Jian Tang

Biography

Jian Tang is an Associate professor at HEC's Department of Decision Sciences. He is also an Adjunct professor at the Department of Computer Science and Operations Research at University of Montreal and a Core Academic member at Mila - Quebec AI Institute. He is a Canada CIFAR AI Chair and the Founder of BioGeometry, an AI startup that focuses on generative AI for antibody discovery. Tang’s main research interests are deep generative models and graph machine learning, and their applications to drug discovery. He is an international leader in graph machine learning, and LINE, his node representation method, has been widely recognized and cited more than five thousand times. He has also done pioneering work on AI for drug discovery, such as developing the first open-source machine learning frameworks for drug discovery, TorchDrug and TorchProtein.

Current Students

Huiyu Cai

PhD - Université de Montréal

huiyu.cai@mila.quebec

Collaborating researcher

Farzaneh Heidari

PhD - Université de Montréal

Principal supervisor :

Guillaume Rabusseau

Jerry Lu

PhD - Université de Montréal

Stephen Lu

Research Intern - McGill University

stephen.lu@mila.quebec

Shentong Mo

Collaborating researcher - Carnegie Mellon University

Chence Shi

PhD - Université de Montréal

Sophie Xhonneux

PhD - Université de Montréal

Principal supervisor :

Gauthier Gidel

lpxhonneux@gmail.com

Minghao Xu

Collaborating researcher

Xinyu Yuan

PhD - Université de Montréal

xinyu.yuan@mila.quebec

Zhihao Zhan

PhD - Université de Montréal

Zuobai Zhang

PhD - Université de Montréal

zhaocheng.zhu@umontreal.ca

Jianan Zhao

PhD - Université de Montréal

PhD - Université de Montréal

Publications

RNNLogic: Learning Logic Rules for Reasoning on Knowledge Graphs

Meng Qu

Junkun Chen

Louis-Pascal Xhonneux

This paper studies learning logic rules for reasoning on knowledge graphs. Logic rules provide interpretable explanations when used for pred… (see more)iction as well as being able to generalize to other tasks, and hence are critical to learn. Existing methods either suffer from the problem of searching in a large search space (e.g., neural logic programming) or ineffective optimization due to sparse rewards (e.g., techniques based on reinforcement learning). To address these limitations, this paper proposes a probabilistic model called RNNLogic. RNNLogic treats logic rules as a latent variable, and simultaneously trains a rule generator as well as a reasoning predictor with logic rules. We develop an EM-based algorithm for optimization. In each iteration, the reasoning predictor is updated to explore some generated logic rules for reasoning. Then in the E-step, we select a set of high-quality rules from all generated rules with both the rule generator and reasoning predictor via posterior inference; and in the M-step, the rule generator is updated with the rules selected in the E-step. Experiments on four datasets prove the effectiveness of RNNLogic.

2021-01-12

ICLR.cc/2021/Conference (poster)

Learning Neural Generative Dynamics for Molecular Conformation Generation

Minkai Xu

Shitong Luo

Jian Peng

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamic… (see more)s, sample conformations via computationally expensive simulations. Recently, machine learning methods have shown great potential by training on a large collection of conformation data. Challenges arise from the limited model capacity for capturing complex distributions of conformations and the difficulty in modeling long-range dependencies between atoms. Inspired by the recent progress in deep generative models, in this paper, we propose a novel probabilistic framework to generate valid and diverse conformations given a molecular graph. We propose a method combining the advantages of both flow-based and energy-based models, enjoying: (1) a high model capacity to estimate the multimodal conformation distribution; (2) explicitly capturing the complex long-range dependencies between atoms in the observation space. Extensive experiments demonstrate the superior performance of the proposed method on several benchmarks, including conformation generation and distance modeling tasks, with a significant improvement over existing generative models for molecular conformation sampling.

2021-01-01

ICLR (published)

GraphMix: Improved Training of GNNs for Semi-Supervised Learning

Vikas Verma

Meng Qu

Kenji Kawaguchi

Alex Lamb

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.

2020-10-11

AAAI Conference on Artificial Intelligence (published)

doi.org

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

Prateek Gupta

Martin Weiss

Nasim Rahaman

Hannah Alsdurf

Abhinav Sharma

Nanor Minoyan

Soren Harnois-Leblanc

Victor Schmidt

Pierre-Luc St-Charles

Tristan Deleu

andrew williams

Akshay Patel

Meng Qu

Olexa Bilaniuk

gaetan caron

pierre luc carrier

satya ortiz gagne

Marc-Andre Rousseau

David Buckeridge … (see 9 more)

Joumana Ghosn

Yang Zhang

Bernhard Schölkopf

Chris Pal

Joanna Merckx

Eilif Benjamin Muller

2020-10-02

OpenReview.net/Anonymous_Preprint (unknown)

COVI White Paper

Hannah Alsdurf

Tristan Deleu

Prateek Gupta

Daphne Ippolito

Richard Janda

Max Jarvie

Tyler J. Kolody

Sekoul Krastev

Robert Obryk

Dan Pilat

Valerie Pisano

Benjamin Prud'homme

Meng Qu

Nasim Rahaman

Jean-franois Rousseau

Abhinav Sharma

Brooke Struck … (see 3 more)

Martin Weiss

Yun William Yu

2020-05-18

ArXiv (preprint)

COVI White Paper

Hannah Alsdurf

Tristan Deleu

Prateek Gupta

Daphne Ippolito

Richard Janda

Max Jarvie

Tyler J. Kolody

Sekoul Krastev

Robert Obryk

Dan Pilat

Valerie Pisano

Benjamin Prud'homme

Meng Qu

Nasim Rahaman

Jean-franois Rousseau

Abhinav Sharma

Brooke Struck … (see 3 more)

Martin Weiss

Yun William Yu

2020-05-18

ArXiv (preprint)

COVI White Paper-Version 1.1

Hannah Alsdurf

Tristan Deleu

Prateek Gupta

Daphne Ippolito

Richard Janda

Max Jarvie

Tyler J. Kolody

Sekoul Krastev

Robert Obryk

Dan Pilat

Valerie Pisano

Benjamin Prud'homme

Meng Qu

Nasim Rahaman

Jean-franois Rousseau

Abhinav Sharma

Brooke Struck … (see 3 more)

Martin Weiss

Yun William Yu

The SARS-CoV-2 (Covid-19) pandemic has resulted in significant strain on health care and public health institutions around the world. Contac… (see more)t tracing is an essential tool for public health officials and local communities to change the course of the Covid-19 pandemic. Standard manual contact tracing of people infected with Covid-19, while the current gold standard, has significant challenges that limit the ability of public health authorities to minimize community infections. Personalized peer-to-peer contact tracing through the use of mobile applications has the potential to shift the paradigm of Covid-19 community spread. Although some countries have deployed centralized tracking systems through either GPS or Bluetooth, more privacy-protecting decentralized systems offer much of the same benefit without concentrating data in the hands of a state authority or in for-profit corporations. Additionally, machine learning methods can be used to circumvent some of the limitations of standard digital tracing by incorporating many clues (including medical conditions, self-reported symptoms, and numerous encounters with people at different risk levels, for different durations and distances) and their uncertainty into a more graded and precise estimation of infection and contagion risk. The estimated risk can be used to provide early risk awareness, personalized recommendations and relevant information to the user and connect them to health services. Finally, the non-identifying data about these risks can inform detailed epidemiological models trained jointly with the machine learning predictor, and these models can provide statistical evidence for the interaction and importance of different factors involved in the transmission of the disease. They can also be used to monitor, evaluate and optimize different health policy and confinement/deconfinement scenarios according to medical and economic productivity indicators. However, such a strategy based on mobile apps and machine learning should proactively mitigate potential ethical and privacy risks, which could have substantial impacts on society (not only impacts on health but also impacts such as stigmatization and abuse of personal data). Here, we present an overview of the rationale, design, ethical considerations and privacy strategy of ‘COVI,’ a Covid-19 public peer-to-peer contact tracing and risk awareness mobile application developed in Canada. Addendum 2020-07-14: The government of Canada has declined to endorse COVI and will be promoting a different app for decentralized contact tracing. In the interest of preventing fragmentation of the app landscape, COVI will therefore not be deployed to end users. We are currently still in the process of finalizing the project, and plan to release our code and models for academic consumption and to make them accessible to other States should they wish to deploy an app based on or inspired by said code and models. University of Ottawa, Mila, Université de Montréal, The Alan Turing Institute, University of Oxford, University of Pennsylvania, McGill University, Borden Ladner Gervais LLP, The Decision Lab, HEC Montréal, Max Planck Institute, Libéo, University of Toronto. Corresponding author general: richard.janda@mcgill.ca Corresponding author for public health: abhinav.sharma@mcgill.ca Corresponding author for privacy: ywyu@math.toronto.edu Corresponding author for machine learning: yoshua.bengio@mila.quebec Corresponding author for user perspective: brooke@thedecisionlab.com Corresponding author for technical implementation: jean-francois.rousseau@libeo.com 1 ar X iv :2 00 5. 08 50 2v 2 [ cs .C R ] 2 7 Ju l 2 02 0

GraphMix: Improved Training of Graph Neural Networks for Semi-Supervised Learning

Vikas Verma

Meng Qu

Alex Lamb

Juho Kannala

We present GraphMix , a regularized training scheme for Graph Neural Network based semi-supervised object classiﬁcation, leveraging the re… (see more)cent advances in the regularization of classical deep neural networks. Speciﬁcally, we pro-pose a uniﬁed approach in which we train a fully-connected network jointly with the graph neural network via parameter sharing, interpolation-based regularization and self-predicted-targets. Our proposed method is architecture agnostic in the sense that it can be applied to any variant of graph neural networks which applies a parametric transformation to the features of the graph nodes. Despite its simplicity, with GraphMix we can consistently improve results and achieve 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.

Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning

Sai Krishna Gottipati

B. Sattarov

Sufeng Niu

Yashaswi Pathak

Haoran Wei

Shengchao Liu

Karam M. J. Thomas

Simon R. Blackburn

Connor Wilson. Coley

Sarath Chandar

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.

2020-01-01

ICML (published)

proceedings.mlr.press

S UPPLEMENTARY M ATERIAL - L EARNING T O N AVIGATE T HE S YNTHETICALLY A CCESSIBLE C HEMICAL S PACE U SING R EINFORCEMENT L EARNING

Sai Krishna

Gottipati

B. Sattarov

Sufeng Niu

Yashaswi Pathak

Haoran Wei

Shengchao Liu

Karam M. J. Thomas

Simon R. Blackburn

Connor Wilson. Coley

Sarath Chandar

While updating the critic network, we multiply the normal random noise vector with policy noise of 0.2 and then clip it in the range -0.2 to… (see more) 0.2. This clipped policy noise is added to the action at the next time step a′ computed by the target actor networks f and π. The actor networks (f and π networks), target critic and target actor networks are updated once every two updates to the critic network.

Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures

Jordan Hoffmann

Louis Maestrati

Yoshihide Sawada

Jean Michel Sellier

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative … (see more)models have led to rapid progress in automated drug discovery. Many of the current methods focus on either 1-D or 2-D representations of typically small, drug-like molecules. However, many molecules require 3-D descriptors and exceed the chemical complexity of commonly used dataset. We present a method to encode and decode the position of atoms in 3-D molecules from a dataset of nearly 50,000 stable crystal unit cells that vary from containing 1 to over 100 atoms. We construct a smooth and continuous 3-D density representation of each crystal based on the positions of different atoms. Two different neural networks were trained on a dataset of over 120,000 three-dimensional samples of single and repeating crystal structures, made by rotating the single unit cells. The first, an Encoder-Decoder pair, constructs a compressed latent space representation of each molecule and then decodes this description into an accurate reconstruction of the input. The second network segments the resulting output into atoms and assigns each atom an atomic number. By generating compressed, continuous latent spaces representations of molecules we are able to decode random samples, interpolate between two molecules, and alter known molecules.

2019-09-03

ArXiv (preprint)

Contextualized Non-local Neural Networks for Sequence Learning

Pengfei Liu

Shuaichen Chang

Xuanjing Huang

Jackie Cheung

Recently, a large number of neural mechanisms and models have been proposed for sequence learning, of which selfattention, as exemplified by… (see more) the Transformer model, and graph neural networks (GNNs) have attracted much attention. In this paper, we propose an approach that combines and draws on the complementary strengths of these two methods. Specifically, we propose contextualized non-local neural networks (CN3), which can both dynamically construct a task-specific structure of a sentence and leverage rich local dependencies within a particular neighbourhood.Experimental results on ten NLP tasks in text classification, semantic matching, and sequence labelling show that our proposed model outperforms competitive baselines and discovers task-specific dependency structures, thus providing better interpretability to users.

2019-07-17

Proceedings of the AAAI Conference on Artificial Intelligence (published)

doi.org