2024
PubTator 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 setChatGPTQueryVerifiabilityRetrievalEnsemble 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 knowledge
2023
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models
Millikin R, Raja K, Steill J, Lock C, Tu X, Ross I, Tsoi L, Kuusisto F, Ni Z, Livny M, Bockelman B, Thomson J, Stewart R. Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models. BMC Bioinformatics 2023, 24: 412. PMID: 37915001, PMCID: PMC10619245, DOI: 10.1186/s12859-023-05539-y.Peer-Reviewed Original ResearchConceptsLiterature-based discoveryKnowledge graphWeb interfaceLiterature-based discovery toolsUser-defined conceptsFunctional web-interfaceOpen-source toolBiomedical domainMachine-learning modelsOpen-source web interfaceBiomedical conceptsType labelsKnowledge domainsLiterature domainTransformation modelAlgorithmBiomedical knowledgeGraphQuerying thousandsPubMed archive
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