Portrait of Jian Tang

Jian Tang

Core Academic Member
Canada CIFAR AI Chair
Associate Professor, HEC Montréal, Department of Decision Sciences
Adjunct Professor, Université de Montréal, Department of Computer Science and Operations Research
Founder, BioGeometry
Research Topics
Computational Biology
Deep Learning
Generative Models
Graph Neural Networks
Molecular Modeling

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

Collaborating researcher
PhD - Université de Montréal
Principal supervisor :
Research Intern - McGill University
PhD - Université de Montréal
Collaborating researcher - Carnegie Mellon University
PhD - Université de Montréal
PhD - Université de Montréal
Principal supervisor :
Collaborating researcher
PhD - Université de Montréal
PhD - Université de Montréal
PhD - Université de Montréal
PhD - Université de Montréal

Publications

The design and technology development of the JUNO central detector
Angel Abusleme
Thomas Adam
Shakeel Ahmad
Rizwan Ahmed
Sebastiano Aiello
Muhammad Akram
Abid Aleem
Tsagkarakis Alexandros
Fengpeng An
Qi An
Giuseppe Andronico
Nikolay Anfimov
Vito Antonelli
Tatiana Antoshkina
Burin Asavapibhop
J. D. de André
João Pedro Athayde Marcondes de André
Didier Auguste
Weidong Bai
Nikita Balashov … (see 616 more)
Wander Baldini
Andrea Barresi
Davide Basilico
Eric Baussan
Marco Bellato
Marco Beretta
Antonio Bergnoli
Daniel Bick
Thilo Birkenfeld
David Blum
Simon Blyth
Anastasia Bolshakova
Mathieu Bongrand
Clément Bordereau
Dominique Breton
Augusto Brigatti
Riccardo Brugnera
Riccardo Bruno
Antonio Budano
Jose Busto
Anatael Cabrera
Barbara Caccianiga
Hao Cai
Xiao Cai
Yanke Cai
Zhiyan Cai
Z. Cai
Stéphane Callier
Antonio Cammi
Agustin Campeny
Chuanya Cao
C. Cao
Guofu Cao
Jun Cao
Rossella Caruso
Cédric Cerna
Vanessa Cerrone
Chi Chan
Jinfan Chang
Yun Chang
Guoming Chen
Pingping Chen
Shaomin Chen
Yixue Chen
Yu Chen
Zhiyuan Chen
Zikang Chen
Jie Cheng
Yaping Cheng
Yu Chin Cheng
Yuanyuan Zhang
Alexander Chepurnov
Alexey Chetverikov
Davide Chiesa
Pietro Chimenti
Ziliang Chu
Artem Chukanov
Gérard Claverie
Catia Clementi
Barbara Clerbaux
Marta Colomer Molla
Selma Conforti Di Lorenzo
Alberto Coppi
Daniele Corti
Flavio Dal Corso
Olivia Dalager
Christophe De La Taille
Zhi Deng
Ziyan Deng
Wilfried Depnering
Marco Diaz
Xuefeng Ding
Yayun Ding
Bayu Dirgantara
Sergey Dmitrievsky
Tadeas Dohnal
Dmitry Dolzhikov
Georgy Donchenko
Jianmeng Dong
Evgeny Doroshkevich
Wei Dou
Marcos Dracos
Frédéric Druillole
Ran Du
S. X. Du
Shuxian Du
Stefano Dusini
Hongyue Duyang
Timo Enqvist
Andrea Fabbri
Ulrike Fahrendholz
Lei Fan
Jian Fang
Wenxing Fang
Marco Fargetta
Dmitry Fedoseev
Zhengyong Fei
Li-Cheng Feng
Qichun Feng
Federico Ferraro
Amélie Fournier
H. Gan
Haonan Gan
Feng Gao
Alberto Garfagnini
Arsenii Gavrikov
Marco Giammarchi
Nunzio Giudice
Maxim Gonchar
Guanghua Gong
Hui Gong
Yuri Gornushkin
Alexandre Göttel
A. Gottel
Marco Grassi
Maxim Gromov
Vasily Gromov
Minghao Gu
Xiaofei Gu
X. Gu
Yu Gu
Yunting Gu
Mengyun Guan
M. Guan
Yuduo Guan
Nunzio Guardone
Cong Guo
Wanlei Guo
Xinheng Guo
Yuhang Guo
Caren Hagner
Ran Han
Yang Han
Jiajun Hao
Miao He
Wei He
Tobias Heinz
Patrick Hellmuth
Yuekun Heng
Rafael Herrera
YuenKeung Hor
Y. Hor
Shaojing Hou
Yee Hsiung
Bei-Zhen Hu
Hang Hu
Jianrun Hu
Jun Hu
Shouyang Hu
Tao Hu
Yuxiang Hu
Zhuojun Hu
Guihong Huang
Hanxiong Huang
Kaixi Huang
Kaixuan Huang
Wenhao Huang
Xin Huang
Xingtao Huang
Yongbo Huang
Jiaqi Hui
Lei Huo
Wenju Huo
Cédric Huss
Safeer Hussain
Ara Ioannisian
Roberto Isocrate
Beatrice Jelmini
Ignacio Jeria
Xiaolu Ji
Huihui Jia
Junji Jia
Siyu Jian
Di Jiang
Wei Jiang
Xiaoshan Jiang
Xiaoping Jing
X. Jing
Cécile Jollet
Philipp Kampmann
Li Kang
Rebin Karaparambil
Narine Kazarian
Ali Khan
Amina Khatun
Khanchai Khosonthongkee
Denis Korablev
Konstantin Kouzakov
Alexey Krasnoperov
Nikolay Kutovskiy
Pasi Kuusiniemi
Tobias Lachenmaier
Cecilia Landini
Sébastien Leblanc
Victor Lebrin
Frederic Lefevre
Rui Li
Rupert Leitner
Jason Leung
Daozheng Li
Demin Li
Fei Li
Yi Wang
Fule Li
Gaosong Li
Huiling Li
Mengzhao Li
Min Li
Nan Li
Qingjiang Li
Ruhui Li
Ruiting Lei
Shanfeng Li
Tao Li
Teng Li
Weidong Li
Weiguo Li
Xiaomei Li
Xiaonan Li
Xinglong Li
Xiwen Li
Yi Li
Yichen Li
Yufeng Li
Zepeng Li
Zhaohan Li
Zhibing Li
Ziyuan Li
Zonghai Li
Hao Liang
Jiaming Yan
Jiajun Liao
Ayut Limphirat
Guey-Lin Lin
Shengxin Lin
Tao Lin
Jiajie Ling
Ivano Lippi
Caimei Liu
Yang Liu
Haidong Liu
Haotian Liu
Hongbang Liu
Hongjuan Liu
Hongtao Liu
Hui Liu
Jianglai Liu
Jinchang Liu
Min Liu
Qian Liu
Qin Liu
Runxuan Liu
Shubin Liu
Shulin Liu
Xiaowei Liu
Xiwen Liu
Yan Liu
Yunzhe Liu
Alexey Lokhov
Paolo Lombardi
Claudio Lombardo
Kai Loo
Chuan Lu
Haoqi Lu
Jingbin Lu
Junguang Lu
Peizhi Lu
Shuxiang Lu
Bayarto Lubsandorzhiev
Sultim Lubsandorzhiev
Livia Ludhova
Arslan Lukanov
Daibin Luo
F. Luo
Fengjiao Luo
Guang Luo
Jianyi Luo
Shu Luo
Wuming Luo
Xiaojie Luo
Xiaolan Luo
Vladimir Lyashuk
B. Ma
Bing Ma
Bangzheng Ma
R. Q. Ma
Si Ma
Qiumei Ma
Xiaoyan Ma
Xubo Ma
Jihane Maalmi
Marco Magoni
Jingyu Mai
Yury Malyshkin
Roberto Carlos Mandujano
Fabio Mantovani
Xin Mao
Yajun Mao
S. Mari
Stefano M. Mari
Filippo Marini
Agnese Martini
Matthias Mayer
Davit Mayilyan
Ints Mednieks
Yu Meng
Anita Meraviglia
Anselmo Meregaglia
Emanuela Meroni
David Meyhöfer
Mauro Mezzetto
Lino Miramonti
Paolo Montini
Michele Montuschi
Axel Muller
M. Nastasi
Massimiliano Nastasi
Dmitry V. Naumov
Elena Naumova
Diana Navas-Nicolas
Igor Nemchenok
Minh Thuan Nguyen Thi
Alexey Nikolaev
F. Ning
Feipeng Ning
Zhe Ning
Hiroshi Nunokawa
Lothar Oberauer
Juan Pedro Ochoa-Ricoux
Alexander Olshevskiy
Domizia Orestano
Fausto Ortica
Rainer Othegraven
A. Paoloni
Alessandro Paoloni
Sergio Parmeggiano
Y. P. Pei
Yatian Pei
Luca Pelicci
Anguo Peng
Yu Peng
Haiping Peng
Yuefeng Peng
Z-R Peng
Frédéric Perrot
Zhaoyuan Peng
P. Petitjean
Pierre-Alexandre Petitjean
Fabrizio Petrucci
Oliver Pilarczyk
Luis Felipe Piñeres Rico
Artyom Popov
Pascal Poussot
Ezio Previtali
Fazhi Qi
Ming Qi
Sen Qian
Xiaohui Qian
Zhen Qian
Hao Qiao
Zhonghua Qin
S. Qiu
Shoukang Qiu
Gioacchino Ranucci
Reem Rasheed
A. Re
Alessandra Re
Abdel Rebii
Mariia Redchuk
Bin Ren
Jie Ren
Barbara Ricci
Mariam Rifai
Mathieu Roche
Narongkiat Rodphai
Aldo Romani
Bedřich Roskovec
Xichao Ruan
Arseniy Rybnikov
Andrey Sadovsky
Paolo Saggese
Simone Sanfilippo
Anut Sangka
Utane Sawangwit
Julia Sawatzki
Michaela Schever
Cédric Schwab
Konstantin Schweizer
Alexandr Selyunin
Andrea Serafini
Giulio Settanta
M. Settimo
Zhuang Shao
Mariangela Settimo
V. Sharov
Arina Shaydurova
Vladislav Sharov
Jingyan Shi
Yanan Shi
Vitaly Shutov
Andrey Sidorenkov
Fedor Šimkovic
Chiara Sirignano
Jaruchit Siripak
Monica Sisti
Maciej Slupecki
Mikhail Smirnov
Oleg Smirnov
Thiago Sogo-Bezerra
Sergey Sokolov
Wuying Song
Julanan Songwadhana
Boonrucksar Soonthornthum
Albert Sotnikov
Ondřej Šrámek
Warintorn Sreethawong
Achim Stahl
Luca Stanco
Konstantin Stankevich
Dušan Štefánik
Hans Steiger
Jochen Steinmann
Tobias Sterr
M. Stock
Virginia Strati
Matthias Raphael Stock
Alexander Studenikin
Jun Su
Shifeng Sun
Xilei Sun
Yongjie Sun
Yongzhao Sun
Zhengyang Sun
Narumon Suwonjandee
Michal Szelezniak
Akira Takenaka
Qiang Tang
Quan Tang
Xiao Tang
Vidhya Thara Hariharan
Eric Theisen
Alexander Tietzsch
Igor Tkachev
Tomas Tmej
M. Torri
Francesco Tortorici
Marco Danilo Claudio Torri
K. Treskov
Andrea Triossi
Konstantin Treskov
Riccardo Triozzi
Giancarlo Troni
Wladyslaw Trzaska
Y. Tung
Cristina Tuve
Nikita Ushakov
Yu-Chen Tung
Vadim Vedin
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
Derun Wang
En Wang
Guoli Wang
Jian Wang
Jun Wang
Lucinda W. Wang
Meng Wang
Ruiguang Wang
Lu Wang
Siguang Wang
Wei Wang
Wenshuai Wang
Xi Wang
Xiangyue Wang
Yangfu Wang
Yaoguang Wang
Yi Xing Wang
Yifang Wang
Yuanqing Wang
Yuman Wang
Zhe Wang
Zheng Wang
Zhimin Wang
Apimook Watcharangkool
Wei Wei
Wenlu Wei
Yadong Wei
K. Wen
Kaile Wen
Jun Weng
Christopher Wiebusch
Rosmarie Wirth
Bjoern Wonsak
Liangjian Wen
Diru Wu
Qun Wu
Shuai Wu
Zhi Wu
Michael Wurm
Jacques Wurtz
Christian Wysotzki
Yufei Xi
Dongmei Xia
Xiang Xiao
Xiaochuan Xie
Yuguang Xie
Zhangquan Xie
Zhao Xin
Zhizhong Xing
Benda Xu
Cheng Xu
Donglian Xu
Fanrong Xu
Hangkun Xu
Jilei Xu
Jing Xu
Meihang Xu
Yin Xu
Yu Xu
Baojun Yan
Qiyu Yan
Taylor Yan
Wenqi Yan
Xiongbo Yan
Yupeng Yan
Changgen Yang
Chengfeng Yang
Jie Yang
Lei Yang
Xiaoyu Yang
Yifan 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
Jing-Yu Tang
Zhenxiong Yuan
Baobiao Yue
Noman Zafar
Vitalii Zavadskyi
Shan Zeng
Tingxuan Zeng
Yuda Zeng
Liang Zhan
Aiqiang Zhang
Bin Zhang
Binting Zhang
Feiyang Zhang
Honghao Zhang
Jiawen Zhang
Jie Zhang
Jin Zhang
Jingbo Zhang
Jinnan Zhang
Mohan Zhang
Peng Zhang
Qingmin Zhang
Shiqi Zhang
Shu Zhang
Tao Zhang
Xiaomei Zhang
Xin Zhang
Xuantong Zhang
Yinhong Zhang
Yiyu Zhang
Yongpeng Zhang
Yu Zhang
Yumei Zhang
Zhenyu Zhang
Zhijian Zhang
Jie Zhao
Rong Zhao
Runze Zhao
Shujun Zhao
Dongqin Zheng
Hua Zheng
Yangheng Zheng
Weirong Zhong
Jing Zhou
Li Zhou
Nan Zhou
Shun Zhou
Tong Zhou
Xiang Zhou
Jingsen Zhu
Kangfu Zhu
Kejun Zhu
Zhihang Zhu
Bo Zhuang
Honglin Zhuang
Liang Zong
Jiaheng Zou
Sebastian Zwickel
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 … (see 1080 more)
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
T. 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
Ning 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
H. Cheng
Huajie Cheng
Hok Chuen Cheng
Shan Cheng
Tongguang Cheng
Yunlong Chi
Pietro Chimenti
Wen Han Chiu
Guk Cho
M. 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
W. 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
Mingyi Dong
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
Muhammad Farooq
A. F. Golfe
Almaz Fazliakhmetov
Angeles Faus Golfe
Rujun Fei
Bo Feng
Chong Feng
Junhua Feng
Xu Feng
Zhuoran Feng
ZhuoranFeng
Luis Roberto Flores Castillo
Etienne Forest
Andrew Fowlie
H. Fox
Harald Fox
Hai-Bing Fu
Jinyu Fu
Benjamin Fuks
Yoshihiro Funakoshi
Emidio Gabrielli
Nan Gan
Li Gang
Jie Gao
Meisen Gao
Wenbin Gao
Wenchun Gao
Yu Gao
Yuanning Gao
Zhanxiang Gao
Yanyan Gao
Kun Ge
Shao-Feng Ge
Zhenwu Ge
Li-Sheng Geng
Qinglin Geng
Hao Zeng
Chao-Qiang Geng
Swagata Ghosh
Antonio Gioiosa
Leonid Gladilin
Ti Gong
Stefania Gori
Quanbu Gou
Sebastian Grinstein
Chenxi Gu
Gerardo Guillermo
Joao Guimaraes da Costa
Dizhou Guo
Fangyi Guo
Jiacheng Guo
Jun Guo
Lei Guo
Xia Guo
Xinyang Guo
Xin-Heng Guo
Yunqiang Guo
Yuping Guo
Yun Guo
Zhi-Hui Guo
Alejandro Gutie´rrez-Rodríguez
Seungkyu Ha
Noman Habib
Jan Hajer
Francois Hammer
Chengcheng Han
Huayong Han
Jifeng Han
Liangliang Han
Liang Han
Rao Zhang
Yang Han
Ruixiong Han
Yezi Han
Yuanying Han
Tao Han
Jiankui Hao
Xiqing Hao
Qiang Zhao
Chuanqi He
Dayong He
Dongbing He
Guangyuan He
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
Y. Hor
YuenKeung Hor
George W. S. Hou
Xiantao Hou
Xiaonan Hou
Zhilong Hou
Suen Hou
Caishi Hu
Chen Hu
Dake Hu
Haiming Hu
Jiagen Hu
Jun Hu
Kun Hu
Shouyang Hu
Yongcai Hu
Yu Hu
Zhen Hu
Z. Hua
Zhehao Hua
Jianfei Hua
Chao-Shang Huang
Fa Peng Huang
Guangshun Huang
Jinshu Huang
Ke Huang
Liangsheng Huang
Shuhui Huang
Xingtao Huang
Xu-Guang Huang
Yanping Huang
Yonggang Huang
Yongsheng Huang
Zimiao Huang
Yuanyuan Wei
Chen Huanyuan
Changgi Huh
Jiaqi Hui
Lihua Huo
Talab Hussain
Kyuyeong Hwang
Ara Ioannisian
Munawar Iqbal
Paul Jackson
Shahriyar Jafarzade
Haeun Jang
Seoyun Jang
Daheng Ji
Q. Ji
Qingping Ji
Quan Ji
Xiaolu Ji
Jingguang Jia
Jinsheng Jia
X. Q. Jia
Xuewei Jia
Zihang Jia
Cailian Jiang
Han Ren Jiang
Houbing Jiang
Jun Jiang
Xiaowei Jiang
Xin Jiang
Xuhui Jiang
Yongcheng Jiang
Zhongjian Jiang
Cheng Jiang
Ruiqi Jiao
Dapeng Jin
Shan Jin
Song Jin
Yi Jin
Junji Jis
Sunghoon Jung
Goran Kacarevic
Eric Kajfasz
Lidia Kalinovskaya
Aleksei Kampf
Wen Kang
Xian-Wei Kang
Xiaolin Kang
Biswajit Karmakar
Zhiyong Ke
Rijeesh Keloth
Alamgir Khan
Hamzeh Khanpour
Khanchai Khosonthongkee
KhanchaiKhosonthongkee
Bobae Kim
Dongwoon Kim
Mi Ran Kim
Minsuk Kim
Sungwon Kim
On Kim
Michael Klasen
Sanghyun Ko
S. Ko
Ivan Koop
Vitaliy Kornienko
Bryan Kortman
Gennady Kozlov
Shiqing Kuang
Mukesh Kumar
Chia Ming Kuo
Tsz Hong Kwok
Franc¸ois Sylvain Ren Lagarde
F. Lagarde
Pei-Zhu Lai
Imad Laktineh
Xiaofei Lan
Zuxiu Lan
Lia Lavezzi
Justin Lee
Junghyun Lee
Sehwook Lee
Ge Lei
Roy Lemmon
Yongxiang Leng
Sze Ching Leung
Hai Tao Li
Bingzhi Li
Bo Li
Changhong Li
Chao Li
Cheng Li
Chunhua Li
Cui Li
Dazhang Li
Dikai Li
Yi Wang
Gang Li
Gaosong Li
Haibo Li
Haifeng Li
Hai-Jun Li
Haotian Li
Hengne Li
Honglei Li
Huijing Li
Jialin Li
Jingyi Li
J. Li
Jun Li
Leyi Li
Liang Li
Jinmian Li
Mei Li
Meng Li
Minxian Li
Ling Li
Pei-Rong Li
Qiang Li
Shaopeng Li
Shenghe Li
Shu Li
Shuo Li
Teng Li
Tiange Li
Tong Li
Weichang Li
Weidong Li
Wenjun Li
Xiaoling Li
Xiaomei Li
Xiaonan Li
Xiaoping Li
Xiaoting Li
Xin Li
Xinqiang Li
Xuekang Li
Yang Li
Yanwei Li
Yiming Li
Ying Li
Ying-Ying Li
Yonggang Li
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
Yi Liao
Yufu Lin
Yugen Lin
Beijiang Liu
Bo Liu
Danning Liu
Dong Liu
Fu-Hu Liu
Hongbang Liu
Huangcheng Liu
Hui Liu
Huiling Liu
Jia Liu
Jiaming Liu
Jianbei Liu
Jianyi Liu
Jingdong Liu
Jinhua Liu
Kai Liu
Kang Liu
Kun Liu
Mengyao Liu
Pengcheng Liu
Qibin Liu
Shan Liu
Shidong Liu
Shuang Liu
Shubin Liu
Peng Liu
Tao Liu
Tong Liu
Wei Liu
Xiang Liu
Xiaohui Liu
Xiaoyu Liu
Xin Liu
Xinglin Liu
Xingquan Liu
Yang Liu
Xiao-Hai Liu
Yanlin Liu
Yao-Bei Liu
Yi Liu
Yiming Liu
Yong Liu
Yonglu Liu
Yu Liu
Yubin Liu
Yudong Liu
Yulong Liu
Zhaofeng Liu
Zhenchao Liu
Zhi Liu
Zhi-Feng Liu
Zhiqing Liu
Zhongfu Liu
Zuowei Liu
Mia Liu
Zhen Liu
Xiaoyang Liu
Xinchou Lou
Cai-Dian Lu
Jun-Xu Lu
Qiu Zhen Lu
Shang Lu
Wenxi Lu
Xiaohan Lu
Yunpeng Lu
Zhiyong Lu
Xianguo Lu
Wei Lu
Bayarto Lubsandorzhiev
Sultim Lubsandorzhiev
Arslan Lukanov
Jinliang Luo
Tao Luo
xiaoan Luo
Xiaofeng Luo
Xiaolan Luo
Jindong Lv
Feng Lyu
Xiao-Rui Lyu
Kun-Feng Lyu
Ande Ma
Hong-Hao Ma
Jun-Li Ma
Kai Ma
Lishuang Ma
Na Ma
Renjie Ma
Weihu Ma
Xinpeng Ma
Yanling Ma
Yan-Qing Ma
Yongsheng Ma
Zhonghui Ma
Zhongjian Ma
Yang Ma
Mousam Maity
Lining Mao
Yanmin Mao
Yaxian Mao
Aure´lien Martens
Caccia Massimo Luigi Maria
Shigeki Matsumoto
Bruce Mellado
Davide Meloni
Cai Meng
Lingxin Meng
Zhenghui Mi
Yuhui Miao
Mauro Migliorati
Lei Ming
Vasiliki A. Mitsou
Laura Monaco
Arthur Moraes
Karabo Mosala
Ahmad Moursy
Lichao Mu
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
Carlo Pagani
Stathes Paganis
Collette Pakuza
Jiangyang Pan
Juntong Pan
Tong Pan
Xiang Pan
Papia Panda
Saraswati Pandey
Mila Pandurovic
Rocco Paparella
Roman Pasechnik
Emilie Passemar
Hua Pei
Xiaohua Peng
Xinye Peng
Yuemei Peng
Jialun Ping
Ronggang Ping
Souvik Priyam Adhya
Baohua Qi
Hang Qi
Huirong Qi
Ming Qi
Sen Qian
Zhuoni Qian
Congfeng Qiao
Guangyou Qin
Jiajia Qin
Laishun Qin
Liqing Qin
Qin Qin
Xiaoshuai Qin
Zhonghua Qin
Guofeng Qu
Antonio Racioppi
Michael Ramsey-Musolf
Shabbar Raza
Vladimir Rekovic
Jing Ren
Ju¨rgen Reuter
Tania Robens
Giancarlo Rossi
Manqi Ruan
Leonid Rumyantsev
Min Sang Ryu
Renat Sadykov
Minjing Sang
Juan Jose´ Sanz-Cillero
Miroslav Saur
Nishil Savla
Michael A. Schmidt
Daniele Sertore
Ron Settles
Peng Sha
Ding-Yu Shao
Ligang Shao
Hua-Sheng Shao
Xin She
Chuang Shen
Hong-Fei Shen
Jian-Ming Shen
Peixun Shen
Qiuping Shen
Zhongtao Shen
Shuqi Sheng
Haoyu Shi
Hua Shi
Qi Shi
Shusu Shi
Xiaolei Shi
Xin Shi
Yukun Shi
Zhan Shi
Ian Shipsey
Gary Shiu
Chang Shu
Zong-Guo Si
Andrei Sidorenkov
Ivan Smiljanić
Aodong Song
Huayang Song
Jiaojiao Song
Jinxing Song
Siyuan Song
Weimin Song
Weizheng Song
Zhi Song
Shashwat Sourav
Paolo Spruzzola
Feng Su
Shengsen Su
Wei Su
Shufang Su
Yanfeng Sui
Zexuan Sui
Michael Sullivan
Baiyang Sun
Guoqiang Sun
Hao Sun
Hao-Kai Sun
Junfeng Sun
Liang Sun
Mengcheng Sun
Pengfei Sun
Sichun Sun
Xianjing Sun
Xiaohu Sun
Xilei Sun
Xingyang Sun
Xin-Yuan Sun
Yanjun Sun
Yongzhao Sun
Yue Sun
Zheng Sun
Narumon Suwonjandee
Elsayed Tag Eldin
Biao Tan
Bo Tang
Chuanxiang Tang
Gao Tang
Guangyi Tang
Jingyu Tang
Liang Tang
Ying’Ao Tang
Junquan Tao
Abdel Nasser Tawfik
Geoffrey Taylor
Valery Telnov
Saike Tian
Riccardo Torre
Wladyslaw Henryk Trzaska
Dmitri Tsybychev
Yanjun Tu
Shengquan Tuo
Michael Tytgat
Ghalib Ul Islam
Nikita Ushakov
German Valencia
Jaap Velthuis
Alessandro Vicini
Trevor Vickey
Ivana Vidakovic
Henri Videau
Raymond Volkas
Dmitry Voronin
Natasa Vukasinovic
Xia Wan
Xuying Wan
Xiao Wang
Anqing Wang
Bin Wang
Chengtao Wang
Chuanye Wang
Ci Wang
Dayong Wang
Dou Wang
En Wang
Guanwen Wang
Guo-Li Wang
Haijing Wang
Haolin Wang
Jianchun Wang
JianLi Wang
Jiawei Wang
Jin Wang
Jin-Wei Wang
Joseph Wang
Kechen Wang
Lechun Wang
Wei Wang
Liguo Wang
Lijiao Wang
Lu Wang
Meng Wang
Na Wang
Pengcheng Wang
Qian Wang
Qun Wang
Shu Lin Wang
Shudong Wang
Taofeng Wang
Tianhong Wang
Tianyang Wang
Xiaolong Wang
Xiaoning Wang
Xiao-Ping Wang
Xiongfei Wang
Xujian Wang
Yaping Wang
Yaqian Wang
Yiao Wang
Yifang Wang
Yilun Wang
Yiwei Wang
You-Kai Wang
Yuanping Wang
Yuexin Wang
Yuhao Wang
Yu-Ming Wang
Yuting Wang
Zhen Wang
Zhigang Wang
Weiping Wang
Zeren Simon Wang
Biao Wang
Hao Wang
Lian-Tao Wang
Zihui Wang
Zirui Wang
Jia Wang
Tong Wang
Daihui Wei
Shujun Wei
Wei Wei
Xiaomin Wei
Yingjie Wei
Liangjian Wen
Xuejun Wen
Yufeng Wen
Martin White
Peter Williams
Zef Wolffs
William John Womersley
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
Lei Xia
Ligang Xia
Shang Xia
Benhou Xiang
Dao Xiang
Zhiyu Xiang
Bo-Wen Xiao
Chu-Wen Xiao
Dong Xiao
Guangyan Xiao
Han Xiao
Meng Xiao
Ouzheng Xiao
Rui-Qing Xiao
Xiang Xiao
Yichen Xiao
Ying Xiao
Yu Xiao
Yunlong Xiao
Zhenjun Xiao
Hengyuan Xiao
Nian Xie
Yuehong Xie
Tianmu Xin
Ye Xing
Zhizhong Xing
Da Xu
Fang Xu
Fanrong Xu
Haisheng Xu
Haocheng Xu
Ji Xu
Miaofu Xu
Qingjin Xu
Qingnian Xu
Wei Xu
Weixi Xu
Xinping Xu
Zhen Xu
Zijun Xu
Zehua Xu
Yaoyuan Xu
Feifei Xue
Baojun Yan
Bin Yan
Fen Yan
Fucheng Yan
Liang Yan
Qi-Shu Yan
Wenbiao Yan
Yupeng Yan
Luping Yan
Haoyue Yan
Dong Yang
Fengying Yang
Guicheng Yang
Haijun Yang
Jin Min Yang
Jing Yang
Lan Yang
Li Yang
Li Lin Yang
Lili Yang
Litao Yang
Mei Yang
Qiaoli Yang
Tiansen Yang
Xiaochen Yang
Yingjun Yang
Yueling Yang
Zhengyong Yang
Zhenwei Yang
Youhua Yang
Xiancong Yang
De-Liang Yao
Shi Yao
Lei Ye
Lingxi Ye
Mei Ye
Rui Ye
Yecheng Ye
Vitaly Yermolchyk
Kai Yi
Li Yi
Yang Yi
Di Yin
Peng-Fei Yin
Shenghua Yin
Ze Yin
Zhongbao Yin
Zhang Yinhong
Hwi Dong Yoo
Zhengyun You
Charles Young
Boxiang Yu
Chenghui Yu
Fusheng Yu
Jie-Sheng Yu
Jinqing Yu
Lingda Yu
Zhao-Huan Yu
Felix Yu
Bingrong Yu
Changzheng Yuan
Li Yuan
Xing-Bo Yuan
Youjin Yuan
Junhui Yue
Qian Yue
Baobiao Yue
Un Nisa Zaib
Riccardo Zanzottera
Ming Zeng
Jian Zhai
Jiyuan Zhai
Xin Zhe Zhai
Xi-Jie Zhan
Ben-Wei Zhang
Bolun Zhang
Di Zhang
Guangyi Zhang
Hao Zhang
Hong-Hao Zhang
Huaqiao Zhang
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
Ning 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
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Rex Ying
Wengong Jin
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (see more)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Rex Ying
Wengong Jin
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (see more)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Rex Ying
Wengong Jin
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (see more)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Rex Ying
Wengong Jin
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (see more)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Rex Ying
Wengong Jin
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (see more)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua
Jiarui Lu
Yong Liu
Odin Zhang
Rex Ying
Wengong Jin
Shuangjia Zheng
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interact… (see more)ion prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.
Cell ontology guided transcriptome foundation model
Xinyu Yuan
Zhihao Zhan
Zuobai Zhang
Manqi Zhou
Jianan Zhao
Boyu Han
Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by… (see more) 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.
GraphText: Graph Reasoning in Text Space
Jianan Zhao
Le Zhuo
Yikang Shen
Meng Qu
Kai Liu
Michael M. Bronstein
Zhaocheng Zhu
Any2Policy: Learning Visuomotor Policy with Any-Modality
Yichen Zhu
Zhicai Ou
Feifei Feng
Humans can communicate and observe media with different modalities, such as texts, sounds, and images. For robots to be more generalizable e… (see more)mbodied agents, they should be capable of following instructions and perceiving the world with adaptation to diverse modalities. Current robotic learning methodologies often focus on single-modal task specification and observation, thereby limiting their ability to process rich multi-modal information. Addressing this limitation, we present an end-to-end general-purpose multi-modal system named Any-to-Policy Embodied Agents. This system empowers robots to handle tasks using various modalities, whether in combinations like text-image, audio-image, text-point cloud, or in isolation. Our innovative approach involves training a versatile modality network that adapts to various inputs and connects with policy networks for effective control. Because of the lack of existing multi-modal robotics datasets for evaluation, we assembled a comprehensive real-world dataset encompassing 30 robotic tasks. Each task in this dataset is richly annotated across multiple modalities, providing a robust foundation for assessment. We conducted extensive validation of our proposed unified modality embodied agent using several simulation benchmarks, including Franka Kitchen, Meta-World, and Maniskill2, as well as in our real-world settings. Our experiments showcase the promising capability of building embodied agents that can adapt to diverse multi-modal in a unified framework.
Cell ontology guided transcriptome foundation model
Xinyu Yuan
Zhihao Zhan
Zuobai Zhang
Manqi Zhou
Jianan Zhao
Boyu Han
Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by… (see more) 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.