Publications

Surveys

Scientific Large Language Models: A Survey on Biological & Chemical Domains

ACM Computing Surveys, 2025

Qiang Zhang, Keyan Ding, Tianwen Lyv, Xinda Wang, Qingyu Yin, Yiwen Zhang, Jing Yu, Yuhao Wang, Xiaotong Li, Zhuoyi Xiang, Xiang Zhuang, Zeyuan Wang, Ming Qin, Mengyao Zhang, Jinlu Zhang, Jiyu Cui, Renjun Xu, Hongyang Chen, Xiaohui Fan, Huabin Xing, Huajun Chen

Paper

GitHub

Agents

SciToolAgent: A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integration

Nature Computational Science, 2025

Keyan Ding, Jing Yu, Junjie Huang, Yuchen Yang, Qiang Zhang, Huajun Chen

Paper

GitHub

AI for Molecules

Advancing biomolecular understanding and design following human instructions

Nature Machine Intelligence, 2025

Xiang Zhuang, Keyan Ding, Tianwen Lyu, Yinuo Jiang, Xiaotong Li, Zhuoyi Xiang, Zeyuan Wang, Ming Qin, Kehua Feng, Jike Wang, Qiang Zhang & Huajun Chen

Paper

GitHub

Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

ICLR, 2024

Yin Fang, Xiaozhuan Liang, Ningyu Zhang, Kangwei Liu, Rui Huang, Zhuo Chen, Xiaohui Fan, Huajun Chen

Paper

GitHub

Knowledge Graph-enhanced Molecular Contrastive learning with Functional Prompt

Nature Machine Intelligence, 2023

Yin Fang, Qiang Zhang, Ningyu Zhang, Zhuo Chen, Xiang Zhuang, Xin Shao, Xiaohui Fan*, Huajun Chen*

Paper

GitHub

Molecular Contrastive Learning with Chemical Element Knowledge Graph

AAAI, 2022

Yin Fang, Qiang Zhang, Haihong Yang, Xiang Zhuang, Shumin Deng, Wen Zhang, Ming Qin, Zhuo Chen, Xiaohui Fan, Huajun Chen

Paper

GitHub

AI for Proteins

Enhancing Safe and Controllable Protein Generation via Knowledge Preference Optimization

ACL, 2025

Yuhao Wang, Keyan Ding, Kehua Feng, Zeyuan Wang, Ming Qin, Xiaotong Li, Qiang Zhang, Huajun Chen

Paper

GitHub

InstructProtein: Aligning Human and Protein Language via Knowledge Instruction

ACL, 2024

Zeyuan Wang, Qiang Zhang, Keyan Ding, Ming Qin, Xiang Zhuang, Xiaotong Li, Huajun Chen

Paper

GitHub

OntoProtein: Protein Pretraining With Gene Ontology Embedding

ICLR, 2022

Ningyu Zhang, Zhen Bi, Xiaozhuan Liang, Siyuan Cheng, Haosen Hong, Shumin Deng, Qiang Zhang, Jiazhang Lian, Huajun Chen

Paper

GitHub

AI for Cells

Knowledge-graph-based Cell-cell Communication Inference for Spatially Resolved Transcriptomic Data with SpaTalk

Nature Communications, 2022

Xin Shao, Chengyu Li, Haihong Yang, Xiaoyan Lu, Jie Liao, Jingyang Qian, Kai Wang, Junyun Cheng, Penghui Yang, Huajun Chen*, Xiao Xu*, Xiaohui Fan*

Paper

GitHub

scDeepSort: A Pre-trained Cell-type Annotation Method for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

Nucleic Acids Research, 2021

Xin Shao, Haihong Yang, Xiang Zhuang, Jie Liao, Huajun Chen*, Xiaohui Fan*

Paper

GitHub