Vipina K. Keloth, PhD
Associate Research Scientist in Biomedical Informatics and Data ScienceDownloadHi-Res Photo
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Associate Research Scientist in Biomedical Informatics and Data Science
Biography
Dr. Vipina Keloth is an Associate Research Scientist at the Section of Biomedical Informatics and Data Science at Yale School of Medicine. Previously, she was a Postdoctoral Associate at Yale BIDS and prior to that a Postdoctoral Research Fellow at the School of Biomedical Informatics at the University of Texas Health Science Center at Houston. Vipina graduated with a doctoral degree in Computer Science from New Jersey Institute of Technology (NJIT) in 2021. She has also worked as an assistant lecturer in the Department of Mathematical and Computational Sciences at the National Institute of Technology Karnataka, India.
Appointments
Biomedical Informatics & Data Science
Associate Research ScientistPrimary
Other Departments & Organizations
Education & Training
- Postdoctoral Associate
- Yale University (2024)
- Postdoctoral Research Fellow
- University of Texas Health Science Center at Houston (2023)
- PhD
- New Jersey Institute of Technology, Computer Science (2021)
- MS
- National Institute of Technology Karnataka, Systems Analysis and Computer Applications (2014)
- MSc
- Mahatma Gandhi University, Computer Applications (2010)
- BS
- Kannur University, Physics (2007)
Research
Research at a Glance
Yale Co-Authors
Frequent collaborators of Vipina K. Keloth's published research.
Publications Timeline
A big-picture view of Vipina K. Keloth's research output by year.
Hua Xu, PhD
Loren Laine, MD
Qingyu Chen, PhD
Jeffrey Zhang
Xinxin (Katie) Zhu, MD, PhD, FAMIA, FIAHSI
25Publications
110Citations
Publications
2024
A Study of Biomedical Relation Extraction Using GPT Models.
Zhang J, Wibert M, Zhou H, Peng X, Chen Q, Keloth V, Hu Y, Zhang R, Xu H, Raja K. A Study of Biomedical Relation Extraction Using GPT Models. AMIA Joint Summits On Translational Science Proceedings 2024, 2024: 391-400. PMID: 38827097, PMCID: PMC11141827.Peer-Reviewed Original ResearchCitations543 IDENTIFYING OVERT SIGNS OF ACUTE GASTROINTESTINAL BLEEDING IN THE ELECTRONIC HEALTH RECORD WITH LARGE LANGUAGE MODELS
Zheng N, Keloth V, You K, Li D, Xu H, Laine L, Shung D. 543 IDENTIFYING OVERT SIGNS OF ACUTE GASTROINTESTINAL BLEEDING IN THE ELECTRONIC HEALTH RECORD WITH LARGE LANGUAGE MODELS. Gastroenterology 2024, 166: s-124-s-125. DOI: 10.1016/s0016-5085(24)00776-5.Peer-Reviewed Original ResearchConcepts1244 AUTOMATED IDENTIFICATION OF RECURRENT GASTROINTESTINAL BLEEDING USING ELECTRONIC HEALTH RECORDS AND LARGE LANGUAGE MODELS
Zheng N, Keloth V, You K, Li D, Xu H, Laine L, Shung D. 1244 AUTOMATED IDENTIFICATION OF RECURRENT GASTROINTESTINAL BLEEDING USING ELECTRONIC HEALTH RECORDS AND LARGE LANGUAGE MODELS. Gastroenterology 2024, 166: s-292. DOI: 10.1016/s0016-5085(24)01152-1.Peer-Reviewed Original ResearchEnsemble pretrained language models to extract biomedical knowledge from literature
Li Z, Wei Q, Huang L, Li J, Hu Y, Chuang Y, He J, Das A, Keloth V, Yang Y, Diala C, Roberts K, Tao C, Jiang X, Zheng W, Xu H. Ensemble pretrained language models to extract biomedical knowledge from literature. Journal Of The American Medical Informatics Association 2024, ocae061. PMID: 38520725, DOI: 10.1093/jamia/ocae061.Peer-Reviewed Original ResearchAltmetricConceptsNatural language processingNatural language processing systemsLanguage modelExpansion of biomedical literatureZero-shot settingManually annotated corpusKnowledge graph developmentTask-specific modelsDomain-specific modelsZero-ShotEntity recognitionBillion parametersEnsemble learningLocation informationKnowledge basesBiomedical entitiesLanguage processingFree textGraph developmentBiomedical conceptsAutomated techniqueBiomedical literatureDetection methodPredictive performanceBiomedical knowledgeAdvancing entity recognition in biomedicine via instruction tuning of large language models
Keloth V, Hu Y, Xie Q, Peng X, Wang Y, Zheng A, Selek M, Raja K, Wei C, Jin Q, Lu Z, Chen Q, Xu H. Advancing entity recognition in biomedicine via instruction tuning of large language models. Bioinformatics 2024, 40: btae163. PMID: 38514400, PMCID: PMC11001490, DOI: 10.1093/bioinformatics/btae163.Peer-Reviewed Original ResearchCitationsAltmetricConceptsNamed Entity RecognitionSequence labeling taskNatural language processingBiomedical NER datasetsLanguage modelNER datasetsEntity recognitionLabeling taskText generationField of natural language processingBiomedical NERFew-shot learning capabilityReasoning tasksMulti-domain scenariosDomain-specific modelsEnd-to-endMinimal fine-tuningSOTA performanceF1 scoreHealthcare applicationsBiomedical entitiesBiomedical domainLanguage processingMulti-taskingPubMedBERT modelFedFSA: Hybrid and federated framework for functional status ascertainment across institutions
Fu S, Jia H, Vassilaki M, Keloth V, Dang Y, Zhou Y, Garg M, Petersen R, St Sauver J, Moon S, Wang L, Wen A, Li F, Xu H, Tao C, Fan J, Liu H, Sohn S. FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. Journal Of Biomedical Informatics 2024, 152: 104623. PMID: 38458578, PMCID: PMC11005095, DOI: 10.1016/j.jbi.2024.104623.Peer-Reviewed Original ResearchCitationsAltmetricConceptsNatural language processingElectronic health recordsStatus informationInformation extractionFunctional status informationRule-based information extractionFederated learning frameworkPrivate local dataNatural language processing frameworkHealthcare sitesPatient's functional statusMultiple healthcare institutionsFederated learningPyTorch libraryConcept normalizationBERT modelLearning frameworkCollaborative development effortsCorpus annotationLanguage processingHealthcare institutionsFunctional statusPredictor of health outcomesActivities of daily livingNatural language processing performanceImproving large language models for clinical named entity recognition via prompt engineering
Hu Y, Chen Q, Du J, Peng X, Keloth V, Zuo X, Zhou Y, Li Z, Jiang X, Lu Z, Roberts K, Xu H. Improving large language models for clinical named entity recognition via prompt engineering. Journal Of The American Medical Informatics Association 2024, ocad259. PMID: 38281112, DOI: 10.1093/jamia/ocad259.Peer-Reviewed Original ResearchCitationsConceptsClinical NER tasksNER taskTask-specific promptsEntity recognitionLanguage modelTraining samplesState-of-the-art modelsFew-shot learningState-of-the-artMinimal training dataTask-specific knowledgeF1-socreAnnotated samplesConcept extractionModel performanceAnnotated datasetsTraining dataF1 scoreTask descriptionFormat specificationsComplex clinical dataOptimal performanceTaskEvaluation schemaGPT modelIntegrating Commercial and Social Determinants of Health: A Unified Ontology for Non-Clinical Determinants of Health.
Kollapally N, Keloth V, Xu J, Geller J. Integrating Commercial and Social Determinants of Health: A Unified Ontology for Non-Clinical Determinants of Health. AMIA Annual Symposium Proceedings 2024, 2023: 446-455. PMID: 38222328, PMCID: PMC10785916.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsDeterminants of healthSocial determinants of healthImpact of social determinants of healthCommercial determinants of healthNon-clinical determinantsFactors affecting healthSocial determinantsHealth outcomesSDoHNonclinical determinantsHealthWell-beingPeople's healthNon-clinicalCDOHPubMed articlesPubMedSystematic approachOutcomesServicesPeopleSkimming of Electronic Health Records Highlighted by an Interface Terminology Curated with Machine Learning Mining
Koohi H. Dehkordi M, Kollapally N, Perl Y, Geller J, Deek F, Liu H, Keloth V, Elhanan G, Einstein A. Skimming of Electronic Health Records Highlighted by an Interface Terminology Curated with Machine Learning Mining. 2024, 498-505. DOI: 10.5220/0012391600003657.Peer-Reviewed Original Research
2023
Using annotation for computerized support for fast skimming of cardiology electronic health record notes
Dehkordi M, Einstein A, Zhou S, Elhanan G, Perl Y, Keloth V, Geller J, Liu H. Using annotation for computerized support for fast skimming of cardiology electronic health record notes. 2023, 00: 4043-4050. DOI: 10.1109/bibm58861.2023.10385289.Peer-Reviewed Original ResearchConceptsElectronic health recordsElectronic health record notesNamed Entity RecognitionTraining dataMining conceptsInterface terminologyMachine learningSNOMED CTEntity recognitionHealth recordsHealthcare professionalsTransfer learningPatient careCurrent healthcareMining techniquesMining phrasesArt techniquesRecord notesSNOMED conceptsMedical specialtiesComputer-SupportedMedical professionalsReference terminologyCritical informationAnnotation
Academic Achievements & Community Involvement
activity American Medical Informatics Association (AMIA)
Professional OrganizationsMemberDetails05/15/2018 - Presentactivity Journal of Biomedical Informatics
Journal ServiceReviewerDetails06/30/2021 - Presentactivity BMC Supplements
Journal ServiceReviewerDetails06/01/2021 - Presentactivity AMIA DEI Communications Subcommittee
Professional OrganizationsMemberDetails10/28/2021 - Presentactivity JAMIA Open
Journal ServiceReviewerDetails04/03/2023 - Present
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