel way to approximate this marginalization by learning an amortized predictor enabling efficient fine-tuning. Extensive experimental results validate the efficacy of our approach, demonstrating the effectiveness of pre-training the OC-GFN, and its ability to swiftly adapt to downstream tasks and discover modes more efficiently. This work may serve as a foundation for further exploration of pre-training strategies in the context of GFlowNets.

2024-01-15

ICLR.cc/2024/Conference (spotlight)

Foundational Challenges in Assuring Alignment and Safety of Large Language Models

Usman Anwar

Abulhair Saparov

Javier Rando

Daniel Paleka

Miles Turpin

Peter Hase

Ekdeep Singh Lubana

Erik Jenner

Stephen Casper

Oliver Sourbut

Benjamin L. Edelman

Zhaowei Zhang

Mario Günther

Anton Korinek

Jose Hernandez-Orallo

Lewis Hammond

Eric Bigelow

Alexander Pan

Lauro Langosco

Tomasz Korbak … (see 22 more)

Heidi Zhang

Ruiqi Zhong

Seán Ó hÉigeartaigh

Gabriel Recchia

Giulio Corsi

Alan Chan

Markus Anderljung

Lilian Edwards

Aleksandar Petrov

Christian Schroeder de Witt

Sumeet Ramesh Motwani

Samuel Albanie

Danqi Chen

Philip H.S. Torr

Tegan Maharaj

Jakob Foerster

Florian Tramèr

He He

Atoosa Kasirzadeh

Yejin Choi

David Krueger

This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are o… (see more)rganized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose

2023-12-31

Trans. Mach. Learn. Res. (published)

Generative Active Learning for the Search of Small-Molecule Protein Binders

Maksym Korablyov

Cheng-Hao Liu

Moksh Jain

Almer Van Der Sloot

Éric Jolicoeur

Edward Ruediger

Andrei Nica

Emmanuel Bengio

Kostiantyn Lapchevskyi

Daniel St-Cyr

Doris Alexandra Schuetz

Victor Ion Butoi

Saikrishna Gottipati

Prateek Gupta

Ladislav Rampasek … (see 14 more)

Sasikanth Avancha

Pierre-Luc Bacon

William Hamilton

Brooks Paige

Sanchit Misra

Stanislaw Jastrzebski

Bharat Kaul

Doina Precup

José Miguel Hernández-Lobato

Marwin Segler

Michael Bronstein

Anne Marinier

Mike Tyers

Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exh… (see more)ibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.

2023-12-31

arXiv (preprint)

arxiv.org

Local Search GFlowNets

Sungsoo Ahn

Jinkyoo Park

Generative Flow Networks (GFlowNets) are amortized sampling methods that learn a distribution over discrete objects proportional to their re… (see more)wards. GFlowNets exhibit a remarkable ability to generate diverse samples, yet occasionally struggle to consistently produce samples with high rewards due to over-exploration on wide sample space. This paper proposes to train GFlowNets with local search, which focuses on exploiting high-rewarded sample space to resolve this issue. Our main idea is to explore the local neighborhood via backtracking and reconstruction guided by backward and forward policies, respectively. This allows biasing the samples toward high-reward solutions, which is not possible for a typical GFlowNet solution generation scheme, which uses the forward policy to generate the solution from scratch. Extensive experiments demonstrate a remarkable performance improvement in several biochemical tasks. Source code is available: https://github.com/dbsxodud-11/ls_gfn.

2023-12-31

ICLR (published)

Machine Learning and Information Theory Concepts Towards an AI Mathematician

Nikolay Malkin

The current state-of-the-art in artificial intelligence is impressive, especially in terms of mastery of language, but not so much in terms … (see more)of mathematical reasoning. What could be missing? Can we learn something useful about that gap from how the brains of mathematicians go about their craft? This essay builds on the idea that current deep learning mostly succeeds at system 1 abilities -- which correspond to our intuition and habitual behaviors -- but still lacks something important regarding system 2 abilities -- which include reasoning and robust uncertainty estimation. It takes an information-theoretical posture to ask questions about what constitutes an interesting mathematical statement, which could guide future work in crafting an AI mathematician. The focus is not on proving a given theorem but on discovering new and interesting conjectures. The central hypothesis is that a desirable body of theorems better summarizes the set of all provable statements, for example by having a small description length while at the same time being close (in terms of number of derivation steps) to many provable statements.

2023-12-31

arXiv (preprint)

arxiv.org

PhAST: Physics-Aware, Scalable, and Task-Specific GNNs for Accelerated Catalyst Design

Alexandre Duval

Victor Schmidt

Santiago Miret

Alex Hernandez-Garcia

David Rolnick

Mitigating the climate crisis requires a rapid transition towards lower-carbon energy. Catalyst materials play a crucial role in the electro… (see more)chemical reactions involved in numerous industrial processes key to this transition, such as renewable energy storage and electrofuel synthesis. To reduce the energy spent on such activities, we must quickly discover more efficient catalysts to drive electrochemical reactions. Machine learning (ML) holds the potential to efficiently model materials properties from large amounts of data, accelerating electrocatalyst design. The Open Catalyst Project OC20 dataset was constructed to that end. However, ML models trained on OC20 are still neither scalable nor accurate enough for practical applications. In this paper, we propose task-specific innovations applicable to most architectures, enhancing both computational efficiency and accuracy. This includes improvements in (1) the graph creation step, (2) atom representations, (3) the energy prediction head, and (4) the force prediction head. We describe these contributions, referred to as PhAST, and evaluate them thoroughly on multiple architectures. Overall, PhAST improves energy MAE by 4 to 42

2023-12-31

J. Mach. Learn. Res. (published)

Simulation-Free Schrödinger Bridges via Score and Flow Matching

Yanlei Zhang

We present simulation-free score and flow matching ([SF]…

2023-12-31

AISTATS (published)

proceedings.mlr.press

Sources of Richness and Ineffability for Phenomenally Conscious States

Xu Ji

Eric Elmoznino

George Deane

Axel Constant

Guillaume Dumas

Guillaume Lajoie

Jonathan Simon

Conscious states (states that there is something it is like to be in) seem both rich or full of detail, and ineffable or hard to fully descr… (see more)ibe or recall. The problem of ineffability, in particular, is a longstanding issue in philosophy that partly motivates the explanatory gap: the belief that consciousness cannot be reduced to underlying physical processes. Here, we provide an information theoretic dynamical systems perspective on the richness and ineffability of consciousness. In our framework, the richness of conscious experience corresponds to the amount of information in a conscious state and ineffability corresponds to the amount of information lost at different stages of processing. We describe how attractor dynamics in working memory would induce impoverished recollections of our original experiences, how the discrete symbolic nature of language is insufficient for describing the rich and high-dimensional structure of experiences, and how similarity in the cognitive function of two individuals relates to improved communicability of their experiences to each other. While our model may not settle all questions relating to the explanatory gap, it makes progress toward a fully physicalist explanation of the richness and ineffability of conscious experience: two important aspects that seem to be part of what makes qualitative character so puzzling.

2023-12-31

Neuroscience of Consciousness (published)