2024
Improving large language models for clinical named entity recognition via prompt engineering
Hu Y, Chen Q, Du J, Peng X, Keloth V, Zuo X, Zhou Y, Li Z, Jiang X, Lu Z, Roberts K, Xu H. Improving large language models for clinical named entity recognition via prompt engineering. Journal Of The American Medical Informatics Association 2024, 31: 1812-1820. PMID: 38281112, PMCID: PMC11339492, DOI: 10.1093/jamia/ocad259.Peer-Reviewed Original ResearchClinical NER tasksNER taskTask-specific promptsEntity recognitionLanguage modelTraining samplesState-of-the-art modelsFew-shot learningState-of-the-artMinimal training dataTask-specific knowledgeF1-socreAnnotated samplesConcept extractionModel performanceAnnotated datasetsTraining dataF1 scoreTask descriptionFormat specificationsComplex clinical dataOptimal performanceTaskEvaluation schemaGPT model
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