Applications

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

Boosting LLM’s Molecular Structure Elucidation with Knowledge Enhanced Tree Search Reasoning

ACL, 2025

Xiang Zhuang, Bin Wu, Jiyu Cui, Kehua Feng, Xiaotong Li, Huabin Xing, Keyan Ding, Qiang Zhang, Huajun Chen

Paper

GitHub

Retrosynthesis Prediction with An Iterative String Editing Model

Nature Communications, 2024

Yuqiang Han, Xiaoyang Xu, Chang-Yu Hsieh, Keyan Ding, Hongxia Xu, Renjun Xu, Tingjun Hou, 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

Domain-Agnostic Molecular Generation with Self-feedback

ICLR, 2024

Yin Fang, Ningyu Zhang, Zhuo Chen, Lingbing Guo, Xiaohui Fan, Huajun Chen

Paper

GitHub

Enhancing Cross Text-Molecule Learning by Self-Augmentation

ACL Findings, 2024

Yinuo Jiang, Xiang Zhuang, Keyan Ding, Qiang Zhang, Huajun Chen

Paper

GitHub

The Future of Molecular Studies through the Lens of Large Language Models

Journal of Chemical Information and Modeling, 2024

Jinlu Zhang, Yin Fang, Xin Shao, Huajun Chen, Ningyu Zhang, Xiaohui Fan

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

Learning Invariant Molecular Representation in Latent Discrete Space

NeurIPS, 2023

Xiang Zhuang, Qiang Zhang, Keyan Ding, Yatao Bian, Xiao Wang, Jingsong Lv, Hongyang Chen, Huajun Chen

Paper

GitHub

Newton–Cotes Graph Neural Networks: On the Time Evolution of Dynamic Systems

NeurIPS, 2023

Lingbing Guo, Weiqing Wang, Zhuo Chen, Ningyu Zhang, Zequn Sun, Yixuan Lai, Qiang Zhang, Huajun Chen

Paper

GitHub

Graph Sampling-based Meta-Learning for Molecular Property Prediction

IJCAI, 2023

Xiang Zhuang, Qiang Zhang, Bin Wu, Keyan Ding, Yin Fang, 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

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

Integrating protein language models and automatic biofoundry for enhanced protein evolution

Nature Communication, 2025

Qiang Zhang, Wanyi Chen, Ming Qin, Yuhao Wang, Zhongji Pu, Keyan Ding, Yuyue Liu, Qunfeng Zhang, Dongfang Li, Xinjia Li, Yu Zhao, Jianhua Yao, Lei Huang, Jianping Wu, Lirong Yang, Huajun Chen & Haoran Yu

Paper

GitHub

DePLM: Denoising Protein Language Models for Property Optimization

NerrIPS, 2024

Zeyuan Wang, Qiang Zhang, Keyan Ding, Ming Qin, Xiaotong Li, Xiang Zhuang, Yu Zhao, Jianhua Yao, Huajun Chen

Paper

GitHub

Knowledge-aware Reinforced Language Models for Protein Directed Evolution

ICML, 2024

Yuhao Wang, Qiang Zhang, Ming Qin, Xiang Zhuang, Xiaotong Li, Zhichen Gong, Zeyuan Wang, Yu Zhao, Jianhua Yao, Keyan Ding, 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

Multi-level Protein Structure Pre-training via Prompt Learning

ICLR, 2023

Zeyuan Wang, Qiang Zhang, Shuang-Wei HU, Haoran Yu, Xurui Jin, Zhichen Gong, Huajun Chen

Paper

GitHub

Active Finetuning Protein Language Model: A Budget-Friendly Method for Directed Evolution

ECAI, 2023

Ming Qin, Keyan Ding, Bin Wu, Zhenping Li, Haihong Yang, Zeyuan Wang, Hongbin Ye, Haoran Yu, Huajun Chen, Qiang Zhang

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

De Novo Analysis of Bulk RNA-seq Data at Spatially Resolved Single-cell Resolution

Nature Communications, 2022

Jie Liao , Jingyang Qian , Yin Fang , Zhuo Chen , Xiang Zhuang , Ningyu Zhang , Xin Shao , Yining Hu , Penghui Yang , Junyun Cheng , Yang Hu , Lingqi Yu , Haihong Yang , Jinlu Zhang , Xiaoyan Lu , Li Shao , Dan Wu , Yue Gao , Huajun Chen*, Xiaohui Fan*

Paper

GitHub

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

Direct Prediction of Gas Adsorption via Spatial Atom Interaction Learning

Nature Communications, 2023

Jiyu Cui, Fang Wu, Wen Zhang, Lifeng Yang, Jianbo Hu, Yin Fang, Peng Ye, Qiang Zhang, Xian Suo, Yiming Mo, Xili Cui, Huajun Chen*, Huabin Xing*

Paper

GitHub