(*=equal contribution)

Journals

Benchmarking and Developing Large Language Models Using One Million Clinical Trials
Zifeng Wang*, Jiacheng Lin*, Qiao Jin*, Junyi Gao, Jathurshan Pradeepkumar, Pengcheng Jiang, Zhiyong Lu, Jimeng Sun
npj Digital Medicine, 2026 • Paper • Project • Dataset • Models

DiffKGW: Stealthy and Robust Diffusion Model Watermarking
Tianxin Wei, Ruizhong Qiu, Yifan Chen, Yunzhe Qi, Jiacheng Lin, Wenxuan Bao, Wenju Xu, Sreyashi Nag, Ruirui Li, Hanqing Lu, Zhengyang Wang, Chen Luo, Hui Liu, Suhang Wang, Jingrui He, Qi He, Xianfeng Tang
TMLR, 2026 • Paper

Rec-R1: Bridging Generative Large Language Models and User-Centric Recommendation Systems via Reinforcement Learning
Jiacheng Lin, Tian Wang, Kun Qian
TMLR, 2025 • Paper • Code

Pisces: A multi-modal data augmentation approach for drug combination synergy prediction
Hanwen Xu*, Jiacheng Lin∗, Addie Woicik, Zixuan Liu, Jianzhu Ma, Sheng Zhang, Hoifung Poon, Liewei Wang, Sheng Wang
Cell Genomics, 2025 • Paper • Code

EpiAgent: Foundation model for single-cell epigenomic data
Xiaoyang Chen, Keyi Li, Xuejian Cui, Zian Wang, Qun Jiang, Jiacheng Lin, Zhen Li, Zijing Gao, Rui Jiang
Nature Methods, 2025 • Paper

R²-DDI: Relation-aware Feature Refinement for Drug-Drug Interaction Prediction
Jiacheng Lin, Lijun Wu, Jinhua Zhu, Xiaobo Liang, Yingce Xia, Shufang Xie, Tao Qin and Tie-Yan Liu
Briefings in Bioinformatics, Volume 24, Issue 1, 2023 • Paper • Code

Learning to branch with Tree-aware Branching Transformers
Jiacheng Lin, Jialin Zhu, Huangang Wang and Tao Zhang
Knowledge-Based Systems, Volume 252, 2022, 109455, ISSN 0950-7051 • Paper • Code

Conferences

SFT Doesn’t Always Hurt General Capabilities: Revisiting Domain-Specific Fine-Tuning in LLMs
Jiacheng Lin, Zhongruo Wang, Kun Qian, Tian Wang, Arvind Srinivasan, Hansi Zeng, Ruocheng Jiao, Xie Zhou, Jiri Gesi, Dakuo Wang, Yufan Guo, Kai Zhong, Weiqi Zhang, Sujay Sanghavi, Changyou Chen, Hyokun Yun, Lihong Li
ICLR, 2026 • Paper

Shop-R1: Rewarding LLMs to Simulate Human Behavior in Online Shopping via Reinforcement Learning
Yimeng Zhang, Tian Wang, Jiri Gesi, Ziyi Wang, Yuxuan Lu, Jiacheng Lin, Sinong Zhan, Vianne Gao, Ruochen Jiao, Junze Liu, Kun Qian, Yuxin Tang, Ran Xue, Houyu Zhang, Qingjun Cui, Yufan Guo, Dakuo Wang
ICLR, 2026 • Paper

s3: You Don’t Need That Much Data to Train a Search Agent via RL
Pengcheng Jiang, Xueqiang Xu, Jiacheng Lin, Jinfeng Xiao, Zifeng Wang, Jimeng Sun, Jiawei Han
EMNLP, 2025 • Paper

DeepRetrieval: Hacking Real Search Engines and Retrievers with Large Language Models via Reinforcement Learning
Pengcheng Jiang*, Jiacheng Lin∗, Lang Cao, Runchu Tian, SeongKu Kang, Zifeng Wang, Jimeng Sun, Jiawei Han
COLM, 2025 • Paper • Code

Cascade Speculative Drafting for Even Faster LLM Inference
Ziyi Chen, Xiaocong Yang, Jiacheng Lin, Chenkai Sun, Kevin Chen-Chuan Chang, and Jie Huang
NeurIPS, 2024 • Paper

HiCRISP: An LLM-Based Hierarchical Closed-Loop Robotic Intelligent Self-Correction Planner
Chenlin Ming, Jiacheng Lin, Pangkit Fong, Han Wang, Xiaoming Duan and Jianping He
CAC, 2024 • Paper • Code

GENRES: Rethinking Evaluation for Generative Relation Extraction in the Era of Large Language Models
Pengcheng Jiang, Jiacheng Lin, Zifeng Wang, Jimeng Sun, and Jiawei Han
NAACL, 2024 • Paper

CAMBranch: Contrastive Learning with Augmented MILPs for Branching
Jiacheng Lin∗, Meng Xu*, Zhihua Xiong, and Huangang Wang
ICLR, 2024 • Paper

Pisces: A cross-modal contrastive learning approach to synergistic drug combination prediction
Jiacheng Lin∗, Hanwen Xu∗, Addie Woicik, Jianzhu Ma and Sheng Wang
RECOMB, 2023 • Paper • Code

GT2VEC: Large Language Models as Multi-Modal Encoders for Text and Graph-Structured Data
Jiacheng Lin, Kun Qian, Haoyu Han, Nurendra Choudhary, Tianxin Wei, Zhongruo Wang, Sahika Genc, Edward W Huang, Sheng Wang, Karthik Subbian, Danai Koutra, Jimeng Sun
KDD 2025 Workshop SKnow-LLM, 2025 • Paper

Preprint

TrialAtlas: Multi-Agent Research Organization for Clinical Trial Design and Optimization
Jiacheng Lin, Zifeng Wang, Zheng Chen, Erick Scott, Ziwei Yang, Fanyang Yu, Sheng Zhong, Jimeng Sun
Preprint, 2026 • Paper

Apodex 1.1: Scaling Agentic Intelligence for Complex Work
Apodex Team
Technical Report, 2026 • Paper • Website • Code • Models

Apodex Discovery: Reality Benchmarks and Environments for Evaluating and Building Discoverative Artificial Intelligence
Brian Wang, Bin Feng, Xiaoman Pan, Chenyang An, Felix Liu, Tangqi Fang, Gongbo Sun, Lingfeng Shen, Ning Wang, Handuo Zhang, Feng Chen, Fuchao Yang, Xiang Wang, Jiacheng Lin, Siting Li, Zixuan Liu, Chi Han, Zhenhailong Wang, Kunlun Zhu, Lawrence Zhao, Yueqi Guo, Kailong Wen, Feng Xing, Yiling Guo, Lidong Bing, David Tan, Bo An, Heng Ji, Sheng Wang
Preprint, 2026 • Paper

Apodex-1.0: A Verification-Centric Agent Team for Discoverative Intelligence
Apodex Team
Technical Report, 2026 • Blog

LLM Agents Enable User-Governed Personalization Beyond Platform Boundaries
Jiacheng Lin, Kun Qian, Arvind Srinivasan, Tian Wang, Fang Han, Changran Hu, Junze Liu, Ziyi Wang, Hanwen Xu, Mengmeng Xue, Shuo Yang, Hansi Zeng, Simon Sinong Zhan, Kai Zhong, Weiqi Zhang, Dakuo Wang, Tianhao Wang, Zhiyuan Li
Preprint, 2026 • Paper

SynPlanResearch-R1: Encouraging Tool Exploration for Deep Research with Synthetic Plans
Hansi Zeng, Zoey Li, Yifan Gao, Chenwei Zhang, Xiaoman Pan, Tao Yang, Fengran Mo, Jiacheng Lin, Xian Li, Jingbo Shang
Preprint, 2026 • Paper

Adaptation of Agentic AI: A Survey of Post-Training, Memory, and Skills
Pengcheng Jiang*, Jiacheng Lin*, Zhiyi Shi*, Zifeng Wang, Luxi He, Yichen Wu, Ming Zhong, Peiyang Song, Qizheng Zhang, Heng Wang, Xueqiang Xu, Hanwen Xu, Pengrui Han, Dylan Zhang, Jiashuo Sun, Chaoqi Yang, Kun Qian, Tian Wang, Changran Hu, Manling Li, Quanzheng Li, Hao Peng, Sheng Wang, Jingbo Shang, Chao Zhang, Jiaxuan You, Liyuan Liu, Pan Lu, Yu Zhang, Heng Ji, Yejin Choi, Dawn Song, Jimeng Sun, Jiawei Han
Preprint, 2025 • Paper

Training LLMs for EHR-Based Reasoning Tasks via Reinforcement Learning
Jiacheng Lin, Zhenbang Wu, Jimeng Sun
Preprint, 2025 • Paper

Panacea: A foundation model for clinical trial search, summarization, design, and recruitment
Jiacheng Lin, Hanwen Xu, Zifeng Wang, Sheng Wang, Jimeng Sun
Preprint, 2024 • Paper • Code

Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on Language, Multimodal, and Scientific GPT Models
Kaiyuan Gao, Sunan He, Zhenyu He, Jiacheng Lin (All authors contribute equally), QiZhi Pei, Jie Shao, Wei Zhang
Preprint, 2023 • Paper • Code