publications

Full list also on Google Scholar.

Below is an updated list of publications and preprints. * indicates joint first authorship; † indicates joint senior authorship.

Statistical Machine Learning and AI

  • Yiqun T. Chen, Lucy L. Gao (2026). Selective Inference for Clustering Under Unknown Covariance. arXiv: 2610.17458. Tutorial.
  • Yiqun T. Chen, Stephanie C. Hicks (2026). Mind the Alignment Gap: A Spatial Transcriptomics Benchmark for Scientific Coding Agents. bioRxiv: 10.64898/2026.07.05.736638.
    • Selected for an oral presentation at MLCB 2026.
  • Can Wang, Hongyu Zhao, Yiqun T. Chen (2026). InferenceEvolve: Towards Automated Causal Effect Estimators through Self-Evolving AI. NeurIPS 2026. arXiv: 2604.04274.
  • Yiqun T. Chen, Moran Guo, Shengyi Li (2026). Power Analysis for Prediction-Powered Inference. arXiv: 2603.16041. Online calculator.
  • Yiqun T. Chen, Sizhu Lu, Sijia Li, Moran Guo, Shengyi Li (2026). Efficient Inference for Noisy LLM-as-a-Judge Evaluation. ICML 2026. arXiv: 2601.05420.
  • Junwei Sun, Yuxun He, Ouyang Zhu, Yiqun T. Chen (2026). Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models. bioRxiv: 10.64898/2026.07.20.739620.
    • Preliminary version (Rethinking Perturbation Prediction Baselines) presented at the ICLR 2026 Workshop on Generative Models and Genomics (Gen2). OpenReview.
  • Yiqun T. Chen, Tyler H. McCormick, Li Liu, Abhirup Datta (2025+). LAVA: Language Model Assisted Verbal Autopsy for Cause-of-Death Determination. arXiv: 2509.09602.
  • Kyle Swanson, Yiqun T. Chen, Aaron Jaech, James Zou (2025). RL-Finetuning of OpenAI o1-mini to Enhance Biomedical Reasoning. bioRxiv: 10.1101/2025.05.19.654988.
  • Yiqun T. Chen, James Zou (2024). GenePert: Leveraging GenePT embeddings for gene perturbation prediction. bioRxiv: 10.1101/2024.10.27.620513.
  • Yiqun T. Chen, James Zou (2025). Simple and effective embedding model for single-cell biology built from ChatGPT. Nature Biomedical Engineering. Journal article.
    • Preliminary version presented as an oral at MLCB 2023 (< 15% acceptance).
  • Yiqun T. Chen, Lucy L. Gao (2025). Testing for a difference in means of a single feature after clustering. Biostatistics. Journal article.
  • Yiqun T. Chen, Daniela M. Witten (2023). Selective inference for k-means clustering. Journal of Machine Learning Research.
  • Yiqun T. Chen, Sean W. Jewell, Daniela M. Witten (2023). More powerful selective inference for the graph fused lasso. Journal of Computational and Graphical Statistics.
  • Yiqun T. Chen, Sean W. Jewell, Daniela M. Witten (2023). Quantifying uncertainty in spikes estimated from calcium imaging data. Biostatistics.

Applications in Data Science

  • Lifeng Lin, Xing Xing, Chong Wu, Yiqun T. Chen, Jiayi Tong, Deborah Jean McClelland, Zhao Chen (2026). Reproducible study identification and selection in systematic reviews: barriers and paths forward. BMJ Open. Journal article.
  • Junhe Yang, Soumyakanti Pan, Hyun Seung Lim, Yue Chu, Yuting Guo, Nishtha Agarwal, Varun Babbar, Gaurav Rajesh Parikh, Yiqun T. Chen, Chris A. Rees, Ziyaad Dangor, Sanjay Govind Lala, Z. Li, Samuel J. Clark, Zhenke Wu, Abhirup Datta, Li Liu, Cynthia D. Rudin, Samuel V. Scarpino, Benjamin M. Gyori, Tyler H. McCormick (2026). A Multimodal Benchmark for Evaluating Cause-of-Death Inference Using Child Health and Mortality Data. medRxiv: 10.64898/2026.07.13.26357980.
  • Jasmin Han, Janardan Devkota, Joseph Waring, Amanda Luken, Felix Naughton, Roger Vilardaga, Jonathan Bricker, Carl Latkin, Meghan Moran, Yiqun T. Chen†, Johannes Thrul† (2026). Personalized Prediction of Perceived Message Effectiveness Using Large Language Model Based Digital Twins. Accepted, Journal of the American Medical Informatics Association. arXiv: 2602.19403.
  • Wenqing Zhang, Trang Quynh Nguyen, Elizabeth A. Stuart, Yiqun T. Chen (2026). Large Language Models for Full-Text Methods Assessment: A Case Study on Mediation Analysis. Journal of the American Medical Informatics Association. Journal article. arXiv: 2510.10762.
  • Can Wang, Yiqun T. Chen (2026). Evaluating Large Language Models for Evidence-Based Clinical Question Answering. Patterns. Journal article. arXiv: 2509.10843.
  • Tianyu Liu, Tianqi Chen, Wangjie Zheng, Xiao Luo, Yiqun T. Chen, Hongyu Zhao (2026). Embeddings from language models are good learners for single-cell data analysis. Patterns. Journal article.
  • Weixin Liang, Nazneen Rajani, Xinyu Yang, Ezinwanne Ozoani, Eric Wu, Yiqun T. Chen, Daniel Scott Smith, James Zou (2024). Systematic analysis of 32,111 AI model cards characterizes documentation practice in AI. Nature Machine Intelligence. Journal article.
  • Yiqun T. Chen, James Zou (2023). TWIGMA: A dataset of AI-generated images with metadata from Twitter. NeurIPS 2023.
  • Yiqun T. Chen, Angela D. R. Smith, Katharina Reinecke, Alexandra To (2023). Why, when, and from whom: considerations for collecting and reporting race and ethnicity data in HCI. CHI 2023. (Best Paper Honorable Mention, Top 5%.)
  • Yiqun T. Chen, Angela D. R. Smith, Katharina Reinecke, Alexandra To (2022). Collecting and reporting race and ethnicity data in HCI. CHI 2022 Extended Abstracts.
  • Yiqun T. Chen, Rahul Gopinath, Anita Tadakamalla, Michael D. Ernst, Reid Holmes, Gordon Fraser, Paul Ammann, René Just (2020). Revisiting the relationship between fault detection, test adequacy criteria, and test set size. ASE 2020.

Applications in Biomedicine

  • Matthew S. Schurr, Yiqun T. Chen, Patrick J. Raue, Patricia A. Areán, George S. Alexopoulos, Brenna N. Renn (2025). Relation Between Executive Function Test Performance and Treatment Outcomes During Brief Psychotherapies for Later-Life Depression. The American Journal of Geriatric Psychiatry: Open Science, Education, and Practice; joint first-author. Journal article.
  • Sonnet Xu, Haiwen Gui, Veronica Rotemberg, Tongzhou Wang, Yiqun T. Chen†, Roxana Daneshjou† (2024+). A framework for evaluating the efficacy of foundation embedding models in healthcare. medRxiv: 10.1101/2024.04.17.24305983.
  • Yiqun T. Chen, Haiwen Gui, et al. (2025). A novel triage and referral pathway for single lesions improves skin cancer risk stratification and efficiency in dermatology clinics. JAMA Dermatology.
  • Iva Veseli, Yiqun T. Chen, Matthew S. Schechter, …, Jessika Füssel, A Murat Eren. (2025). Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. eLife.
  • Yiqun T. Chen, Brian D. Williamson, Taylor Okonek, …, Amy Willis. (2023). rigr: Regression, Inference, and General Data Analysis Tools in R. Journal of Open Source Software, 7(80), 4847.
  • Yiqun T. Chen, Carina Marquez, Moses Atukunda, …, Maya Petersen (2023). The association between social network characteristics and TB infection among adults in nine rural Ugandan communities. Clinical Infectious Diseases.
    • Preliminary results presented at the 23rd International AIDS Conference (oral, 2019).
  • Yiqun T. Chen, Lillian B. Brown, Gabriel Chamie, et al. (2021). Social networks and HIV care outcomes in rural Kenya and Uganda. Epidemiology, 32(4):551-559.
    • New Investigator Scholarship for CROI 2020.
  • Lillian Brown, Laura B. Balzer, …, Yiqun Chen, et al. (2020). The influence of social networks on antiretroviral therapy initiation among HIV-infected antiretroviral therapy-naive youth in rural Kenya and Uganda. Journal of Acquired Immune Deficiency Syndromes, 83(1):9-15.
  • Yiqun Chen, Wenjing Zheng, Lillian B. Brown, et al. (2019). Semi-supervised record linkage for construction of large-scale sociocentric networks in resource-limited settings: an application to the SEARCH study in rural Uganda and Kenya. arXiv: 1908.09059.
  • Christopher M. Jakobson, Yiqun Chen, Marilyn F. Slininger, et al. (2016). Tuning the catalytic activity of subcellular nanoreactors. Journal of Molecular Biology, 428(15):2989-2996.