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Register a new userCross-Domain Data Integration for Named Entity Disambiguation in Biomedical Text
تكامل البيانات عبر المجال ل Disambiguation الكيان المسمى في النص الطبي الطبيعي
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إن إزالة الكيانات المسماة (NED)، والتي تنطوي على رسم الخرائط النصية للكيانات الهيكلية، تحديا بشكل خاص في المجال الطبي بسبب وجود كيانات نادرة.تقتصر الأساليب الحالية بوجود الموارد الهيكلية الخشونة في قواعد المعرفة الطبية الحيوية وكذلك استخدام مجموعات البيانات التدريبية التي توفر تغطية منخفضة على الموارد غير الشائعة.في هذا العمل، نتعلم هذه المشكلات من خلال اقتراح طريقة تكامل بيانات عبر المجال التي تنقل المعرفة الهيكلية من قاعدة معارف النص العامة إلى المجال الطبي.نحن نستخدم مخطط الاندماج لدينا لزيادة الموارد الهيكلية وتوليد مجموعة بيانات كبيرة بييوميديا للأحاد المحاكمة.يحقق نموذج عائليتنا مع المعرفة الهيكلية المحقونة أداء حديثة على مجموعة بيانات القياس الطبية القياسية: التوصيلات و BC5CDR.علاوة على ذلك، فإننا نحسن الغموض من كيانات نادرة تصل إلى 57 نقطة دقة.
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-grained structural resources in biomedical knowledge bases as well as the use of training datasets that provide low coverage over uncommon resources. In this work, we address these issues by proposing a cross-domain data integration method that transfers structural knowledge from a general text knowledge base to the medical domain. We utilize our integration scheme to augment structural resources and generate a large biomedical NED dataset for pretraining. Our pretrained model with injected structural knowledge achieves state-of-the-art performance on two benchmark medical NED datasets: MedMentions and BC5CDR. Furthermore, we improve disambiguation of rare entities by up to 57 accuracy points.
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Current work in named entity recognition (NER) shows that data augmentation techniques can produce more robust models. However, most existing techniques focus on augmenting in-domain data in low-resource scenarios where annotated data is quite limite
d. In this work, we take this research direction to the opposite and study cross-domain data augmentation for the NER task. We investigate the possibility of leveraging data from high-resource domains by projecting it into the low-resource domains. Specifically, we propose a novel neural architecture to transform the data representation from a high-resource to a low-resource domain by learning the patterns (e.g. style, noise, abbreviations, etc.) in the text that differentiate them and a shared feature space where both domains are aligned. We experiment with diverse datasets and show that transforming the data to the low-resource domain representation achieves significant improvements over only using data from high-resource domains.
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.
It has been shown that named entity recognition (NER) could benefit from incorporating the long-distance structured information captured by dependency trees. We believe this is because both types of features - the contextual information captured by t
he linear sequences and the structured information captured by the dependency trees may complement each other. However, existing approaches largely focused on stacking the LSTM and graph neural networks such as graph convolutional networks (GCNs) for building improved NER models, where the exact interaction mechanism between the two types of features is not very clear, and the performance gain does not appear to be significant. In this work, we propose a simple and robust solution to incorporate both types of features with our Synergized-LSTM (Syn-LSTM), which clearly captures how the two types of features interact. We conduct extensive experiments on several standard datasets across four languages. The results demonstrate that the proposed model achieves better performance than previous approaches while requiring fewer parameters. Our further analysis demonstrates that our model can capture longer dependencies compared with strong baselines.
Cross-domain Named Entity Recognition (NER) transfers the NER knowledge from high-resource domains to the low-resource target domain. Due to limited labeled resources and domain shift, cross-domain NER is a challenging task. To address these challeng
es, we propose a progressive domain adaptation Knowledge Distillation (KD) approach -- PDALN. It achieves superior domain adaptability by employing three components: (1) Adaptive data augmentation techniques, which alleviate cross-domain gap and label sparsity simultaneously; (2) Multi-level Domain invariant features, derived from a multi-grained MMD (Maximum Mean Discrepancy) approach, to enable knowledge transfer across domains; (3) Advanced KD schema, which progressively enables powerful pre-trained language models to perform domain adaptation. Extensive experiments on four benchmarks show that PDALN can effectively adapt high-resource domains to low-resource target domains, even if they are diverse in terms and writing styles. Comparison with other baselines indicates the state-of-the-art performance of PDALN.
Named Entity Recognition is an essential task in natural language processing to detect entities and classify them into predetermined categories. An entity is a meaningful word, or phrase that refers to proper nouns. Named Entities play an important r
ole in different NLP tasks such as Information Extraction, Question Answering and Machine Translation. In Machine Translation, named entities often cause translation failures regardless of local context, affecting the output quality of translation. Annotating named entities is a time-consuming and expensive process especially for low-resource languages. One solution for this problem is to use word alignment methods in bilingual parallel corpora in which just one side has been annotated. The goal is to extract named entities in the target language by using the annotated corpus of the source language. In this paper, we compare the performance of two alignment methods, Grow-diag-final-and and Intersect Symmetrisation heuristics, to exploit the annotation projection of English-Brazilian Portuguese bilingual corpus to detect named entities in Brazilian Portuguese. A NER model that is trained on annotated data extracted from the alignment methods, is used to evaluate the performance of aligners. Experimental results show the Intersect Symmetrisation is able to achieve superior performance scores compared to the Grow-diag-final-and heuristic in Brazilian Portuguese.
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