Portrait of Emmanuel Bengio

Emmanuel Bengio

Associate Industry Member
Staff Machine Learning Scientist, Recursion
Research Topics
Deep Learning
Generative Models
GFlowNets
Molecular Modeling
Reinforcement Learning

Biography

Emmanuel Bengio is an ML Scientist at Valence Labs/Recursion, working on the intersection of GFlowNets and drug discovery. He did his PhD under Joelle Pineau and Doina Precup at McGill/Mila - Quebec Artificial Intelligence Institute, focusing on understanding generalization in deep RL.

Publications

SynFlowNet: Towards Molecule Design with Guaranteed Synthesis Pathways
M. Cretu
Charles Harris
Julien Roy
Pietro Lio
A community effort in SARS-CoV-2 drug discovery.
Johannes Schimunek
Philipp Seidl
Katarina Elez
Tim Hempel
Tuan Le
Frank Noé
Simon Olsson
Lluís Raich
Robin Winter
Hatice Gokcan
Filipp Gusev
Evgeny M. Gutkin
Olexandr Isayev
Maria G. Kurnikova
Chamali H. Narangoda
Roman Zubatyuk
Ivan P. Bosko
Konstantin V. Furs
Anna D. Karpenko
Yury V. Kornoushenko … (see 133 more)
Mikita Shuldau
Artsemi Yushkevich
Mohammed B. Benabderrahmane
Patrick Bousquet‐Melou
Ronan Bureau
Beatrice Charton
Bertrand C. Cirou
Gérard Gil
William J. Allen
Suman Sirimulla
Stanley Watowich
Nick Antonopoulos
Nikolaos Epitropakis
Agamemnon Krasoulis
Vassilis Pitsikalis
Stavros Theodorakis
Igor Kozlovskii
Anton Maliutin
Alexander Medvedev
Petr Popov
Mark Zaretckii
Hamid Eghbal‐Zadeh
Christina Halmich
Sepp Hochreiter
Andreas Mayr
Peter Ruch
Michael Widrich
Francois Berenger
Ashutosh Kumar
Yoshihiro Yamanishi
Kam Y. J. Zhang
Moksh J. Jain
Maksym Korablyov
Cheng-Hao Liu
Gilles Marcou
Marcous Gilles
Enrico Glaab
Kelly Barnsley
Suhasini M. Iyengar
Mary Jo Ondrechen
V. Joachim Haupt
Florian Kaiser
Michael Schroeder
Luisa Pugliese
Simone Albani
Christina Athanasiou
Andrea Beccari
Paolo Carloni
Giulia D'Arrigo
Eleonora Gianquinto
Jonas Goßen
Anton Hanke
Benjamin P. Joseph
Daria B. Kokh
Sandra Kovachka
Candida Manelfi
Goutam Mukherjee
Abraham Muñiz‐Chicharro
Francesco Musiani
Ariane Nunes‐Alves
Giulia Paiardi
Giulia Rossetti
S. Kashif Sadiq
Francesca Spyrakis
Carmine Talarico
Alexandros Tsengenes
Rebecca C. Wade
Conner Copeland
Jeremiah Gaiser
Daniel R. Olson
Amitava Roy
Vishwesh Venkatraman
Travis J. Wheeler
Haribabu Arthanari
Klara Blaschitz
Marco Cespugli
Vedat Durmaz
Konstantin Fackeldey
Patrick D. Fischer
Christoph Gorgulla
Christian Gruber
Karl Gruber
Michael Hetmann
Jamie E. Kinney
Krishna M. Padmanabha Das
Shreya Pandita
Amit Singh
Georg Steinkellner
Guilhem Tesseyre
Gerhard Wagner
Zi‐Fu Wang
Ryan J. Yust
Dmitry S. Druzhilovskiy
Dmitry A. Filimonov
Pavel V. Pogodin
Vladimir Poroikov
Anastassia V. Rudik
Leonid A. Stolbov
Alexander V. Veselovsky
Maria De Rosa
Giada De Simone
Maria R. Gulotta
Jessica Lombino
Nedra Mekni
Ugo Perricone
Arturo Casini
Amanda Embree
D. Benjamin Gordon
David Lei
Katelin Pratt
Christopher A. Voigt
Kuang‐Yu Chen
Yves Jacob
Tim Krischuns
Pierre Lafaye
Agnès Zettor
M. Luis Rodríguez
Kris M. White
Daren Fearon
Frank Von Delft
Martin A. Walsh
Dragos Horvath
Charles L. Brooks
Babak Falsafi
Bryan Ford
Adolfo García‐Sastre
Sang Yup Lee
Nadia Naffakh
Alexandre Varnek
Günter Klambauer
Thomas M. Hermans
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availabili… (see more)ty of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against Covid-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.
Baking Symmetry into GFlowNets
George Ma
Dinghuai Zhang
GFlowNets have exhibited promising performance in generating diverse candidates with high rewards. These networks generate objects increment… (see more)ally and aim to learn a policy that assigns probability of sampling objects in proportion to rewards. However, the current training pipelines of GFlowNets do not consider the presence of isomorphic actions, which are actions resulting in symmetric or isomorphic states. This lack of symmetry increases the amount of samples required for training GFlowNets and can result in inefficient and potentially incorrect flow functions. As a consequence, the reward and diversity of the generated objects decrease. In this study, our objective is to integrate symmetries into GFlowNets by identifying equivalent actions during the generation process. Experimental results using synthetic data demonstrate the promising performance of our proposed approaches.
Baking Symmetry into GFlowNets
George Ma
Dinghuai Zhang
GFlowNets have exhibited promising performance in generating diverse candidates with high rewards. These networks generate objects increment… (see more)ally and aim to learn a policy that assigns probability of sampling objects in proportion to rewards. However, the current training pipelines of GFlowNets do not consider the presence of isomorphic actions, which are actions resulting in symmetric or isomorphic states. This lack of symmetry increases the amount of samples required for training GFlowNets and can result in inefficient and potentially incorrect flow functions. As a consequence, the reward and diversity of the generated objects decrease. In this study, our objective is to integrate symmetries into GFlowNets by identifying equivalent actions during the generation process. Experimental results using synthetic data demonstrate the promising performance of our proposed approaches.
DGFN: Double Generative Flow Networks
Elaine Lau
Nikhil Murali Vemgal
Local Search GFlowNets
Minsu Kim
Taeyoung Yun
Dinghuai Zhang
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.
Local Search GFlowNets
Minsu Kim
Taeyoung Yun
Dinghuai Zhang
Sungsoo Ahn
Jinkyoo Park
Goal-conditioned GFlowNets for Controllable Multi-Objective Molecular Design
In recent years, in-silico molecular design has received much attention from the machine learning community. When designing a new compound f… (see more)or pharmaceutical applications, there are usually multiple properties of such molecules that need to be optimised: binding energy to the target, synthesizability, toxicity, EC50, and so on. While previous approaches have employed a scalarization scheme to turn the multi-objective problem into a preference-conditioned single objective, it has been established that this kind of reduction may produce solutions that tend to slide towards the extreme points of the objective space when presented with a problem that exhibits a concave Pareto front. In this work we experiment with an alternative formulation of goal-conditioned molecular generation to obtain a more controllable conditional model that can uniformly explore solutions along the entire Pareto front.
Multi-Objective GFlowNets
Moksh J. Jain
Sharath Chandra Raparthy
Alex Hernandez-Garcia
Jarrid Rector-Brooks
Santiago Miret
We study the problem of generating diverse candidates in the context of Multi-Objective Optimization. In many applications of machine learni… (see more)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.
GFlowNet Foundations
Salem Lahlou
Tristan Deleu
Edward J Hu
Mo Tiwari
Learning GFlowNets from partial episodes for improved convergence and stability
Kanika Madan
Jarrid Rector-Brooks
Maksym Korablyov
Moksh J. Jain
Andrei Cristian Nica
Tom Bosc
Nikolay Malkin
Generative flow networks (GFlowNets) are a family of algorithms for training a sequential sampler of discrete objects under an unnormalized … (see more)target density and have been successfully used for various probabilistic modeling tasks. Existing training objectives for GFlowNets are either local to states or transitions, or propagate a reward signal over an entire sampling trajectory. We argue that these alternatives represent opposite ends of a gradient bias-variance tradeoff and propose a way to exploit this tradeoff to mitigate its harmful effects. Inspired by the TD(
Noisy Pairing and Partial Supervision for Stylized Opinion Summarization
Reinald Kim
Mirella Lapata. 2020
Un-611
Maxinder S. Kan-620
Asja Fischer
Somnath Basu
Roy Chowdhury
Chao Zhao
Tanya Goyal
Junyi Jiacheng Xu
Jessy Li
Ivor W. Tsang
James T. Kwok
Neil Houlsby
Andrei Giurgiu
Stanisław Jastrzębski … (see 22 more)
Bruna Morrone
Quentin de Laroussilhe
Mona Gesmundo
Attariyan Sylvain
Gelly
Thomas Wolf
Lysandre Debut
Julien Victor Sanh
Clement Chaumond
Anthony Delangue
Pier-339 Moi
Tim ric Cistac
R´emi Rault
Morgan Louf
Funtow-900 Joe
Sam Davison
Patrick Shleifer
Von Platen
Clara Ma
Yacine Jernite
Julien Plu
Canwen Xu
Opinion summarization research has primar-001 ily focused on generating summaries reflect-002 ing important opinions from customer reviews 0… (see more)03 without paying much attention to the writing 004 style. In this paper, we propose the stylized 005 opinion summarization task, which aims to 006 generate a summary of customer reviews in 007 the desired (e.g., professional) writing style. 008 To tackle the difficulty in collecting customer 009 and professional review pairs, we develop a 010 non-parallel training framework, Noisy Pair-011 ing and Partial Supervision ( NAPA ), which 012 trains a stylized opinion summarization sys-013 tem from non-parallel customer and profes-014 sional review sets. We create a benchmark P RO - 015 S UM by collecting customer and professional 016 reviews from Yelp and Michelin. Experimental 017 results on P RO S UM and FewSum demonstrate 018 that our non-parallel training framework con-019 sistently improves both automatic and human 020 evaluations, successfully building a stylized 021 opinion summarization model that can gener-022 ate professionally-written summaries from cus-023 tomer reviews. 024