Nathanael R. Fillmore
Themes / Natural Language Processing for Clinical Phenotyping
Line of work

Natural Language Processing for Clinical Phenotyping

This line of work develops rule-based and transformer-based NLP models to extract critical clinical data from unstructured notes. Applications include the extraction of cancer staging, PD-L1 expression, and VTE events.

Clinical Notes Natural Language Processing Rule-Based Algorithms Health Informatics

Anchor result

The VTE-BERT model achieved a precision of 95% and recall of 91% in external validation for detecting incident VTE events.

Related publications

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

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

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

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

Validation of algorithms to select patients with multiple myeloma and patients initiating myeloma treatment in the national Veterans Affairs Healthcare System.

Jennifer La†, Clark DuMontier†, Hamza Hassan, Maya Abdallah, Camille Edwards, Karina Verma, Grace Ferri, Mayuri Dharne, Cenk Yildirim, June Corrigan, J. Michael Gaziano, Nhan V. Do, Mary T. Brophy, Jane A. Driver, Nikhil C. Munshi, Nathanael R. Fillmore† Equal first authorship

Pharmacoepidemiology and Drug Safety32(5), 558-566
U.S. Veterans and VA Data Electronic Health Records Multiple Myeloma VA Cancer Registry Algorithm Validation