2024
Ascle—A Python Natural Language Processing Toolkit for Medical Text Generation: Development and Evaluation Study
Yang R, Zeng Q, You K, Qiao Y, Huang L, Hsieh C, Rosand B, Goldwasser J, Dave A, Keenan T, Ke Y, Hong C, Liu N, Chew E, Radev D, Lu Z, Xu H, Chen Q, Li I. Ascle—A Python Natural Language Processing Toolkit for Medical Text Generation: Development and Evaluation Study. Journal Of Medical Internet Research 2024, 26: e60601. PMID: 39361955, PMCID: PMC11487205, DOI: 10.2196/60601.Peer-Reviewed Original ResearchConceptsNatural language processingNatural language processing toolkitQuestion-answering taskLanguage modelText generationText processingDomain-specific language modelsNatural language processing functionsMinimal programming expertiseText generation tasksMedical knowledge graphMachine translation tasksROUGE-L scoreDomain-specific challengesAll-in-one solutionROUGE-LText summarizationBLEU scoreKnowledge graphMachine translationUnstructured textQuestion-answeringHugging FaceProcessing toolkitLanguage processingRepurposing non-pharmacological interventions for Alzheimer's disease through link prediction on biomedical literature
Xiao Y, Hou Y, Zhou H, Diallo G, Fiszman M, Wolfson J, Zhou L, Kilicoglu H, Chen Y, Su C, Xu H, Mantyh W, Zhang R. Repurposing non-pharmacological interventions for Alzheimer's disease through link prediction on biomedical literature. Scientific Reports 2024, 14: 8693. PMID: 38622164, PMCID: PMC11018822, DOI: 10.1038/s41598-024-58604-8.Peer-Reviewed Original ResearchConceptsAlzheimer's diseaseManual therapy techniquesR-GCNKnowledge graphAD preventionNon-pharmacological interventionsBiomedical literatureGraph convolutional network modelKG embedding modelsTest setLink prediction modelIntegrated healthConvolutional network modelImprove cognitive functionHighest scoring candidatesDomain expertsEmbedding modelNon-pharmaceutical interventionsReal-world data analysisGround truthPrevent ADCognitive functionTherapy techniquesNetwork modelDiscovery patternsPrompt Tuning in Biomedical Relation Extraction
He J, Li F, Li J, Hu X, Nian Y, Xiang Y, Wang J, Wei Q, Li Y, Xu H, Tao C. Prompt Tuning in Biomedical Relation Extraction. Journal Of Healthcare Informatics Research 2024, 8: 206-224. PMID: 38681754, PMCID: PMC11052745, DOI: 10.1007/s41666-024-00162-9.Peer-Reviewed Original ResearchFew-shot scenariosBiomedical relation extractionNatural language processingBiomedical RERelation extractionPrompt tuningState-of-the-art performanceText mining applicationsTuning modelBioCreative VISemEval-2013Knowledge graphLanguage modelMining applicationsBiomedical textOriginal inputComputational resourcesLanguage processingExternal knowledgeSpecific textsSuperior performanceDatasetEfficient approachTaskModel performance
2023
Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature
Xiao Y, Hou Y, Zhou H, Diallo G, Fiszman M, Wolfson J, Kilicoglu H, Chen Y, Xu H, Mantyh W, Zhang R. Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature. 2023, 00: 750-752. DOI: 10.1109/ichi57859.2023.00137.Peer-Reviewed Original ResearchAlzheimer's diseaseKnowledge graphKnowledge graph embedding modelsGraph convolutional network modelComputational drug repurposingGraph embedding modelsTest setConvolutional network modelBiomedical knowledge graphComprehensive knowledge graphDietary supplementsR-GCNEmbedding modelDrug repurposingLink predictionPrediction taskSemantic triplesNetwork modelAlzheimerBiomedical literatureNovel drugsRepurposed drugsGraph
2022
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature
Schutte D, Vasilakes J, Bompelli A, Zhou Y, Fiszman M, Xu H, Kilicoglu H, Bishop J, Adam T, Zhang R. Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. Journal Of Biomedical Informatics 2022, 131: 104120. PMID: 35709900, PMCID: PMC9335448, DOI: 10.1016/j.jbi.2022.104120.Peer-Reviewed Original ResearchConceptsUnified Medical Language SystemComprehensive knowledge graphDomain terminologyKnowledge graphSemantic relationsNatural language processing technologyLanguage processing technologyNLP toolsDownstream tasksF1 scoreSemantic relationshipsDiscovery patternsPubMed abstractsLimited coverageBiomedical literatureProcessing technologyLanguage systemSemRepDietary supplement informationManual reviewNovel methodologyGraphNodesDomainTask