Jian Tang

Biographie

Jian Tang est professeur agrégé au département de sciences de la décision de HEC. Il est aussi professeur associé au département informatique et recherche opérationnelle (DIRO) de l'Université de Montréal et un membre académique principal à Mila – Institut québécois d’intelligence artificielle. Il est titulaire d'une chaire de recherche en IA Canada-CIFAR et le fondateur de BioGeometry, une entreprise en démarrage spécialisée dans l'IA générative pour la découverte d'anticorps. Ses principaux domaines de recherche sont les modèles génératifs profonds, l'apprentissage automatique des graphes et leurs applications à la découverte de médicaments. Il est un leader international dans le domaine de l'apprentissage automatique des graphes, et son travail représentatif sur l'apprentissage de la représentation des nœuds, LINE, a été largement reconnu et cité plus de 5 000 fois. Il a également réalisé de nombreux travaux pionniers sur l'IA pour la découverte de médicaments, notamment le premier cadre d'apprentissage automatique à source ouverte pour la découverte de médicaments, TorchDrug et TorchProtein.

Étudiants actuels

Huiyu Cai

Doctorat - UdeM

Doctorat - UdeM

Superviseur⋅e principal⋅e :

Xixian Liu

Doctorat - Université de Montréal

Jiarui Lu

Doctorat - UdeM

Github

Chence Shi

Doctorat - UdeM

Sophie Xhonneux

Doctorat - UdeM

Superviseur⋅e principal⋅e :

Gauthier Gidel

Xinyu Yuan

Doctorat - UdeM

Github

Zhihao Zhan

Doctorat - UdeM

Doctorat - UdeM

Doctorat - HEC

Jianan Zhao

Doctorat - UdeM

Github

Publications

Origin of Nonlinear Circular Photocurrent in 2D Semiconductor MoS_{2}.

Yanchong Zhao

Fengyu Chen

Jing Liang

Mohammad Saeed Bahramy

Mingwei Yang

Yao Guang

Xiaomei Li

Zheng Wei

Jiaojiao Zhao

Mengzhou Liao

Cheng Shen

Qinqin Wang

Rong Yang

Kenji Watanabe

Takashi Taniguchi

Zhiheng Huang

Dongxia Shi

Kaihui Liu

Zhipei Sun … (voir 3 de plus)

Ji Feng

Luojun Du

Guangyu Zhang

2025-02-25

Physical Review Letters (publié)

Author Correction: Isospin competitions and valley polarized correlated insulators in twisted double bilayer graphene

Le Liu

Shihao Zhang

Yanbang Chu

Cheng Shen

Yuan Huang

Yalong Yuan

Jinpeng Tian

Yiru Ji

Rong Yang

Kenji Watanabe

Takashi Taniguchi

Dongxia Shi

Jianpeng Liu

Wei Yang

Guangyu Zhang

2025-02-11

Nature Communications (publié)

Rapid restoration of potent neutralization activity against the latest Omicron variant JN.1 via AI rational design and antibody engineering

Yunji Liao

Hang Ma

Zhenyu Wang

Shusheng Wang

Yang He

Yunsong Chang

Huifang Zong

Haoneng Tang

Lei Wang

Yong Ke

Huiyu Cai

Ping Li

Yunsheng Yuan

Aleksandra Drelich

Bi-Hung Peng

Jason Hsu

Vivian Tat

Chien-Te K. Tseng

Jingjing Song … (voir 20 de plus)

Yunsheng Yuan

Mingyuan Wu

Junjun Liu

Yali Yue

Xiaoju Zhang

Ziqi Wang

Yang He

Jing Li

Xiaodan Ni

Hongshi Li

Yuning Xiang

Yanlin Bian

Baohong Zhang

Haiyang Yin

Dimiter S. Dimitrov

John Gilly

Lei Han

Hua Jiang

Yueqing Xie

Jianwei Zhu

Owing to the ongoing mutation of SARS-CoV-2, the vast majority of therapeutic antibodies developed in the early stages have lost their neutr… (voir plus)alizing effects. Here, we have developed neutralizing antibodies, including 8G3 isolated from patients infected with the wild-type SARS-CoV-2 and its mutants from computational rational design. Following the mutations of 8G3 through computational technology, the neutralizing activity of the antibody was enhanced by approximately 1,500-fold. Our experimental results offer a case study for the optimization of neutralizing antibodies against SARS-CoV-2 guided by computational technology.

2025-02-04

Proceedings of the National Academy of Sciences (publié)

Rapid restoration of potent neutralization activity against the latest Omicron variant JN.1 via AI rational design and antibody engineering

Yunji Liao

Hang Ma

Zhenyu Wang

Shusheng Wang

Yang He

Yunsong Chang

Huifang Zong

Haoneng Tang

Lei Wang

Yong Ke

Huiyu Cai

Ping Li

Yunsheng Yuan

Aleksandra Drelich

Bi-Hung Peng

Jason Hsu

Vivian Tat

Chien-Te K. Tseng

Jingjing Song … (voir 22 de plus)

Yunsheng Yuan

Mingyuan Wu

Junjun Liu

Yali Yue

Xiaoju Zhang

Ziqi Wang

Yang He

Jing Li

Xiaodan Ni

Hongshi Li

Yuning Xiang

Yanlin Bian

Baohong Zhang

Haiyang Yin

Dimiter S. Dimitrov

John Gilly

Lei Han

Hua Jiang

Yueqing Xie

Jianwei Zhu

Yueqing Xie

Jianwei Zhu

The rapid evolution of the viral genome has led to the continual generation of new variants of SARS-CoV-2. Developing antibody drugs with br… (voir plus)oad-spectrum and high efficiency is a long-term task. It is promising but challenging to develop therapeutic neutralizing antibodies (nAbs) through in vitro evolution based on antigen–antibody binding interactions. From an early B cell antibody repertoire, we isolated antibody 8G3 that retains its nonregressive neutralizing activity against Omicron BA.1 and various other strains in vitro. 8G3 protected ACE2 transgenic mice from BA.1 and WA1/2020 virus infection without adverse clinical manifestations and completely cleared viral load in the lungs. Similar to most IGHV3–53 antibodies, the binding sites of 8G3 and ACE2 largely overlap, enabling competition with ACE2 for binding to RBD. By comprehensively considering the binding free energy changes of the antigen–antibody complexes, the biological environment of their interactions, and the evolutionary direction of the antibodies, we were able to select 50 mutants. Among them, 11 were validated by experiments showing better neutralizing activities. Further, a combination of four mutations were identified in 8G3 that increased its neutralization potency against JN.1, the latest Omicron mutant, by approximately 1,500-fold, and one of the mutations led to an improvement in activity against multiple variants to a certain extent. Together, we established a procedure of rapid selection of neutralizing antibodies with potent SARS-CoV-2 neutralization activity. Our results provide a reference for engineering neutralizing antibodies against future SARS-CoV-2 variants and even other pandemic viruses.

2025-02-04

Proceedings of the National Academy of Sciences (publié)

Fully-Inductive Node Classification on Arbitrary Graphs

Hesham Mostafa

Michael Bronstein

One fundamental challenge in graph machine learning is generalizing to new graphs. Many existing methods following the inductive setup can g… (voir plus)eneralize to test graphs with new structures, but assuming the feature and label spaces remain the same as the training ones. This paper introduces a fully-inductive setup, where models should perform inference on arbitrary test graphs with new structures, feature and label spaces. We propose GraphAny as the first attempt at this challenging setup. GraphAny models inference on a new graph as an analytical solution to a LinearGNN, which can be naturally applied to graphs with any feature and label spaces. To further build a stronger model with learning capacity, we fuse multiple LinearGNN predictions with learned inductive attention scores. Specifically, the attention module is carefully parameterized as a function of the entropy-normalized distance features between pairs of LinearGNN predictions to ensure generalization to new graphs. Empirically, GraphAny trained on a single Wisconsin dataset with only 120 labeled nodes can generalize to 30 new graphs with an average accuracy of 67.26%, surpassing not only all inductive baselines, but also strong transductive methods trained separately on each of the 30 test graphs.

2025-01-21

ICLR.cc/2025/Conference (poster)

GlycanML: A Multi-task and Multi-structure Benchmark for Glycan Machine Learning

Minghao Xu

Yunteng Geng

Yihang Zhang

Ling Yang

Wentao Zhang

Glycans are basic biomolecules and perform essential functions within living organisms. The rapid increase of functional glycan data provide… (voir plus)s a good opportunity for machine learning solutions to glycan understanding. However, there still lacks a standard machine learning benchmark for glycan property and function prediction. In this work, we fill this blank by building a comprehensive benchmark for Glycan Machine Learning (GlycanML). The GlycanML benchmark consists of diverse types of tasks including glycan taxonomy prediction, glycan immunogenicity prediction, glycosylation type prediction, and protein-glycan interaction prediction. Glycans can be represented by both sequences and graphs in GlycanML, which enables us to extensively evaluate sequence-based models and graph neural networks (GNNs) on benchmark tasks. Furthermore, by concurrently performing eight glycan taxonomy prediction tasks, we introduce the GlycanML-MTL testbed for multi-task learning (MTL) algorithms. Also, we evaluate how taxonomy prediction can boost other three function prediction tasks by MTL. Experimental results show the superiority of modeling glycans with multi-relational GNNs, and suitable MTL methods can further boost model performance. We provide all datasets and source codes at https://github.com/GlycanML/GlycanML and maintain a leaderboard at https://GlycanML.github.io/project

2025-01-21

ICLR.cc/2025/Conference (poster)

Structure Language Models for Protein Conformation Generation

Stephen Z. Lu

Hongyu Guo

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is cru… (voir plus)cial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

2025-01-21

ICLR.cc/2025/Conference (poster)

JUNO sensitivity to invisible decay modes of neutrons

Juno Collaboration Angel Abusleme

Angel Abusleme

Thomas Adam

Kai Adamowicz

Shakeel Ahmad

Rizwan Ahmed

Sebastiano Aiello

Fengpeng An

Qi An

Giuseppe Andronico

Nikolay Anfimov

Vito Antonelli

Tatiana Antoshkina

João Pedro Athayde Marcondes de André

Didier Auguste

Weidong Bai

Nikita Balashov

Wander Baldini

Andrea Barresi

Davide Basilico … (voir 648 de plus)

Eric Baussan

Marco Bellato

Marco Beretta

Antonio Bergnoli

Daniel Bick

Lukas Bieger

Svetlana Biktemerova

Thilo Birkenfeld

Iwan Blake

Simon Blyth

Anastasia Bolshakova

Mathieu Bongrand

Dominique Breton

Augusto Brigatti

Riccardo Brugnera

Riccardo Bruno

Antonio Budano

Jose Busto

Anatael Cabrera

Barbara Caccianiga

Hao Cai

Xiao Cai

Yanke Cai

Zucong Cai

Zhiyan Cai

Stéphane Callier

Steven Calvez

Antonio Cammi

Agustin Campeny

Chuanya Cao

Guofu Cao

Jun Cao

Rossella Caruso

Cédric Cerna

Vanessa Cerrone

Jinfan Chang

Yun Chang

Auttakit Chatrabhuti

Chao Chen

Guoming Chen

Pingping Chen

Shaomin Chen

Xin Chen

Yiming Chen

Yixue Chen

Yu Chen

Zelin Chen

Zhangming Chen

Zhiyuan Chen

Zikang Chen

Jie Cheng

Yaping Cheng

Yu Chin Cheng

Yuanyuan Zhang

Alexander Chepurnov

Alexey Chetverikov

Davide Chiesa

Pietro Chimenti

Yen-Ting Chin

Po-Lin Chou

Ziliang Chu

Artem Chukanov

Gérard Claverie

Catia Clementi

Barbara Clerbaux

Marta Colomer Molla

Selma Conforti Di Lorenzo

Alberto Coppi

Daniele Corti

Simon Csakli

Chenyang Cui

Flavio Dal Corso

Olivia Dalager

Jaydeep Datta

Christophe De La Taille

C. Taille

Zhi Deng

Ziyan Deng

Xiaoyu Ding

Xuefeng Ding

Yayun Ding

Bayu Dirgantara

Carsten Dittrich

Sergey Dmitrievsky

Tadeas Dohnal

Dmitry Dolzhikov

Georgy Donchenko

Jianmeng Dong

Evgeny Doroshkevich

Wei Dou

Marcos Dracos

Frédéric Druillole

Ran Du

S. X. Du

Yujie Duan

Katherine Dugas

Stefano Dusini

Hongyue Duyang

Jessica Eck

Timo Enqvist

Andrea Fabbri

Ulrike Fahrendholz

Lei Fan

Jian Fang

W. X. Fang

Dmitry Fedoseev

Haiping Peng

Li-Cheng Feng

Qichun Feng

Federico Ferraro

Amélie Fournier

Fritsch Fritsch

Haonan Gan

Feng Gao

Alberto Garfagnini

Arsenii Gavrikov

Marco Giammarchi

Nunzio Giudice

Maxim Gonchar

G. Gong

Hui Gong

Guanghua Gong

Yuri Gornushkin

Marco Grassi

Maxim Gromov

Vasily Gromov

Minghao Gu

Xiang Zhou

Xiaofei Gu

Yunting Gu

Mengyun Guan

Yu Gu

Yuduo Guan

Nunzio Guardone

Rosa Maria Guizzetti

Cong Guo

Wanlei Guo

Caren Hagner

Hechong Han

Ran Han

Yang Han

Jinhong He

Miao He

Wei He

Xinhai He

Tobias Heinz

Patrick Hellmuth

Rafael Herrera

Yuenkeung Hor

Shaojing Hou

Yee Hsiung

Bei-Zhen Hu

Hang Hu

Jun Hu

Peng Hu

Shouyang Hu

T. Hu

Yuxiang Hu

Zhuojun Hu

Guihong Huang

Hanxiong Huang

Jinhao Huang

Jun-Hao Huang

Xin Huang

Kaixuan Huang

Shengheng Huang

Wenhao Huang

X. T. Huang

Yongbo Huang

Jiaqi Hui

Lei Huo

Wenju Huo

Cédric Huss

Safeer Hussain

Leonard Imbert

Ara Ioannisian

Roberto Isocrate

Arshak Jafar

Beatrice Jelmini

Ignacio Jeria

Xiaolu Ji

Huihui Jia

Junji Jia

Siyu Jian

Cailian Jiang

Di Jiang

Guangzheng Jiang

Wei Jiang

Xiaoshan Jiang

Xiaozhao Jiang

Yixuan Jiang

Xiang Jing

Cécile Jollet

Li Kang

Rebin Karaparabil

Narine Kazarian

Ali Khan

Amina Khatun

Khanchai Khosonthongkee

Denis Korablev

Konstantin Kouzakov

Alexey Krasnoperov

Sergey Kuleshov

Sindhujha Kumaran

Nikolay Kutovskiy

Loïc Labit

Tobias Lachenmaier

Haojing Lai

Cecilia Landini

Sébastien Leblanc

Frederic Lefevre

Rupert Leitner

Jason Leung

Demin Li

Yi Wang

Fule Li

Fei Li

Gaosong Li

Hongjian Li

Huang Li

Jiajun Li

Min Li

Nan Li

Qingjiang Li

Ruhui Li

Rui Li

Shanfeng Li

Shuo Li

Tao Li

Teng Li

Weidong Li

Weiguo Li

Xiaomei Li

Xiao-Nan Li

Xinglong Li

Yi Li

Yichen Li

Yufeng Li

Zhaohan Li

Zhibing Li

Ziyuan Li

Zonghai Li

An-An Liang

Hao Liang

Jiaming Yan

Yilin Liao

Jiajun Liao

Y. P. Liao

Ayut Limphirat

Guey-Lin Lin

Yuzhong Liao

Shengxin Lin

Tao Lin

Jiajie Ling

Xin Ling

Ivano Lippi

Caimei Liu

Yang Liu

Fengcheng Liu

Haidong Liu

Haotian Liu

Hongbang Liu

Hongjuan Liu

Hongtao Liu

Hongyang Liu

Jianglai Liu

Jiaxi Liu

Jinchang Liu

Min Liu

Qian Liu

Qin Liu

Runxuan Liu

Sheng Liu

Shubin Liu

Shulin Liu

Xiaowei Liu

Xiwen Liu

Xuewei Liu

Yankai Liu

Zhen Liu

Lorenzo Loi

Alexey Lokhov

Paolo Lombardi

Claudio Lombardo

Kai Loo

Chuan Lu

Haoqi Lu

Jingbin Lu

Junguang Lu

Meishu Lu

Peizhi Lu

Shuxian Du

Xianguo Lu

Bayarto Lubsandorzhiev

Sultim Lubsandorzhiev

Livia Ludhova

Arslan Lukanov

Feng Luo

Guang Luo

Fengjiao Luo

Jianyi Luo

Shu Luo

Wuming Luo

Xiaojie Luo

Vladimir Lyashuk

Biao Ma

Bing Ma

Qiumei Ma

Bangzheng Ma

Si Ma

Xiaoyan Ma

Xubo Ma

Jihane Maalmi

Jingyu Mai

Marco Malabarba

Yury Malyshkin

Roberto Carlos Mandujano

Fabio Mantovani

Xin Mao

Yajun Mao

S. Mari

Filippo Marini

Stefano M. Mari

Agnese Martini

Matthias Mayer

Davit Mayilyan

Ints Mednieks

Yu Meng

Anita Meraviglia

Anselmo Meregaglia

Emanuela Meroni

Lino Miramonti

Nikhil Mohan

Michele Montuschi

Cristobal Morales Reveco

Massimiliano Nastasi

Dmitry V. Naumov

Elena Naumova

Diana Navas-Nicolas

Igor Nemchenok

Minh Thuan Nguyen Thi

Alexey Nikolaev

Feipeng Ning

Zhe Ning

Hiroshi Nunokawa

Lothar Oberauer

Juan Pedro Ochoa-Ricoux

Alexander Olshevskiy

Domizia Orestano

Fausto Ortica

Rainer Othegraven

Alessandro Paoloni

George Parker

Sergio Parmeggiano

Achilleas Patsias

Y. P. Pei

Luca Pelicci

Yatian Pei

Anguo Peng

Zhaoyuan Peng

Elisa Percalli

Willy Perrin

Frédéric Perrot

P. Petitjean

Fabrizio Petrucci

Pierre-Alexandre Petitjean

Oliver Pilarczyk

Luis Felipe Piñeres Rico

Artyom Popov

Pascal Poussot

Ezio Previtali

Fazhi Qi

M. Qi

Xiaohui Qi

Sen Qian

Xiangyang Qian

Zhen Qian

Hao Qiao

Xiaohui Qian

Zhonghua Qin

Shoukang Qiu

Manhao Qu

Z. Qu

Gioacchino Ranucci

A. Re

Zhenning Qu

Abdel Rebii

Mariia Redchuk

Alessandra Re

Gioele Reina

Bin Ren

Jie Ren

Yuhan Ren

Barbara Ricci

Komkrit Rientong

Mariam Rifai

Mathieu Roche

Narongkiat Rodphai

Aldo Romani

Bedřich Roskovec

Xichao Ruan

Arseniy Rybnikov

Andrey Sadovsky

Paolo Saggese

Deshan Sandanayake

Anut Sangka

Giuseppe Sava

Utane Sawangwit

Michaela Schever

Cédric Schwab

Konstantin Schweizer

Alexandr Selyunin

Andrea Serafini

Mariangela Settimo

Junyu Shao

Vladislav Sharov

Hexi Shi

Jingyan Shi

Yanan Shi

Vitaly Shutov

Andrey Sidorenkov

Fedor Šimkovic

Apeksha Singhal

Chiara Sirignano

Jaruchit Siripak

Monica Sisti

Mikhail Smirnov

Oleg Smirnov

Sergey Sokolov

Julanan Songwadhana

Boonrucksar Soonthornthum

Albert Sotnikov

Warintorn Sreethawong

Achim Stahl

Luca Stanco

Konstantin Stankevich

Hans Steiger

Jochen Steinmann

Tobias Sterr

M. Stock

Virginia Strati

Matthias Raphael Stock

Michail Strizh

Alexander Studenikin

Aoqi Su

Jun Su

G. X. Sun

Shifeng Sun

Xilei Sun

Yongjie Sun

Guangbao Sun

Yongzhao Sun

Zhengyang Sun

Narumon Suwonjandee

Akira Takenaka

Xiaohan Tan

Jing-Yu Tang

Qiang Tang

Quan Tang

Jingzhe Tang

Xiao Tang

Vidhya Thara Hariharan

Igor Tkachev

Tomas Tmej

M. Torri

Andrea Triossi

Wladyslaw Trzaska

Marco Danilo Claudio Torri

Y. Tung

Cristina Tuve

Nikita Ushakov

Vadim Vedin

Yu-Chen Tung

Carlo Venettacci

Giuseppe Verde

Maxim Vialkov

Benoit Viaud

Cornelius Moritz Vollbrecht

Katharina von Sturm

Vit Vorobel

Dmitriy Voronin

Lucia Votano

Pablo Walker

Caishen Wang

Chung-Hsiang Wang

En Wang

Guoli Wang

Yuekun Heng

Jian Wang

Jun Wang

Li Wang

Lucinda W. Wang

Meng Wang

Mingyuan Wang

Qianchuan Wang

Lu Wang

Ruiguang Wang

Sibo Wang

Siguang Wang

Wei Wang

Wenshuai Wang

Xi Wang

Xiangyue Wang

Yangfu Wang

Yaoguang Wang

Yifang Wang

Yong Wang

Yuyi Wang

Zhe Wang

Z. Wang

Zhimin Wang

Apimook Watcharangkool

Wei Wei

Wenlu Wei

Yadong Wei

Yuehuan Wei

Liangjian Wen

Jun Weng

Christopher Wiebusch

Rosmarie Wirth

Chengxin Wu

Diru Wu

Qun Wu

Yinhui Wu

Yiyang Wu

Zhi Wu

Michael Wurm

Jacques Wurtz

Christian Wysotzki

Yufei Xi

Dongmei Xia

Shishen Xian

Ziqian Xiang

Fei Xiao

Xiang Xiao

Xiaochuan Xie

Yijun Xie

Yuguang Xie

Zhao Xin

Zhizhong Xing

Benda Xu

Cheng Xu

Donglian Xu

Fanrong Xu

Hangkun Xu

Jiayang Xu

Jilei Xu

Jing Xu

Jinghuan Xu

Meihang Xu

Xunjie Xu

Yin Xu

Yu Xu

Baojun Yan

Qiyu Yan

Taylor Yan

Xiongbo Yan

Yupeng Yan

Changgen Yang

Chengfeng Yang

Fengfan Yang

Jie Yang

Lei Yang

Pengfei Yang

Xiaoyu Yang

Yifan Yang

Yixiang Yang

Zekun Yang

Haifeng Yao

Jiaxuan Ye

Mei Ye

Ziping Ye

Frédéric Yermia

Zhengyun You

Boxiang Yu

Chiye Yu

Chunxu Yu

Guojun Yu

Hongzhao Yu

Miao Yu

Xianghui Yu

Zeyuan Yu

Zezhong Yu

Cenxi Yuan

Chengzhuo Yuan

Zhenxiong Yuan

Baobiao Yue

Noman Zafar

Kirill Zamogilnyi

Vitalii Zavadskyi

Fanrui Zeng

Shan Zeng

Tingxuan Zeng

Yuda Zeng

Liang Zhan

Aiqiang Zhang

Bin Zhang

Binting Zhang

Feiyang Zhang

Hangchang Zhang

Haosen Zhang

Honghao Zhang

Jiawen Zhang

Jie Zhang

Jingbo Zhang

Jinnan Zhang

Junwei Zhang

Lei Zhang

Ping Zhang

Qingmin Zhang

Shiqi Zhang

Shu Zhang

Shuihan Zhang

Siyuan Zhang

Tao Zhang

Xiaomei Zhang

Xin Zhang

Xuantong Zhang

Yibing Zhang

Yinhong Zhang

Yiyu Zhang

Yongpeng Zhang

Yu Zhang

Yumei Zhang

Zhenyu Zhang

Zhijian Zhang

Jie Zhao

Rong Zhao

Runze Zhao

Shujun Zhao

Tianhao Zhao

Hua Zheng

Yangheng Zheng

Jing Zhou

Li Zhou

Nan Zhou

Shun Zhou

Tong Zhou

Xing Zhou

Jingsen Zhu

Kangfu Zhu

Kejun Zhu

Zhihang Zhu

Bo Zhuang

Honglin Zhuang

Liang Zong

Jiaheng Zou

2025-01-03

The European Physical Journal C (publié)

arxiv.org

A Text-guided Protein Design Framework

Shengchao Liu

Yutao Zhu

Yanjing Li

Zhuoxinran Li

Jiarui Lu

Zhao Xu

Weili Nie

Anthony Gitter

Chaowei Xiao

Arvind Ramanathan

Hongyu Guo

Anima Anandkumar

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowled… (voir plus)ge curated by humans in the text format describing proteins' high-level functionalities. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP which aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that creates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We quantitatively verify the effectiveness of ProteinDT on three challenging tasks: (1) over 90% accuracy for text-guided protein generation; (2) best hit ratio on 12 zero-shot text-guided protein editing tasks; (3) superior performance on four out of six protein property prediction benchmarks.

2024-12-31

Nat. Mac. Intell. (publié)

arxiv.org

Sliding ferroelectric memories and synapses based on rhombohedral-stacked bilayer MoS2

Xiuzhen Li

Biao Qin

Yaxian Wang

Yue Xi

Zhiheng Huang

Mengze Zhao

Yalin Peng

Zitao Chen

Zitian Pan

Jundong Zhu

Chenyang Cui

Rong Yang

Wei Yang

Sheng Meng

Dongxia Shi

Xuedong Bai

Can Liu

Na Li

Kaihui Liu … (voir 3 de plus)

Kai-Wen Liu

Luojun Du

Guangyu Zhang

2024-12-29

Nature Communications (publié)

arxiv.org

Correction: CEPC Technical Design Report: Accelerator

Waleed Abdallah

Tiago CarlosAdorno de Freitas

Konstantin Afanaciev

Shakeel Ahmad

Ijaz Ahmed

Xiaocong Ai

Abid Aleem

Wolfgang Altmannshofer

Fabio Alves

Weiming An

Rui An

Daniele Paolo Anderle

D. Anderle

Stefan Antusch

Yasuo Arai

Andrej Arbuzov

Abdesslam Arhrib

A. Arhrib

Mustafa Ashry

Sha Bai … (voir 1076 de plus)

Yu Bai

Yang Bai

Vipul Bairathi

Csaba Balazs

Philip Bambade

Yong Ban

Triparno Bandyopadhyay

Shou-Shan Bao

Desmond P. Barber

Ays¸e Bat

Varvara Batozskaya

Subash Chandra Behera

Alexander Belyaev

Michele Bertucci

Xiao-Jun Bi

Yuanjie Bi

Tianjian Bian

Tingting Bian

Fabrizio Bianchi

Thomas Bieko¨tter

Michela Biglietti

Shalva Bilanishvili

Deng Binglin

Lingling Men

Denis Bodrov

Anton Bogomyagkov

Serge Bondarenko

Stewart Boogert

Maarten Boonekamp

Marcello Borri

M. Borri

Angelo Bosotti

Vincent Boudry

Mohammed Boukidi

Igor Boyko

Ivanka Bozovic

Giuseppe Bozzi

Jean-Claude Brient

J. Brient

Anastasiia Budzinskaya

Masroor Bukhari

Vladimir Bytev

Giacomo Cacciapaglia

Hua Cai

Wenyong Cai

Wujun Cai

Yijian Cai

Yizhou Cai

Yuchen Cai

Haiying Cai

Huacheng Cai

Lorenzo Calibbi

Junsong Cang

Guofu Cao

Jianshe Cao

Antoine Chance

Xuejun Chang

Yue Chang

Zhe Chang

Xinyuan Chang

Wei Chao

Auttakit Chatrabhuti

Yimin Che

Yuzhi Che

Bin Chen

Danping Chen

Fuqing Chen

Fusan Chen

Gang Chen

Guoming Chen

Hua-Xing Chen

Huirun Chen

Jinhui Chen

Ji-Yuan Chen

Kai Chen

Mali Chen

Mingjun Chen

Mingshui Chen

Nanying Chen

Shanhong Chen

Shanzhen Chen

Shao-Long Chen

Shaomin Chen

Shiqiang Chen

Tianlu Chen

Wei Chen

Xiang Chen

Xiaoyu Chen

Xin Chen

Xun Chen

Xurong Chen

Ye Chen

Ying Chen

Yukai Chen

Zelin Chen

Zilin Chen

Boping Chen

Chunhui Chen

Haifeng Cheng

Huajie Cheng

Hok Chuen Cheng

Shan Cheng

Tongguang Cheng

Yunlong Chi

Pietro Chimenti

Wen Han Chiu

Guk Cho

Mingxing Chu

Ming-Chung Chu

X. Chu

Xiaotong Chu

Ziliang Chu

Guglielmo Coloretti

Andreas Crivellin

Hanhua Cui

Xiaohao Cui

Zhaoyuan Cui

B. D’Anzi

Brunella D’Anzi

Ling-Yun Dai

Xinchen Dai

Xuwen Dai

Antonio De Maria

Nicola De Filippis

Christophe De La Taille

Francesca De Mori

Chiara De Sio

Elisa Del Core

Shuangxue Deng

Wei Deng

Wei-Tian Deng

Zhi Deng

Ziyan Deng

Bhupal Dev

Tang Dewen

Biagio Di Micco

Ran Ding

Siqin Ding

Yadong Ding

Haiyi Dong

Jianing Dong

Jing Dong

Lan Dong

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Xu Dong

Yipei Dong

Yubing Dong

Milos Dordevic

Marco Drewes

Mingxuan Du

Qianqian Du

Xiaokang Du

Yanyan Du

Yong Du

Yunfei Du

Chun-Gui Duan

Zhe Duan

Yahor Dydyshka

Ulrik Egede

Walaa Elmetenawee

Yun Eo

Ka Yan Fan

Kuanjun Fan

Yunyun Fan

Bo Fang

Shuangshi Fang

Yuquan Fang

Ada Farilla

Riccardo Farinelli

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Xu Feng

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Etienne Forest

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Harald Fox

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Jinyu Fu

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Xia Guo

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Zhi-Hui Guo

Alejandro Gutie´rrez-Rodríguez

Seungkyu Ha

Noman Habib

Jan Hajer

Francois Hammer

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Huayong Han

Jifeng Han

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Liang Han

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Ruixiong Han

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Yuanying Han

T. T. Han

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Xiqing Hao

Qiang Zhao

Chuanqi He

Dayong He

Dongbing He

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Hong-Jian He

Jibo He

Jun He

Longyan He

Xiang He

Xiao-Gang He

Zhenqiang He

Klaus Heinemann

Sven Heinemeyer

Yuekun Heng

María A. Herna´ndez-Ruíz

Jiamin Hong

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George W. S. Hou

Xiantao Hou

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Suen Hou

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Dake Hu

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Jun Hu

Kun Hu

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Yu Hu

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Ke Huang

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Yuanyuan Wei

Chen Huanyuan

Changgi Huh

Jiaqi Hui

Lihua Huo

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Kyuyeong Hwang

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Munawar Iqbal

Paul Jackson

Shahriyar Jafarzade

Haeun Jang

Seoyun Jang

Daheng Ji

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Qingping Ji

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Jun Jiang

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On Kim

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Tong Li

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Xiaoling Li

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Xiao-Nan Li

Xiaoping Li

Xiaoting Li

Xin Li

Xinqiang Li

Xuekang Li

Yang Li

Yanwei Li

Yiming Li

Ying Li

Ying-Ying Li

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Yonglin Li

Yufeng Li

Yuhui Li

Zhan Li

Zhao Li

Zhiji Li

Lingfeng Li

Jing Liang

Jinhan Liang

Zhijun Liang

Guangrui Liao

Hean Liao

Jiaming Yan

Fei Li

Libo Liao

Longzhou Liao

Yipu Liao

Ayut Limphirat

AyutLimphirat

Jiajun Liao

Tao Lin

Weiping Lin

Yufu Lin

Y. P. Liao

Yugen Lin

Beijiang Liu

Bo Liu

Danning Liu

Dong Liu

Fu-Hu Liu

Hongbang Liu

Huangcheng Liu

H. Liu

Huiling Liu

Jia Liu

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Kang Liu

Kun Liu

Mengyao Liu

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Shidong Liu

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Shubin Liu

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xiaoan Luo

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Shigeki Matsumoto

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Lingxin Meng

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Yuhui Miao

Mauro Migliorati

Lei Ming

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Arthur Moraes

Karabo Mosala

Ahmad Moursy

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Zhihui Mu

Nickolai Muchnoi

Daniel Muenstermann

Pankaj Munbodh

William John Murray

Jérôme Nanni

Dmitry Nanzanov

Changshan Nie

Sergei Nikitin

Feipeng Ning

Guozhu Ning

Jia-Shu Niu

Juan-Juan Niu

Yan Niu

Edward Khomotso Nkadimeng

Kazuhito Ohmi

Katsunobu Oide

Hideki Okawa

Mohamed Ouchemhou

Qun Ouyang

Daniele Paesani

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Stathes Paganis

Collette Pakuza

Jiangyang Pan

Juntong Pan

Tong Pan

Xiang Pan

Papia Panda

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Hua Pei

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Xinye Peng

Yuemei Peng

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M. Qi

Sen Qian

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Guangyou Qin

Jiajia Qin

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Guofeng Qu

Antonio Racioppi

Michael Ramsey-Musolf

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Tania Robens

Giancarlo Rossi

Manqi Ruan

Leonid Rumyantsev

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Renat Sadykov

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Juan Jose´ Sanz-Cillero

Miroslav Saur

Nishil Savla

Michael A. Schmidt

Daniele Sertore

Ron Settles

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Hua-Sheng Shao

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Chuang Shen

Hong-Fei Shen

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Shuqi Sheng

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Andrei Sidorenkov

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Weiping Wang

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Biao Wang

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Lian-Tao Wang

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Zirui Wang

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Tong Wang

Daihui Wei

Shujun Wei

Wei Wei

Xiaomin Wei

Yingjie Wei

Liangjian Wen

Xuejun Wen

Yufeng Wen

Martin White

Peter Williams

Zef Wolffs

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Baona Wu

Bobing Wu

Guanjian Wu

Jinfei Wu

Lei Wu

Lina Wu

Linghui Wu

Minlin Wu

Peiwen Wu

Qi Wu

Qun Wu

Tianya Wu

Xiang Wu

Xiaohong Wu

Xing-Gang Wu

Xuehui Wu

Yaru Wu

Yongcheng Wu

Yuwen Wu

Zhi Wu

Xin Wu

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Ligang Xia

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Felix Yu

Bingrong Yu

Changzheng Yuan

Li Yuan

Xing-Bo Yuan

Youjin Yuan

Junhui Yue

Qian Yue

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Un Nisa Zaib

Riccardo Zanzottera

Min Zeng

Jian Zhai

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Xi-Jie Zhan

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Di Zhang

Guangyi Zhang

Hao Zhang

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Hui Zhang

Jian Wang

Jianzhong Zhang

Jiehao Zhang

Jielei Zhang

Jingru Zhang

Jinxian Zhang

Junsong Zhang

Junxing Zhang

Lei Zhang

Liang Zhang

Licheng Zhang

Liming Zhang

Linhao Zhang

Mengchao Zhang

Shulei Zhang

Wan Zhang

Wenchao Zhang

Xiangzhen Zhang

Xiaomei Zhang

Xiaoming Zhang

Xiaoxu Zhang

Xiaoyu Zhang

Xuantong Zhang

Xueyao Zhang

Yang Zhang

Yanxi Zhang

Yao Zhang

Ying Zhang

Yixiang Zhang

Yizhou Zhang

Yongchao Zhang

Yu Zhang

Yuan Zhang

Yujie Zhang

Yulei Zhang

Yumei Zhang

Yunlong Zhang

Zhandong Zhang

Zhaoru Zhang

Zhen-Hua Zhang

Zhenyu Zhang

Zhichao Zhang

Zhi-Qing Zhang

Zhuo Zhang

Zhiqing Zhang

Cong Zhang

Tianliang Zhang

Luyan Zhang

Guang Zhao

Hongyun Zhao

Jie Zhao

Jingxia Zhao

Jingyi Zhao

Ling Zhao

Luyang Zhao

Mei Zhao

Minggang Zhao

Mingrui Zhao

Ruiguang Zhao

Tongxian Zhao

Yaliang Zhao

Ying Zhao

Yue Zhao

Zhiyu Zhao

Zhuo Zhao

Alexey Zhemchugov

Hongjuan Zheng

Jinchao Zheng

Liang Zheng

Ran Zheng

shanxi zheng

Xu-Chang Zheng

Wang Zhile

Weicai Zhong

Yi-Ming Zhong

Chen Zhou

Daicui Zhou

Jianxin Zhou

Jing Zhou

Na Zhou

Qi-Dong Zhou

Shiyu Zhou

Shun Zhou

Sihong Zhou

Xiang Zhou

Xingyu Zhou

Yang Zhou

Yong Zhou

Yu-Feng Zhou

Zusheng Zhou

Demin Zhou

Dechong Zhu

Hongbo Zhu

Huaxing Zhu

Jingya Zhu

Kai Zhu

Pengxuan Zhu

Ruilin Zhu

Xianglei Zhu

Yingshun Zhu

Yongfeng Zhu

Xiao Zhuang

Xuai Zhuang

Mikhail Zobov

Zhanguo Zong

Cong Zou

Hongying Zou

2024-12-15

Radiation Detection Technology and Methods (publié)

Cell ontology guided transcriptome foundation model

Manqi Zhou

Boyu Han

Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by… (voir plus) self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present **s**ingle **c**ell, **Cell**-**o**ntology guided TFM (scCello). We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses. Source code and model weights are available at https://github.com/DeepGraphLearning/scCello.

2024-12-10

Conference on Neural Information Processing Systems (Accept (spotlight))