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

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

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

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

The SARS-CoV-2 (Covid-19) pandemic has caused significant strain on public health institutions around the world. Contact tracing is an essen… (see more)tial tool to change the course of the Covid-19 pandemic. Manual contact tracing of Covid-19 cases 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 apps has the potential to shift the paradigm. Some countries have deployed centralized tracking systems, but more privacy-protecting decentralized systems offer much of the same benefit without concentrating data in the hands of a state authority or for-profit corporations. Machine learning methods can circumvent some of the limitations of standard digital tracing by incorporating many clues and their uncertainty into a more graded and precise estimation of infection risk. The estimated risk can provide early risk awareness, personalized recommendations and relevant information to the user. Finally, non-identifying risk data can inform epidemiological models trained jointly with the machine learning predictor. These models can provide statistical evidence for the importance of factors involved in disease transmission. They can also be used to monitor, evaluate and optimize health policy and (de)confinement 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.

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)

openreview.net

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

Learning Powerful Policies by Using Consistent Dynamics Model

Shagun Sodhani

Anirudh Goyal

Tristan Deleu

Sergey Levine

Model-based Reinforcement Learning approaches have the promise of being sample efficient. Much of the progress in learning dynamics models i… (see more)n RL has been made by learning models via supervised learning. But traditional model-based approaches lead to `compounding errors' when the model is unrolled step by step. Essentially, the state transitions that the learner predicts (by unrolling the model for multiple steps) and the state transitions that the learner experiences (by acting in the environment) may not be consistent. There is enough evidence that humans build a model of the environment, not only by observing the environment but also by interacting with the environment. Interaction with the environment allows humans to carry out experiments: taking actions that help uncover true causal relationships which can be used for building better dynamics models. Analogously, we would expect such interactions to be helpful for a learning agent while learning to model the environment dynamics. In this paper, we build upon this intuition by using an auxiliary cost function to ensure consistency between what the agent observes (by acting in the real world) and what it imagines (by acting in the `learned' world). We consider several tasks - Mujoco based control tasks and Atari games - and show that the proposed approach helps to train powerful policies and better dynamics models.

2019-06-11

ArXiv (preprint)

GMNN: Graph Markov Neural Networks

Meng Qu

This paper studies semi-supervised object classification in relational data, which is a fundamental problem in relational data modeling. The… (see more) problem has been extensively studied in the literature of both statistical relational learning (e.g. relational Markov networks) and graph neural networks (e.g. graph convolutional networks). Statistical relational learning methods can effectively model the dependency of object labels through conditional random fields for collective classification, whereas graph neural networks learn effective object representations for classification through end-to-end training. In this paper, we propose the Graph Markov Neural Network (GMNN) that combines the advantages of both worlds. A GMNN models the joint distribution of object labels with a conditional random field, which can be effectively trained with the variational EM algorithm. In the E-step, one graph neural network learns effective object representations for approximating the posterior distributions of object labels. In the M-step, another graph neural network is used to model the local label dependency. Experiments on object classification, link classification, and unsupervised node representation learning show that GMNN achieves state-of-the-art results.

2019-05-24

Proceedings of the 36th International Conference on Machine Learning (published)

proceedings.mlr.press

Session-Based Social Recommendation via Dynamic Graph Attention Networks

Weiping Song

Zhiping Xiao

Yifan Wang

Laurent Charlin

Ming Zhang

Online communities such as Facebook and Twitter are enormously popular and have become an essential part of the daily life of many of their … (see more)users. Through these platforms, users can discover and create information that others will then consume. In that context, recommending relevant information to users becomes critical for viability. However, recommendation in online communities is a challenging problem: 1) users' interests are dynamic, and 2) users are influenced by their friends. Moreover, the influencers may be context-dependent. That is, different friends may be relied upon for different topics. Modeling both signals is therefore essential for recommendations. We propose a recommender system for online communities based on a dynamic-graph-attention neural network. We model dynamic user behaviors with a recurrent neural network, and context-dependent social influence with a graph-attention neural network, which dynamically infers the influencers based on users' current interests. The whole model can be efficiently fit on large-scale data. Experimental results on several real-world data sets demonstrate the effectiveness of our proposed approach over several competitive baselines including state-of-the-art models.

2019-01-30

Proceedings of the Twelfth ACM International Conference on Web Search and Data Mining (published)

doi.org