Our chemical chain-of-thought study is online. Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad ↗
AI × Molecular Science
Jiatong Li
From molecular learning to science agents.
I build language models that learn molecules, assist chemists, reason over structure, and execute verifiable scientific workflows.
Latest updates
News
Our analysis of molecular LLM generalization is online. Do LLMs Truly Generalize in the Molecular Domain? ↗
Our medical reasoning survey is accepted by Machine Intelligence Research. Aligning Clinical Needs and AI Capabilities ↗
Two papers are accepted by KDD 2026: Speak-to-Structure ↗ and Chem-R ↗, my first work as a co-corresponding author.
MolViBench is released, introducing a benchmark for molecular vibe coding across real-world drug-discovery workflows. Code ↗
MolReFlect is accepted by IEEE TKDE. Code ↗
CMPhysBench is accepted by ICLR 2026. Paper ↗
My research line
Can a model complete the scientific loop?
Each generation of my work moves the research object outward—from molecular representations, to reasoning processes, to workflows and verifiable deliverables.
Learn molecules
Can LLMs learn molecular mappings from a handful of local examples?
MolReGPT · ICMA · MolReFlectAssist chemists
Can a model translate natural-language requirements into valid molecular designs?
Speak-to-Structure (S²-Bench)Reason—and audit it
Can we improve chemical reasoning while checking which intermediate states truly matter?
Mol-R1 · Chem-R · Chemical CoTExecute workflows
Can models organize tools, state, chemistry, and artifacts into an end-to-end workflow?
MolViBench Grounded reasoning Executable workflows Reproducible artifacts
New in 2026
Latest research
Browse recent work across faithful reasoning, molecular generalization, scientific agents, open-ended design, and clinically grounded capability. Scroll sideways for more.
arXiv · Jul 2026 01
Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad
Chemical CoT can be causally useful as a structural scratchpad while remaining an unreliable explanation of how an answer was reached.
arXiv · Jul 2026 02
Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis
Controlled graph edits reveal a narrow local trust region in molecular LLMs and show how in-context tuning can partially stabilize it.
Machine Intelligence Research · 2026 03
Aligning Clinical Needs and AI Capabilities: A Survey on LLMs for Medical Reasoning
A dual clinical–computational view of medical reasoning, paired with a five-level benchmark across 18 state-of-the-art models.
arXiv · May 2026 04
MolViBench: Evaluating LLMs on Molecular Vibe Coding
A benchmark for executable molecular coding across 12 real-world drug-discovery workflows.
KDD · 2026 05
Speak-to-Structure: Open-Domain Natural Language-Driven Molecule Generation
S²-Bench evaluates one-to-many molecular design from natural-language requirements.
KDD · 2026 06
Chem-R: Learning to Reason as a Chemist
A three-phase chemical reasoning model spanning molecular- and reaction-level tasks.
IEEE TKDE · 2026 07
MolReFlect: Fine-Grained Alignments Between Molecules and Texts
An in-context reflection framework for precise molecule–text alignment.
ICLR · 2026 08
CMPhysBench: Evaluating LLMs in Condensed Matter Physics
A fine-grained benchmark for calculation-intensive reasoning in condensed matter physics.
Selected
Recent publications
A selection spanning molecular language models, scientific reasoning, alignment, and multimodal robustness.
- 2026arXiv
Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad
Jiatong Li, Yuxuan Ren, Weida Wang, Xiaoyong Wei, Yatao Bian
- 2026arXiv
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, Qing Li
- 2026MIR
Aligning Clinical Needs and AI Capabilities: A Survey on LLMs for Medical Reasoning
Qi Peng*, Jiatong Li*, Sirui Huang, Yiyang Jiang, Kaisong Gong, et al.
- 2026arXiv
MolViBench: Evaluating LLMs on Molecular Vibe Coding
Jiatong Li, Yuxuan Ren, Weida Wang, Changmeng Zheng, Xiao-yong Wei, Qing Li, Yatao Bian
- 2026IEEE TKDE
MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts
Jiatong Li, Yunqing Liu, Wei Liu, Jingdi Lei, Di Zhang, Wenqi Fan, Dongzhan Zhou, Yuqiang Li, Qing Li
- 2026KDD
Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation
Jiatong Li, Junxian Li, Weida Wang, Yunqing Liu, Changmeng Zheng, Yatao Bian, et al.
- 2026KDD
Chem-R: Learning to Reason as a Chemist
Weida Wang, Benteng Chen, Di Zhang, et al., Jiatong Li, et al. · Co-corresponding author
- 2026ICLR
CMPhysBench: A Benchmark for Evaluating Large Language Models in Condensed Matter Physics
Weida Wang*, Dongchen Huang*, Jiatong Li*, Tengchao Yang, et al. · Co-first author
- 2026CVPR
IAG: Input-Aware Backdoor Attack on VLM-Based Visual Grounding
Junxian Li, Beining Xu, Simin Chen, Jiatong Li, Jingdi Lei, Haodong Zhao, Di Zhang
- 2025IEEE TKDE
Large Language Models are In-Context Molecule Learners
Jiatong Li, Wei Liu, Zhihao Ding, Wenqi Fan, Yuqiang Li, Qing Li
- 2025arXiv
Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery
Jiatong Li, Weida Wang, Qinggang Zhang, Junxian Li, Di Zhang, Changmeng Zheng, et al.
Background
Research journey
Training across information security, natural language processing, and AI-driven molecular discovery.
Education
- 2023—Now Ph.D. Candidate, Computing
The Hong Kong Polytechnic University · HKPFS
- 2021—2022 Master of Information Technology
The University of Melbourne · Dean’s Honor List
- 2017—2021 B.Eng. in Information Security
Shanghai Jiao Tong University
Research experience
- 2026—Now Visiting Scholar
BlueWhale Lab ↗ · National University of Singapore
- 2023—2024 Algorithm Researcher
Shanghai AI Laboratory
- 2021—2022 Algorithm Researcher
Noah’s Ark Lab
Beyond papers
Teaching & service
Teaching Assistant · PolyU
- COMP2411 Database Systems
- COMP4434 Big Data Analytics
- COMP6703 Advanced Topics in Data Analytics
- COMP6713 Advanced Large Language Models and Beyond
Program committees & reviewing
PC: AAAI 2024–2026, IIAI AAI 2026, PRICAI 2024–2025, WISE 2024.
Reviewer: ICLR, NeurIPS, ICML, ACL, KDD, AISTATS, IEEE TKDE, Journal of Cheminformatics, npj Digital Medicine, and more.
Tutorials & workshops
Recognition
Honors
HKSAR Government
The University of Melbourne
Mathematical Contest in Modeling
On repeat
A little life beyond the lab.
When I am not working with molecules and models, there is usually music somewhere nearby.
Collaborate
Let’s make scientific AI more capable—and more honest.
I am always happy to talk about molecular language models, scientific reasoning, and potential collaborations.
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