2024
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information
Jin Q, Yang Y, Chen Q, Lu Z. GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. Bioinformatics 2024, 40: btae075. PMID: 38341654, PMCID: PMC10904143, DOI: 10.1093/bioinformatics/btae075.Peer-Reviewed Original ResearchAPI callsWeb APIsLanguage modelState-of-the-art performanceMulti-hop questionsState-of-the-artDomain-specific toolsDecoding algorithmNational Center for Biotechnology InformationGPT-3Biomedical informationDatabase utilizationExperimental resultsAPITaskDomain toolsLearningChatGPTSpecialized knowledgeInformationLanguageGenomic questionsAlgorithmDatasetBiotechnology Information
2020
LitCovid: an open database of COVID-19 literature
Chen Q, Allot A, Lu Z. LitCovid: an open database of COVID-19 literature. Nucleic Acids Research 2020, 49: d1534-d1540. PMID: 33166392, PMCID: PMC7778958, DOI: 10.1093/nar/gkaa952.Peer-Reviewed Original ResearchConceptsSerious information overloadCuration workflowData miningInformation overloadCollected articlesInformation needsOpen databaseManual curationNews articlesCOVID-19 literatureLiterature resourcesRapid growthUsersCOVID-19 researchMiningWorkflowAlgorithmCurationDate scientific informationDatabaseInformationGeneral publicResourcesAccessText
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