Xinyuan Zhu 朱心远 Research Engineer Ant Group Email: zhuxinyuan.zxy@antgroup.com xyzhu2001@gmail.com [Google Scholar]

Publications

paper

Hierarchical Progressive Learning for Zero-Shot Peptide-HLA Binding Prediction and Automated Antigenic Peptide Design Xinyuan Zhu, Jiadong Lu, Xinting Hu, Tengchuan Jin, Shan Lu and Fuli Feng Cell Reports, 2025

paper

Machine Learning Dataset and Benchmark for Accurate T Cell Receptor-pHLA Binding Prediction Xinyuan Zhu, Jiadong Lu, Yeqing Lu, Yuyan Zhang and Fuli Feng Nature Computational Science (in press).

paper

Generative Design of High-affinity T-cell Receptors by Progressive Learning with Structural Confidence Xinyuan Zhu, Qingshuo Jin, Jiadong Lu, Jun Wu, Lixia Zhu, Yuhua Shang, Tengchuan Jin and Fuli Feng Under reivew of Nature Communications

paper

Improving Prostate Cancer Risk Prediction through Partial AUC Optimization Xinyuan Zhu, Xiaohan Ren, Wentao Shi, Changming Wang, Xuehan Liu, Yuqing Liu, Tao Tao, Fuli Feng The Web Conference (WWW) 2024 - Health Day

paper

Mitigating Hidden Confounding Effects for Causal Recommendation Xinyuan Zhu, Yang Zhang, Fuli Feng, Xun Yang, Dingxian Wang, Xiangnan He IEEE Transactions on Knowledge and Data Engineering (TKDE), 2024

paper

Benchmarking TCR-pMHC Structure Prediction: a Unified Evaluation and CDR3-based Functional Insights Jiadong Lu, Xinyuan Zhu, Xinting Hu, Cheng Zhang and Fuli Feng Briefings in Bioinformatics, 2026

paper

DrugTrail: Interpretable Drug Discovery via Structured Reasoning and Druggability-Tailored Preference Optimization Yurou Liu, Mingyang Li, Xinyuan Zhu, Rui Jiao, Yiming Dong, Xinyu Tang, Yang Liu, Jieping Ye, Bing Su, Zheng Wang The Fourteenth International Conference on Learning Representations (ICLR 2026)

paper

Probing RLVR Training Instability through the Lens of Objective-level Hacking Yiming Dong, Kun Fu, Haoyu Li, Xinyuan Zhu, Yurou Liu, Lijing Shao, Jieping Ye, Zheng Wang The Forty-Third International Conference on Machine Learning (ICML 2026)

paper

HEAL: Latent Head Alignment for Post-Training Quantization of Large Language Models Mingzhe Yang, Sihao Lin, Ruibo Zhang, Xinyuan Zhu, Lei Chen, Weidong Chen, Xiaojun Chang The 2026 Conference on Empirical Methods in Natural Language Processing (EMNLP 2026)

paper

Machine Learning-enhanced Preoperative Assessment of Spontaneous Ventilation Risk in Diverse Video-assisted Thoracoscopic Surgeries Xiaohan Ren, Fengfa Yang, Jiayu Li, Shujun Wu, Xinyuan Zhu, Fuli Feng, Xinting Hu, Lan Lan The Journal of Thoracic and Cardiovascular Surgery Open, 2026

paper

An Agentic Framework for Gravitational-Wave Counterpart Association in the Multi-Messenger Era Yiming Dong, Yacheng Kang, Junjie Zhao, Xinyuan Zhu, Ziming Wang, Lijing Shao The Innovation, 2026

paper

PPBoost: Progressive Prompt Boosting for Text-Driven Medical Image Segmentation Xuchen Li, Hengrui Gu, Mohan Zhang, Qin Liu, Zhen Tan, Xinyuan Zhu, Huixue Zhou, Tianlong Chen, Kaixiong Zhou Preprint

Education

University of Science and Technology of China Ph.D. in Artificial Intelligence                                                                                       Sep 2021 - Jun 2026, Hefei, Anhui, China Advisor: Prof. Xiangnan He and Prof. Fuli Feng.

University of Science and Technology of China B.Eng. in Information Security and Artificial Intelligence                                      Sep 2017 - Jun 2021, Hefei, Anhui, China Advisor: Prof.Xiangnan He and Prof.Fuli Feng.

Industry Experience

Research Intern, Shanghai Artificial Intelligence Laboratory, May 2026 - June 2026 • Developed LLM-based agent workflows for AI-driven vaccine research, focusing on broad-spectrum vaccine development, antigenic epitope identification and screening, and vaccine candidate prioritization.

Research Intern, AI for Science, Tongyi Laboratory, Alibaba Token Hub (ATH), Apr 2025 - Apr 2026 • Led the development of an LLM-based drug discovery agent that autonomously orchestrated target retrieval, protein structure assessment, pocket detection, molecular docking, ML-based rescoring, and candidate ranking for large-scale virtual screening. • Applied the agent to screen more than 500 cancer-related targets and over 100 billion synthesizable molecules, yielding 12 of 24 tested KRAS G12D and FGFR4 candidates with IC50 values below 1 μM in wet-lab validation, with the best reaching 8 nM.

Research Intern, BioGeometry, Mar 2023 - Aug 2023 Mentors: Dr. Meng Qu and Prof. Jian Tang • Led the design and development of a biomedical RAG system for disease target discovery, covering literature parsing, knowledge base construction, vector indexing, hybrid retrieval, reranking, and response generation. • Built a local knowledge base containing approximately 20 million biomedical research papers and patents. • Developed a hybrid retrieval pipeline combining semantic search, keyword search, metadata filtering, and reranking to improve evidence retrieval from large-scale biomedical corpora.

Research Intern, Theory Dept., 2012 Lab, Huawei, Jan 2020 - Aug 2020 Mentors: Dr. Sen Wang and Dr. Peng Wang • Contributed to privacy-preserving learning mechanisms based on local differential privacy for edge-cloud collaborative learning and evaluated system privacy using model inversion and membership inference attacks. • Contributed to the development of MistNet, an edge-cloud collaborative learning prototype whose related components were later integrated into the open-source federated learning framework Plato.

Selected Awards

Silver Reviewer for ICML 2025 USTC Chuying Fund Support, 2024 USTC Outstanding Student Scholarship, 2021-2026 USTC Outstanding Graduate 2021 Qiangwei Scholarship, 2021 Cyrus Tang Scholarship, 2017 - 2021 Challenge Cup, National Third Prize, 2020 Neural Network Intelligence (NNI) by MSRA, Outstanding Project 2020 Robotics Competition of USTC, Bronze Medal, 2019

Activities/Services

Reviewer ICLR, ICML, NeurIPS, KDD, AAAI, etc.

Invited Talk CCL 2025, etc.

Teaching Assistant Probability and Statistics / Advanced Computer Programming / Introduction to Cryptography. 2020.1 - 2021.6 @USTC