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

  • Yiqun T. Chen, Tyler McCormick, Li Liu, Abhirup Datta (2025+). LAVA: Language Model Assisted Verbal Autopsy for Cause-of-Death Determination. arXiv: 2509.09602.
  • Yiqun Chen, James Zou (2024). GenePert: Leveraging GenePT embeddings for gene perturbation prediction. bioRxiv preprint.
  • Yiqun T. Chen, James Zou (2025). Simple and effective embedding model for genes and cells built from ChatGPT. Nature Biomedical Engineering.
    • 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.
  • Yiqun T. Chen, Daniela M. Witten (2024). 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

  • Wenqin Zhang, Thu Nguyen, Elizabeth A. Stuart, Yiqun T. Chen (2025+). Large Language Models for Full-Text Methods Quality Assessment: A Case Study on Causal Mediation Analysis Research.
  • Can Wang, Yiqun T. Chen (2025+). Evaluating Large Language Models for Evidence-Based Clinical Question Answering. arXiv: 2509.10843.
  • Yiqun T. Chen, James Zou (2023). TWIGMA: A dataset of AI-generated images with metadata from Twitter. NeurIPS 2023.
  • Weixin Liang, Nazneen Rajani, Xingyao Yang, Ezinwanne Ozoani, Eric Wu, Yiqun T. Chen, Daniel Scott Smith, James Zou (2025). What’s documented in AI? Systematic analysis of 32K AI model cards. Nature Machine Intelligence.
  • 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). Changes in executive dysfunction during the course of brief psychotherapies for late-life depression and relation to treatment response. The American Journal of Geriatric Psychiatry: Open Science, Education, and Practice; joint first-author.
  • 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.