How Sustainable are Biomedical Ontologies? - James Geller; Vipina Kuttichi Keloth; Mark A. Musen (AMIA, 2018)

Leveraging Horizontal Density Differences between Ontologies to Identify Missing Child Concepts: A Proof of Concept. - Vipina Kuttichi Keloth; Zhe He 001; Yan Chen 009; James Geller (AMIA, 2018)

Extended Analysis of Topological-Pattern-Based Ontology Enrichment. - Zhe He 001; Vipina Kuttichi Keloth; Yan Chen 009; James Geller (BIBM, 2018)

Measuring and Avoiding Information Loss During Concept Import from a Source to a Target Ontology. - James Geller; Shmuel T. Klein; Vipina Kuttichi Keloth (KEOD, 2019)

Alternative classification of identical concepts in different terminologies: Different ways to view the world. - Vipina Kuttichi Keloth; Zhe He 001; Gai Elhanan; James Geller (J. Biomed. Informatics, 2019)

Generating Training Data for Concept-Mining for an 'Interface Terminology' Annotating Cardiology EHRs. - Vipina Kuttichi Keloth; Shuxin Zhou; Andrew J. Einstein; Gai Elhanan; Yan Chen 009; James Geller; Yehoshua Perl (BIBM, 2020)

Mining Concepts for a COVID Interface Terminology for Annotation of EHRs. - Vipina Kuttichi Keloth; Shuxin Zhou; Luke Lindemann; Gai Elhanan; Andrew J. Einstein; James Geller; Yehoshua Perl (IEEE BigData, 2020)

A review of auditing techniques for the Unified Medical Language System. - Ling Zheng; Zhe He 001; Duo Helen Wei; Vipina Kuttichi Keloth; Jungwei Fan 001; Luke Lindemann; Xinxin Zhu; James J. Cimino; Yehoshua Perl (J. Am. Medical Informatics Assoc., 2020)

Extending import detection algorithms for concept import from two to three biomedical terminologies. - Vipina Kuttichi Keloth; James Geller; Yan Chen 009; Julia Xu (BMC Medical Informatics Decis. Mak., 2020)

Outlier concepts auditing methodology for a large family of biomedical ontologies. - Ling Zheng; Hua Min; Yan Chen 009; Vipina Kuttichi Keloth; James Geller; Yehoshua Perl; George Hripcsak (BMC Medical Informatics Decis. Mak., 2020)

Visual comprehension and orientation into the COVID-19 CIDO ontology. - Ling Zheng; Yehoshua Perl; Yongqun He; Christopher Ochs; James Geller; Hao Liu 025; Vipina Kuttichi Keloth (J. Biomed. Informatics, 2021)

Section-specific Annotation of PICO for Medical Evidence Extraction: Applications to Articles of Randomized Controlled Trials for Alzheimer's Disease and COVID-19. - Yan Hu; Vipina Kuttichi Keloth; Hua Xu 001 (AMIA, 2022)

Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues. - Avisha Das; Salih Selek; Alia R. Warner; Xu Zuo; Yan Hu; Vipina Kuttichi Keloth; Jianfu Li; W. Jim Zheng; Hua Xu 001 (BioNLP@ACL, 2022)

Systematic Design and Evaluation of Social Determinants of Health Ontology (SDoHO). - Yifang Dang; Fang Li 011; Xinyue Hu 002; Vipina Kuttichi Keloth; Meng Zhang; Sunyang Fu; Jingcheng Du; J. Wilfred Fan; Muhammad F. Amith; Evan Yu; Hongfang Liu; Xiaoqian Jiang; et al. (CoRR, 2022)

Using annotation for computerized support for fast skimming of cardiology electronic health record notes. - Mahshad Koohi H. Dehkordi; Andrew J. Einstein; Shuxin Zhou; Gai Elhanan; Yehoshua Perl; Vipina Kuttichi Keloth; James Geller; Hao Liu 025 (BIBM, 2023)

Integrating Commercial and Social Determinants of Health: A Unified Ontology for Non-Clinical Determinants of Health. - Navya Martin Kollapally; Vipina Kuttichi Keloth; Julia Xu; James Geller (CoRR, 2023)

Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations. - Qingyu Chen 001; Jingcheng Du; Yan Hu; Vipina Kuttichi Keloth; Xueqing Peng; Kalpana Raja; Rui Zhang 028; Zhiyong Lu; Hua Xu 001 (CoRR, 2023)

Representing and utilizing clinical textual data for real world studies: An OHDSI approach. - Vipina Kuttichi Keloth; Juan M. Banda; Michael J. Gurley; Paul M. Heider; Georgina Kennedy; Hongfang Liu; Feifan Liu; Timothy Miller 002; Karthik Natarajan; Olga V. Patterson; Yifan Peng 002; Kalpana Raja; et al. (J. Biomed. Informatics, 2023)

Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO). - Yifang Dang; Fang Li 011; Xinyue Hu 002; Vipina Kuttichi Keloth; Meng Zhang; Sunyang Fu; Muhammad F. Amith; J. Wilfred Fan; Jingcheng Du; Evan Yu; Hongfang Liu; Xiaoqian Jiang; et al. (J. Am. Medical Informatics Assoc., 2023)

Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach. - Yan Hu; Vipina Kuttichi Keloth; Kalpana Raja; Yong Chen 016; Hua Xu 001 (Bioinform., 2023)

Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients. - Vipina Kuttichi Keloth; Shuxin Zhou; Luke Lindemann; Ling Zheng; Gai Elhanan; Andrew J. Einstein; James Geller; Yehoshua Perl (BMC Medical Informatics Decis. Mak., 2023)

Using clinical entity recognition for curating an interface terminology to aid fast skimming of EHRs. - Navya Martin Kollapally; Mahshad Koohi H. Dehkordi; Yehoshua Perl; James Geller; Fadi P. Deek; Hao Liu 025; Vipina Kuttichi Keloth; Gai Elhanan; Andrew J. Einstein; Shuxin Zhou (BIBM, 2024)

Skimming of Electronic Health Records Highlighted by an Interface Terminology Curated with Machine Learning Mining. - Mahshad Koohi H. Dehkordi; Navya Martin Kollapally; Yehoshua Perl; James Geller; Fadi P. Deek; Hao Liu 025; Vipina Kuttichi Keloth; Gai Elhanan; Andrew J. Einstein (BIOSTEC (2), 2024)

Me LLaMA: Foundation Large Language Models for Medical Applications. - Qianqian Xie; Qingyu Chen 001; Aokun Chen; Cheng Peng 009; Yan Hu; Fongci Lin; Xueqing Peng; Jimin Huang; Jeffrey Zhang 010; Vipina Kuttichi Keloth; Xingyu Zhou; Huan He; et al. (CoRR, 2024)

Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models? - Yan Hu; Xu Zuo; Yujia Zhou 003; Xueqing Peng; Jimin Huang; Vipina Kuttichi Keloth; Vincent J. Zhang; Ruey-Ling Weng; Qingyu Chen 001; Xiaoqian Jiang; Kirk E. Roberts; Hua Xu 001 (CoRR, 2024)

Improving large language models for clinical named entity recognition via prompt engineering. - Yan Hu; Qingyu Chen 001; Jingcheng Du; Xueqing Peng; Vipina Kuttichi Keloth; Xu Zuo; Yujia Zhou 003; Zehan Li; Xiaoqian Jiang; Zhiyong Lu; Kirk Roberts; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2024)

Ensemble pretrained language models to extract biomedical knowledge from literature. - Zhao Li; Qiang Wei 002; Liang-Chin Huang; Jianfu Li; Yan Hu; Yao-Shun Chuang; Jianping He 002; Avisha Das; Vipina Kuttichi Keloth; Yuntao Yang; Chiamaka S. Diala; Kirk E. Roberts; et al. (J. Am. Medical Informatics Assoc., 2024)

FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. - Sunyang Fu; Heling Jia; Maria Vassilaki; Vipina Kuttichi Keloth; Yifang Dang; Yujia Zhou 003; Muskan Garg; Ronald C. Petersen; Jennifer St Sauver; Sungrim Moon; Liwei Wang 010; Andrew Wen; et al. (J. Biomed. Informatics, 2024)

Developing and sustaining inclusive language in biomedical informatics communications: an AMIA Board of Directors endorsed paper on the Inclusive Language and Context Style Guidelines. - Oliver J. Bear Don't Walk IV; Shefali Haldar; Duo Helen Wei; Hu Huang 004; Rebecca L. Rivera; Jungwei W. Fan 001; Vipina Kuttichi Keloth; Tiffany I. Leung; Pooja M. Desai; Diane M. Korngiebel; Lisa Grossman Liu; Adrienne Pichon; et al. (J. Am. Medical Informatics Assoc., 2025)

Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement. - Navya Martin Kollapally; James Geller; Vipina Kuttichi Keloth; Zhe He 001; Julia Xu (J. Biomed. Informatics, 2025)

Social determinants of health extraction from clinical notes across institutions using large language models. - Vipina Kuttichi Keloth; Salih Selek; Qingyu Chen 001; Christopher Gilman; Sunyang Fu; Yifang Dang; Xinghan Chen; Xinyue Hu 002; Yujia Zhou 003; Huan He; Jungwei W. Fan 001; Karen Wang; et al. (npj Digit. Medicine, 2025)

Medical foundation large language models for comprehensive text analysis and beyond. - Qianqian Xie; Qingyu Chen 001; Aokun Chen; Cheng Peng 009; Yan Hu; Fongci Lin; Xueqing Peng; Jimin Huang; Jeffrey Zhang 010; Vipina Kuttichi Keloth; Xinyu Zhou; Lingfei Qian; et al. (npj Digit. Medicine, 2025)