2025
AdFair-CLIP: Adversarial Fair Contrastive Language-Image Pre-training for Chest X-Rays
Yi C, Xiong Z, Qi Q, Wei X, Bathla G, Lin C, Mortazavi B, Yang T. AdFair-CLIP: Adversarial Fair Contrastive Language-Image Pre-training for Chest X-Rays. Lecture Notes In Computer Science 2025, 15965: 13-23. DOI: 10.1007/978-3-032-04978-0_2.Peer-Reviewed Original ResearchContrastive Language-Image Pre-trainingFairness-aware learningFew-shot scenariosMedical image classificationMedical diagnostic modelsChest X-ray analysisZero-ShotImage classificationComprehensive experimentsSensitive attributesPre-trainingSuperior performancePredictive fairnessRobust generalizationVisual tasksClip modelSpurious correlationsDemographic biasFairnessDiagnostic modelDatasetReduced reliabilityInstruction-Tuned Large Language Models for Clinical Data Extraction: Creating an Aortic Measurement Database from CT Radiology Reports
Erez E, Dankwa S, Tuttle M, Nasir A, Vallabhajosyula P, Schneider E, Assi R, Ong C. Instruction-Tuned Large Language Models for Clinical Data Extraction: Creating an Aortic Measurement Database from CT Radiology Reports. Journal Of Healthcare Informatics Research 2025, 1-19. DOI: 10.1007/s41666-025-00210-y.Peer-Reviewed Original ResearchLanguage modelFew-shotZero-ShotInformation extraction tasksMacro F1-scoreBERT-based modelsExtraction taskBERT modelChest Computed TomographyF1 scoreElectronic health recordsMinimal annotationStructure extractionTest setAortic measurementsAortic diameterHealth recordsThoracic aortic dilatationCT radiology reportsRelevant informationChest CT reportsHigh performanceAortic dilatationCT reportsAortic diseasePHSOP12 Presentation Time: 9:55 AM No Training Set Required: Concept and Benchmarking of BrachyGPT, the First Fully-Automated AI Zero-Shot Brachytherapy Treatment Planning Framework
Li Z, Carlson D, Liu X, Damast S, Fakhri G, Tien C. PHSOP12 Presentation Time: 9:55 AM No Training Set Required: Concept and Benchmarking of BrachyGPT, the First Fully-Automated AI Zero-Shot Brachytherapy Treatment Planning Framework. Brachytherapy 2025, 24: s41-s42. DOI: 10.1016/j.brachy.2025.06.070.Peer-Reviewed Original ResearchDose-volume indicesHR-CTVDose distributionDwell positionsHDR-BTClinically acceptable plansTreatment planning systemDose-volume histogramsClinical criteriaTreatment planning frameworkApplication programming interfaceHigh-dose-rate brachytherapyTreatment planningReconstructed cathetersTG-43Dose kernelsZero-ShotIsodose comparisonEMBRACE IIAcceptable plansTraining setOARsPlanning systemAI approachesSeed modelBenchmarking large language models for biomedical natural language processing applications and recommendations
Chen Q, Hu Y, Peng X, Xie Q, Jin Q, Gilson A, Singer M, Ai X, Lai P, Wang Z, Keloth V, Raja K, Huang J, He H, Lin F, Du J, Zhang R, Zheng W, Adelman R, Lu Z, Xu H. Benchmarking large language models for biomedical natural language processing applications and recommendations. Nature Communications 2025, 16: 3280. PMID: 40188094, PMCID: PMC11972378, DOI: 10.1038/s41467-025-56989-2.Peer-Reviewed Original ResearchConceptsLanguage modelNatural language processing applicationsBiomedical natural language processingMedical question answeringLanguage processing applicationsNatural language processingGrowth of biomedical literatureMissing informationFew-shotQuestion AnsweringZero-ShotKnowledge curationLanguage processingProcessing applicationsBioNLPBART modelPerformance gapBiomedical literatureGeneral domainTaskBenchmarksBERTInformationPerformanceLLMMedical foundation large language models for comprehensive text analysis and beyond
Xie Q, Chen Q, Chen A, Peng C, Hu Y, Lin F, Peng X, Huang J, Zhang J, Keloth V, Zhou X, Qian L, He H, Shung D, Ohno-Machado L, Wu Y, Xu H, Bian J. Medical foundation large language models for comprehensive text analysis and beyond. Npj Digital Medicine 2025, 8: 141. PMID: 40044845, PMCID: PMC11882967, DOI: 10.1038/s41746-025-01533-1.Peer-Reviewed Original ResearchText analysis tasksAnalysis tasksLanguage modelDomain-specific knowledgeZero-ShotHuman evaluationSupervised settingTask-specific instructionsClinical data sourcesSpecialized medical knowledgeChatGPTText analysisPretrainingTaskData sourcesMedical applicationsMedical knowledgeEnhanced performanceTextPerformance
2024
Large language models for biomedicine: foundations, opportunities, challenges, and best practices
Sahoo S, Plasek J, Xu H, Uzuner Ö, Cohen T, Yetisgen M, Liu H, Meystre S, Wang Y. Large language models for biomedicine: foundations, opportunities, challenges, and best practices. Journal Of The American Medical Informatics Association 2024, 31: 2114-2124. PMID: 38657567, PMCID: PMC11339493, DOI: 10.1093/jamia/ocae074.Peer-Reviewed Original ResearchNatural language processingPrompt tuningNLP applicationsLanguage modelState-of-the-art performanceNLP practitionersNatural language processing applicationsBiomedical NLP applicationsPre-training datasetNatural language understandingNeural network architecture modelNatural language generationBiomedical informatics communityNetwork architecture modelAmerican Medical Informatics Association (AMIAPrompt-tuningFew-shotZero-ShotNLP challengeNLP tasksReinforcement learningHuman feedbackLanguage generationLanguage understandingEvaluation metricsEnsemble 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, 31: 1904-1911. PMID: 38520725, PMCID: PMC11339500, DOI: 10.1093/jamia/ocae061.Peer-Reviewed Original ResearchNatural 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 knowledgeIdentifying and Extracting Rare Diseases and Their Phenotypes with Large Language Models
Shyr C, Hu Y, Bastarache L, Cheng A, Hamid R, Harris P, Xu H. Identifying and Extracting Rare Diseases and Their Phenotypes with Large Language Models. Journal Of Healthcare Informatics Research 2024, 8: 438-461. PMID: 38681753, PMCID: PMC11052982, DOI: 10.1007/s41666-023-00155-0.Peer-Reviewed Original Research
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