Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userClustering-based Inference for Biomedical Entity Linking
الاستدلال القائم على التجميع للكيان الطبي الطبيعي
264
0 0
0.0
(
0
)
Created by
Shamra Editor
Ask ChatGPT about the research
نظرا لعدد كبير من الكيانات في قواعد المعرفة الطبية الحيوية، فإن جزء بسيط من الكيانات الصغيرة فقط بيانات التدريب المسمى. وهذا يستلزم كيان ربط النماذج التي يمكن أن تصل إلى ربط تذكر الكيانات غير المرئية باستخدام التمثيلات المستفادة للكيانات. يتذكر كل منهما السابقة بشكل مستقل، وتجاهل العلاقات داخل الوثائق وعبر الوثائق بين الكيان. يمكن أن تكون هذه العلاقات مفيدة للغاية لربط الذكور في النص الطبي الطبيعي حيث غالبا ما تذكر القرارات ذات الصلة وجود نموذج عام أو متخصص للغاية. في هذه الورقة، نقدم نموذجا يمكن فيه إلقاء النموذج الذي يمكن فيه اتخاذ قرارات مرتبطة فقط بالربط بالكيان الأساسي المعرفي ولكن أيضا من خلال تجميع تذكر معا عبر التجميع والاشتراك في ربط التوقعات. في تجارب في أكبر مجموعة بيانات بيئية متوفرة للجمهور، نحسن أفضل التنبؤ المستقل للكيان الذي يربط بمقدار 3.0 نقطة من الدقة، ويحسن نموذج الاستدلال القائم على التجميع كيان يربط بمقدار 2.3 نقطة.
Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using learned representations of entities. Previous approaches link each mention independently, ignoring the relationships within and across documents between the entity mentions. These relations can be very useful for linking mentions in biomedical text where linking decisions are often difficult due mentions having a generic or a highly specialized form. In this paper, we introduce a model in which linking decisions can be made not merely by linking to a knowledge base entity but also by grouping multiple mentions together via clustering and jointly making linking predictions. In experiments on the largest publicly available biomedical dataset, we improve the best independent prediction for entity linking by 3.0 points of accuracy, and our clustering-based inference model further improves entity linking by 2.3 points.
References used
https://aclanthology.org/
rate research
Read More
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.
Many open-domain question answering problems can be cast as a textual entailment task, where a question and candidate answers are concatenated to form hypotheses. A QA system then determines if the supporting knowledge bases, regarded as potential pr
emises, entail the hypotheses. In this paper, we investigate a neural-symbolic QA approach that integrates natural logic reasoning within deep learning architectures, towards developing effective and yet explainable question answering models. The proposed model gradually bridges a hypothesis and candidate premises following natural logic inference steps to build proof paths. Entailment scores between the acquired intermediate hypotheses and candidate premises are measured to determine if a premise entails the hypothesis. As the natural logic reasoning process forms a tree-like, hierarchical structure, we embed hypotheses and premises in a Hyperbolic space rather than Euclidean space to acquire more precise representations. Empirically, our method outperforms prior work on answering multiple-choice science questions, achieving the best results on two publicly available datasets. The natural logic inference process inherently provides evidence to help explain the prediction process.
Biomedical Concept Normalization (BCN) is widely used in biomedical text processing as a fundamental module. Owing to numerous surface variants of biomedical concepts, BCN still remains challenging and unsolved. In this paper, we exploit biomedical c
oncept hypernyms to facilitate BCN. We propose Biomedical Concept Normalizer with Hypernyms (BCNH), a novel framework that adopts list-wise training to make use of both hypernyms and synonyms, and also employs norm constraint on the representation of hypernym-hyponym entity pairs. The experimental results show that BCNH outperforms the previous state-of-the-art model on the NCBI dataset.
Natural language inference (NLI) is the task of determining whether a piece of text is entailed, contradicted by or unrelated to another piece of text. In this paper, we investigate how to tease systematic inferences (i.e., items for which people agr
ee on the NLI label) apart from disagreement items (i.e., items which lead to different annotations), which most prior work has overlooked. To distinguish systematic inferences from disagreement items, we propose Artificial Annotators (AAs) to simulate the uncertainty in the annotation process by capturing the modes in annotations. Results on the CommitmentBank, a corpus of naturally occurring discourses in English, confirm that our approach performs statistically significantly better than all baselines. We further show that AAs learn linguistic patterns and context-dependent reasoning.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
