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Register a new userRelation Extraction Using Multiple Pre-Training Models in Biomedical Domain
استخراج العلاقة باستخدام نماذج متعددة التدريب مسبقا في المجال الطبي الطبيعي
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يزداد عدد الوثائق الطبية الحيوية بسرعة.وفقا لذلك، يتزايد الطلب على استخراج المعرفة من النصوص الطبية الحيوية على نطاق واسع.تعرف النماذج القائمة على بيرت بأدائها عالية في المهام المختلفة.ومع ذلك، غالبا ما يكون باهظ الثمن بشكل حسابي.بيئة GPU متطورة غير متوفرة في العديد من المواقف.لتحقيق كل من الدقة عالية وسرعة الاستخراج السريع، نقترح مجموعات من النماذج المبهب المدربة مسبقا.تتفوق طريقةنا على أحدث طراز أحدث نماذج ومقرها بيرت على جاد كوربوس.بالإضافة إلى ذلك، تظهر طريقةنا بسرعة ما يقرب من ثلاث مرات سرعة استخراج أسرع من النماذج القائمة على Bert
The number of biomedical documents is increasing rapidly. Accordingly, a demand for extracting knowledge from large-scale biomedical texts is also increasing. BERT-based models are known for their high performance in various tasks. However, it is often computationally expensive. A high-end GPU environment is not available in many situations. To attain both high accuracy and fast extraction speed, we propose combinations of simpler pre-trained models. Our method outperforms the latest state-of-the-art model and BERT-based models on the GAD corpus. In addition, our method shows approximately three times faster extraction speed than the BERT-based models on the ChemProt corpus and reduces the memory size to one sixth of the BERT ones.
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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.
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
ed 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.
As it has been unveiled that pre-trained language models (PLMs) are to some extent capable of recognizing syntactic concepts in natural language, much effort has been made to develop a method for extracting complete (binary) parses from PLMs without
training separate parsers. We improve upon this paradigm by proposing a novel chart-based method and an effective top-K ensemble technique. Moreover, we demonstrate that we can broaden the scope of application of the approach into multilingual settings. Specifically, we show that by applying our method on multilingual PLMs, it becomes possible to induce non-trivial parses for sentences from nine languages in an integrated and language-agnostic manner, attaining performance superior or comparable to that of unsupervised PCFGs. We also verify that our approach is robust to cross-lingual transfer. Finally, we provide analyses on the inner workings of our method. For instance, we discover universal attention heads which are consistently sensitive to syntactic information irrespective of the input language.
To alleviate human efforts from obtaining large-scale annotations, Semi-Supervised Relation Extraction methods aim to leverage unlabeled data in addition to learning from limited samples. Existing self-training methods suffer from the gradual drift p
roblem, where noisy pseudo labels on unlabeled data are incorporated during training. To alleviate the noise in pseudo labels, we propose a method called MetaSRE, where a Relation Label Generation Network generates accurate quality assessment on pseudo labels by (meta) learning from the successful and failed attempts on Relation Classification Network as an additional meta-objective. To reduce the influence of noisy pseudo labels, MetaSRE adopts a pseudo label selection and exploitation scheme which assesses pseudo label quality on unlabeled samples and only exploits high-quality pseudo labels in a self-training fashion to incrementally augment labeled samples for both robustness and accuracy. Experimental results on two public datasets demonstrate the effectiveness of the proposed approach.
The rise of pre-trained language models has yielded substantial progress in the vast majority of Natural Language Processing (NLP) tasks. However, a generic approach towards the pre-training procedure can naturally be sub-optimal in some cases. Parti
cularly, fine-tuning a pre-trained language model on a source domain and then applying it to a different target domain, results in a sharp performance decline of the eventual classifier for many source-target domain pairs. Moreover, in some NLP tasks, the output categories substantially differ between domains, making adaptation even more challenging. This, for example, happens in the task of aspect extraction, where the aspects of interest of reviews of, e.g., restaurants or electronic devices may be very different. This paper presents a new fine-tuning scheme for BERT, which aims to address the above challenges. We name this scheme DILBERT: Domain Invariant Learning with BERT, and customize it for aspect extraction in the unsupervised domain adaptation setting. DILBERT harnesses the categorical information of both the source and the target domains to guide the pre-training process towards a more domain and category invariant representation, thus closing the gap between the domains. We show that DILBERT yields substantial improvements over state-of-the-art baselines while using a fraction of the unlabeled data, particularly in more challenging domain adaptation setups.
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