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Terminologies augmented recurrent neural network model for clinical named entity recognition
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In: ISSN: 1532-0464 ; EISSN: 1532-0480 ; Journal of Biomedical Informatics ; https://hal.archives-ouvertes.fr/hal-02428771 ; Journal of Biomedical Informatics, Elsevier, 2020, 102, pp.103356. ⟨10.1016/j.jbi.2019.103356⟩ (2020)
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Abstract:
International audience ; OBJECTIVE:We aimed to enhance the performance of a supervised model for clinical named-entity recognition (NER) using medical terminologies. In order to evaluate our system in French, we built a corpus for 5 types of clinical entities.METHODS:We used a terminology-based system as baseline, built upon UMLS and SNOMED. Then, we evaluated a biGRU-CRF, and a hybrid system using the prediction of the terminology-based system as feature for the biGRU-CRF. In French, we built APcNER, a corpus of 147 documents annotated for 5 entities (Drug names, Signs or symptoms, Diseases or disorders, Diagnostic procedures or lab tests and Therapeutic procedures). We evaluated each NER systems using exact and partial match definition of F-measure for NER. The APcNER contains 4,837 entities, which took 28 h to annotate. The inter-annotator agreement as measured by Cohen's Kappa was substantial for non-exact match (Κ = 0.61) and moderate considering exact match (Κ = 0.42). In English, we evaluated the NER systems on the i2b2-2009 Medication Challenge for Drug name recognition, which contained 8,573 entities for 268 documents, and i2b2-small a version reduced to match APcNER number of entities.RESULTS:For drug name recognition on both i2b2-2009 and APcNER, the biGRU-CRF performed better that the terminology-based system, with an exact-match F-measure of 91.1% versus 73% and 81.9% versus 75% respectively. For i2b2-small and APcNER, the hybrid system outperformed the biGRU-CRF, with an exact-match F-measure of 87.8% versus 85.6% and 86.4% versus 81.9% respectively. On APcNER corpus, the micro-average F-measure of the hybrid system on the 5 entities was 69.5% in exact match and 84.1% in non-exact match.CONCLUSION:APcNER is a French corpus for clinical-NER of five types of entities which covers a large variety of document types. The extension of the supervised model with terminology has allowed an easy increase in performance, especially for rare entities, and established near state of the art results on the i2b2-2009 corpus.
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Keyword:
[INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL]; APcNER; Clinical natural language processing; Information extraction; Machine learning; Named entity recognition
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URL: https://hal.archives-ouvertes.fr/hal-02428771
https://doi.org/10.1016/j.jbi.2019.103356
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| 2 |
Inference Annotation of a Chinese Corpus for Opinion Mining
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In: LREC ; https://hal-inalco.archives-ouvertes.fr/hal-02507170 ; LREC, May 2020, Marseille, France (2020)
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The Multilingual Anonymisation Toolkit for Public Administrations (MAPA) Project
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In: Annual Conference of the European Association for Machine Translation ; https://hal.archives-ouvertes.fr/hal-03103205 ; Annual Conference of the European Association for Machine Translation, Nov 2020, Lisbon, Portugal. pp.471-472 (2020)
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The language industry at the age of data ; La industria del lenguaje en la era del dato
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In: Revista Abaco ; https://hal.archives-ouvertes.fr/hal-02912828 ; Revista Abaco, 2020 (2020)
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Inference Annotation of a Chinese Corpus for Opinion Mining
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In: LREC ; https://hal-inalco.archives-ouvertes.fr/hal-02507170 ; LREC, May 2020, Marseille, France (2020)
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The NLP4NLP Corpus (II): 50 Years of Research in Speech and Language Processing
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In: ISSN: 2504-0537 ; EISSN: 2504-0537 ; Frontiers in Research Metrics and Analytics ; https://hal.archives-ouvertes.fr/hal-02413749 ; Frontiers in Research Metrics and Analytics, Frontiers Media, 2019, 3, pp.1-30 (2019)
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French Levothyrox® Crisis: Retrospective Analysis of Social Media
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In: International Society of Pharmacovigilance ; https://hal.archives-ouvertes.fr/hal-02411632 ; International Society of Pharmacovigilance, Springer International Publishing, Oct 2019, Bogota, Colombia (2019)
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The NLP4NLP Corpus (I): 50 Years of Publication, Collaboration and Citation in Speech and Language Processing
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In: ISSN: 2504-0537 ; EISSN: 2504-0537 ; Frontiers in Research Metrics and Analytics ; https://hal.archives-ouvertes.fr/hal-02413751 ; Frontiers in Research Metrics and Analytics, Frontiers Media, 2019, 3, pp.1-30 (2019)
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Unsupervised learning of natural language morphology using non-parametric bayesian models ; Apprentissage non-supervisé de la morphologie des langues à l’aide de modèles bayésiens non-paramétriques
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In: https://tel.archives-ouvertes.fr/tel-02354184 ; Informatique et langage [cs.CL]. Université Paris Saclay (COmUE), 2019. Français. ⟨NNT : 2019SACLS203⟩ (2019)
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A Comparison between NMT and PBSMT Performance for Translating Noisy User-Generated Content
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In: The 22nd Nordic Conference on Computational Linguistics (NoDaLiDa’19) ; https://hal.archives-ouvertes.fr/hal-02270524 ; The 22nd Nordic Conference on Computational Linguistics (NoDaLiDa’19), Sep 2019, Turku, Finland ; https://nodalida2019.org/index.html (2019)
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Recognition of sub-sentential translation techniques : from resources to validation ; Reconnaissance des procédés de traduction sous-phrastiques : des ressources aux validations
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In: https://tel.archives-ouvertes.fr/tel-02460548 ; Informatique et langage [cs.CL]. Université Paris Saclay (COmUE), 2019. Français. ⟨NNT : 2019SACLS489⟩ (2019)
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Clinical Natural Language Processing in languages other than English: opportunities and challenges.
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In: ISSN: 2041-1480 ; Journal of Biomedical Semantics ; https://hal.archives-ouvertes.fr/hal-01842518 ; Journal of Biomedical Semantics, BioMed Central, 2018, 9, 13p. ⟨10.1186/s13326-018-0179-8⟩ (2018)
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| 13 |
User profile detection in health online fora
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In: International Congress of the European Federation for Medical Informatics ; https://hal.archives-ouvertes.fr/hal-01971156 ; International Congress of the European Federation for Medical Informatics, Adrien Ugon, Daniel Karlsson, Gunnar O. Klein, Anne Moen, Apr 2018, Gothenburg, Sweden (2018)
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| 14 |
Sign Language Video Analysis For Automatic Recognition and Detection
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In: 20th International ACM SIGACCESS Conference on Computers and Accessibility ; https://hal.archives-ouvertes.fr/hal-02146365 ; 20th International ACM SIGACCESS Conference on Computers and Accessibility, Oct 2018, Galway, Ireland (2018)
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Knowledge Base Population based on Entity Graph Analysis ; Peuplement d'une base de connaissance fondé sur l'exploitation d'un graphe d'entités
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In: https://tel.archives-ouvertes.fr/tel-01810983 ; Computation and Language [cs.CL]. Université Paris Saclay (COmUE), 2018. English. ⟨NNT : 2018SACLS092⟩ (2018)
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A Multilingual Dataset for Evaluating Parallel Sentence Extraction from Comparable Corpora
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In: International Conference on Language Resources and Evaluation ; https://hal.archives-ouvertes.fr/hal-01898362 ; International Conference on Language Resources and Evaluation, May 2018, Miyazaki, Japan (2018)
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IRIT at e-Risk 2018
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In: CLEF 2018 Working Notes ; 9th Conference and Labs of the Evaluation Forum, Living Labs (CLEF 2018) ; https://hal.archives-ouvertes.fr/hal-02290007 ; 9th Conference and Labs of the Evaluation Forum, Living Labs (CLEF 2018), Sep 2018, Avignon, France. pp.1-12 (2018)
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| 18 |
Expanding the Diversity of Texts and Applications: Findings from the Section on Clinical Natural Language Processing of the International Medical Informatics Association Yearbook.
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In: ISSN: 0943-4747 ; EISSN: 2364-0502 ; IMIA Yearbook of Medical Informatics ; https://hal.archives-ouvertes.fr/hal-01990501 ; IMIA Yearbook of Medical Informatics, Schattauer, 2018, 27, pp.193-198 (2018)
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| 19 |
Reuse and Plagiarism in Speech and Natural Language Processing
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In: ISSN: 1432-5012 ; EISSN: 1432-1300 ; International Journal on Digital Libraries ; https://hal.archives-ouvertes.fr/hal-01840700 ; International Journal on Digital Libraries, Springer Verlag, 2017, 18, pp.1-14 (2017)
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Creation of a multilingual aligned corpus with Ukrainian as the target language and its exploitation
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In: Computational Linguistics and Intelligent Systems ; https://hal.archives-ouvertes.fr/hal-01736363 ; Computational Linguistics and Intelligent Systems, Apr 2017, Kharkiv, Ukraine (2017)
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