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Register a new userA Comparison between Named Entity Recognition Models in the Biomedical Domain
مقارنة بين نماذج التعرف على الكيانات المسماة في المجال الطبي الطبيعي
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يعرف تطبيق المتخصص في مجال التعرف على الكيان المسمى (ner) باسم الطيوميدي (Bioner)، الذي يهدف إلى تحديد وتصنيف المفاهيم الطبية الحيوية التي تهم الباحثين، مثل الجينات والبروتينات والمركبات الكيميائية والمخدرات والطفرات والأمراض ، وما إلى ذلك وهلم جرا. تشبه المهمة Bioner إلى حد كبير عام NER ولكن الاعتراف بالكيانات الطبية الحيوية المسماة (BNES) أكثر تحديا من الاعتراف بالأسماء المناسبة من الصحف بسبب خصائص التسميات الطبية الحيوية. من أجل معالجة التحديات التي تطرحها Bioner، تم تنفيذ سبع نماذج تعليمية في سبع آلات مقارنة نهج تعلم النقل بناء على برت ضبط صقل مع النماذج العصبية التي تعتمد عليها BI-LSTM وطراز CRF يستخدم كناسما أساسيا. تم استخدام الدقة والتذكر و F1-Score نظرا لأن درجات الأداء التي تقوم بتقييم النماذج على اثنين من الأطباق الطبية الحيوية المعروفة: Jnlpba و Biocreative IV (BC-IV). تعتبر مطابقة صارمة جزئية معايير تقييم. تشير النتائج المبلغ عنها إلى أن نهج التعلم عبر النقل يعتمد على بيرت المصنفات التي تم ضبطها تتفوق جميع أساليب الآخرين على تحقيق أعلى درجات لجميع المقاييس على كلا الشريعة.
The domain-specialised application of Named Entity Recognition (NER) is known as Biomedical NER (BioNER), which aims to identify and classify biomedical concepts that are of interest to researchers, such as genes, proteins, chemical compounds, drugs, mutations, diseases, and so on. The BioNER task is very similar to general NER but recognising Biomedical Named Entities (BNEs) is more challenging than recognising proper names from newspapers due to the characteristics of biomedical nomenclature. In order to address the challenges posed by BioNER, seven machine learning models were implemented comparing a transfer learning approach based on fine-tuned BERT with Bi-LSTM based neural models and a CRF model used as baseline. Precision, Recall and F1-score were used as performance scores evaluating the models on two well-known biomedical corpora: JNLPBA and BIOCREATIVE IV (BC-IV). Strict and partial matching were considered as evaluation criteria. The reported results show that a transfer learning approach based on fine-tuned BERT outperforms all others methods achieving the highest scores for all metrics on both corpora.
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Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of coarse-grain
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