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Register a new userApplication of Deep Learning Methods to SNOMED CT Encoding of Clinical Texts: From Data Collection to Extreme Multi-Label Text-Based Classification
تطبيق طرق التعلم العميق للترميز CT SNOMED من النصوص السريرية: من مجموعة البيانات إلى تصنيف النص المتطرف متعدد الملصقات
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يعد تطبيع المفهوم للنصوص السريرية للتصنيفات الطبية القياسية والاتجاهات مهمة ذات أهمية عالية للبحث الطبي للرعاية الصحية. نحاول حل هذه المشكلة من خلال ترميز CT التلقائي CT، حيث يعد CT Snomed CT أحد أونولوجيات المصطلحات السريرية الأكثر استخداما وشاملة على نطاق واسع. ومع ذلك، فإن تطبيق نماذج التعلم العميق الأساسية يؤدي إلى نتائج غير مرغوب فيها بسبب الطبيعة غير المتوازنة للبيانات والعدد المتطرف من الفصول الدراسية. نقترح إجراء التصنيف الذي يحتوي على سير عمل متعدد الخطوات يتكون من تجميع الملصقات، والتصنيف متعدد الكتلة، ورسم الخرائط عن المجموعات إلى الملصقات. بالنسبة للتصنيف متعدد المجموعات، BioBert يتم ضبطه بشكل جيد على مجموعة بياناتنا المخصصة. يتم إجراء تعيين مجموعات إلى التسميات من قبل A One-VS-All Mederifier (SVC) المطبق على كل كتلة واحدة. نقدم أيضا خطوات لتوليد البيانات التلقائي من الأوصاف النصية المشروحة مع رموز CT Conomed بناء على البيانات العامة والبيانات المفتوحة المرتبطة. من أجل التعامل مع المشكلة أن DataSet لدينا غير متوازنة للغاية، يتم تطبيق بعض طرق تكبير البيانات. تظهر النتائج من التجارب التي أجريت دقة عالية وموثوقية نهجنا للتنبؤ برموز CT Conomed ذات الصلة بنص سريري.
Concept normalization of clinical texts to standard medical classifications and ontologies is a task with high importance for healthcare and medical research. We attempt to solve this problem through automatic SNOMED CT encoding, where SNOMED CT is one of the most widely used and comprehensive clinical term ontologies. Applying basic Deep Learning models, however, leads to undesirable results due to the unbalanced nature of the data and the extreme number of classes. We propose a classification procedure that features a multiple-step workflow consisting of label clustering, multi-cluster classification, and clusters-to-labels mapping. For multi-cluster classification, BioBERT is fine-tuned over our custom dataset. The clusters-to-labels mapping is carried out by a one-vs-all classifier (SVC) applied to every single cluster. We also present the steps for automatic dataset generation of textual descriptions annotated with SNOMED CT codes based on public data and linked open data. In order to cope with the problem that our dataset is highly unbalanced, some data augmentation methods are applied. The results from the conducted experiments show high accuracy and reliability of our approach for prediction of SNOMED CT codes relevant to a clinical text.
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