2025
A Generative Artificial Intelligence Copilot for Biomedical Nanoengineering
Wang Y, Song H, Teng Y, Huang G, Qian J, Wang H, Dong S, Ha J, Ma Y, Chang M, Jeong S, Deng W, Schrank B, Grippin A, Wu A, Edwards J, Zhang Y, Lin Y, Poon W, Wilhelm S, Bi Y, Teng L, Wang Z, Kim B, Jiang W. A Generative Artificial Intelligence Copilot for Biomedical Nanoengineering. ACS Nano 2025, 19: 19394-19407. PMID: 40367350, DOI: 10.1021/acsnano.5c03454.Peer-Reviewed Original ResearchConceptsArtificial intelligenceNatural language processing tasksExtract contextual informationLanguage processing tasksAutomatically extract knowledgeAI-based methodsGenerative artificial intelligenceInformation extractionLanguage modelAutomated learningContextual informationProcessing tasksIntelligent copilotBaseline modelAI toolsDesign tasksTaskQueryScientific queriesAutomaticallyCopilotIntelligenceScientific researchLLMLearningImage-Based Search in Radiology: Identification of Brain Tumor Subtypes within Databases Using MRI-Based Radiomic Features.
von Reppert M, Chadha S, Willms K, Avesta A, Maleki N, Zeevi T, Lost J, Tillmanns N, Jekel L, Merkaj S, Lin M, Hoffmann K, Aneja S, Aboian M. Image-Based Search in Radiology: Identification of Brain Tumor Subtypes within Databases Using MRI-Based Radiomic Features. American Journal Of Neuroradiology 2025, 46: 1421-1428. PMID: 40250848, DOI: 10.3174/ajnr.a8805.Peer-Reviewed Original ResearchConceptsDimensionality reduction techniquesQuery caseImage search enginesImage-based searchReduction techniquesQuery subsetsRetrieval performanceQuery onesDimensionality reductionVisual similarityQuerySearch enginesSearch approachSearch methodTumor segmentationImage-basedRadiomic featuresNearest neighborsTumor typesDimensionalityBrain tumorsData setsNinety-five patientsLikert scoresMRI-based radiomic featuresRouterRetriever: Routing over a Mixture of Expert Embedding Models
Lee H, Soldaini L, Cohan A, Seo M, Lo K. RouterRetriever: Routing over a Mixture of Expert Embedding Models. Proceedings Of The AAAI Conference On Artificial Intelligence 2025, 39: 11995-12003. DOI: 10.1609/aaai.v39i11.33306.Peer-Reviewed Original ResearchEmbedding modelRouting mechanismGeneral domain datasetsMulti-task trainingDomain-specific dataInformation retrieval methodsMulti-task modelDomain-specific expertsExpert retrievalInformation retrievalLanguage modelRouting techniquesRetrieval modelUnderperforming modelsRetrieval methodRetrievalSpecialized domainsDatasetGeneration researchExpertsQueryInformationLanguageTrainingEmbeddingmFollowIR: A Multilingual Benchmark for Instruction Following in Retrieval
Weller O, Chang B, Yang E, Yarmohammadi M, Barham S, MacAvaney S, Cohan A, Soldaini L, Van Durme B, Lawrie D. mFollowIR: A Multilingual Benchmark for Instruction Following in Retrieval. Lecture Notes In Computer Science 2025, 15573: 295-310. DOI: 10.1007/978-3-031-88711-6_19.Peer-Reviewed Original Research
2024
Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network
Yu Y, Edelson M, Pham A, Pekar J, Johnson B, Post K, Kuo T. Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network. Journal Of The American Medical Informatics Association 2024, 32: 296-307. PMID: 39569448, PMCID: PMC11756586, DOI: 10.1093/jamia/ocae288.Peer-Reviewed Original ResearchBlockchain-based systemSmart contractsMedical data managementData access processReal-world scenariosData access historyRuntime metricsAccess transparencyAudit logMetadata InitiativeNetwork speedPerformance gainsSharing requestsAccess historyRequest managementHardware specificationsComputing capacityAverage runtimeData managementSharing processSynthetic dataRequest timeQueryAudit trailData linksPubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature
Tian S, Chen Q, Comeau D, Wilbur W, Lu Z. PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature. Bioinformatics 2024, 40: btae672. PMID: 39520405, PMCID: PMC11588201, DOI: 10.1093/bioinformatics/btae672.Peer-Reviewed Original ResearchAuthor name disambiguationAuthor namesBiomedical literature searchWeb APIsEnhancement algorithmAuthority datasetsQueryBiomedical literatureDatasetAuthors' algorithmImproved accuracyIndividual researchersAlgorithmPubMed articlesSupplementary dataDisambiguationORCIDLiterature retrievalDownloadRetrievalWebAPIComprehensive datasetBioinformaticsFrom Queries to Transformations: A Correlation Analysis of Google Trends Search Data of Cosmetic Dermatologic Surgery
Rajanala S, Dover J. From Queries to Transformations: A Correlation Analysis of Google Trends Search Data of Cosmetic Dermatologic Surgery. Dermatologic Surgery 2024, 51: 340-342. PMID: 39404124, DOI: 10.1097/dss.0000000000004449.Peer-Reviewed Original ResearchDigital contentQueryDistributed management of patient data-sharing informed consents for clinical research
Pham A, Edelson M, Nouri A, Kuo T. Distributed management of patient data-sharing informed consents for clinical research. Computers In Biology And Medicine 2024, 180: 108956. PMID: 39121682, PMCID: PMC11380755, DOI: 10.1016/j.compbiomed.2024.108956.Peer-Reviewed Original ResearchBenefits of immutabilityBlockchain-based infrastructureMulti-site scenarioResearch Data AccessNode parallelismOn-chainNetwork nodesData accessAudit trailPatient privacyDistribution managementConsent mechanismsData categoriesNodesEfficient wayNetworkAutomated channelAccuracyQueryPrivacyImmutabilityOrchestrationConsent protocolDataExhaustive listPubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge
Wei C, Allot A, Lai P, Leaman R, Tian S, Luo L, Jin Q, Wang Z, Chen Q, Lu Z. PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic Acids Research 2024, 52: w540-w546. PMID: 38572754, PMCID: PMC11223843, DOI: 10.1093/nar/gkae235.Peer-Reviewed Original ResearchState-of-the-art AI techniquesState-of-the-artComplex information needsAdvanced search capabilitiesPairs queriesEntity relationsRetrieval qualitySearch capabilityAI techniquesLiterature resourcesPubTatorInformation needsPubMed abstractsBiomedical literatureOnline interfaceLarge-scale analysisGenetic variantsBiomedical knowledgeAPIScientific discoveryComprehensive setChatGPTQueryVerifiabilityRetrievalChatGPT for Automated Cross‐Checking of Authors' Conflicts of Interest Against Industry Payments
Safranek C, Liu C, Richmond R, Boyi T, Rimmer R, Manes R. ChatGPT for Automated Cross‐Checking of Authors' Conflicts of Interest Against Industry Payments. Otolaryngology 2024, 170: 1512-1518. PMID: 38488302, DOI: 10.1002/ohn.720.Peer-Reviewed Original ResearchAuthor affiliationLanguage modelChatGPTManual verificationManually cross-checkedAuthor namesChronic rhinosinusitisMetadataNasal polyposisObservational studyRandom subsetAccuracyMedical publicationsRelevant articlesLabor-intensiveUS physiciansDatabaseQueryAuthor conflictsData extractionMedical research articlesResearch articlesEMPATHIC: Emulating Human-Like Multimodal Personality Architecture Through Thoughtful Human-AI Conversation
Devi V, Oviya I, Raja K. EMPATHIC: Emulating Human-Like Multimodal Personality Architecture Through Thoughtful Human-AI Conversation. 2024, 00: 79-85. DOI: 10.1109/confluence60223.2024.10463330.Peer-Reviewed Original ResearchHigh-quality training dataReal-time faceHuman-computer interactionNatural language processingChatbot systemGeneral queriesConversational agentsTraining dataObject countingHuman instructionsEmotion recognitionLow-rankLanguage processingDialogue performanceChatbotFine-tuningInstruction templatesLanguage dataPersonality architectureFrameworkCustomer service experienceOperational efficiencyTuning methodologyLoRaQuery
2023
LeafAI: query generator for clinical cohort discovery rivaling a human programmer
Dobbins N, Han B, Zhou W, Lan K, Kim H, Harrington R, Uzuner Ö, Yetisgen M. LeafAI: query generator for clinical cohort discovery rivaling a human programmer. Journal Of The American Medical Informatics Association 2023, 30: 1954-1964. PMID: 37550244, PMCID: PMC10654856, DOI: 10.1093/jamia/ocad149.Peer-Reviewed Original ResearchConceptsUnified Medical Language SystemHuman programmersQuery creationDatabase programmersText processing problemsUnified Medical Language System conceptsState-of-the-artLogical reasoning capabilityKnowledge baseMedical Language SystemRule-based moduleHybrid deep learningQuery generationSchema elementsEntity recognitionReasoning capabilitiesQuery designDeep learningQueryCohort discoveryClinical trial eligibility criteriaLanguage systemConditional reasoningClinical trialsSequence-to-sequence transformationChatGPT and Artificial Intelligence in Transplantation Research: Is It Always Correct?
Rawashdeh B, Kim J, AlRyalat S, Prasad R, Cooper M. ChatGPT and Artificial Intelligence in Transplantation Research: Is It Always Correct? Cureus 2023, 15: e42150. PMID: 37602076, PMCID: PMC10438857, DOI: 10.7759/cureus.42150.Peer-Reviewed Original Research
2022
ABNIRML: Analyzing the Behavior of Neural IR Models
MacAvaney S, Feldman S, Goharian N, Downey D, Cohan A. ABNIRML: Analyzing the Behavior of Neural IR Models. Transactions Of The Association For Computational Linguistics 2022, 10: 224-239. DOI: 10.1162/tacl_a_00457.Peer-Reviewed Original ResearchNeural IR modelsLanguage modelBase language modelNeural ranking modelsContextual language modelsIR modelExtensive empirical studyRanking modelsModel trainingLinguistic informationSensitivity to wordUnintended biasWriting styleComprehensive frameworkEmpirical studiesBERTQueryModel gainsFrameworkWordsParaphrasingModel
2018
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions
Chen Q, Zhang X, Wan Y, Zobel J, Verspoor K. Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. Journal Of Computational Biology 2018, 26: 605-617. PMID: 30585742, DOI: 10.1089/cmb.2018.0198.Peer-Reviewed Original ResearchConceptsSearch effectivenessGroup similar sequencesBiological sequence databasesUser behaviorEvaluation metricsEffective search timeSearch timeClustering methodMatched clustersUsersAnnotation similarityMember recordsDatabaseIncreasing databaseSequence clustering methodsQueryAggregation sequenceRecallPrecisionNonredundant databaseSequence databasesSearchSimilar sequencesClustersNonredundant sequence databaseOvercoming low-utility facets for complex answer retrieval
MacAvaney S, Yates A, Cohan A, Soldaini L, Hui K, Goharian N, Frieder O. Overcoming low-utility facets for complex answer retrieval. Discover Computing 2018, 22: 395-418. DOI: 10.1007/s10791-018-9343-0.Peer-Reviewed Original ResearchComplex Answer RetrievalAnswer RetrievalTREC CAR datasetEntity similarity scoresRetrieval of answersNeural rankerCar datasetDifficult queriesKnowledge graphRetrieval performanceTraining dataSimilarity scoresRanking techniqueFrequency informationQueryRetrievalHierarchical structureTRECRankersPerformanceEmbeddingAnswersDatasetGraphEntitiesCharacterizing Question Facets for Complex Answer Retrieval
MacAvaney S, Yates A, Cohan A, Soldaini L, Hui K, Goharian N, Frieder O. Characterizing Question Facets for Complex Answer Retrieval. 2018, 1205-1208. DOI: 10.1145/3209978.3210135.Peer-Reviewed Original Research
2017
Scientific document summarization via citation contextualization and scientific discourse
Cohan A, Goharian N. Scientific document summarization via citation contextualization and scientific discourse. International Journal On Digital Libraries 2017, 19: 1-17. DOI: 10.1007/s00799-017-0216-8.Peer-Reviewed Original ResearchScientific summarizationCitation textContributions of scientific papersComputational linguistics domainGrowth of scientific literatureScientific document summarizationSummarization datasetsDocument summarizationQuery reformulationProblem of inaccuracySupervised learningWord embeddingsCiting paperDiscourse facetsScientific papersContextualizing citationsSummarizationEvaluation resultsCitationsDiscourse structureQueryTextEmbeddingDatasetLinguistic domains
2015
Retrieving Medical Literature for Clinical Decision Support
Soldaini L, Cohan A, Yates A, Goharian N, Frieder O. Retrieving Medical Literature for Clinical Decision Support. Lecture Notes In Computer Science 2015, 9022: 538-549. DOI: 10.1007/978-3-319-16354-3_59.Peer-Reviewed Original ResearchClinical decision supportDecision supportQuery reformulation techniquesState-of-the-artQueryVast volumeSearch taskReformulation techniquesTaskStatistically significant improvementHealthcare professionalsMedical case reportsPoseMedical literatureSearchMedical professionalsClinical decisionsLiterature searchSystemSignificant improvementProfessionalsRelevant medical literatureCase reportSupport
2014
On clinical decision support
Cohan A, Soldaini L, Yates A, Goharian N, Frieder O. On clinical decision support. 2014, 651-652. DOI: 10.1145/2649387.2660820.Peer-Reviewed Original Research
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