Nathanael R. Fillmore
Topics / Natural Language Processing
Topic

Natural Language Processing

Fillmore has developed and validated a variety of rule-based and machine learning natural language processing tools to extract critical clinical data from unstructured electronic health records. His work focuses on automating the identification of disease staging, biomarker expression, and treatment history, as well as improving the efficiency of clinical trial recruitment. Additionally, he has applied sentiment analysis and linguistic modeling to better understand patient experiences and behavioral patterns within large medical datasets.

U.S. Veterans and VA Data 11 Electronic Health Records 10 Clinical Notes 6 Health Informatics 6 Model Validation 4 Rule-Based Algorithms 4 Radiology and Pathology Reports 3 VA Cancer Registry 3 Race and Ethnicity 3 Machine Learning 3 External Validation 2 Cancer Patients 2

Publications (14)

2026

Development and validation of venous thromboembolism-bidirectional encoder representations from transformers (VTE-BERT) natural language processing model.

Omid Jafari, Shengling Ma, Barbara D. Lam, Jun Y. Jiang, Emily Zhou, Mrinal Ranjan, Justine Ryu, Raka Bandyo, Arash Maghsoudi, Bo Peng, Christopher I. Amos, Abiodun Oluyomi, Nathanael R. Fillmore, Jennifer La‡, Ang Li‡‡ Equal senior authorship

Journal of Thrombosis and Haemostasis24(7), 2522-2531
Natural Language Processing External Validation Clinical Notes Radiology and Pathology Reports Cancer Patients
2026

Identification of Risk Factors for Acral Melanoma in US Veterans.

Jonathan C. Hwang†, Linden B. Huhmann†, Kelly Cho, Sergey D. Goryachev, Nicholas Starink, Martin A. Weinstock, Maryam M. Asgari, Christy Zheng, Charles Lu, Theodore C. Feldman, Nhan V. Do, John M. Gaziano, Yevgeniy R. Semenov, Marc S. Hurlbert, Nathanael R. Fillmore‡, Rebecca I. Hartman‡† Equal first authorship · ‡ Equal senior authorship

JAMA Dermatology162(3), 279-291
Acral Melanoma Agent Orange Exposure U.S. Veterans and VA Data VA Cancer Registry Nested Case-Control Study
2026

Magnetic Resonance Imaging or Confirmatory Biopsy for Patients With Prostate Cancer Receiving Active Surveillance.

Matthew R. Cooperberg†, John R. Bihn†, John M. Culnan, Jennifer La, Sergey D. Goryachev, Daniel C. R. Chen, Oleg Soloviev, Grace Lee, June K. Corrigan, Kaitlin N. Swinnerton, Nicholas G. Nickols, Karlynn N. Dulberger, Pedro Barata, Rhonda L. Bitting, Mary T. Brophy, Heather H. Cheng, Hoedt Amanda De, Nhan V. Do, Stephen J. Freedland, Isla P. Garraway, J. Michael Gaziano, Susan Halabi, Richard L. Hauger, Stacy Loeb, David M. Nanus, Timothy R. Rebbeck, Matthew B. Rettig, Chong-Xian Pan, Kenute Myrie, Rachel B. Ramoni, Nathanael R. Fillmore‡, Channing J. Paller‡† Equal first authorship · ‡ Equal senior authorship

JAMA Oncology12(1), 111-113
U.S. Veterans and VA Data Retrospective Cohort Study Electronic Health Records Prostate Cancer Active Surveillance
2026

Rule-based natural language processing to extract clinical trial and research study enrollment history from unstructured notes.

Sergey D. Goryachev†, Julie Tsu-Yu Wu†, Eric Lin†, Daphne R. Friedman, Robert Zwolinski, Rupali Dhond, Danne C. Elbers, Jennifer La, Cenk Yildirim, June K. Corrigan, Daniel C. R. Chen, Mary T. Brophy, Nhan V. Do‡, Nathanael R. Fillmore‡† Equal first authorship · ‡ Equal senior authorship

Health Informatics Journal32(1), 14604582261430614
U.S. Veterans and VA Data Electronic Health Records Natural Language Processing Rule-Based Algorithms Clinical Notes
2025

Rapid Support and Implementation of an Application for the Prediction Augmented Screening Initiative (PASI) Planning Phase Through the Enabling Technologies for Rapid Learning Health Systems Platform (ENTHRALL) at the Department of Veterans Affairs (VA).

Hannah M. Tosi, Chunlei Zheng, Amelia H. Tarren, Meghana Yellanki, Stephen J. Miller, Oleg V. Soloviev, June K. Corrigan, George R. Schneeloch, Hormuzd A. Katki, Lauren E. Kearney, Tanner J. Caverly, Nichole T. Tanner, Renda Soylemez Wiener, Mary Brophy, Nathanael R. Fillmore, Nhan V. Do, Danne C. Elbers

Cancer Informatics24, 11769351251389781
U.S. Veterans and VA Data Electronic Health Records Lung Cancer Natural Language Processing Learning Health Systems
2025

Automated Extraction of Imaging and Pathology Data From Diverse Prostate Cancer Electronic Records.

John M. Culnan, Sergey D. Goryachev, John R. Bihn, Grace Lee, Daniel C. R. Chen, Oleg Soloviev, Robert Zwolinski, Karlynn N. Dulberger, Nhan V. Do, Channing J. Paller, Matthew R. Cooperberg‡, Nathanael R. Fillmore‡‡ Equal senior authorship

JCO Clinical Cancer Informatics9, e2500085
U.S. Veterans and VA Data Electronic Health Records Prostate Cancer Natural Language Processing VA Cancer Registry
2024

Natural Language Processing Algorithm to Extract Multiple Myeloma Stage From Oncology Notes in the Veterans Affairs Healthcare System.

Sergey D. Goryachev†, Cenk Yildirim†, Clark DuMontier†, Jennifer La†, Mayuri Dharne, J. Michael Gaziano, Mary T. Brophy, Nikhil C. Munshi, Jane A. Driver, Nhan V. Do‡, Nathanael R. Fillmore‡† Equal first authorship · ‡ Equal senior authorship

JCO Clinical Cancer Informatics8, e2300197
U.S. Veterans and VA Data Electronic Health Records Multiple Myeloma Natural Language Processing VA Cancer Registry
2024

Matching Patients to Accelerate Clinical Trials (MPACT): Enabling Technology for Oncology Clinical Trial Workflow.

Nhan V. Do, Danne C. Elbers, Nathanael R. Fillmore, Samuel Ajjarapu, Steven J. Bergstrom, John Bihn, June K. Corrigan, Rupali Dhond, Svitlana Dipietro, Arkadiy Dolgin, Theodore C. Feldman, Sergey D. Goryachev, Linden B. Huhmann, Jennifer La, Paul A. Marcantonio, Kyle M. McGrath, Stephen J. Miller, Vinh Q. Nguyen, George R. Schneeloch, Feng-Chi Sung, Kaitlin N. Swinnerton, Amelia H. Tarren, Hannah M. Tosi, Danielle Valley, Austin D. Vo, Cenk Yildirim, Chunlei Zheng, Robert Zwolinski, Gisele A. Sarosy, David Loose, Colleen Shannon, Mary T. Brophy

Studies in Health Technology and Informatics310, 1086-1090
U.S. Veterans and VA Data Electronic Health Records Natural Language Processing Clinical Trial Enrollment Patient Screening Workflow
2023

External validation of a novel electronic risk score for cancer-associated thrombosis in a comprehensive cancer center.

Ang Li, Las Pozas Giordana De, Clark R. Andersen, Chijioke C. Nze, Katy M. Toale, Emily M. Milner, Nathanael R. Fillmore, Elizabeth Yu Chiao, Hernandez Cristhiam Rojas, Michael H. Kroll, Kelly W. Merriman‡, Christopher R. Flowers‡‡ Equal senior authorship

American Journal of Hematology98(7), 1052-1057
Cancer-Associated Thrombosis Electronic Health Records External Validation Model Validation Natural Language Processing
2023

Machine learning-based natural language processing to extract PD-L1 expression levels from clinical notes.

Eric Lin†, Robert Zwolinski†, Julie Tsu-Yu Wu, Jennifer La, Sergey Goryachev, Linden Huhmann, Cenk Yildrim, David P. Tuck, Danne C. Elbers, Mary T. Brophy, Nhan V. Do‡, Nathanael R. Fillmore‡† Equal first authorship · ‡ Equal senior authorship

Health Informatics Journal29(3), 14604582231198021
U.S. Veterans and VA Data Electronic Health Records Natural Language Processing Machine Learning PD-L1 Expression
2023

Epidemiology of Cancer-Associated Venous Thromboembolism in Patients With Solid and Hematologic Neoplasms in the Veterans Affairs Health Care System.

Kylee L. Martens†, Ang Li†, Jennifer La, Sarah B. May, Kaitlin N. Swinnerton, Hannah Tosi, Danne C. Elbers, Nhan V. Do, Mary T. Brophy, J. Michael Gaziano, Saran Lotfollahzadeh, Vipul Chitalia, Katya Ravid, Nathanael R. Fillmore† Equal first authorship

JAMA Network Open6(6), e2317945
U.S. Veterans and VA Data Retrospective Cohort Study Electronic Health Records Cancer-Associated Thrombosis Health Disparities