Open Science: Tools, Approaches, and Implications. - Cameron Neylon; Shirley Wu (Pacific Symposium on Biocomputing, 2009)

Microblogging the ISMB: A New Approach to Conference Reporting. - Neil F. W. Saunders; Pedro Beltrão; Lars Juhl Jensen; Daniel Jurczak; Roland Krause; Michael Kuhn 004; Shirley Wu (PLoS Comput. Biol., 2009)

Efficient Automatic Machine Learning via Design Graphs. - Shirley Wu; Jiaxuan You; Jure Leskovec; Rex Ying (CoRR, 2022)

Discover and Cure: Concept-aware Mitigation of Spurious Correlation. - Shirley Wu; Mert Yüksekgönül; Linjun Zhang; James Zou 001 (ICML, 2023)

Med-Flamingo: a Multimodal Medical Few-shot Learner. - Michael Moor; Qian Huang; Shirley Wu; Michihiro Yasunaga; Yash Dalmia; Jure Leskovec; Cyril Zakka; Eduardo Pontes Reis; Pranav Rajpurkar (ML4H@NeurIPS, 2023)

D4Explainer: In-distribution Explanations of Graph Neural Network via Discrete Denoising Diffusion. - Jialin Chen; Shirley Wu; Abhijit Gupta; Rex Ying (NeurIPS, 2023)

Communication-Free Distributed GNN Training with Vertex Cut. - Kaidi Cao; Rui Deng; Shirley Wu; Edward W. Huang; Karthik Subbian; Jure Leskovec (CoRR, 2023)

D4Explainer: In-Distribution GNN Explanations via Discrete Denoising Diffusion. - Jialin Chen; Shirley Wu; Abhijit Gupta; Rex Ying (CoRR, 2023)

Holistic Analysis of Hallucination in GPT-4V(ision): Bias and Interference Challenges. - Chenhang Cui; Yiyang Zhou; Xinyu Yang 002; Shirley Wu; Linjun Zhang; James Zou 001; Huaxiu Yao (CoRR, 2023)

GraphMETRO: Mitigating Complex Distribution Shifts in GNNs via Mixture of Aligned Experts. - Shirley Wu; Kaidi Cao; Bruno Ribeiro 001; James Zou 001; Jure Leskovec (CoRR, 2023)

GraphMETRO: Mitigating Complex Graph Distribution Shifts via Mixture of Aligned Experts. - Shirley Wu; Kaidi Cao; Bruno Ribeiro 001; James Y. Zou; Jure Leskovec (NeurIPS, 2024)

AvaTaR: Optimizing LLM Agents for Tool Usage via Contrastive Reasoning. - Shirley Wu; Shiyu Zhao; Qian Huang; Kexin Huang; Michihiro Yasunaga; Kaidi Cao; Vassilis N. Ioannidis; Karthik Subbian; Jure Leskovec; James Y. Zou (NeurIPS, 2024)

STaRK: Benchmarking LLM Retrieval on Textual and Relational Knowledge Bases. - Shirley Wu; Shiyu Zhao; Michihiro Yasunaga; Kexin Huang; Kaidi Cao; Qian Huang; Vassilis N. Ioannidis; Karthik Subbian; James Y. Zou; Jure Leskovec (NeurIPS, 2024)

AvaTaR: Optimizing LLM Agents for Tool-Assisted Knowledge Retrieval. - Shirley Wu; Shiyu Zhao; Qian Huang; Kexin Huang; Michihiro Yasunaga; Kaidi Cao; Vassilis N. Ioannidis; Karthik Subbian; Jure Leskovec; James Zou 001 (CoRR, 2024)

CollabLLM: From Passive Responders to Active Collaborators. - Shirley Wu; Michel Galley; Baolin Peng; Hao Cheng 002; Gavin Li; Yao Dou; Weixin Cai; James Zou 001; Jure Leskovec; Jianfeng Gao 001 (CoRR, 2025)

SiriuS: Self-improving Multi-agent Systems via Bootstrapped Reasoning. - Wanjia Zhao; Mert Yüksekgönül; Shirley Wu; James Zou 001 (CoRR, 2025)

Optimas: Optimizing Compound AI Systems with Globally Aligned Local Rewards. - Shirley Wu; Parth Sarthi; Shiyu Zhao; Aaron Lee; Herumb Shandilya; Adrian Mladenic Grobelnik; Nurendra Choudhary; Edward W. Huang; Karthik Subbian; Linjun Zhang; Diyi Yang; James Zou 001; et al. (CoRR, 2025)

Finance Agent Benchmark: Benchmarking LLMs on Real-world Financial Research Tasks. - Antoine Bigeard; Langston Nashold; Rayan Krishnan; Shirley Wu (CoRR, 2025)