2023
Opportunities and challenges for ChatGPT and large language models in biomedicine and health
Tian S, Jin Q, Yeganova L, Lai P, Zhu Q, Chen X, Yang Y, Chen Q, Kim W, Comeau D, Islamaj R, Kapoor A, Gao X, Lu Z. Opportunities and challenges for ChatGPT and large language models in biomedicine and health. Briefings In Bioinformatics 2023, 25: bbad493. PMID: 38168838, PMCID: PMC10762511, DOI: 10.1093/bib/bbad493.Peer-Reviewed Original ResearchConceptsLarge language modelsLanguage modelSensitive patient dataBiomedical information retrievalText generation tasksInformation retrievalPrivacy concernsDomain expertsInformation extractionText summarizationBiomedical domainArt methodsDiverse applicationsPrevious stateBiomedical researchersGeneration taskPatient dataSuch methodsTaskDistinct complexityGeneration capabilityExtensive literature surveySummarizationRecent rapid progressChallengesMedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval
Jin Q, Kim W, Chen Q, Comeau D, Yeganova L, Wilbur W, Lu Z. MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. Bioinformatics 2023, 39: btad651. PMID: 37930897, PMCID: PMC10627406, DOI: 10.1093/bioinformatics/btad651.Peer-Reviewed Original ResearchConceptsInformation retrievalIR tasksUser click logsSemantic information retrievalBiomedical information retrievalBiomedical knowledge acquisitionPre-trained TransformerClinical decision supportClick logsSearch logsContrastive learningLexical matchingArt performanceIR systemsSemantic retrievalBiomedical articlesDecision supportSentence representationModel encoderKnowledge acquisitionLarge modelsSemantic evaluationRetrievalTransformer modelUnprecedented scale
2021
Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing
Chen Q, Leaman R, Allot A, Luo L, Wei C, Yan S, Lu Z. Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing. Annual Review Of Biomedical Data Science 2021, 4: 1-27. PMID: 34465169, DOI: 10.1146/annurev-biodatasci-021821-061045.Peer-Reviewed Original ResearchConceptsNatural language processingArtificial intelligenceLanguage processingInformation needsLiterature-based discoveryInformation retrievalEntity recognitionMisinformation detectionInformation overloadNLP studiesNLP tasksEmotion analysisTopic modelingCOVID-19 pandemicIntelligenceAdditional tasksHuman languagePublic health measuresTaskHealth measuresProcessingSerious health effectsHealth effectsRetrievalDataset
2019
BioWordVec, improving biomedical word embeddings with subword information and MeSH
Zhang Y, Chen Q, Yang Z, Lin H, Lu Z. BioWordVec, improving biomedical word embeddings with subword information and MeSH. Scientific Data 2019, 6: 52. PMID: 31076572, PMCID: PMC6510737, DOI: 10.1038/s41597-019-0055-0.Peer-Reviewed Original ResearchConceptsWord embeddingsSubword informationWord representationsBiomedical natural language processingNatural language processingMultiple NLP tasksBiomedical word embeddingsInformation retrievalUnlabeled textBiomedical textText miningBiomedical domainLanguage processingNLP tasksStructured resourcesChallenging taskPrevious stateBenchmarking resultsLarge corpusEmbeddingWord levelBioWordVecSuch informationTaskInformation