2023
MedCPT: 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 scaleAIONER: all-in-one scheme-based biomedical named entity recognition using deep learning
Luo L, Wei C, Lai P, Leaman R, Chen Q, Lu Z. AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. Bioinformatics 2023, 39: btad310. PMID: 37171899, PMCID: PMC10212279, DOI: 10.1093/bioinformatics/btad310.Peer-Reviewed Original ResearchConceptsDeep learningEntity recognitionTraining dataEntity typesLabeling training dataNatural language textText mining tasksSignificant domain expertiseMulti-task learningMining tasksInformation extractionBioNER taskDomain expertiseBiomedical entitiesIndependent tasksSource codeBenchmark tasksLanguage textBiomedical textArt approachesAccurate annotationExternal dataData scarcityTaskLearning
2022
Multi-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
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 publicResourcesAccessTextBetter synonyms for enriching biomedical search
Yeganova L, Kim S, Chen Q, Balasanov G, Wilbur W, Lu Z. Better synonyms for enriching biomedical search. Journal Of The American Medical Informatics Association 2020, 27: 1894-1902. PMID: 33083825, PMCID: PMC7727334, DOI: 10.1093/jamia/ocaa151.Peer-Reviewed Original ResearchDeep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records
Chen Q, Du J, Kim S, Wilbur W, Lu Z. Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. BMC Medical Informatics And Decision Making 2020, 20: 73. PMID: 32349758, PMCID: PMC7191680, DOI: 10.1186/s12911-020-1044-0.Peer-Reviewed Original ResearchConceptsEnd deep learning modelEncoder networkDeep learning modelsSentence embeddingsBiomedical corporaLearning modelRandom forestTraditional machineText mining applicationsDeep learning approachSimilar sentencesMachine learning modelsHigh performanceMining applicationsRelated datasetsClinical notesLearning approachSentence semanticsPubMed abstractsChallenge taskEnsembled modelBest submissionSentence pairsNetworkTest setBioConceptVec: 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