Biography

An avatar photo

I am a Ph.D. student at Mila - Quebec AI Institute / Université de Montréal and advised by Prof. Jian Tang. Before that, I received my bachelor of science degrees majoring in chemsitry plus mathematics from Shanghai Jiao Tong University (SJTU). During my undergraduate, I worked with Prof.Yang Yang and interned at the AI-Lab of ByteDance.

(The avatar photo was taken @Chena, Alaska)

Scholar / Linkedin / Github / Twitter

Work Email: jiarui [dot] lu [at] mila [dot] quebec


Research Interest

I am passionate about the very junction between learning 🔨 and scientific problems 🧪 🧬. I specially pay my attention to the generative modeling and representation learning of the molecular geometry.

Currently I am open to possible collaboration about the general AI for Science projects. You are sincerely welcome to reach out via the Email, Linkedin or WeChat.


Education

Mila - Quebec AI Institute
Ph.D. in Computer Science
Affiliation: Université de Montréal
Sept. 2021 - Present


Shanghai Jiao Tong University
B.Sc. in Chemistry &
B.Sc. in Mathematics and Applied Mathematics
Sept. 2017 - Jun. 2021

Publication

(Preprint)

ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, Jian Tang

A text-guided protein design framework
Shengchao Liu, Yutao Zhu, Jiarui Lu, Zhao Xu, Weili Nie, Anthony Gitter, Chaowei Xiao, Jian Tang, Hongyu Guo, Anima Anandkumar

Torchdrug: A powerful and flexible machine learning platform for drug discovery
Zhaocheng Zhu, Chence Shi, Zuobai Zhang, Shengchao Liu, Minghao Xu, Xinyu Yuan, Yangtian Zhang, Junkun Chen, Huiyu Cai, Jiarui Lu, Chang Ma, Runcheng Liu, Louis-Pascal Xhonneux, Meng Qu, Jian Tang


(Conference / Journal)

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu, Zuobai Zhang, Bozitao Zhong, Chence Shi, Jian Tang
GEM Bio Workshop at ICLR 2024

Structure-Informed Protein Language Model
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie Lozano, Payel Das, Jian Tang
GEM Bio Workshop at ICLR 2024

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang
The 12th International Conference on Learning Representations (ICLR) 2024

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets
Dominique Beaini, Shenyang Huang, Joao Alex Cunha, Gabriela Moisescu-Pareja, Oleksandr Dymov, Samuel Maddrell-Mander, Callum McLean, Frederik Wenkel, Luis Müller, Jama Hussein Mohamud, Ali Parviz, Michael Craig, Michał Koziarski, Jiarui Lu, Zhaocheng Zhu, Cristian Gabellini, Kerstin Klaser, Josef Dean, Cas Wognum, Maciej Sypetkowski, Guillaume Rabusseau, Reihaneh Rabbany, Jian Tang, Christopher Morris, Ioannis Koutis, Mirco Ravanelli, Guy Wolf, Prudencio Tossou, Hadrien Mary, Therence Bois, Andrew Fitzgibbon, Błażej Banaszewski, Chad Martin, Dominic Masters
The 12th International Conference on Learning Representations (ICLR) 2024

Score-based Enhanced Sampling for Protein Molecular Dynamics
Jiarui Lu, Bozitao Zhong, Jian Tang
International conference on machine learning (ICML) Workshop on SPIGM 2023

Multi-modal molecule structure–text model for text-based retrieval and editing
Shengchao Liu, Weili Nie, Chengpeng Wang, Jiarui Lu, Zhuoran Qiao, Ling Liu, Jian Tang, Chaowei Xiao, Animashree Anandkumar
Nature Machine Intelligence 5 (12), 1447-1457

Protein Sequence and Structure Co-Design with Equivariant Translation
Chence Shi, Chuanrui Wang, Jiarui Lu, Bozitao Zhong, Jian Tang
The 11th International Conference on Learning Representations (ICLR) 2023

Unsupervised Discovery of Steerable Factors When Graph Deep Generative Models Are Entangled
Shengchao Liu, Chengpeng Wang, Jiarui Lu, Weili Nie, Hanchen Wang, Zhuoxinran Li, Bolei Zhou, Jian Tang
Transactions on Machine Learning Research (01/2024)

Peer: a comprehensive and multi-task benchmark for protein sequence understanding
Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Ma Chang, Runcheng Liu, Jian Tang
Advances in Neural Information Processing Systems 35, 35156-35173

ReLMole: Molecular representation learning based on two-level graph similarities
Zewei Ji, Runhan Shi, Jiarui Lu, Fang Li, Yang Yang
Journal of Chemical Information and Modeling 62 (22), 5361-5372

EmbedDTI: Enhancing the Molecular Representations via Sequence Embedding and Graph Convolutional Network for the Prediction of Drug-Target Interaction
Yuan Jin, Jiarui Lu, Runhan Shi, Yang Yang
Biomolecules 11 (12), 1783

KenDTI: an ensemble model based on network integration and CNN for drug-target interaction prediction
Zhimiao Yu, Jiarui Lu, Yuan Jin, and Yang Yang
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 4, pp. 1305-1314


Open-source Library

TorchDrug: A powerful and flexible machine learning platform for drug discovery
Homepage Github

TorchProtein: Protein machine learning accessible to everyone
Homepage Github

Graphium: Protein machine learning accessible to everyone
Homepage Github Paper (ICLR'24)


Service

Reviewer: ICLR, NeurIPS, ICML, KDD, LoG

Area chair: NeurIPS GenBio Workshop

Teaching assistant (TA):


Award