TGSA: protein-protein association-based twin graph neural networks for drug response prediction with similarity augmentation. - Yiheng Zhu 002; Zhenqiu Ouyang; Wenbo Chen; Ruiwei Feng; Danny Z. Chen; Ji Cao; Jian Wu 001 (Bioinform., 2022)

MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation. - Yiheng Zhu 002; Zhenqiu Ouyang; Ben Liao; Jialu Wu; Yixuan Wu; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (IJCAI, 2023)

GCL: Gradient-Guided Contrastive Learning for Medical Image Segmentation with Multi-Perspective Meta Labels. - Yixuan Wu; Jintai Chen; Jiahuan Yan; Yiheng Zhu 002; Danny Z. Chen; Jian Wu 001 (ACM Multimedia, 2023)

Sample-efficient Multi-objective Molecular Optimization with GFlowNets. - Yiheng Zhu 002; Jialu Wu; Chaowen Hu; Jiahuan Yan; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (NeurIPS, 2023)

Making Pre-trained Language Models Great on Tabular Prediction. - Jiahuan Yan; Bo Zheng 011; Hongxia Xu; Yiheng Zhu 002; Danny Z. Chen; Jimeng Sun 001; Jian Wu 001; Jintai Chen (ICLR, 2024)

Generative AI for Controllable Protein Sequence Design: A Survey. - Yiheng Zhu 002; Zitai Kong; Jialu Wu; Weize Liu; Yuqiang Han; Mingze Yin; Hongxia Xu; Chang-Yu Hsieh; Tingjun Hou (CoRR, 2024)

Multi-Modal CLIP-Informed Protein Editing. - Mingze Yin; Hanjing Zhou; Yiheng Zhu 002; Miao Lin; Yixuan Wu; Jialu Wu; Hongxia Xu; Chang-Yu Hsieh; Tingjun Hou; Jintai Chen; Jian Wu 001 (CoRR, 2024)

Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding. - Wei Wu 045; Chao Wang 086; Liyi Chen 001; Mingze Yin; Yiheng Zhu 002; Kun Fu; Jieping Ye; Hui Xiong 001; Zheng Wang 027 (CoRR, 2024)

S2ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning. - Mingze Yin; Hanjing Zhou; Jialu Wu; Yiheng Zhu 002; Yuxuan Zhan; Zitai Kong; Hongxia Xu; Chang-Yu Hsieh; Jintai Chen; Tingjun Hou; Jian Wu 001 (CoRR, 2024)

Synergy of GFlowNet and Protein Language Model Makes a Diverse Antibody Designer. - Mingze Yin; Hanjing Zhou; Yiheng Zhu 002; Jialu Wu; Wei Wu 045; Mingyang Li; Kun Fu; Zheng Wang 027; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (AAAI, 2025)

ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings. - Zitai Kong; Yiheng Zhu 002; Yinlong Xu; Hanjing Zhou; Mingzhe Yin; Jialu Wu; Hongxia Xu; Chang-Yu Hsieh; Tingjun Hou; Jian Wu 001 (CoRR, 2025)