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

Experience Grounds Language

Yonatan Bisk

Ari Holtzman

Jesse D. Thomason

Jacob Andreas

Joyce Yue Chai

Mirella Lapata

Angeliki Lazaridou

Jonathan May

Aleksandr Nisnevich

Nicolas Pinto

Joseph Turian

2020-10-31

Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP) (published)

The Bottleneck Simulator: A Model-based Deep Reinforcement Learning Approach

Iulian Vlad Serban

Chinnadhurai Sankar

Michael Pieper

Joelle Pineau

Deep reinforcement learning has recently shown many impressive successes. However, one major obstacle towards applying such methods to real-… (see more)world problems is their lack of data-efficiency. To this end, we propose the Bottleneck Simulator: a model-based reinforcement learning method which combines a learned, factorized transition model of the environment with rollout simulations to learn an effective policy from few examples. The learned transition model employs an abstract, discrete (bottleneck) state, which increases sample efficiency by reducing the number of model parameters and by exploiting structural properties of the environment. We provide a mathematical analysis of the Bottleneck Simulator in terms of fixed points of the learned policy, which reveals how performance is affected by four distinct sources of error: an error related to the abstract space structure, an error related to the transition model estimation variance, an error related to the transition model estimation bias, and an error related to the transition model class bias. Finally, we evaluate the Bottleneck Simulator on two natural language processing tasks: a text adventure game and a real-world, complex dialogue response selection task. On both tasks, the Bottleneck Simulator yields excellent performance beating competing approaches.

2020-10-26

Journal of Artificial Intelligence Research (published)

NU-GAN: High resolution neural upsampling with GAN

In this paper, we propose NU-GAN, a new method for resampling audio from lower to higher sampling rates (upsampling). Audio upsampling is an… (see more) important problem since productionizing generative speech technology requires operating at high sampling rates. Such applications use audio at a resolution of 44.1 kHz or 48 kHz, whereas current speech synthesis methods are equipped to handle a maximum of 24 kHz resolution. NU-GAN takes a leap towards solving audio upsampling as a separate component in the text-to-speech (TTS) pipeline by leveraging techniques for audio generation using GANs. ABX preference tests indicate that our NU-GAN resampler is capable of resampling 22 kHz to 44.1 kHz audio that is distinguishable from original audio only 7.4% higher than random chance for single speaker dataset, and 10.8% higher than chance for multi-speaker dataset.

2020-10-21

ArXiv (preprint)

Cross-Modal Information Maximization for Medical Imaging: CMIM

Tristan Sylvain

Francis Dutil

Tess Berthier

Lisa Di Jorio

Margaux Luck

R Devon Hjelm

2020-10-19

ArXiv (preprint)

GraphMix: Improved Training of GNNs for Semi-Supervised Learning

Juho Kannala

We present GraphMix, a regularization method for Graph Neural Network based semi-supervised object classification, whereby we propose to tra… (see more)in a fully-connected network jointly with the graph neural network via parameter sharing and interpolation-based regularization. Further, we provide a theoretical analysis of how GraphMix improves the generalization bounds of the underlying graph neural network, without making any assumptions about the "aggregation" layer or the depth of the graph neural networks. We experimentally validate this analysis by applying GraphMix to various architectures such as Graph Convolutional Networks, Graph Attention Networks and Graph-U-Net. Despite its simplicity, we demonstrate that GraphMix can consistently improve or closely match state-of-the-art performance using even simpler architectures such as Graph Convolutional Networks, across three established graph benchmarks: Cora, Citeseer and Pubmed citation network datasets, as well as three newly proposed datasets: Cora-Full, Co-author-CS and Co-author-Physics.

2020-10-10

AAAI Conference on Artificial Intelligence (published)

COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing

Prateek Gupta

Tegan Maharaj

Martin Weiss

Nasim Rahaman

Hannah Alsdurf

Abhinav Sharma

Nanor Minoyan

Soren Harnois Leblanc

Victor Schmidt

Pierre-Luc St. Charles

Akshay Patel

David Buckeridge … (see 9 more)

Joumana Ghosn

Yang Zhang

Bernhard Schölkopf

Jian Tang

Irina Rish

Christopher Pal

Joanna Merckx

Eilif B. Muller

The rapid global spread of COVID-19 has led to an unprecedented demand for effective methods to mitigate the spread of the disease, and vari… (see more)ous digital contact tracing (DCT) methods have emerged as a component of the solution. In order to make informed public health choices, there is a need for tools which allow evaluation and comparison of DCT methods. We introduce an agent-based compartmental simulator we call COVI-AgentSim, integrating detailed consideration of virology, disease progression, social contact networks, and mobility patterns, based on parameters derived from empirical research. We verify by comparing to real data that COVI-AgentSim is able to reproduce realistic COVID-19 spread dynamics, and perform a sensitivity analysis to verify that the relative performance of contact tracing methods are consistent across a range of settings. We use COVI-AgentSim to perform cost-benefit analyses comparing no DCT to: 1) standard binary contact tracing (BCT) that assigns binary recommendations based on binary test results; and 2) a rule-based method for feature-based contact tracing (FCT) that assigns a graded level of recommendation based on diverse individual features. We find all DCT methods consistently reduce the spread of the disease, and that the advantage of FCT over BCT is maintained over a wide range of adoption rates. Feature-based methods of contact tracing avert more disability-adjusted life years (DALYs) per socioeconomic cost (measured by productive hours lost). Our results suggest any DCT method can help save lives, support re-opening of economies, and prevent second-wave outbreaks, and that FCT methods are a promising direction for enriching BCT using self-reported symptoms, yielding earlier warning signals and a significantly reduced spread of the virus per socioeconomic cost.

2020-10-01

OpenReview.net/Anonymous_Preprint (unknown)

openreview.net

Generating Multiscale Amorphous Molecular Structures Using Deep Learning: A Study in 2D.

Michael Kilgour

Nicolas Gastellu

David Y. T. Hui

Lena Simine

Amorphous molecular assemblies appear in a vast array of systems: from living cells to chemical plants and from everyday items to new device… (see more)s. The absence of long-range order in amorphous materials implies that precise knowledge of their underlying structures throughout is needed to rationalize and control their properties at the mesoscale. Standard computational simulations suffer from exponentially unfavorable scaling of the required compute with system size. We present a method based on deep learning that leverages the finite range of structural correlations for an autoregressive generation of disordered molecular aggregates up to arbitrary size from small-scale computational or experimental samples. We benchmark performance on self-assembled nanoparticle aggregates and proceed to simulate monolayer amorphous carbon with atomistic resolution. This method bridges the gap between the nanoscale and mesoscale simulations of amorphous molecular systems.

2020-09-23

Journal of Physical Chemistry Letters (published)

A learning-based algorithm to quickly compute good primal solutions for Stochastic Integer Programs

Emma Frejinger

Andrea Lodi

Rahul Patel

Sriram Sankaranarayanan

We propose a novel approach using supervised learning to obtain near-optimal primal solutions for two-stage stochastic integer programming (… (see more)2SIP) problems with constraints in the first and second stages. The goal of the algorithm is to predict a "representative scenario" (RS) for the problem such that, deterministically solving the 2SIP with the random realization equal to the RS, gives a near-optimal solution to the original 2SIP. Predicting an RS, instead of directly predicting a solution ensures first-stage feasibility of the solution. If the problem is known to have complete recourse, second-stage feasibility is also guaranteed. For computational testing, we learn to find an RS for a two-stage stochastic facility location problem with integer variables and linear constraints in both stages and consistently provide near-optimal solutions. Our computing times are very competitive with those of general-purpose integer programming solvers to achieve a similar solution quality.

2020-09-18

Integration of Constraint Programming, Artificial Intelligence, and Operations Research (published)

Mastering Rate based Curriculum Learning

Lucas Willems

Salem Lahlou

2020-08-13

ArXiv (preprint)

Deriving Differential Target Propagation from Iterating Approximate Inverses

2020-07-28

ArXiv (preprint)

Predicting COVID-19 Pneumonia Severity on Chest X-ray With Deep Learning

Beiyi Shen

Almas F Abbasi

Hoshmand Kochi Mahsa

Marzyeh Ghassemi

Haifang Li

Tim Q Duong

Introduction The need to streamline patient management for coronavirus disease-19 (COVID-19) has become more pressing than ever. Chest X-ray… (see more)s (CXRs) provide a non-invasive (potentially bedside) tool to monitor the progression of the disease. In this study, we present a severity score prediction model for COVID-19 pneumonia for frontal chest X-ray images. Such a tool can gauge the severity of COVID-19 lung infections (and pneumonia in general) that can be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the ICU. Methods Images from a public COVID-19 database were scored retrospectively by three blinded experts in terms of the extent of lung involvement as well as the degree of opacity. A neural network model that was pre-trained on large (non-COVID-19) chest X-ray datasets is used to construct features for COVID-19 images which are predictive for our task. Results This study finds that training a regression model on a subset of the outputs from this pre-trained chest X-ray model predicts our geographic extent score (range 0-8) with 1.14 mean absolute error (MAE) and our lung opacity score (range 0-6) with 0.78 MAE. Conclusions These results indicate that our model’s ability to gauge the severity of COVID-19 lung infections could be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the ICU. To enable follow up work, we make our code, labels, and data available online.

2020-07-27

Cureus (published)

Learning to Navigate the Synthetically Accessible Chemical Space Using Reinforcement Learning

Sai Krishna Gottipati

Boris Sattarov

Sufeng Niu

Yashaswi Pathak

Haoran Wei

Karam J. Thomas

Connor W. Coley

Over the last decade, there has been significant progress in the field of machine learning for de novo drug design, particularly in deep gen… (see more)erative models. However, current generative approaches exhibit a significant challenge as they do not ensure that the proposed molecular structures can be feasibly synthesized nor do they provide the synthesis routes of the proposed small molecules, thereby seriously limiting their practical applicability. In this work, we propose a novel forward synthesis framework powered by reinforcement learning (RL) for de novo drug design, Policy Gradient for Forward Synthesis (PGFS), that addresses this challenge by embedding the concept of synthetic accessibility directly into the de novo drug design system. In this setup, the agent learns to navigate through the immense synthetically accessible chemical space by subjecting commercially available small molecule building blocks to valid chemical reactions at every time step of the iterative virtual multi-step synthesis process. The proposed environment for drug discovery provides a highly challenging test-bed for RL algorithms owing to the large state space and high-dimensional continuous action space with hierarchical actions. PGFS achieves state-of-the-art performance in generating structures with high QED and penalized clogP. Moreover, we validate PGFS in an in-silico proof-of-concept associated with three HIV targets. Finally, we describe how the end-to-end training conceptualized in this study represents an important paradigm in radically expanding the synthesizable chemical space and automating the drug discovery process.

2020-07-13

ICML (Accept)