📄 Selected Publications

The full list can be accessed on my Google Scholar profile.

• [Advanced Science 2025] A Multi-Objective Molecular Generation Method Based on Pareto Algorithm and Monte Carlo Tree Search
  Yifei Liu, Yiheng Zhu, Jike Wang, Renling Hu, Chao Shen, Wanglin Qu, Gaoang Wang, Qun Su, Yuchen Zhu, Yu Kang, Peichen Pan, Chang‐Yu Hsieh, Tingjun Hou

• [JACS Au 2025] HiCLR: Knowledge-Induced Hierarchical Contrastive Learning with Retrosynthesis Prediction Yields a Reaction Foundation Model [Code]
  Jialu Wu, Yiheng Zhu, Xiaorui Wang, Yitong Li, Mingze Yin, Tianyue Wang, Yuqiang Han, Yu Kang, Yafeng Deng, Jian Wu, Chang-Yu Hsieh, Tingjun Hou

• [AAAI 2025] Synergy of GFlowNet and Protein Language Model Makes a Diverse Antibody Designer
  Mingze Yin, Hanjing Zhou, Yiheng Zhu, Jialu Wu, Wei Wu, Mingyang Li, Kun Fu, Zheng Wang, Chang-Yu Hsieh, Tingjun Hou, Jian Wu

• [NeurIPS 2024] Bridge-IF: Learning Inverse Protein Folding with Markov Bridges [Code]
  Yiheng Zhu, Jialu Wu, Qiuyi Li, Jiahuan Yan, Mingze Yin, Wei Wu, Mingyang Li, Jieping Ye, Zheng Wang, Jian Wu

• [Health Data Science 2024] Multi-Modal CLIP-Informed Protein Editing [Code]
  Mingze Yin, Hanjing Zhou, Yiheng Zhu, Miao Lin, Yixuan Wu, Jialu Wu, Hongxia Xu, Chang-Yu Hsieh, Tingjun Hou, Jintai Chen, Jian Wu

• [NeurIPS 2023] Sample-efficient Multi-objective Molecular Optimization with GFlowNets [Code]
  Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Chang-Yu Hsieh, Tingjun Hou, Jian Wu

• [IJCAI 2023] MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation [Code]
  Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh, Tingjun Hou, Jian Wu

• [arXiv] GENERator: A Long-Context Generative Genomic Foundation Model [Code]
  Wei Wu, Qiuyi Li, Yuanyuan Zhang, Zhihao Zhan, Ruipu Chen, Mingyang Li, Kun Fu, Junyan Qi, Yongzhou Bao, Chao Wang, Yiheng Zhu, Zhiyun Zhang, Jian Tang, Fuli Feng, Jieping Ye, Yuwen Liu, Hui Xiong, Zheng Wang

• [bioRxiv] Functional In-Context Learning in Genomic Language Models with Nucleotide-Level Supervision and Genome Compression
  Qiuyi Li, Zhihao Zhan, Shikun Feng, Yiheng Zhu, Yuan He, Wei Wu, Zhenghang Shi, Shengjie Wang, Zongyong Hu, Zhao Yang, Jiaoyang Li, Jian Tang, Haiguang Liu, Tao Qin

• [bioRxiv] Generanno: A Genomic Foundation Model for Metagenomic Annotation [Code]
  Qiuyi Li, Wei Wu, Yiheng Zhu, Fuli Feng, Jieping Ye, Zheng Wang

• [Genome Biology 2025] Biology-driven insights into the power of single-cell foundation models [Code]
  Jialu Wu, Qing Ye, Yilin Wang, Renling Hu, Yiheng Zhu, Mingze Yin, Tianyue Wang, Jike Wang, Chang-Yu Hsieh, Tingjun Hou

• [Bioinformatics 2022] TGSA: protein–protein association-based twin graph neural networks for drug response prediction with similarity augmentation [Code]
  Yiheng Zhu, Zhenqiu Ouyang, Wenbo Chen, Ruiwei Feng, Danny Z Chen, Ji Cao, Jian Wu