2022
Assigning species information to corresponding genes by a sequence labeling framework
Luo L, Wei C, Lai P, Chen Q, Islamaj R, Lu Z. Assigning species information to corresponding genes by a sequence labeling framework. Database 2022, 2022: baac090. PMID: 36227127, PMCID: PMC9558450, DOI: 10.1093/database/baac090.Peer-Reviewed Original ResearchConceptsNovel deep learning-based frameworkDeep learning-based frameworkLearning-based frameworkText mining algorithmsSequence labeling taskGene normalization taskSequence labeling frameworkBinary classification frameworkSource codeBaseline methodsNormalization taskClassification frameworkLabeling taskLabeling frameworkAutomatic assignmentHigh-performance methodHeuristic rulesGene mentionsBenchmarking resultsDatabase URLDatabase recordsAssignment task
2019
BioSentVec: creating sentence embeddings for biomedical texts
Chen Q, Peng Y, Lu Z. BioSentVec: creating sentence embeddings for biomedical texts. 2019, 00: 1-5. DOI: 10.1109/ichi.2019.8904728.Peer-Reviewed Original ResearchNatural language processing systemsSentence embeddingsBiomedical textAdvanced deep learning methodsDeep learning methodsBiomedical text miningBiomedical word embeddingsLanguage processing systemPre-trained sentence encodersText miningArt performanceLearning methodsSentence semanticsSentence encoderWord embeddingsProcessing systemBenchmarking resultsEmbeddingSimilarity taskClinical notesTaskEssential partGeneral domainsClinical databaseSemanticsBioWordVec, improving biomedical word embeddings with subword information and MeSH
Zhang Y, Chen Q, Yang Z, Lin H, Lu Z. BioWordVec, improving biomedical word embeddings with subword information and MeSH. Scientific Data 2019, 6: 52. PMID: 31076572, PMCID: PMC6510737, DOI: 10.1038/s41597-019-0055-0.Peer-Reviewed Original ResearchConceptsWord embeddingsSubword informationWord representationsBiomedical natural language processingNatural language processingMultiple NLP tasksBiomedical word embeddingsInformation retrievalUnlabeled textBiomedical textText miningBiomedical domainLanguage processingNLP tasksStructured resourcesChallenging taskPrevious stateBenchmarking resultsLarge corpusEmbeddingWord levelBioWordVecSuch informationTaskInformation