Synthesis of Probability Theory Based on Molecular Computation. - Ziyuan Shen; Chuan Zhang 001; Lulu Ge; Yuchen Zhuang; Bo Yuan 001; Xiaohu You 001 (SiPS, 2016)

A synthesis flow for fast convolution unit based on molecular reactions. - Yuchen Zhuang; Lulu Ge; Wei Wei; Jing Zhao; Xiaohu You 001; Chuan Zhang 001 (WCSP, 2017)

Arithmetic Computations Based on Chemical Reaction Networks. - Yuchen Zhuang; Chongzhou Fang; Zaichen Zhang; Xiaohu You 001; Chuan Zhang 001 (SiPS, 2018)

DNA computing for combinational logic. - Chuan Zhang 001; Lulu Ge; Yuchen Zhuang; Ziyuan Shen; Zhiwei Zhong; Zaichen Zhang; Xiaohu You 001 (Sci. China Inf. Sci., 2019)

EXAM: An Explainable Attention-based Model for COVID-19 Automatic Diagnosis. - Wenqi Shi; Li Tong 001; Yuchen Zhuang; Yuanda Zhu; May D. Wang (BCB, 2020)

Calibrated Language Model Fine-Tuning for In- and Out-of-Distribution Data. - Lingkai Kong; Haoming Jiang; Yuchen Zhuang; Jie Lyu 005; Tuo Zhao; Chao Zhang 014 (EMNLP (1), 2020)

ReSel: N-ary Relation Extraction from Scientific Text and Tables by Learning to Retrieve and Select. - Yuchen Zhuang; Yinghao Li; Junyang Zhang; Yue Yu 001; Yingjun Mou; Xiang Chen; Le Song; Chao Zhang 014 (EMNLP, 2022)

End-to-end Stochastic Optimization with Energy-based Model. - Lingkai Kong; Jiaming Cui; Yuchen Zhuang; Rui Feng; B. Aditya Prakash; Chao Zhang 014 (NeurIPS, 2022)

ReSel: N-ary Relation Extraction from Scientific Text and Tables by Learning to Retrieve and Select. - Yuchen Zhuang; Yinghao Li; Jerry Junyang Cheung; Yue Yu 001; Yingjun Mou; Xiang Chen; Le Song; Chao Zhang 014 (CoRR, 2022)

ReGen: Zero-Shot Text Classification via Training Data Generation with Progressive Dense Retrieval. - Yue Yu 001; Yuchen Zhuang; Rongzhi Zhang; Yu Meng 001; Jiaming Shen; Chao Zhang 014 (ACL (Findings), 2023)

Retrieval-Augmented Large Language Models for Adolescent Idiopathic Scoliosis Patients in Shared Decision-Making. - Wenqi Shi; Yuchen Zhuang; Yuanda Zhu; Henry J. Iwinski; J. Michael Wattenbarger; May Dongmei Wang (BCB, 2023)

G-STO: Sequential Main Shopping Intention Detection via Graph-Regularized Stochastic Transformer. - Yuchen Zhuang; Xin Shen; Yan Zhao; Chaosheng Dong; Ming Wang; Jin Li 003; Chao Zhang 014 (CIKM, 2023)

Autoregressive Diffusion Model for Graph Generation. - Lingkai Kong; Jiaming Cui; Haotian Sun; Yuchen Zhuang; B. Aditya Prakash; Chao Zhang 014 (ICML, 2023)

DyGen: Learning from Noisy Labels via Dynamics-Enhanced Generative Modeling. - Yuchen Zhuang; Yue Yu 001; Lingkai Kong; Xiang Chen; Chao Zhang 014 (KDD, 2023)

AdaPlanner: Adaptive Planning from Feedback with Language Models. - Haotian Sun; Yuchen Zhuang; Lingkai Kong; Bo Dai 001; Chao Zhang 014 (NeurIPS, 2023)

Large Language Model as Attributed Training Data Generator: A Tale of Diversity and Bias. - Yue Yu 001; Yuchen Zhuang; Jieyu Zhang 001; Yu Meng 001; Alexander J. Ratner; Ranjay Krishna; Jiaming Shen; Chao Zhang 014 (NeurIPS, 2023)

ToolQA: A Dataset for LLM Question Answering with External Tools. - Yuchen Zhuang; Yue Yu 001; Kuan Wang; Haotian Sun; Chao Zhang 014 (NeurIPS, 2023)

MUBen: Benchmarking the Uncertainty of Pre-Trained Models for Molecular Property Prediction. - Yinghao Li; Lingkai Kong; Yuanqi Du; Yue Yu 001; Yuchen Zhuang; Wenhao Mu; Chao Zhang 014 (CoRR, 2023)

DF2: Distribution-Free Decision-Focused Learning. - Lingkai Kong; Wenhao Mu; Jiaming Cui; Yuchen Zhuang; B. Aditya Prakash; Bo Dai 001; Chao Zhang 014 (CoRR, 2023)

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models. - Ran Xu 002; Hejie Cui; Yue Yu 001; Xuan Kan; Wenqi Shi; Yuchen Zhuang; Wei Jin 009; Joyce C. Ho; Carl Yang 001 (CoRR, 2023)

How Many Validation Labels Do You Need? Exploring the Design Space of Label-Efficient Model Ranking. - Zhengyu Hu; Jieyu Zhang 001; Yue Yu 001; Yuchen Zhuang; Hui Xiong 001 (CoRR, 2023)

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models. - Ran Xu 002; Hejie Cui; Yue Yu 001; Xuan Kan; Wenqi Shi; Yuchen Zhuang; May Dongmei Wang; Wei Jin 009; Joyce C. Ho; Carl Yang 001 (ACL (Findings), 2024)

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records. - Ran Xu 002; Wenqi Shi; Yue Yu 001; Yuchen Zhuang; Bowen Jin; May Dongmei Wang; Joyce C. Ho; Carl Yang 001 (ACL (Short Papers), 2024)

Two Birds with One Stone: Enhancing Uncertainty Quantification and Interpretability with Graph Functional Neural Process. - Lingkai Kong; Haotian Sun; Yuchen Zhuang; Haorui Wang; Wenhao Mu; Chao Zhang 014 (AISTATS, 2024)

HiGen: Hierarchy-Aware Sequence Generation for Hierarchical Text Classification. - Vidit Jain; Mukund Rungta; Yuchen Zhuang; Yue Yu 001; Zeyu Wang; Mu Gao; Jeffrey Skolnick; Chao Zhang 014 (EACL (1), 2024)

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers. - Ran Xu 002; Wenqi Shi; Yue Yu 001; Yuchen Zhuang; Yanqiao Zhu 001; May Dongmei Wang; Joyce C. Ho; Chao Zhang 014; Carl Yang 001 (EMNLP, 2024)

MedAdapter: Efficient Test-Time Adaptation of Large Language Models Towards Medical Reasoning. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Haotian Sun; Hang Wu; Carl Yang 001; May Dongmei Wang (EMNLP, 2024)

EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Jieyu Zhang 001; Hang Wu; Yuanda Zhu; Joyce C. Ho; Carl Yang 001; May Dongmei Wang (EMNLP, 2024)

ToolChain*: Efficient Action Space Navigation in Large Language Models with A* Search. - Yuchen Zhuang; Xiang Chen; Tong Yu 001; Saayan Mitra; Victor S. Bursztyn; Ryan A. Rossi; Somdeb Sarkhel; Chao Zhang 014 (ICLR, 2024)

BBox-Adapter: Lightweight Adapting for Black-Box Large Language Models. - Haotian Sun; Yuchen Zhuang; Wei Wei 019; Chao Zhang 014; Bo Dai 001 (ICML, 2024)

POLYIE: A Dataset of Information Extraction from Polymer Material Scientific Literature. - Jerry Junyang Cheung; Yuchen Zhuang; Yinghao Li; Pranav Shetty; Wantian Zhao; Sanjeev Grampurohit; Rampi Ramprasad; Chao Zhang 014 (NAACL-HLT, 2024)

Aligning Large Language Models with Representation Editing: A Control Perspective. - Lingkai Kong; Haorui Wang; Wenhao Mu; Yuanqi Du; Yuchen Zhuang; Yifei Zhou; Yue Song; Rongzhi Zhang; Kai Wang; Chao Zhang 014 (NeurIPS, 2024)

HYDRA: Model Factorization Framework for Black-Box LLM Personalization. - Yuchen Zhuang; Haotian Sun; Yue Yu 001; Rushi Qiang; Qifan Wang 001; Chao Zhang 014; Bo Dai 001 (NeurIPS, 2024)

EHRAgent: Code Empowers Large Language Models for Complex Tabular Reasoning on Electronic Health Records. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Jieyu Zhang 001; Hang Wu; Yuanda Zhu; Joyce C. Ho; Carl Yang 001; May D. Wang (CoRR, 2024)

TPD: Enhancing Student Language Model Reasoning via Principle Discovery and Guidance. - Haorui Wang; Rongzhi Zhang; Yinghao Li; Lingkai Kong; Yuchen Zhuang; Xiusi Chen; Chao Zhang 014 (CoRR, 2024)

MedAdapter: Efficient Test-Time Adaptation of Large Language Models towards Medical Reasoning. - Wenqi Shi; Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Hang Wu; Carl Yang 001; May D. Wang (CoRR, 2024)

Efficient Evolutionary Search Over Chemical Space with Large Language Models. - Haorui Wang; Marta Skreta; Cher Tian Ser; Wenhao Gao 001; Lingkai Kong; Felix Streith-Kalthoff; Chenru Duan; Yuchen Zhuang; Yue Yu 001; Yanqiao Zhu 001; Yuanqi Du; Alán Aspuru-Guzik; et al. (CoRR, 2024)

Matryoshka: Learning to Drive Black-Box LLMs with LLMs. - Changhao Li; Yuchen Zhuang; Rushi Qiang; Haotian Sun; Hanjun Dai; Chao Zhang 014; Bo Dai 001 (CoRR, 2024)

MUBen: Benchmarking the Uncertainty of Molecular Representation Models. - Yinghao Li; Lingkai Kong; Yuanqi Du; Yue Yu 001; Yuchen Zhuang; Wenhao Mu; Chao Zhang 014 (Trans. Mach. Learn. Res., 2024)

Efficient Evolutionary Search Over Chemical Space with Large Language Models. - Haorui Wang; Marta Skreta; Cher Tian Ser; Wenhao Gao 001; Lingkai Kong; Felix Strieth-Kalthoff; Chenru Duan; Yuchen Zhuang; Yue Yu 001; Yanqiao Zhu 001; Yuanqi Du; Alán Aspuru-Guzik; et al. (ICLR, 2025)

Hephaestus: Improving Fundamental Agent Capabilities of Large Language Models through Continual Pre-Training. - Yuchen Zhuang; Jingfeng Yang 001; Haoming Jiang; Xin Liu 039; Kewei Cheng; Sanket Lokegaonkar; Yifan Gao 001; Qing Ping; Tianyi Liu; Binxuan Huang; Zheng Li 018; Zhengyang Wang; et al. (NAACL (Long Papers), 2025)

DF2: Distribution-Free Decision-Focused Learning. - Lingkai Kong; Wenhao Mu; Jiaming Cui; Yuchen Zhuang; B. Aditya Prakash; Bo Dai 001; Chao Zhang 014 (UAI, 2025)

Frame Extraction Person Retrieval Framework Based on Improved YOLOv8s and the Stage-Wise Clustering Person Re-Identification. - Jianjun Zhuang; Nan Wang; Yuchen Zhuang; Yong Hao (IET Image Process., 2025)

Collab-RAG: Boosting Retrieval-Augmented Generation for Complex Question Answering via White-Box and Black-Box LLM Collaboration. - Ran Xu 002; Wenqi Shi; Yuchen Zhuang; Yue Yu 001; Joyce C. Ho; Haoyu Wang; Carl Yang 001 (CoRR, 2025)

MLE-Dojo: Interactive Environments for Empowering LLM Agents in Machine Learning Engineering. - Rushi Qiang; Yuchen Zhuang; Yinghao Li; Dingu Sagar V. K; Rongzhi Zhang; Changhao Li; Ian Shu-Hei Wong; Sherry Yang 001; Percy Liang; Chao Zhang 014; Bo Dai 001 (CoRR, 2025)

AmorLIP: Efficient Language-Image Pretraining via Amortization. - Haotian Sun; Yitong Li; Yuchen Zhuang; Niao He; Hanjun Dai; Bo Dai 001 (CoRR, 2025)

Towards Better Instruction Following Retrieval Models. - Yuchen Zhuang; Aaron Trinh; Rushi Qiang; Haotian Sun; Chao Zhang 014; Hanjun Dai; Bo Dai 001 (CoRR, 2025)

WorkForceAgent-R1: Incentivizing Reasoning Capability in LLM-based Web Agents via Reinforcement Learning. - Yuchen Zhuang; Di Jin; Jiaao Chen; Wenqi Shi; Hanrui Wang; Chao Zhang (CoRR, 2025)

MSQA: Benchmarking LLMs on Graduate-Level Materials Science Reasoning and Knowledge. - Jerry Junyang Cheung; Shiyao Shen; Yuchen Zhuang; Yinghao Li; Rampi Ramprasad; Chao Zhang 014 (CoRR, 2025)

MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale. - Ran Xu 002; Yuchen Zhuang; Yishan Zhong; Yue Yu 001; Xiangru Tang; Hang Wu; May D. Wang; Peifeng Ruan; Donghan Yang; Tao Wang 006; Guanghua Xiao; Carl Yang 001; et al. (CoRR, 2025)

RAG in the Wild: On the (In)effectiveness of LLMs with Mixture-of-Knowledge Retrieval Augmentation. - Ran Xu 002; Yuchen Zhuang; Yue Yu 001; Haoyu Wang; Wenqi Shi; Carl Yang 001 (CoRR, 2025)

CellForge: Agentic Design of Virtual Cell Models. - Xiangru Tang; Zhuoyun Yu; Jiapeng Chen; Yan Cui; Daniel Shao; Weixu Wang; Fang Wu; Yuchen Zhuang; Wenqi Shi; Zhi Huang; Arman Cohan; Xihong Lin; et al. (CoRR, 2025)