Publications

2026

Improving Cross-Format Robustness in Language Models with Multi-Format Training

June M. Liu, S Zheng, H Cao, D Jin, Q Cui, J Zhou

arXiv preprint arXiv:2606.11643, 2026.

2026

From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models

H Guo, H Li, H Cao, G Zhang, L Yuan

arXiv preprint arXiv:2606.03660, 2026.

2026

MolGram: Molecular Language Models with Conditional n-gram Memory

X Zhang, Z Liu, H Cao, Y Li, Irwin King

2026

Beyond Fitting: Knowledge-Guided LLM Reasoning for Combinatorial Gene Perturbation Prediction

Z Jiang, X Zhi, H Cao, Z liu, M Peng, Z Gao

2026

Divergence Decoding: Training-Free Capability Fusion

Y Wang, H Li, S Yang, H Cao, C Zhang, Z Wu, Z Yan, F mo, L Yuan

2026

FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization

Q Zhang, H Cao, H Li, Y Shao, Z Liu, S Wang, S Xie, S Gao, X Ye

ICML2026 GenBio Workshop

2026

ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design

Y Zhang, H Cao, Z Jiang, C Zi, Z Zhou, Z Liu, Y Li, J Li, Z Gao

arXiv preprint arXiv:2605.10189, 2026.

2026

Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization

X Ye, H Cao, H Li, B Feng, Z Liu, X Tang, Y Li, S Gao

ICML2026 GenBio Workshop

2026

Beyond chemical qa: Evaluating llm's chemical reasoning with modular chemical operations

L Hao, H Cao, B Feng, D Shao, R Tang, Z Yan, Y Tian, L Yuan, Y Li

Advances in Neural Information Processing Systems 38, 2026.

2026

Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis

H Li, H Cao, S Peng, Z Liu, B Feng, Y Wang, Z Yan, Y Tian, Y Li, L Yuan

arXiv preprint arXiv:2601.17687, 2026.

2026

BioClaw: Human-Bot Research Collaboration Ecosystems in Group Chats

M Xu, J Yan, R Feng, Q Cai, P Zhang, C Zhao, C He, Z Wei, J Li, S Lin, ...

bioRxiv, 2026.04.11.716807, 2026.

2026

Mozi: Governed autonomy for drug discovery llm agents

H Cao, S Liu, F Zhang, Z Liu, H Li, B Feng, S Bai, L Chen, K Xie, Y Li

arXiv preprint arXiv:2603.03655, 2026.

2026

ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams

Q Xu, S Bai, Y Wang, H Cao, L Chen, Y Liu, B Feng, Z Liu, Y Li

arXiv preprint arXiv:2604.15994, 2026.

2026

Test-Time Self-Evolution in Multi-Agent Systems for Materials Discovery

T Wen, S Liu, B Hu, B YE, H Cao, DJ Srolovitz

AI4X 2026 Conference (Oral), 2026.

2025

Hierarchical affinity landscape navigation through learning a shared pocket-ligand space

B Feng, Z Liu, H Li, M Yang, J Zou, H Cao, Y Li, L Zhang, S Wang

Patterns 6 (10), 2025.

2025

How to detect and defeat molecular mirage: A metric-driven benchmark for hallucination in llm-based molecular comprehension

H Li, L Lv, H Cao, Z Liu, Z Yan, Y Wang, Y Tian, Y Li, L Yuan

NeurIPS 2025 AI4S Discovery Workshop

2025

A foundation model for protein-ligand affinity prediction through jointly optimizing virtual screening and hit-to-lead optimization

B Feng, Z Liu, M Yang, J Zou, H Cao, Y Li, L Zhang, S Wang

bioRxiv, 2025.02.17.638554, 2025.

2025

Rethinking Text-based Protein Understanding: Retrieval or LLM?

J Wu, Z Liu, H Cao, H Li, B Feng, Z Shu, K Yu, L Yuan, Y Li

EMNLP 2025 Oral, 2025.

2025

Dynamic guided and domain applicable safeguards for enhanced security in large language models

W Luo, H Cao, Z Liu, Y Wang, A Wong, B Feng, Y Yao, Y Li

NAACL 2025

2025

CAPE: A Chinese Dataset for Appraisal-based Emotional Generation in Large Language Models

JM Liu, H Cao, R Sun, R Wang, Y Li, J Zhang

NAACL 2025

2025

ControlMol: Adding Substructure Control To Molecule Diffusion Models

Z Qi, Z Liu, J Zhang, H Cao, X Xu, Y Li

ICASSP 2025 IEEE International Conference on Acoustics, Speech and Signal Processing, 2025.

2025

From Static Structures to Ensembles: Studying and Harnessing Protein Structure Tokenization

Z Liu, B Feng, H Cao, Y Li

NeurIPS 2025 AI4S Discovery Workshop

2024

Grounded sam: Assembling open-world models for diverse visual tasks

T Ren, S Liu, A Zeng, J Lin, K Li, H Cao, J Chen, X Huang, Y Chen, F Yan, ...

ICCV 2023 Demo Track

2024

Moleculeqa: A dataset to evaluate factual accuracy in molecular comprehension

X Lu, H Cao, Z Liu, S Bai, L Chen, Y Yao, HT Zheng, Y Li

EMNLP 2024

2024

PRESTO: Progressive pretraining enhances synthetic chemistry outcomes

H Cao, Y Shao, Z Liu, Z Liu, X Tang, Y Yao, Y Li

EMNLP 2024

2024

Smiles-prompting: A novel approach to llm jailbreak attacks in chemical synthesis

A Wong, H Cao, Z Liu, Y Li

arXiv preprint arXiv:2410.15641, 2024.

2024

Efficient antibody structure refinement using energy-guided se (3) flow matching

J Zhang, Z Liu, S Bai, H Cao, Y Li, L Zhang

IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2024.

2023

Chatcounselor: A large language models for mental health support

JM Liu, H Cao, D Li, T Ren, Z Liao, J Wu

International Workshop on Personalized Generative AI @ CIKM 2023.

2023

Instructmol: Multi-modal integration for building a versatile and reliable molecular assistant in drug discovery

H Cao, Z Liu, X Lu, Y Yao, Y Li

COLING 2025

2023

Dreamwaltz: Make a scene with complex 3d animatable avatars

Y Huang, J Wang, A Zeng, H Cao, X Qi, Y Shi, ZJ Zha, L Zhang

Advances in Neural Information Processing Systems 36, 4566-4584, 2023.

2023

Inducing neural collapse in deep long-tailed learning

X Liu, J Zhang, T Hu, H Cao, Y Yao, L Pan

International Conference on Artificial Intelligence and Statistics, 11534-11544, 2023.

2023

detrex: Benchmarking detection transformers

T Ren, S Liu, F Li, H Zhang, A Zeng, J Yang, X Liao, D Jia, H Li, H Cao, ...

arXiv preprint arXiv:2306.07265, 2023.

2023

Toss: High-quality text-guided novel view synthesis from a single image

Y Shi, H Cao, J Wang, B Tang, X Qi, T Yang, Y Huang, S Liu, L Zhang, ...

ICLR 2023

2023

Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches

J Wu, H Cao, Y Yao

arXiv preprint arXiv:2309.16684, 2023.

2022

Exploring vision transformers as diffusion learners

H Cao, J Wang, T Ren, X Qi, Y Chen, Y Yao, L Zhang

arXiv preprint arXiv:2212.13771, 2022.