Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. - Lia X. Harrington; Gregory P. Way; Jennifer A. Doherty; Casey S. Greene (PSB, 2018)

Building a tobacco user registry by extracting multiple smoking behaviors from clinical notes. - Ellen L. Palmer; Saeed Hassanpour; John H. Higgins; Jennifer A. Doherty; Tracy Onega (BMC Medical Informatics Decis. Mak., 2019)

Assessing data availability and quality within an electronic health record system through external validation against an external clinical data source. - Ellen L. Palmer; John H. Higgins; Saeed Hassanpour; James Sargent; Christina M. Robinson; Jennifer A. Doherty; Tracy Onega (BMC Medical Informatics Decis. Mak., 2019)

Privacy-Preserving Knowledge Transfer with Bootstrap Aggregation of Teacher Ensembles. - Hong-Jun Yoon; Hilda B. Klasky; Eric B. Durbin; Xiao-Cheng Wu; Antoinette Stroup; Jennifer A. Doherty; Linda Coyle; Lynne Penberthy; Christopher B. Stanley; James Blair Christian; Georgia D. Tourassi (Poly/DMAH@VLDB, 2020)

Why I'm not Answering: Understanding Determinants of Classification of an Abstaining Classifier for Cancer Pathology Reports. - Sayera Dhaubhadel; Jamaludin Mohd-Yusof; Kumkum Ganguly; Gopinath Chennupati; Sunil Thulasidasan; Nicolas W. Hengartner; Brent J. Mumphrey; Eric B. Durbin; Jennifer A. Doherty; Mireille Lemieux; Noah Schaefferkoetter; Georgia D. Tourassi; et al. (CoRR, 2020)

Accelerated training of bootstrap aggregation-based deep information extraction systems from cancer pathology reports. - Hong-Jun Yoon; Hilda B. Klasky; John P. Gounley; Mohammed M. Alawad; Shang Gao 008; Eric B. Durbin; Xiao-Cheng Wu; Antoinette Stroup; Jennifer A. Doherty; Linda Coyle; Lynne Penberthy; James Blair Christian; et al. (J. Biomed. Informatics, 2020)

Deep active learning for classifying cancer pathology reports. - Kevin De Angeli; Shang Gao 008; Mohammed M. Alawad; Hong-Jun Yoon; Noah Schaefferkoetter; Xiao-Cheng Wu; Eric B. Durbin; Jennifer A. Doherty; Antoinette Stroup; Linda Coyle; Lynne Penberthy; Georgia D. Tourassi (BMC Bioinform., 2021)

Integration of Domain Knowledge using Medical Knowledge Graph Deep Learning for Cancer Phenotyping. - Mohammed M. Alawad; Shang Gao 008; Mayanka Chandra Shekar; S. M. Shamimul Hasan; James Blair Christian; Xiao-Cheng Wu; Eric B. Durbin; Jennifer A. Doherty; Antoinette Stroup; Linda Coyle; Lynne Penberthy; Georgia D. Tourassi (CoRR, 2021)

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. - Ariel A. Hippen; Matias M. Falco; Lukas M. Weber; Erdogan Pekcan Erkan; Kaiyang Zhang; Jennifer Anne Doherty; Anna Vähärautio; Casey S. Greene; Stephanie C. Hicks (PLoS Comput. Biol., 2021)

Limitations of Transformers on Clinical Text Classification. - Shang Gao 008; Mohammed M. Alawad; M. Todd Young; John Gounley; Noah Schaefferkoetter; Hong-Jun Yoon; Xiao-Cheng Wu; Eric B. Durbin; Jennifer A. Doherty; Antoinette Stroup; Linda Coyle; Georgia D. Tourassi (IEEE J. Biomed. Health Informatics, 2021)

Iam hiQ - a novel pair of accuracy indices for imputed genotypes. - Albert Rosenberger; Viola Tozzi; Heike Bickeböller; Rayjean J. Hung; David C. Christiani; Neil E. Caporaso; Geoffrey Liu; Stig E. Bojesen; Loic Le Marchand; Demetrios Albanes; Melinda C. Aldrich; Adonina Tardon; et al. (BMC Bioinform., 2022)

Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types. - Kevin De Angeli; Shang Gao 008; Ioana Danciu; Eric B. Durbin; Xiao-Cheng Wu; Antoinette Stroup; Jennifer A. Doherty; Stephen M. Schwartz; Charles Wiggins; Mark Damesyn; Linda Coyle; Lynne Penberthy; et al. (J. Biomed. Informatics, 2022)

A Keyword-Enhanced Approach to Handle Class Imbalance in Clinical Text Classification. - Andrew E. Blanchard; Shang Gao 008; Hong-Jun Yoon; James Blair Christian; Eric B. Durbin; Xiao-Cheng Wu; Antoinette Stroup; Jennifer A. Doherty; Stephen M. Schwartz; Charles Wiggins; Linda Coyle; Lynne Penberthy; et al. (IEEE J. Biomed. Health Informatics, 2022)

Deep learning uncertainty quantification for clinical text classification. - Alina Peluso; Ioana Danciu; Hong-Jun Yoon; Jamaludin Mohd-Yusof; Tanmoy Bhattacharya 001; Adam Spannaus; Noah Schaefferkoetter; Eric B. Durbin; Xiao-Cheng Wu; Antoinette Stroup; Jennifer A. Doherty; Stephen M. Schwartz; et al. (J. Biomed. Informatics, 2024)

Development of message passing-based graph convolutional networks for classifying cancer pathology reports. - Hong-Jun Yoon; Hilda B. Klasky; Andrew E. Blanchard; James Blair Christian; Eric B. Durbin; Xiao-Cheng Wu; Antoinette Stroup; Jennifer A. Doherty; Linda Coyle; Lynne Penberthy; Georgia D. Tourassi (BMC Medical Informatics Decis. Mak., 2024)