2024
Augmenting biomedical named entity recognition with general-domain resources
Yin Y, Kim H, Xiao X, Wei C, Kang J, Lu Z, Xu H, Fang M, Chen Q. Augmenting biomedical named entity recognition with general-domain resources. Journal Of Biomedical Informatics 2024, 159: 104731. PMID: 39368529, DOI: 10.1016/j.jbi.2024.104731.Peer-Reviewed Original ResearchBioNER datasetsMulti-task learningNER datasetsEntity typesBiomedical datasetsBaseline modelGeneral domain datasetsBiomedical language modelNeural network-basedYield performance improvementsBioNER modelsEntity recognitionBiomedical corporaHuman annotatorsLabel ambiguityLanguage modelTransfer learningF1 scoreBioNERHuman effortNetwork-basedBiomedical resourcesPerformance improvementDatasetSuperior performance
2020
Deep 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 set
2019
Evaluation of Five Sentence Similarity Models on Electronic Medical Records
Chen Q, Du J, Kim S, Wilbur W, Lu Z. Evaluation of Five Sentence Similarity Models on Electronic Medical Records. 2019, 533-533. DOI: 10.1145/3307339.3343239.Peer-Reviewed Original ResearchSentence similarity modelSimilarity modelLarge biomedical corporaLarge public datasetsTraditional machineClinical domainsBiomedical corporaText summarizationBidirectional transformersPublic datasetsSemantic similaritySmall datasetsSentence similarityDataset consistingSentence pairsDatasetElectronic medical recordsPrimary applicationCNNSummarizationBERTVital roleMachineDomainEmbedding