Recent Publications

Peer-reviewed articles by Computational Precision Health faculty and students (select list).

Leone, M., Martin-Loeches, I., & Pirracchio, R. (2025). Humans versus machine learning models: improving the outcome of trauma patients. The Lancet Regional Health-Europe, 55, 101356. 

Aiken, E., Ashraf, A., Blumenstock, J., Guiteras, R., & Mobarak, A. M. (2025). Scalable Targeting of Social Protection: When Do Algorithms Out-Perform Surveys and Community Knowledge? (No. w33919). National Bureau of Economic Research.

Rudrapatna, V.A., Ravindranath, V.G., Arneson, D.V. … Butte, A. J., Wang, S. From trial data to personalized medicine: a validated framework with an application to Crohn’s disease. npj Digit. Med. 8, 327 (2025).  

Barrios, J., Porter, E., Capaldi, D. P., Upadhaya, T., Chen, W. C., Perks, J. R., Apte, A., Aristophanous, M., LoCastro, E., Hsu, D., Stone, P. H., Villanueva-Meyer, J. E., Valdes, G., Jiang, F., Maddalena, M., Ballangrud, A., Prezelski, K., Lin, H., Sun, J. Y., … Sheng, K., … Morin, O. (2025). Multi-institutional Atlas of brain metastases informs spatial modeling for Precision Imaging and personalized therapy. Nature Communications, 16(1).

Chang, C., Chen, J. J., Feng, J., Friesner, I., Mohindra, S., Boreta, L., Rabow, M. W., Braunstein, S. E., Benson, R., & Hong, J. C. (2025). Patterns in symptoms preceding acute care in patients with cancer. JAMA Network Open, 8(4).

Dorfner, F. J., Dada, A., Busch, F., Makowski, M. R., Han, T., Truhn, D., Kleesiek, J., Sushil, M., Adams, L. C., & Bressem, K. K. (2025). Evaluating the effectiveness of biomedical fine-tuning for large language models on clinical tasks. Journal of the American Medical Informatics Association. 

Ghosh, S., Cai, C., Hashemi, A., Gao, Y., Haufe, S., Sekihara, K., Raj, A., & Nagarajan, S. S. (2025). Structured noise champagne: An empirical bayesian algorithm for electromagnetic brain imaging with Structured Noise. Frontiers in Human Neuroscience, 19. 

Miao, B. Y., Williams, C. Y., Chinedu-Eneh, E., Zack, T., Alsentzer, E., Butte, A. J., & Chen, I. Y. (2025). Understanding contraceptive switching rationales from real world clinical notes using large language models. Npj Digital Medicine, 8(1).

Nugent, J. R., Kakande, E., Chamie, G., Kabami, J., Owaraganise, A., Havlir, D. V., Kamya, M., & Balzer, L. B. (2025). Causal inference in randomized trials with partial clustering. Clinical Trials. 

Pace, W. A., Jahangirizadeh, P., Liu, A., Carlisle, M. N., Krumm, R., Cowan, J. E., Carroll, P. R., Cooperberg, M. R., & Odisho, A. Y. (2025). PD32-03 Generative artificial intelligence applications in data abstraction and pattern analysis for kidney cancer pathology reports. Journal of Urology, 213(5S). 

Poole, S., Sisodia, N., Koshal, K., Henderson, K., Wijangco, J., Paredes, D., Chen, C., Rowles, W., Akula, A., Wuerfel, J., Sharma, V., UCSF Multiple Sclerosis and Neuroinflammation Center clinicians, Rauschecker, A. M., Henry, R. G., & Bove, R. (2025). Detecting New Lesions Using a Large Language Model: Applications in Real-World Multiple Sclerosis Datasets. Annals of neurology, 10.1002/ana.27251.

Dorfner, F. J., Dada, A., Busch, F., Makowski, M. R., Han, T., Truhn, D., … Sushi, M., … & Bressem, K. K. (2025). Evaluating the effectiveness of biomedical fine-tuning for large language models on clinical tasks. Journal of the American Medical Informatics Association, ocaf045. 

Tawfik, D., Rule, A., Alexanian, A., Cross, D., Holmgren, A. J., Lou, S. S., … & Apathy, N. C. (2025). Emerging Domains for Measuring Health Care Delivery With Electronic Health Record Metadata. Journal of medical Internet research, 27, e64721.

Mandair, D., Elia, M. V., & Hong, J. C. (2025). Considerations in Translating AI to Improve Care. JAMA Network Open, 8(4), e252023-e252023. 

Miao, B. Y., Williams, C. Y., Chinedu-Eneh, E., Zack, T., Alsentzer, E., Butte, A. J., & Chen, I. Y. (2025). Understanding contraceptive switching rationales from real world clinical notes using large language models. npj Digital Medicine, 8(1), 221.

Poole, S., Sisodia, N., Koshal, K., Henderson, K., Wijangco, J., Paredes, D., … Rauschecker, A.M., … & Bove, R. (2025). Detecting New Lesions Using a Large Language Model: Applications in Real‐World Multiple Sclerosis Datasets. Annals of Neurology.

Fong, N., Lipnick, M. S., Behnke, E., Chou, Y., Elmankabadi, S., Ortiz, L., … Pirracchio, R., … & Law, T. J. (2025). Open Access Dataset and Common Data Model for Pulse Oximeter Performance Data. Scientific data, 12(1), 1-8.

Phillips, R. V., & van der Laan, M. J. (2025). Commentary on” Nonparametric identification is not enough, but randomized controlled trials are”: Statistical considerations for generating reliable evidence across a spectrum of studies that increasingly involve real-world elements. Observational Studies, 11(1), 61-75. 

Tawfik, D., Rule, A., Alexanian, A., Cross, D., Holmgren, A. J., Lou, S. S., … & Apathy, N. C. (2025). Emerging Domains for Measuring Health Care Delivery With Electronic Health Record Metadata. Journal of Medical Internet Research, 27, e64721. 

Bennett, D. J., Feng, J., Goldman, S., Kothari, A., Gottlieb, L. M., Durstenfeld, M. S., Marks, J., Ehrlich, S., Davis, J., & Zier, L. S. (2025). Reducing readmissions in the safety net through AI and automation. The American journal of managed care, 31(3), 142–148. https://doi.org/10.37765/ajmc.2025.89697

Phongpreecha, T., Ghanem, M., Reiss, J. D., Oskotsky, T., Mataraso, S. J., De Francesco, D., … Sirota, M., … & Aghaeepour, N. (2025). AI-guided precision parenteral nutrition for neonatal intensive care units. Nature Medicine, 1-13.

Kalimouttou, A., Kennedy, J. N., Feng, J., Singh, H., Saria, S., Angus, D. C., … & Pirracchio, R. (2025). Optimal Vasopressin Initiation in Septic Shock: The OVISS Reinforcement Learning Study. JAMA. 

Hathaway, Q. A., Kasaeian, A., Pan, T., Bluemke, D. A., Ghotbi, E., Klein, J. G., … Tison, G. H., … & Demehri, S. (2025). A Deep Learning Model for Three-Dimensional Determination of Whole Thoracic Vertebral Bone Mineral Density from Noncontrast Chest CT: The Multi-Ethnic Study of Atherosclerosis. Radiology, 314(3), e242133

Chen, I.Y. and Zink, A., 2025. AI Tools in Human Hands: Measuring Real-World Impact in the Emergency Department. NEJM AI, 2(3), p.AIe2500083.

Subramaniam, S., Rizvi, S., Ramesh, R., Sehgal, V., Gurusamy, B., Arif, H., Tran, J., Thamman, R., Anyanwu, E.C., Mastouri, R., Mackensen, G.B., and Arnaout R. 2025. Ontology-guided machine learning outperforms zero-shot foundation models for cardiac ultrasound text reports. Scientific Reports, 15(1), p.5456.

Nezhat, C.R., Oskotsky, T.T., Robinson, J.F., Fisher, S.J., Tsuei, A., Liu, B., Irwin, J.C., Gaudilliere, B., Sirota, M., Stevenson, D.K. and Giudice, L.C., 2025. Real world perspectives on endometriosis disease phenotyping through surgery, omics, health data, and artificial intelligence. npj Women’s Health, 3(1), p.8.

Nauka, P.C., Kennedy, J.N., Brant, E.B., Komorowski, M., Pirracchio, R., Angus, D.C. and Seymour, C.W., 2025. Challenges with reinforcement learning model transportability for sepsis treatment in emergency care. npj Digital Medicine, 8(1), pp.1-5.

Tsukamoto, S. and Mofrad, M.R., 2025. Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function. The Journal of Chemical Physics, 162(5).

Li, H., Apathy, N.C., Holmgren, A.J., Melnick, E.R., McDougal, R.A. 2025. Imputation of missing aggregate EHR audit log data across individual and multiple organizations. Journal of Biomedical Informatics, 163, p.104805. 

Wyss, R., van der Laan, M., Gruber, S. Shi, X., Lee, H…. 2025. Note on targeted learning with an undersmoothed Lasso propensity score model for large-scale covariate adjustment in health care database studies. American Journal of Epidemiology, kwaf024.

Miao, B. Y., Chen, I. Y., Williams, C. Y. K., Davidson, J., Garcia-Agundez, A., Sun, S., Zack, T., Saria, S., Arnaout, R., Quer, G., Sadaei, H. J., Torkamani, A., Beaulieu-Jones, B., Yu, B., Gianfrancesco, M., Butte, A. J., Norgeot, B., & Sushil, M. (2025). The MI-CLAIM-GEN checklist for generative artificial intelligence in health. Nature medicine, 10.1038/s41591-024-03470-0. Advance online publication.