2023
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets
Lai P, Wei C, Luo L, Chen Q, Lu Z. BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. Journal Of Biomedical Informatics 2023, 146: 104487. PMID: 37673376, DOI: 10.1016/j.jbi.2023.104487.Peer-Reviewed Original ResearchBiomedical relation extractionRelation extractionRE tasksNatural language processing researchData-centric approachKnowledge graph constructionMulti-task learningLanguage processing researchIndividual datasetsLiterature-based discoveryChemical-induced disease relationsDataset annotationDomain knowledgeTransfer learningTraining dataHeterogeneous datasetsArt methodsNovel frameworkGraph constructionFree textData heterogeneityLarge datasetsBiomedical conceptsProcessing researchDataset
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
2020
BioConceptVec: 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