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
2016
Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature
Zhang Y, Wu H, Xu J, Wang J, Soysal E, Li L, Xu H. Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. BMC Systems Biology 2016, 10: 67. PMID: 27585838, PMCID: PMC5009562, DOI: 10.1186/s12918-016-0311-2.Peer-Reviewed Original ResearchConceptsPaths graph kernelGraph kernelsSemantic classesSemantic informationBiomedical literatureShallow semantic representationsText mining techniquesBest F-scoreAutomatic DDI extractionProblem of sparsenessDependency structureSemantic graphDDI detectionKnowledge basesDDI corpusF-scoreDDI extractionSemantic representationNovel approachExperimental resultsKernelHigh precisionInformationSparsenessGraph