Do you want to publish a course? Click here

Biomedical Concept Normalization by Leveraging Hypernyms

تطبيع المفهوم الطبي الطبيعي من خلال الاستفادة من الارتفاع

147   0   0   0.0 ( 0 )
 Publication date 2021
and research's language is English
 Created by Shamra Editor




Ask ChatGPT about the research

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 concept 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.

References used
https://aclanthology.org/
rate research

Read More

Integrating knowledge into text is a promising way to enrich text representation, especially in the medical field. However, undifferentiated knowledge not only confuses the text representation but also imports unexpected noises. In this paper, to all eviate this problem, we propose leveraging capsule routing to associate knowledge with medical literature hierarchically (called HiCapsRKL). Firstly, HiCapsRKL extracts two empirically designed text fragments from medical literature and encodes them into fragment representations respectively. Secondly, the capsule routing algorithm is applied to two fragment representations. Through the capsule computing and dynamic routing, each representation is processed into a new representation (denoted as caps-representation), and we integrate the caps-representations as information gain to associate knowledge with medical literature hierarchically. Finally, HiCapsRKL are validated on relevance prediction and medical literature retrieval test sets. The experimental results and analyses show that HiCapsRKLcan more accurately associate knowledge with medical literature than mainstream methods. In summary, HiCapsRKL can efficiently help selecting the most relevant knowledge to the medical literature, which may be an alternative attempt to improve knowledge-based text representation. Source code is released on GitHub.
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 repre sentations 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.
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 oft en 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.
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.
The rapid growth in published clinical trials makes it difficult to maintain up-to-date systematic reviews, which require finding all relevant trials. This leads to policy and practice decisions based on out-of-date, incomplete, and biased subsets of available clinical evidence. Extracting and then normalising Population, Intervention, Comparator, and Outcome (PICO) information from clinical trial articles may be an effective way to automatically assign trials to systematic reviews and avoid searching and screening---the two most time-consuming systematic review processes. We propose and test a novel approach to PICO span detection. The major difference between our proposed method and previous approaches comes from detecting spans without needing annotated span data and using only crowdsourced sentence-level annotations. Experiments on two datasets show that PICO span detection results achieve much higher results for recall when compared to fully supervised methods with PICO sentence detection at least as good as human annotations. By removing the reliance on expert annotations for span detection, this work could be used in a human-machine pipeline for turning low-quality, crowdsourced, and sentence-level PICO annotations into structured information that can be used to quickly assign trials to relevant systematic reviews.

suggested questions

comments
Fetching comments Fetching comments
Sign in to be able to follow your search criteria
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا