About Me

Siyuan Chen (陈思远) is currently a Ph.D. candidate in Computer Science at King Abdullah University of Science and Technology (KAUST), supervised by Professor Xin Gao in the Structural and Functional Bioinformatics (SFB) Group, and co-supervised by Professor Yu Li from CUHK. His research focuses on developing advanced AI algorithms and computational frameworks to address complex challenges in healthcare. Before that, he did his bachelors at UESTC, advised by Professor Yang Hu and Professor Yan Chen.

Research Interests

  • Agentic Workflow and Large Language Models for Healthcare
  • Medical Image Analysis
  • AI for Science

News

  • 2026.08 One paper on safety evaluation of large reasoning models was accepted to the EMNLP Main Conference.
  • 2026.03 One paper on a foundation model for generalizable cytogenetics was accepted by npj Precision Oncology.
  • 2025.12 One review on large language models in biomedicine and healthcare was accepted by npj Artificial Intelligence.
  • 2025.08 One paper on noise-tolerant cleaning of bone marrow karyotyping data was accepted by IEEE Journal of Biomedical and Health Informatics.
  • 2024.08 One paper on genome-wide chromatin loop mapping was accepted by Genome Research.
  • 2024.02 One paper on privacy-preserving federated learning for omic data was accepted by Science Advances.

Publications

Journal & Conference (* equal contribution, # correspondence)

  1. TRACE: An Evidence-Grounded Benchmark for Safety Evaluation of Large Reasoning Models Zhenyu Wu, Siyuan Chen, Changchun Yang, Jiaqi Dong, Min Zhou, Ali Almadan, Talal Hammad, Faisal Wahbo, Aminullah Tora, Mona Alshahrani, Xin Gao EMNLP Main Conference, 2026paper
  2. A comprehensive foundation model for generalizable cytogenetics in precision oncology with CHROMA Changchun Yang, Weiqian Dai, Yilan Zhang, Siyuan Chen, Jingdong Hu, Junkai Su, Yuxuan Chen, Ao Xu, Na Li, Xin Gao, Yongguo Yu# npj Precision Oncology, 2026paper
  3. Large Language Models in Biomedicine and Healthcare Juexiao Zhou, Haoyang Li, Siyuan Chen, Zhangtianyi Chen, Zhongyi Han, Xin Gao# npj Artificial Intelligence, 2025paper
  4. NoTAC: A Noise-Tolerance Automatic Cleaning Framework for Bone Marrow Karyotyping Data Rihan Huang*, Siyuan Chen*, Yafei Li, Chunling Zhang, Yilan Zhang, Changchun Yang, Na Li, Jingdong Hu, Ao Xu, Junkai Su, Xin Gao#, Huidan Li#, Jiatao Lou# IEEE-JBHI, 2025paper
  5. A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data Siyuan Chen*, Jiuming Wang*, Inkyung Jung, Zhaowen Qiu, Xin Gao#, Yu Li# Genome Research, 2024paper
  6. BR-CHromNet: Banding Resolution localization of CHromosome structural abnormality with conditional random field Siyuan Chen*, Tingting Hu*, Na Li, Xin Gao, Yongguo Yu# Journal of Molecular Biology, 2024paper
  7. KaryoXpert: An accurate chromosome segmentation and classification framework for karyotyping analysis without training with manually labeled metaphase-image mask annotations Siyuan Chen*, Kaichuang Zhang*, Jingdong Hu, Na Li, Ao Xu, Haoyang Li, Juexiao Zhou, Chao Huang, Yongguo Yu#, Xin Gao# Computers in Biology and Medicine, 2024paper
  8. PPML-Omics: a Privacy-Preserving federated Machine Learning system protects patients’ privacy from omic data Juexiao Zhou*, Siyuan Chen*, Yulian Wu*, Haoyang Li, Bin Zhang, Longxi Zhou, Yan Hu, Zihang Xiang, Zhongxiao Li, Ningning Chen, Wenkai Han, Di Wang#, Xin Gao# Science Advances, 2024papernews
  9. An AI Agent for Fully Automated Multi-omic Analyses Juexiao Zhou, Bin Zhang, Guowei Li, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Liwei Liu, Xin Gao# Advanced Science, 2024paper
  10. ProNet DB: A proteome-wise database for protein surface property representations and RNA-binding profiles Junkang Wei*, Jin Xiao*, Siyuan Chen*, Licheng Zong, Xin Gao#, Yu Li# Database: The Journal of Biological Databases and Curation, 2024paper
  11. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics Haoyang Li*, Juexiao Zhou*, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao# Nature Communications, 2023paper
  12. Deep learning identifies and quantifies recombination hotspot determinants Yu Li*, Siyuan Chen*, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao# Bioinformatics, 2022paper
  13. The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity Shaorong Fan, Wenju Sun, Ligang Fan, Nan Wu, Wei Sun, Haiqian Ma, Siyuan Chen, Zitong Li, Yu Li, Jilin Zhang, Jian Yan# Computational and Structural Biotechnology Journal, 2022paper
  14. Self-supervised contrastive learning for integrative single cell RNA-seq data analysis Wenkai Han, Yuqi Cheng, Jiayang Chen, Huawen Zhong, Zhihang Hu, Siyuan Chen, Licheng Zong, Ting-Fung Chan, Kevin Lip, Irwin King, Xin Gao#, Yu Li# Briefings in Bioinformatics, 2022paper
  15. Protein-RNA interaction prediction with deep learning: Structure matters Junkang Wei*, Siyuan Chen*, Licheng Zong*, Xin Gao#, Yu Li# Briefings in Bioinformatics, 2021paper
  16. Lunar features detection for energy discovery via deep learning Siyuan Chen*, Yu Li*, Tao Zhang, Xingyu Zhu, Shuyu Sun, Xin Gao# Applied Energy, 2021papernews

Preprint / Under Review (* equal contribution)

  1. Perturb-and-Restore: Simulation-driven Structural Augmentation Framework for Imbalance Chromosomal Anomaly Detection Yilan Zhang, Chen Hanbiao, Changchun Yang, Yuetan Chu, Siyuan Chen, Wu Jun, Jingdong Hu, Junkai Su, Yuxuan Chen, Ao Xu, Na Li, Xin Gao# 2025

Education

Ph.D. candidate in Computer Science
King Abdullah University of Science and Technology, Saudi Arabia
Jan 2022 – Present
M.S. in Computer Science
King Abdullah University of Science and Technology, Saudi Arabia
Aug 2020 – Dec 2021
B.E. in Engineering
University of Electronic Science and Technology of China, China
Sept 2016 – Jun 2020
B.E. in Finance (Double Degree)
University of Electronic Science and Technology of China, China
Sept 2016 – Jun 2020

Experiences

  • Sep 2025 – Dec 2025 On-campus Teaching Assistant, CS220 Data Analytics King Abdullah University of Science and Technology (KAUST), Riyadh, Saudi Arabia
  • Sep 2023 – Dec 2023 On-campus Teaching Assistant, CS398 Graduate Seminar King Abdullah University of Science and Technology (KAUST), Saudi Arabia
  • Sep 2023 – Dec 2023 Teaching Assistant, CS220 Data Analytics Ministry of Interior (MOI), King Fahad Security College (KFSC), Riyadh, Saudi Arabia
  • May 2023 Teaching Assistant, DSA009 Data Analytics Saudi Aramco, Dammam, Saudi Arabia
  • Jan 2023 Administrator, The 21st International Conference on Bioinformatics (InCoB2022) KAUST, Saudi Arabia
  • Jul 2022 – Sep 2022 Visiting Scholar The Chinese University of Hong Kong, Hong Kong, China