Jian Tang

farzaneh.heidari@mila.quebec

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

PhD - Université de Montréal

Principal supervisor :

Guillaume Rabusseau

Xixian Liu

PhD - Université de Montréal

xixian.liu@mila.quebec

Jiarui Lu

PhD - Université de Montréal

jiarui.lu@mila.quebec

PhD - Université de Montréal

Principal supervisor :

Gauthier Gidel

lpxhonneux@gmail.com

Jinxi Yang

Collaborating researcher - Wuhan University

jinxi.yang@mila.quebec

Xinyu Yuan

PhD - Université de Montréal

xinyu.yuan@mila.quebec

Zhihao Zhan

PhD - Université de Montréal

zhihao.zhan@mila.quebec

Ya-Shi Zhang

PhD - HEC Montréal

ya-shi.zhang@mila.quebec

PhD - Université de Montréal

zuobai.zhang@mila.quebec

Jianan Zhao

PhD - Université de Montréal

jianan.zhao@mila.quebec

Publications

Predicting Infectiousness for Proactive Contact Tracing

Prateek Gupta

Nasim Rahaman

Pierre-Luc St-Charles

Hannah Alsdurf

Olexa Bilanuik

David Buckeridge

Gaétan Marceau Caron

Pierre-Luc Carrier

Joumana Ghosn

Satya Ortiz-Gagné

Chris Pal

Irina Rish

Bernhard Schölkopf … (see 3 more)

Abhinav Sharma

Andrew Williams

The COVID-19 pandemic has spread rapidly worldwide, overwhelming manual contact tracing in many countries and resulting in widespread lockdo… (see more)wns for emergency containment. Large-scale digital contact tracing (DCT) has emerged as a potential solution to resume economic and social activity while minimizing spread of the virus. Various DCT methods have been proposed, each making trade-offs between privacy, mobility restrictions, and public health. The most common approach, binary contact tracing (BCT), models infection as a binary event, informed only by an individual's test results, with corresponding binary recommendations that either all or none of the individual's contacts quarantine. BCT ignores the inherent uncertainty in contacts and the infection process, which could be used to tailor messaging to high-risk individuals, and prompt proactive testing or earlier warnings. It also does not make use of observations such as symptoms or pre-existing medical conditions, which could be used to make more accurate infectiousness predictions. In this paper, we use a recently-proposed COVID-19 epidemiological simulator to develop and test methods that can be deployed to a smartphone to locally and proactively predict an individual's infectiousness (risk of infecting others) based on their contact history and other information, while respecting strong privacy constraints. Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT). We find a deep-learning based PCT method which improves over BCT for equivalent average mobility, suggesting PCT could help in safe re-opening and second-wave prevention.

2021-05-02

International Conference on Learning Representations (Spotlight)

RNNLogic: Learning Logic Rules for Reasoning on Knowledge Graphs

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 first 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.

2021-05-02

International Conference on Learning Representations (Poster)

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

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)

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

International Conference on Machine Learning (Accept)

proceedings.mlr.press

COVI White Paper - Version 1.1

Hannah Alsdurf

Edmond Belliveau

Tristan Deleu

Prateek Gupta

Daphne Ippolito

Richard Janda

Max Jarvie

Tyler Kolody

Sekoul Krastev

Tegan Maharaj

Robert Obryk

Dan Pilat

Valérie Pisano

Benjamin Prud’homme

Nasim Rahaman

Irina Rish

Jean-François Rousseau

Victor Schmidt … (see 5 more)

Abhinav Sharma

Brooke Struck

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.

2019-12-31

International Conference on Machine Learning (published)

arxiv.org

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

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.

2019-12-31

(published)

www.semanticscholar.org

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

A. 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.

2019-12-31

(published)

www.semanticscholar.org

Data-Driven Approach to Encoding and De-Coding 3-D Crystal Structures

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.

2019-09-02

ArXiv (preprint)

Contextualized Non-local Neural Networks for Sequence Learning

Pengfei Liu

Shuaichen Chang

Xuanjing Huang

Jackie CK 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.

2019-07-16

Proceedings of the AAAI Conference on Artificial Intelligence (published)

arxiv.org

Weakly-supervised Knowledge Graph Alignment with Adversarial Learning

This paper studies aligning knowledge graphs from different sources or languages. Most existing methods train supervised methods for the ali… (see more)gnment, which usually require a large number of aligned knowledge triplets. However, such a large number of aligned knowledge triplets may not be available or are expensive to obtain in many domains. Therefore, in this paper we propose to study aligning knowledge graphs in fully-unsupervised or weakly-supervised fashion, i.e., without or with only a few aligned triplets. We propose an unsupervised framework to align the entity and relation embddings of different knowledge graphs with an adversarial learning framework. Moreover, a regularization term which maximizes the mutual information between the embeddings of different knowledge graphs is used to mitigate the problem of mode collapse when learning the alignment functions. Such a framework can be further seamlessly integrated with existing supervised methods by utilizing a limited number of aligned triples as guidance. Experimental results on multiple datasets prove the effectiveness of our proposed approach in both the unsupervised and the weakly-supervised settings.

2019-07-05

ArXiv (preprint)

Learning Powerful Policies by Using Consistent Dynamics Model

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.

2019-06-10

arXiv (preprint)

arxiv.org

GMNN: Graph Markov Neural Networks

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.

2019-05-23

International Conference on Machine Learning (published)