Publications by authors named "Chang-Yu Hsieh"

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Interpretable PROTAC Degradation Prediction With Structure-Informed Deep Ternary Attention Framework.
Zhenglu Chen, Chunbin Gu, Shuoyan Tan, Xiaorui Wang, Yuquan Li, Chang-Yu Hsieh

Adv Sci (Weinh)· December 2025

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Unlocking the application potential of AlphaFold3-like approaches in virtual screening.
Chao Shen, Xujun Zhang, Shukai Gu, Odin Zhang, Qinghan Wang, Chang-Yu Hsieh

Chem Sci· December 2025

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ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design.
Odin Zhang, Jieyu Jin, Zhenxing Wu, Jintu Zhang, Po Yuan, Chang-Yu Hsieh

Nat Comput Sci· November 2025

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SynGFN: learning across chemical space with generative flow-based molecular discovery.
Yuchen Zhu, Shuwang Li, Jihong Chen, Donghai Zhao, Xiaorui Wang, Chang-Yu Hsieh

Nat Comput Sci· November 2025

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mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset.
Ying Xiong, Aowen Wang, Yu Kang, Chao Shen, Chang-Yu Hsieh

Nat Commun· November 2025

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A virtual platform for automated hybrid organic-enzymatic synthesis planning.
Xiaorui Wang, Xiaodan Yin, Xujun Zhang, Huifeng Zhao, Shukai Gu, Chang-Yu Hsieh

Nat Commun· November 2025

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ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction.
Qiaolin Gou, Qun Su, Jike Wang, Hui Zhang, Huiyong Sun, Chang-Yu Hsieh

J Chem Inf Model· October 2025

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Graph Neural Networks in Modern AI-Aided Drug Discovery.
Odin Zhang, Haitao Lin, Xujun Zhang, Xiaorui Wang, Zhenxing Wu, Chang-Yu Hsieh

Chem Rev· October 2025

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Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions.
De-Jun Jiang, Hui-Feng Zhao, Hong-Yan Du, Yu Kang, Pei-Chen Pan, Chang-Yu Hsieh

Acta Pharmacol Sin· October 2025

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Biology-driven insights into the power of single-cell foundation models.
Jialu Wu, Qing Ye, Yilin Wang, Renling Hu, Yiheng Zhu, Chang-Yu Hsieh

Genome Biol· October 2025

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SALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning.
Mingze Yin, Hanjing Zhou, Jialu Wu, Yiheng Zhu, Yuxuan Zhan, Chang-Yu Hsieh

Research (Wash D C)· September 2025

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PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide-Protein Interaction Prediction.
Shuaiyan Li, Xiaorui Wang, Yuchen Zhu, Jingxuan Ge, Donghai Zhao, Chang-Yu Hsieh

J Chem Inf Model· September 2025

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DGMM: A Deep Learning-Genetic Algorithm Framework for Efficient Lead Optimization in Drug Discovery.
Jiebin Fang, Churu Mao, Yuchen Zhu, Xiaoming Chen, Yun Huang, Chang-Yu Hsieh

J Chem Inf Model· August 2025

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RSGPT: a generative transformer model for retrosynthesis planning pre-trained on ten billion datapoints.
Yafeng Deng, Xinda Zhao, Hanyu Sun, Yu Chen, Xiaorui Wang, Chang-Yu Hsieh

Nat Commun· July 2025

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HiCLR: Knowledge-Induced Hierarchical Contrastive Learning with Retrosynthesis Prediction Yields a Reaction Foundation Model.
Jialu Wu, Yiheng Zhu, Xiaorui Wang, Yitong Li, Mingze Yin, Chang-Yu Hsieh

JACS Au· July 2025

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TRAP: a contrastive learning-enhanced framework for robust TCR-pMHC binding prediction with improved generalizability.
Jingxuan Ge, Jike Wang, Qing Ye, Liqiang Pan, Yu Kang, Chang-Yu Hsieh

Chem Sci· June 2025

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LumiCharge: Spherical Harmonic Convolutional Networks for Atomic Charge Prediction in Drug Discovery.
Qun Su, Hui Zhang, Qiaolin Gou, Huiyong Sun, Meijing Fang, Chang-Yu Hsieh

J Phys Chem Lett· June 2025

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AI-Guided Design of Antimicrobial Peptide Hydrogels for Precise Treatment of Drug-resistant Bacterial Infections.
Zhihui Jiang, Jianwen Feng, Fan Wang, Jike Wang, Ningtao Wang, Chang-Yu Hsieh

Adv Mater· May 2025

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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, Chang-Yu Hsieh

Adv Sci (Weinh)· May 2025

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Token-Mol 1.0: tokenized drug design with large language models.
Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Chang-Yu Hsieh

Nat Commun· May 2025

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scHeteroNet: A Heterophily-Aware Graph Neural Network for Accurate Cell Type Annotation and Novel Cell Detection.
Jiacheng Liu, Xingyu Fan, Chunbin Gu, Yaodong Yang, Bian Wu, Chang-Yu Hsieh

Adv Sci (Weinh)· April 2025

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A Knowledge-Guided Graph Learning Approach Bridging Phenotype- and Target-Based Drug Discovery.
Qing Ye, Yundian Zeng, Linlong Jiang, Yu Kang, Peichen Pan, Chang-Yu Hsieh

Adv Sci (Weinh)· April 2025

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Guselkumab: a safe treatment option for patients with comorbid psoriasis and multiple sclerosis.
Chang-Yu Hsieh, Tsen-Fang Tsai

Ital J Dermatol Venerol· April 2025

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Discovery of antimicrobial peptides with notable antibacterial potency by an LLM-based foundation model.
Jike Wang, Jianwen Feng, Yu Kang, Peichen Pan, Jingxuan Ge, Chang-Yu Hsieh

Sci Adv· March 2025

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Clinical Experience of Risankizumab in Patients With a History of Erythrodermic Psoriasis.
Che-Chia Hsu, Chang-Yu Hsieh, Tsen-Fang Tsai

Exp Dermatol· March 2025

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