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
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 researchDatasetAIONER: 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