Vivek Rudrapatna, MD, PhD

Assistant Professor In Res

Vivek Rudrapatna is a physician-scientist and Inflammatory Bowel Disease specialist in the Division of Gastroenterology. His research group develops methods for analyzing healthcare data with the goal of improving clinical decision making. Towards these goals, his team draws inspiration from a variety of disciplines within the data sciences, including biostatistics, natural language processing, machine learning, and artificial intelligence.

Current areas of focus include:
-Information extraction from clinical notes using Large Language Models
-Retrospective emulation of clinical trials using EHR data
-Reducing diagnostic delays using machine learning
-Personalizing treatment selection using EHR and RCT data
-Reinforcement learning for optimal clinical decision making

Education
Fellowship, 06/2020 - Gastroenterology, Clinical Data Science, University of California
Residency, 06/2016 - Internal Medicine, Baylor College of Medicine
M.D., Ph.D., 05/2014 - Medicine, Cancer Biology, Icahn School of Medicine at Mount Sinai
A.B., 05/2006 - Biophysics, Harvard University
Honors and Awards
  • Vivli Pioneer Award, 2020
Websites
Publications

  1. Perseus V. Patel, Conner Davis, Amariel Ralbovsky, Daniel Tinoco, Christopher Y.K. Williams, Shadera Slatter, Behzad Naderalvojoud, Michael J. Rosen, Tina Hernandez-Boussard, Vivek Rudrapatna. Large language models outperform traditional natural language processing methods in extracting patient-reported outcomes in IBD. Gastro Hep Advances 2024. PMID:


  2. Patel PV, Davis C, Ralbovsky A, Tinoco D, Williams CYK, Slatter S, Naderalvojoud B, Rosen MJ, Hernandez-Boussard T, Rudrapatna V. Large language models outperform traditional natural language processing methods in extracting patient-reported outcomes in IBD. medRxiv : the preprint server for health sciences 2024. PMID: 39281744


  3. Bhasuran B, Schmolly K, Kapoor Y, Jayakumar NL, Doan R, Amin J, Meninger S, Cheng N, Deering R, Anderson K, Beaven SW, Wang B, Rudrapatna VA. Reducing diagnostic delays in acute hepatic porphyria using health records data and machine learning. Journal of the American Medical Informatics Association : JAMIA 2024. PMID: 38946554


  4. Yannis Lombardi, Vivek Rudrapatna, Agathe Truchot, Gillian Divard, Charlotte Debiais, Marc Raynaud, Atul Butte, Alexandre Loupy. #955 Real-world validation of the mortality box score to predict death following kidney transplantation: an international study. Nephrology Dialysis Transplantation 2024. PMID:


  5. Tzu An Wang, Kaiyi Wang, Nathan Alhalel, Parsia Vazirnia, Shadera Slatter, Gunnar Mattson, Amy E. Becker, Ching-Ying Oon, Shan Wang, William Karlon, Scott V. Pasternak, Cassandra L. Thiel, Seema Gandhi, Sean Woolen, Vivek A. Rudrapatna. 1088 A COMPARATIVE ENVIRONMENTAL IMPACT ANALYSIS OF SCREENING TESTS FOR COLORECTAL CANCER. Gastroenterology 2024. PMID:


  6. Perseus V. Patel, Conner Davis, Amariel Ralbovsky, Daniel Tinoco, Christopher Y. Williams, Shadera Slatter, Behzad Naderalvojoud, Michael J. Rosen, Tina Hernandez-Boussard, Vivek A. Rudrapatna. 313 ENHANCING PATIENT-REPORTED OUTCOMES ASSESSMENT IN INFLAMMATORY BOWEL DISEASE: A COMPARATIVE STUDY OF NATURAL LANAUGE PROCESSING METHODS AND GPT-4 INTEGRATION. Gastroenterology 2024. PMID:


  7. Vivek A. Rudrapatna, Vignesh G. Ravindranath, Douglas Arneson, Arman Mosenia, Atul Butte, Shan Wang. Tu1834 PERSONALIZING TREATMENT SELECTION IN CROHN'S DISEASE: A META-ANALYSIS OF INDIVIDUAL PARTICIPANT DATA FROM FIFTEEN RANDOMIZED CONTROLLED TRIALS. Gastroenterology 2024. PMID:


  8. Silverman AL, Bhasuran B, Mosenia A, Yasini F, Ramasamy G, Banerjee I, Gupta S, Mardirossian T, Narain R, Sewell J, Butte AJ, Rudrapatna VA. Accurate, Robust, and Scalable Machine Abstraction of Mayo Endoscopic Subscores From Colonoscopy Reports. Inflammatory bowel diseases 2024. PMID: 38533919


  9. Patel PV, Zhang A, Bhasuran B, Ravindranath VG, Heyman MB, Verstraete SG, Butte AJ, Rosen MJ, Rudrapatna VA, ImproveCareNow Pediatric IBD Learning Health System. Real-world effectiveness of ustekinumab and vedolizumab in TNF-exposed pediatric patients with ulcerative colitis. Journal of pediatric gastroenterology and nutrition 2024. PMID: 38482890


  10. Silverman AL, Sushil M, Bhasuran B, Ludwig D, Buchanan J, Racz R, Parakala M, El-Kamary S, Ahima O, Belov A, Choi L, Billings M, Li Y, Habal N, Liu Q, Tiwari J, Butte AJ, Rudrapatna VA. Algorithmic Identification of Treatment-Emergent Adverse Events From Clinical Notes Using Large Language Models: A Pilot Study in Inflammatory Bowel Disease. Clinical pharmacology and therapeutics 2024. PMID: 38459719


  11. Miao BY, Sushil M, Xu A, Wang M, Arneson D, Berkley E, Subash M, Vashisht R, Rudrapatna V, Butte AJ. Characterisation of digital therapeutic clinical trials: a systematic review with natural language processing. The Lancet. Digital health 2024. PMID: 38395542


  12. Hunter Mills, Christoper Yuen, Cecilia Arana-Yi, Vivek Rudrapatna. Quantifying Diagnostic Delays in Patients with Indolent and Aggressive Systemic Mastocytosis. Journal of Allergy and Clinical Immunology 2024. PMID:


  13. Odufalu FD, Sewell JL, Rudrapatna V, Somsouk M, Mahadevan U. Assessing the Impact of COVID-19 on IBD Outcomes Among Vulnerable Patient Populations in a Large Metropolitan Center. Inflammatory bowel diseases 2023. PMID: 36943305


  14. Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S. Personalizing treatment selection in Crohn's disease: a meta-analysis of individual participant data from fifteen randomized controlled trials. medRxiv : the preprint server for health sciences 2023. PMID: 37986977


  15. Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S. Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group. BMC medical research methodology 2023. PMID: 37789257


  16. Anna L. Silverman, Madhumita Sushil, Balu Bhasuran, Dana Ludwig, James Buchanan, Rebecca Racz, Mahalakshmi Parakala, Samer El-Kamary, Ohenewaa Ahima, Artur Belov, Lauren Choi, Monisha Billings, Yan Li, Nadia Habal, Qi Liu, Jawahar Tiwari, Atul Butte, Vivek Rudrapatna. S1012 Algorithmic Identification of Treatment-Emergent Adverse Events From Clinical Notes Using Large Language Models: A Pilot Study in Inflammatory Bowel Disease. The American journal of gastroenterology 2023. PMID:


  17. Balu Bhasuran, Shadera Slatter, Gail Fernandes, Boshu Ru, Joe Yang, Xiao Zhang, Ravi Shankar, Jin Ge, Vivek Rudrapatna. S1394 NASHDetection: A Natural Language Processing Method for Identifying Patients With Non-alcoholic Steatohepatitis Using Clinical Notes. The American journal of gastroenterology 2023. PMID:


  18. Balu Bhasuran, Shadera Slatter, Gail Fernandes, Boshu Ru, Joe Yang, Xiao Zhang, Ravi Shankar, Vivek Rudrapatna, Jin Ge. S1395 Uncontrolled Diabetes and Hypertension Are Associated With the Risk of New-Onset Cirrhosis in Patients With Nonalcoholic Steatohepatitis. The American journal of gastroenterology 2023. PMID:


  19. Vivek Rudrapatna, Vignesh Ravindranath, Douglas Arneson, Arman Mosenia, Atul Butte, Shan Wang. S936 Optimizing Treatment Selection in Crohn’s Disease Using Patient-Specific Features: An Individual Participant Data Meta-Analysis of Fifteen Randomized Controlled Trials. The American journal of gastroenterology 2023. PMID:


  20. Silverman AL, Sushil M, Bhasuran B, Ludwig D, Buchanan J, Racz R, Parakala M, El-Kamary S, Ahima O, Belov A, Choi L, Billings M, Li Y, Habal N, Liu Q, Tiwari J, Butte AJ, Rudrapatna VA. Algorithmic identification of treatment-emergent adverse events from clinical notes using large language models: a pilot study in inflammatory bowel disease. medRxiv : the preprint server for health sciences 2023. PMID: 37732220


  21. Bhasuran B, Schmolly K, Kapoor Y, Jayakumar NL, Doan R, Amin J, Meninger S, Cheng N, Deering R, Anderson K, Beaven SW, Wang B, Rudrapatna VA. Reducing diagnostic delays in Acute Hepatic Porphyria using electronic health records data and machine learning: a multicenter development and validation study. medRxiv : the preprint server for health sciences 2023. PMID: 37693437


  22. Wang M, Slatter S, Sussell J, Lin CW, Ogale S, Datta D, Butte AJ, Bazhenova L, Rudrapatna VA. ALK Inhibitor Treatment Patterns and Outcomes in Real-World Patients with ALK-Positive Non-Small-Cell Lung Cancer: A Retrospective Cohort Study. Targeted oncology 2023. PMID: 37341856


  23. Rudrapatna VA, Cheng YW, Feuille C, Mosenia A, Shih J, Shi Y, Roberson O, Rubin B, Butte AJ, Mahadevan U, Skomrock N, Erondu N, Chehoud C, Rahim S, Apfel D, Curran M, Khan NS, O'Brien C, Terry N, Martini BD. Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study. PloS one 2023. PMID: 36862717


  24. Singh S, Kim J, Luo J, Paul P, Rudrapatna V, Park S, Zheng K, Syal G, Ha C, Fleshner P, McGovern D, Sauk JS, Limketkai B, Dulai PS, Boland BS, Eisenstein S, Ramamoorthy S, Melmed G, Mahadevan U, Sandborn WJ, Ohno-Machado L. Comparative Safety and Effectiveness of Biologic Therapy for Crohn's Disease: A CA-IBD Cohort Study. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association 2022. PMID: 36343846


  25. Gu P, Luo J, Kim J, Paul P, Limketkai B, Sauk JS, Park S, Parekh N, Zheng K, Rudrapatna V, Syal G, Ha C, McGovern DP, Melmed GY, Fleshner P, Eisenstein S, Ramamoorthy S, Dulai PS, Boland BS, Grunvald E, Mahadevan U, Ohno-Machado L, Sandborn WJ, Singh S. Effect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. The American journal of gastroenterology 2022. PMID: 35973139


  26. Nguyen NH, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk J, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Dulai P, Boland B, Mahadevan U, Sandborn WJ, Ohno-Machado L, McGovern D, Singh S. Unplanned healthcare utilization and safety of biologic therapy in Hispanic vs. non-Hispanic patients with IBD: A CA-IBD Cohort Study. 2022. PMID: 35644340


  27. Phillip Gu, Jiyu Luo, Paulina Paul, Berkeley N. Limketkai, Jenny S. Sauk, Sunhee Park, Nimisha K. Parekh, Kai Zheng, Vivek A. Rudrapatna, Gaurav Syal, Christina Ha, Dermot P.B. Mcgovern, Gil Melmed, Phillip Fleshner, Samuel Eisenstein, Sonia Ramamoorthy, Parambir Dulai, Brigid Boland, Uma Mahadevan, Lucila Ohno-Machado, William J. Sandborn, Siddharth Singh. 454: OBESITY IS NOT ASSOCIATED WITH INCREASED RISK OF ADVERSE TREATMENT OUTCOMES OR SERIOUS INFECTION IN INFLAMMATORY BOWEL DISEASES PATIENTS (IBD) STARTING NEW BIOLOGIC THERAPY. Gastroenterology 2022. PMID:


  28. Nghia H. Nguyen, Jiyu Luo, Paulina Paul, Jihoon Kim, Gaurav Syal, Christina Ha, Vivek A. Rudrapatna, Sunhee Park, Nimisha K. Parekh, Kai Zheng, Jenny S. Sauk, Berkeley N. Limketkai, Phillip Fleshner, Samuel Eisenstein, Sonia Ramamoorthy, Gil Melmed, Brigid Boland, Uma Mahadevan, William J. Sandborn, Lucila Ohno-Machado, Dermot P.B. Mcgovern, Siddharth Singh. Su1018: UNPLANNED HEALTHCARE UTILIZATION AND SAFETY OF BIOLOGIC THERAPY IN HISPANIC VS. NON-HISPANIC PATIENTS WITH IBD. Gastroenterology 2022. PMID:


  29. Anna L. Silverman, Balu Bhasuran, Arman Mosenia, Fatema Yasini, Saransh Gupta, Narbe Mardirossian, Rohan Narain, Justin L. Sewell, Atul Butte, Vivek A. Rudrapatna. Su1534: ACCURATE, ROBUST, AND SCALABLE ABSTRACTION OF MAYO ENDOSCOPIC SUBSCORES FROM COLONOSCOPY REPORTS. Gastroenterology 2022. PMID:


  30. Zhang B, Silverman AL, Bangaru S, Arneson D, Dasharathy S, Nguyen N, Rodden D, Shih J, Butte AJ, El-Nachef WN, Boland BS, Rudrapatna VA. Case-control study of the association of chronic acid suppression and social determinants of health with COVID-19 infection. 2021. PMID: 34697319


  31. Anna L. Silverman, Douglas Arneson, Saroja Bangaru, Bing Zhang, Diane Rodden, Sonya Dasharathy, Jonathan Shih, Nghia H. Nguyen, Wael N. El-Nachef, Brigid Boland, Vivek Rudrapatna. Fr001 PROTON PUMP INHIBITOR AND RISK OF SARS-COV-2 INFECTION: A MULTI-CENTER EXPERIENCE. 2021. PMID:


  32. Rudrapatna VA, Glicksberg BS, Butte AJ. Utility of routinely collected electronic health records data to support effectiveness evaluations in inflammatory bowel disease: a pilot study of tofacitinib. 2021. PMID: 34011632


  33. Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties. 2020. PMID: 33199721


  34. Vivek Rudrapatna, Myung Ko, Arman Mosenia, Kavita Radhakrishnan, Atul Butte, Priya Kathpalia. S0525 An Electronic Health Records-Based Intervention Improves Appropriate Referrals for Upper Endoscopy: A Prospective, Single Center Study. 2020. PMID:


  35. Vivek Rudrapatna, Saransh Gupta, Taline Mardirossian, Rohan Narain, Arman Mosenia, Atul Butte. S0818 Accurate Machine Classification of Ulcerative Colitis Mayo Subscores From Electronic Health Record Procedure Reports. 2020. PMID:


  36. Arneson D, Elliott M, Mosenia A, Oskotsky B, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties. medRxiv : the preprint server for health sciences 2020. PMID: 32511606


  37. Myung S. Ko, Vivek Rudrapatna, Arman Mosenia, Kavita Radhakrishnan, Priya Kathpalia. 518 AN ELECTRONIC MEDICAL RECORDS-BASED INTERVENTION REDUCES UNNECESSARY ENDOSCOPIES FOR HEARTBURN AND DYSPEPSIA. 2020. PMID:


  38. Emilie Regner, Vivek Rudrapatna, Sofia G. Verstraete, Bilal Hameed, Uma Mahadevan. Sa1851 LOW PREVALENCE OF NONALCOHOLIC FATTY LIVER DISEASE IN ADOLESCENTS WITH INFLAMMATORY BOWEL DISEASE. 2020. PMID:


  39. Rudrapatna VA, Glicksberg BS, Avila P, Harding-Theobald E, Wang C, Butte AJ. Accuracy of medical billing data against the electronic health record in the measurement of colorectal cancer screening rates. Volume 9 of Issue 1. BMJ open quality 2020. PMID: 32209595


  40. Ko MS, Rudrapatna VA, Avila P, Mahadevan U. Safety of Flexible Sigmoidoscopy in Pregnant Patients with Known or Suspected Inflammatory Bowel Disease. Digestive diseases and sciences 2020. PMID: 32034603


  41. Rudrapatna VA, Butte AJ. Opportunities and challenges in using real-world data for health care. Volume 130 of Issue 2. The Journal of clinical investigation 2020. PMID: 32011317


  42. Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna VA, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, Israni S, Larsen R, Percha B, Li L, Dudley JT, Tatonetti NP, Butte AJ. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Volume 35 of Issue 21. Bioinformatics (Oxford, England) 2019. PMID: 31214700


  43. Colin Feuille, Patrick Avila, Myung S. Ko, Dena Goldberg, Vivek A. Rudrapatna, Aparajita Singh. 302 Increasing Appropriate Referrals to Genetic Counseling at the Time of Endoscopy. 2019. PMID:


  44. Vivek A. Rudrapatna, Atul J. Butte. 861 Mind the Gap: A Comparison of the Randomized Clinical Trial Efficacy and Real World Effectiveness of Tofacitinib for the Treatment of Inflammatory Bowel Disease. 2019. PMID:


  45. Myung S. Ko, Vivek Rudrapatna, Patrick Avila, Uma Mahadevan. 46 – Safety of Flexible Sigmoidoscopy in Pregnant Patients with Inflammatory Bowel Disease – a 10 Year Study. Gastroenterology 2019. PMID:


  46. Vivek Rudrapatna, Benjamin Glicksberg, Patrick Avila, Emily Harding-Theobald, Connie Wang, Atul Butte. Tu1650 – Accuracy of Electronic Health Record Billing Data in the Measurement of Colorectal Cancer Screening Rates. Gastroenterology 2019. PMID:


  47. Rudrapatna VA, Velayos F. Biosimilars for the Treatment of Inflammatory Bowel Disease. Volume 43 of Issue 4. Practical gastroenterology 2019. PMID: 31435122


  48. Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ. ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. Volume 2 of Issue 1. JAMIA Open 2019. PMID: 31633087


  49. Rudrapatna VA, Butte AJ. Open data informatics and data repurposing for IBD. Volume 15 of Issue 12. Nature reviews. Gastroenterology & hepatology 2018. PMID: 30061595


  50. Feagins LA, Waljee A, Hou JK, Gu P, Kanjo S, Rudrapatna V, Cipher DJ, Govani S, Gaidos J. Incidence of and Predictors for Early Discontinuation of Biological Therapies in Veteran Patients with Inflammatory Bowel Disease. Volume 23 of Issue 8. Inflammatory bowel diseases 2017. PMID: 28570429


  51. Dunn T, Rudrapatna VA, Hesse S, Sargsyan Z. Arterial Thromboses Heralding Cholangiocarcinoma. Volume 130 of Issue 8. The American journal of medicine 2017. PMID: 28344146


  52. Linda A. Feagins, Akbar K. Waljee, Jason K. Hou, Phillip Gu, Steven Kanjo, Vivek Rudrapatna, Amanda Ellis, Shail M. Govani, Jill Gaidos. Sa1885 Incidence of and Predictors for Early Discontinuation of Biologic Therapies in Veteran Patients with Inflammatory Bowel Disease. Gastroenterology 2016. PMID:


  53. Rudrapatna VA, Bangi E, Cagan RL. A Jnk-Rho-Actin remodeling positive feedback network directs Src-driven invasion. Volume 33 of Issue 21. Oncogene 2013. PMID: 23831567


  54. Rudrapatna VA, Bangi E, Cagan RL. Caspase signalling in the absence of apoptosis drives Jnk-dependent invasion. Volume 14 of Issue 2. EMBO reports 2013. PMID: 23306653


  55. Rudrapatna VA, Cagan RL, Das TK. Drosophila cancer models. Volume 241 of Issue 1. Developmental dynamics : an official publication of the American Association of Anatomists 2011. PMID: 22038952