2022
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation
Chen Q, Du J, Allot A, Lu Z. LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2022, 19: 2584-2595. PMID: 35536809, PMCID: PMC9647722, DOI: 10.1109/tcbb.2022.3173562.Peer-Reviewed Original ResearchMulti-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
Chen Q, Allot A, Leaman R, Islamaj R, Du J, Fang L, Wang K, Xu S, Zhang Y, Bagherzadeh P, Bergler S, Bhatnagar A, Bhavsar N, Chang Y, Lin S, Tang W, Zhang H, Tavchioski I, Pollak S, Tian S, Zhang J, Otmakhova Y, Yepes A, Dong H, Wu H, Dufour R, Labrak Y, Chatterjee N, Tandon K, Laleye F, Rakotoson L, Chersoni E, Gu J, Friedrich A, Pujari S, Chizhikova M, Sivadasan N, Vg S, Lu Z. Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database 2022, 2022: baac069. PMID: 36043400, PMCID: PMC9428574, DOI: 10.1093/database/baac069.Peer-Reviewed Original Research
2021
LitSuggest: a web-based system for literature recommendation and curation using machine learning
Allot A, Lee K, Chen Q, Luo L, Lu Z. LitSuggest: a web-based system for literature recommendation and curation using machine learning. Nucleic Acids Research 2021, 49: w352-w358. PMID: 33950204, PMCID: PMC8262723, DOI: 10.1093/nar/gkab326.Peer-Reviewed Original ResearchMeSH KeywordsCOVID-19Data CurationHealthcare DisparitiesHumansInternetLiver NeoplasmsMachine LearningPublicationsSoftwareConceptsNatural language processingWeb-based systemQuery methodSearch systemSearch queriesMachine learningWeb serverCuration servicesAdvanced machineUser projectsLanguage processingClassification resultsTraining corpusSingle interfaceUsersBiomedical researchersCollaborative analysisHigh accuracyLiterature recommendationsPubMed articlesMachineCurationComputational methodsSpecialized knowledgeKeywords
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 publicResourcesAccessTextBioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale
Chen Q, Lee K, Yan S, Kim S, Wei C, Lu Z. BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLOS Computational Biology 2020, 16: e1007617. PMID: 32324731, PMCID: PMC7237030, DOI: 10.1371/journal.pcbi.1007617.Peer-Reviewed Original ResearchConceptsConcept embeddingsNER toolsLearning modelBiomedical text mining applicationsAdvanced deep learning modelsDifferent machine learning modelsEvaluation resultsText mining applicationsDeep learning modelsSemantics of conceptsMachine learning modelsLiterature-based discoveryConcept recognitionDifferent machineProtein-protein interaction predictionPubMed abstractsRecognition toolsMassive numberVector representationBiomedical conceptsLarge marginExtrinsic evaluationBiomedical literatureIntrinsic evaluationSemantic relatedness
2019
LitSense: making sense of biomedical literature at sentence level
Allot A, Chen Q, Kim S, Alvarez R, Comeau D, Wilbur W, Lu Z. LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Research 2019, 47: w594-w599. PMID: 31020319, PMCID: PMC6602490, DOI: 10.1093/nar/gkz289.Peer-Reviewed Original ResearchConceptsFirst web-based systemFilter search resultsNeural embedding approachBiomedical literatureUser-friendly interfaceWeb-based systemTerm-weighting approachUser queriesQuery formulationUnified accessKeyword matchesBiomedical entitiesSentence retrievalResults visualizationSearch resultsEmbedding approachCurrent toolsQueriesRetrievalSentence levelRare termsRelevant resultsSignificant effortsPrevious knowledgePubTator