arXiv preprint
MolLean: A Process-Verifiable Language for Chemical Reasoning
Jiatong Li and Yatao Bian. (2026). MolLean: A Process-Verifiable Language for Chemical Reasoning. arXiv:2610.20459.
Cite this work View paper
Academic record / 04
CV
Education, research appointments, publications, and academic service.
I am a Ph.D. candidate in Computing at The Hong Kong Polytechnic University and an incoming Research Fellow at the National University of Singapore. I was a Visiting Scholar at NUS from January to July 2026. I work on AI co-scientists for molecular discovery, with a focus on molecular representations, chemical reasoning, and scientific tool use.
Education
- Ph.D. Candidate in Computing, The Hong Kong Polytechnic University, 2023.01–Present
- Hong Kong PhD Fellowship Scheme (HKPFS)
- Master of Information Technology, The University of Melbourne, 2021.07–2022.12
- Dean’s Honor List
- Bachelor of Engineering, Shanghai Jiao Tong University, 2017.09–2021.06
Research experience
- Incoming Research Fellow, BlueWhale Lab, National University of Singapore
- Visiting Scholar, BlueWhale Lab, National University of Singapore, 2026.01–2026.07
- Algorithm Researcher, Shanghai AI Laboratory, 2023.08–2024.12
- Algorithm Researcher, Noah’s Ark Lab, 2021.11–2022.02
Publications
CCF classifications and journal impact factors accompany the relevant papers.
arXiv preprint
STAMP as a topology-aware molecular language for fragment-level learning and editing
Yuxuan Ren, Jiatong Li, Ziqiao Meng, and Yatao Bian. (2026). STAMP as a topology-aware molecular language for fragment-level learning and editing. arXiv:2610.18438.
Cite this work View paper
arXiv preprint
Molecular LLM Agents: From Architectural Design to Scientific Autonomy
Jiatong Li, Wengyu Zhang, Weida Wang, Yuxuan Ren, Wei Liu, Chenyang Mao, Yuqiang Li, Yatao Bian, Changmeng Zheng, Xiaoyong Wei, and Qing Li. (2026). Molecular LLM Agents: From Architectural Design to Scientific Autonomy. arXiv:2608.23104.
Cite this work View paper
arXiv preprint
Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad
Jiatong Li, Yuxuan Ren, Weida Wang, Xiaoyong Wei, and Yatao Bian. (2026). Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad. arXiv:2607.20935.
Cite this work View paper
Machine Intelligence Research
Aligning Clinical Needs and AI Capabilities: A Survey on LLMs for Medical Reasoning
IF 10.0Qi Peng, Jiatong Li, Sirui Huang, Yiyang Jiang, Kaisong Gong, Ronger Ding, Shijie Ye, Changmeng Zheng, Yi Cai, Xiaobo Yang, Jin Huang, Xiao-Yong Wei, and Qing Li. (2026). Aligning Clinical Needs and AI Capabilities: A Survey on LLMs for Medical Reasoning. Machine Intelligence Research.
Cite this work View paper
arXiv preprint
Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis
Jiatong Li, Weida Wang, Changmeng Zheng, Shufei Zhang, Yatao Bian, Xiao-yong Wei, and Qing Li. (2026). Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis. arXiv:2607.01800.
Cite this work View paper
arXiv preprint
MolViBench: Evaluating LLMs on Molecular Vibe Coding
Jiatong Li*, Yuxuan Ren, Weida Wang, Changmeng Zheng, Xiao-yong Wei, Qing Li, and Yatao Bian. (2026). MolViBench: Evaluating LLMs on Molecular Vibe Coding. arXiv preprint arXiv:2605.02351.
Cite this work View paper
KDD 2026
Chem-R: Learning to Reason as a Chemist
CCF AWeida Wang, Benteng Chen, Di Zhang, Wanhao Liu, Shuchen Pu, Ben Gao, Jin Zeng, Xiaoyong Wei, Tianshu Yu, Shuzhou Sun, Tianfan Fu, Wanli Ouyang, Lei Bai, Jiatong Li, Zifu Wang, Yuqiang Li, Shufei Zhang. (2026). Chem-R: Learning to Reason as a Chemist. KDD 2026.
Cite this work
KDD 2026
Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation
CCF AJiatong Li*, Junxian Li*, Yunqing Liu, Dongzhan Zhou, and Qing Li. (2026). Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation. KDD 2026.
Cite this work View paper
IEEE TKDE
MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts
CCF A IF 10.4Jiatong Li, Yunqing Liu, Wei Liu, Jingdi Le, Di Zhang, Wenqi Fan, Dongzhan Zhou, Yuqiang Li, and Qing Li. (2026). MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts. IEEE TKDE.
Cite this work View paper
CVPR 2026
IAG: Input-Aware Backdoor Attack on VLM-Based Visual Grounding
CCF AJunxian Li, Beining Xu, Simin Chen, Jiatong Li, Jingdi Lei, Haodong Zhao, and Di Zhang. (2026). IAG: Input-Aware Backdoor Attack on VLM-Based Visual Grounding. CVPR 2026.
Cite this work View paper
ICLR 2026
CMPhysBench: A Benchmark for Evaluating Large Language Models in Condensed Matter Physics
CCF AWeida Wang*, Dongchen Huang*, Jiatong Li*, Tengchao Yang, Ziyang Zheng, Di Zhang, Dong Han et al. (2026). CMPhysBench: A Benchmark for Evaluating Large Language Models in Condensed Matter Physics. ICLR 2026. (Co-First Author)
Cite this work View paper
arXiv preprint
Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery
Jiatong Li, Weida Wang*, Qinggang Zhang, Junxian Li, Di Zhang, Changmeng Zheng, Shufei Zhang, Xiaoyong Wei, and Qing Li. (2025). Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery. arXiv preprint arXiv:2508.08401.
Cite this work View paper
CVPR 2025
Critic-V: VLM Critics Help Catch VLM Errors in Multimodal Reasoning
CCF ADi Zhang, Jingdi Lei, Junxian Li, Xunzhi Wang, Yujie Liu, Zonglin Yang, Jiatong Li, Weida Wang, Suorong Yang, Jianbo Wu, Peng Ye, Wanli Ouyang, Dongzhan Zhou. (2025). Critic-V: VLM Critics Help Catch VLM Errors in Multimodal Reasoning. CVPR 2025.
Cite this work View paper
NAACL 2025
Llama-berry: Pairwise optimization for o1-like olympiad-level mathematical reasoning
CCF BDi Zhang, Jianbo Wu, Jingdi Lei, Tong Che, Jiatong Li, Tong Xie, Xiaoshui Huang, Shufei Zhang, Marco Pavone, Yuqiang Li, Wanli Ouyang, Dongzhan Zhou. (2025). Llama-Berry: Pairwise Optimization for O1-like Olympiad-Level Mathematical Reasoning. NAACL 2025.
Cite this work View paper
IEEE TKDE
Large Language Models are In-Context Molecule Learners
CCF A IF 10.4Jiatong Li, Wei Liu, Zhihao Ding, Wenqi Fan, Yuqiang Li, Qing Li. (2025). Large Language Models are In-Context Molecule Learners. IEEE TKDE.
Cite this work View paper
CBDCom 2025
Search Engine Augmented Chinese Named Entity Recognition for Big Data Content Security
Qinghua Mao, Jiatong Li, Kui Meng, Yuanyuan Sun, Pengjiao Wang, Jianhua Li. (2025). Search Engine Augmented Chinese Named Entity Recognition for Big Data Content Security. CBDCom 2025.
Cite this work View paper
IEEE TKDE
Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective
CCF A IF 10.4Jiatong Li, Yunqing Liu, Wenqi Fan, Xiao-yong Wei, Hui Liu, Jiliang Tang, and Qing Li. (2024). Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective. IEEE TKDE.
Cite this work View paper
IEEE TKDE
Recommender Systems in the Era of Large Language Models (LLMs)
CCF A IF 10.4Wenqi Fan, Zihuai Zhao, Jiatong Li, Yunqing Liu, Xiaowei Mei, Yiqi Wang, Jiliang Tang, and Qing Li. (2024). Recommender Systems in the Era of Large Language Models (LLMs). IEEE TKDE.
Cite this work View paper
arXiv preprint
Chemllm: A chemical large language model
Di Zhang, Wei Liu, Qian Tan, Jingdan Chen, Hang Yan, Yuliang Yan, Jiatong Li, Weiran Huang, Xiangyu Yue, Wanli Ouyang, Dongzhan Zhou, Shufei Zhang, Mao Su, Han-Sen Zhong, Yuqiang Li. (2024). Chemllm: A chemical large language model. arXiv preprint arXiv:2402.06852.
Cite this work View paper
WWW 2024
Fast graph condensation with structure-based neural tangent kernel
CCF ALin Wang, Wenqi Fan, Jiatong Li, Yao Ma, and Qing Li. (2023). Fast graph condensation with structure-based neural tangent kernel. arXiv preprint arXiv:2310.11046. (Accepted by WWW 24)
Cite this work View paper
CCL 2024
MFE-NER: Multi-feature Fusion Embedding for Chinese Named Entity Recognition
CCF CJiatong Li, Kui Meng. (2024). MFE-NER: Multi-feature Fusion Embedding for Chinese Named Entity Recognition. In Proceedings of the 23rd Chinese National Conference on Computational Linguistics (Volume 1: Main Conference) (pp. 1112-1122). CCL 2024.
Cite this work View paper
ACL 2023
Conflicts, Villains, Resolutions: Towards models of Narrative Media Framing
CCF ALea Ferrmann, Jiatong Li, Shima Khanehzar, Gosia Mikolajczak. (2023). Conflicts, Villains, Resolutions: Towards models of Narrative Media Framing. ACL 2023.
Cite this work View paper
IJCAI 2023
Generative Diffusion Models on Graphs: Methods and Applications
CCF AWenqi Fan, Chengyi Liu, Yunqing Liu, Jiatong Li, Hang Li, Hui Liu, Jiliang Tang, Qing Li. (2023). Generative Diffusion Models on Graphs: Methods and Applications. IJCAI 2023.
Cite this work View paper
arXiv preprint
Improving Chinese Named Entity Recognition by Search Engine Augmentation
Mao, Q., Li, J., & Meng, K. (2022). Improving Chinese Named Entity Recognition by Search Engine Augmentation. arXiv preprint arXiv:2210.12662.
Cite this work View paper
arXiv preprint
Exploring Effective Information Utilization in Multi-Turn Topic-Driven Conversations
Li, J., He, B., & Mi, F. (2022). Exploring Effective Information Utilization in Multi-Turn Topic-Driven Conversations. arXiv preprint arXiv:2209.00250.
Cite this work View paper
Journal of Building Engineering
Generation of Hospital Emergency Department Layouts Based on Generative Adversarial Networks
IF 7.4Zhao, C. W., Yang, J., & Li, J. (2021). Generation of hospital emergency department layouts based on generative adversarial networks. Journal of Building Engineering, 43, 102539.
Cite this work View paper
Journal of Shanghai Jiaotong University (Science)
Two Generative Design Methods of Hospital Operating Department Layouts Based on Healthcare Systematic Layout Planning and Generative Adversarial Network
Zhao, C., Yang, J., Xiong, W., & Li, J. (2021). Two generative design methods of hospital operating department layouts based on healthcare systematic layout planning and generative adversarial network. Journal of Shanghai Jiaotong University (Science), 26, 103-115.
Cite this work View paper
Tutorials & workshops
- LLM Reasoning on Medicine: Challenges, Opportunities, and Future, INLG 2025 Workshop, Hanoi, Vietnam
- Recommender Systems in the Era of Large Language Models (LLMs), ICDM 2023 Tutorial, Shanghai, China
Teaching
Teaching Assistant at The Hong Kong Polytechnic University:
- COMP5584 Large Language Models for Agents, 2026/27 Semester 1
- COMP2411 Database Systems, 2023/24 Semester 1 and 2025/26 Semester 1
- COMP4434 Big Data Analytics, 2023/24 Semester 2
- COMP6703 Advanced Topics in Data Analytics, 2024/25 Semester 1
- COMP6713 Advanced Large Language Models and Beyond, 2024/25 Semester 2
Awards & honors
- Hong Kong PhD Fellowship Scheme, HKSAR Government, 2022
- Melbourne Graduate Grant, The University of Melbourne, 2021
- Finalist Award, Mathematical Contest in Modeling, 2020
Professional service
- Program Committee: AAAI 2024–2026, IIAI AAI 2026, PRICAI 2024–2025, WISE 2024
- Conference Reviewer: ICLR, NeurIPS, ICML, ACL, KDD, AISTATS
- Journal Reviewer: IEEE Transactions on Knowledge and Data Engineering, Journal of Cheminformatics, npj Digital Medicine, npj Artificial Intelligence, Language Resources and Evaluation, Knowledge and Information Systems