2024
Development of Clinical NLP Systems
Xu H, Demner Fushman D. Development of Clinical NLP Systems. Cognitive Informatics In Biomedicine And Healthcare 2024, 301-324. DOI: 10.1007/978-3-031-55865-8_11.Peer-Reviewed Original Research
2019
Recognizing software names in biomedical literature using machine learning
Wei Q, Zhang Y, Amith M, Lin R, Lapeyrolerie J, Tao C, Xu H. Recognizing software names in biomedical literature using machine learning. Health Informatics Journal 2019, 26: 21-33. PMID: 31566474, PMCID: PMC7334865, DOI: 10.1177/1460458219869490.Peer-Reviewed Original ResearchConceptsSoftware namesF-measureNatural language processing methodsBiomedical literatureWord representation featuresLanguage processing methodsEntity recognition systemSoftware catalogSoftware repositoriesFeature engineeringBiomedical softwareRecognition systemSoftware toolsBiomedical domainRepresentation featuresMEDLINE abstractsWord embeddingsKnowledge featuresManual curationSoftwareMachineProcessing methodsBest systemRepositorySystem
2017
Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification
Amith M, Zhang Y, Xu H, Tao C. Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification. Lecture Notes In Computer Science 2017, 10351: 386-395. DOI: 10.1007/978-3-319-60045-1_40.Peer-Reviewed Original ResearchEntity recognitionNatural language processingContextual semantic informationNamed Entity RecognitionEntity recognition methodFeatures of ontologyMachine learning approachesKnowledge-based approachSoftware entitiesSoftware namesInformation extractionUse casesBiomedical softwareSemantic informationSoftware identificationLanguage processingRecognition methodLearning approachBiomedical literatureRecognitionOntologyEntitiesSoftwareResearch abstractsTaskExpressing Biomedical Ontologies in Natural Language for Expert Evaluation.
Amith M, Manion F, Harris M, Zhang Y, Xu H, Tao C. Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. 2017, 245: 838-842. PMID: 29295217, PMCID: PMC6644701.Peer-Reviewed Original Research
2014
Open Source Clinical NLP - More than Any Single System.
Masanz J, Pakhomov S, Xu H, Wu S, Chute C, Liu H. Open Source Clinical NLP - More than Any Single System. AMIA Joint Summits On Translational Science Proceedings 2014, 2014: 76-82. PMID: 25954581, PMCID: PMC4419764.Peer-Reviewed Original ResearchClinical NLPNLP systemsNatural language processing toolsOpen source softwareLanguage processing toolsInformation technology practicesPluggable componentsSource softwareNLP softwareProcessing capabilitiesProcessing toolsResearch communityNLPCollaborative communitySingle systemSoftwareTechnology practicesNLP activityUIMAAnnotatorsSystemApacheOngoing activityFrameworkCapability