scholarly journals Named Entity Recognition in Chinese Medical Literature Using Pretraining Models

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Yu Wang ◽  
Yining Sun ◽  
Zuchang Ma ◽  
Lisheng Gao ◽  
Yang Xu
Keyword(s):  
Large Scale ◽  
Data Augmentation ◽  
Medical Literature ◽  
Named Entity Recognition ◽  
Semantic Knowledge ◽  
Training Data ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Small Scale ◽  
Named Entity

The medical literature contains valuable knowledge, such as the clinical symptoms, diagnosis, and treatments of a particular disease. Named Entity Recognition (NER) is the initial step in extracting this knowledge from unstructured text and presenting it as a Knowledge Graph (KG). However, the previous approaches of NER have often suffered from small-scale human-labelled training data. Furthermore, extracting knowledge from Chinese medical literature is a more complex task because there is no segmentation between Chinese characters. Recently, the pretraining models, which obtain representations with the prior semantic knowledge on large-scale unlabelled corpora, have achieved state-of-the-art results for a wide variety of Natural Language Processing (NLP) tasks. However, the capabilities of pretraining models have not been fully exploited, and applications of other pretraining models except BERT in specific domains, such as NER in Chinese medical literature, are also of interest. In this paper, we enhance the performance of NER in Chinese medical literature using pretraining models. First, we propose a method of data augmentation by replacing the words in the training set with synonyms through the Mask Language Model (MLM), which is a pretraining task. Then, we consider NER as the downstream task of the pretraining model and transfer the prior semantic knowledge obtained during pretraining to it. Finally, we conduct experiments to compare the performances of six pretraining models (BERT, BERT-WWM, BERT-WWM-EXT, ERNIE, ERNIE-tiny, and RoBERTa) in recognizing named entities from Chinese medical literature. The effects of feature extraction and fine-tuning, as well as different downstream model structures, are also explored. Experimental results demonstrate that the method of data augmentation we proposed can obtain meaningful improvements in the performance of recognition. Besides, RoBERTa-CRF achieves the highest F1-score compared with the previous methods and other pretraining models.

scholarly journals Zero-Resource Cross-Lingual Named Entity Recognition

2020 ◽  
Vol 34 (05) ◽  
pp. 7415-7423
Author(s):  
M Saiful Bari ◽  
Shafiq Joty ◽  
Prathyusha Jwalapuram
Keyword(s):  
Named Entity Recognition ◽  
Training Data ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Adversarial Learning ◽  
Named Entity ◽  
Word Level ◽  
Parallel Data ◽  
Feature Augmentation ◽  
Cross Lingual

Recently, neural methods have achieved state-of-the-art (SOTA) results in Named Entity Recognition (NER) tasks for many languages without the need for manually crafted features. However, these models still require manually annotated training data, which is not available for many languages. In this paper, we propose an unsupervised cross-lingual NER model that can transfer NER knowledge from one language to another in a completely unsupervised way without relying on any bilingual dictionary or parallel data. Our model achieves this through word-level adversarial learning and augmented fine-tuning with parameter sharing and feature augmentation. Experiments on five different languages demonstrate the effectiveness of our approach, outperforming existing models by a good margin and setting a new SOTA for each language pair.

scholarly journals Low-Resource Named Entity Recognition via the Pre-Training Model

Symmetry ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 786
Author(s):  
Siqi Chen ◽  
Yijie Pei ◽  
Zunwang Ke ◽  
Wushour Silamu
Keyword(s):  
Data Augmentation ◽  
Language Model ◽  
Named Entity Recognition ◽  
Name Entity Recognition ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Language Models ◽  
Low Resource ◽  
Named Entity ◽  
High Resource

Named entity recognition (NER) is an important task in the processing of natural language, which needs to determine entity boundaries and classify them into pre-defined categories. For low-resource languages, most state-of-the-art systems require tens of thousands of annotated sentences to obtain high performance. However, there is minimal annotated data available about Uyghur and Hungarian (UH languages) NER tasks. There are also specificities in each task—differences in words and word order across languages make it a challenging problem. In this paper, we present an effective solution to providing a meaningful and easy-to-use feature extractor for named entity recognition tasks: fine-tuning the pre-trained language model. Therefore, we propose a fine-tuning method for a low-resource language model, which constructs a fine-tuning dataset through data augmentation; then the dataset of a high-resource language is added; and finally the cross-language pre-trained model is fine-tuned on this dataset. In addition, we propose an attention-based fine-tuning strategy that uses symmetry to better select relevant semantic and syntactic information from pre-trained language models and apply these symmetry features to name entity recognition tasks. We evaluated our approach on Uyghur and Hungarian datasets, which showed wonderful performance compared to some strong baselines. We close with an overview of the available resources for named entity recognition and some of the open research questions.

scholarly journals Improving Biomedical Named Entity Recognition with Syntactic Information

2020 ◽  
Author(s):  
YUANHE TIAN ◽  
Wang Shen ◽  
Yan Song ◽  
Fei Xia ◽  
Min He ◽  
...  
Keyword(s):  
Domain Knowledge ◽  
Large Scale ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entity ◽  
Syntactic Information ◽  
Biomedical Texts ◽  
Biomedical Named Entity Recognition

Abstract Background Biomedical named entity recognition (BioNER) is an important task for understanding biomedical texts. The task can be challenging due to the lack of large-scale labeled training data and domain knowledge. Previous studies have shown that syntactic information can be useful for named entity recognition; however, most of them fail to weigh that information with respect to its contribution as they treat the syntactic information as gold reference. Results In this paper, we propose BioKMNER, a BioNER model for biomedical texts with key-value memory networks to incorporate syntactic information, which is extracted from syntactic structures automatically generated by existing toolkits. Our approach outperforms baselines without memories and achieves new state-of-the-art results on on four biomedical datasets compared with previous studies, i.e., 85.67% on BC2GM, 94.22% on BC5CDR-chemical, 90.11% on NCBI-diease, and 76.33% on Species-800. Conclusion Experimental results on four benchmark datasets demonstrate the effectiveness of our method, where the state-of-the-art performance is achieved on all of them.

scholarly journals Data Augmentation Techniques on Arabic Data for Named Entity Recognition

2021 ◽  
Vol 189 ◽  
pp. 292-299
Author(s):  
Caroline Sabty ◽  
Islam Omar ◽  
Fady Wasfalla ◽  
Mohamed Islam ◽  
Slim Abdennadher
Keyword(s):  
Data Augmentation ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity ◽  
Augmentation Techniques

scholarly journals An Attention-Based Model Using Character Composition of Entities in Chinese Relation Extraction

Information ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 79 ◽  
Author(s):  
Xiaoyu Han ◽  
Yue Zhang ◽  
Wenkai Zhang ◽  
Tinglei Huang
Keyword(s):  
Language Processing ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Additional Information ◽  
Named Entity ◽  
Proposed Model ◽  
The Relationship ◽  
Crucial Part

Relation extraction is a vital task in natural language processing. It aims to identify the relationship between two specified entities in a sentence. Besides information contained in the sentence, additional information about the entities is verified to be helpful in relation extraction. Additional information such as entity type getting by NER (Named Entity Recognition) and description provided by knowledge base both have their limitations. Nevertheless, there exists another way to provide additional information which can overcome these limitations in Chinese relation extraction. As Chinese characters usually have explicit meanings and can carry more information than English letters. We suggest that characters that constitute the entities can provide additional information which is helpful for the relation extraction task, especially in large scale datasets. This assumption has never been verified before. The main obstacle is the lack of large-scale Chinese relation datasets. In this paper, first, we generate a large scale Chinese relation extraction dataset based on a Chinese encyclopedia. Second, we propose an attention-based model using the characters that compose the entities. The result on the generated dataset shows that these characters can provide useful information for the Chinese relation extraction task. By using this information, the attention mechanism we used can recognize the crucial part of the sentence that can express the relation. The proposed model outperforms other baseline models on our Chinese relation extraction dataset.

scholarly journals Learning Task-Specific Representation for Novel Words in Sequence Labeling

2019 ◽  
Author(s):  
Minlong Peng ◽  
Qi Zhang ◽  
Xiaoyu Xing ◽  
Tao Gui ◽  
Jinlan Fu ◽  
...  
Keyword(s):  
Empirical Studies ◽  
Named Entity Recognition ◽  
Learning Task ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entity ◽  
Part Of Speech Tagging ◽  
Sequence Labeling ◽  
Part Of Speech ◽  
Word Representation

Word representation is a key component in neural-network-based sequence labeling systems. However, representations of unseen or rare words trained on the end task are usually poor for appreciable performance. This is commonly referred to as the out-of-vocabulary (OOV) problem. In this work, we address the OOV problem in sequence labeling using only training data of the task. To this end, we propose a novel method to predict representations for OOV words from their surface-forms (e.g., character sequence) and contexts. The method is specifically designed to avoid the error propagation problem suffered by existing approaches in the same paradigm. To evaluate its effectiveness, we performed extensive empirical studies on four part-of-speech tagging (POS) tasks and four named entity recognition (NER) tasks. Experimental results show that the proposed method can achieve better or competitive performance on the OOV problem compared with existing state-of-the-art methods.

scholarly journals BioALBERT: A Simple and Effective Pre-trained Language Model for Biomedical Named Entity Recognition

2020 ◽  
Author(s):  
Usman Naseem ◽  
Matloob Khushi ◽  
Vinay Reddy ◽  
Sakthivel Rajendran ◽  
Imran Razzak ◽  
...  
Keyword(s):  
State Of The Art ◽  
Language Model ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Future Research ◽  
Named Entity ◽  
Domain Specific ◽  
Context Dependent ◽  
Biomedical Named Entity Recognition

Abstract Background: In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER research is challenging as NER in the biomedical domain are: (i) often restricted due to limited amount of training data, (ii) an entity can refer to multiple types and concepts depending on its context and, (iii) heavy reliance on acronyms that are sub-domain specific. Existing BioNER approaches often neglect these issues and directly adopt the state-of-the-art (SOTA) models trained in general corpora which often yields unsatisfactory results. Results: We propose biomedical ALBERT (A Lite Bidirectional Encoder Representations from Transformers for Biomedical Text Mining) - bioALBERT - an effective domain-specific pre-trained language model trained on huge biomedical corpus designed to capture biomedical context-dependent NER. We adopted self-supervised loss function used in ALBERT that targets on modelling inter-sentence coherence to better learn context-dependent representations and incorporated parameter reduction strategies to minimise memory usage and enhance the training time in BioNER. In our experiments, BioALBERT outperformed comparative SOTA BioNER models on eight biomedical NER benchmark datasets with four different entity types. The performance is increased for; (i) disease type corpora by 7.47% (NCBI-disease) and 10.63% (BC5CDR-disease); (ii) drug-chem type corpora by 4.61% (BC5CDR-Chem) and 3.89 (BC4CHEMD); (iii) gene-protein type corpora by 12.25% (BC2GM) and 6.42% (JNLPBA); and (iv) Species type corpora by 6.19% (LINNAEUS) and 23.71% (Species-800) is observed which leads to a state-of-the-art results. Conclusions: The performance of proposed model on four different biomedical entity types shows that our model is robust and generalizable in recognizing biomedical entities in text. We trained four different variants of BioALBERT models which are available for the research community to be used in future research.

scholarly journals Deep Learning-Based Named Entity Recognition and Knowledge Graph Construction for Geological Hazards

2019 ◽  
Vol 9 (1) ◽  
pp. 15 ◽  
Author(s):  
Runyu Fan ◽  
Lizhe Wang ◽  
Jining Yan ◽  
Weijing Song ◽  
Yingqian Zhu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Conditional Random Field ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Knowledge Graph ◽  
Geological Hazard ◽  
Geological Hazards ◽  
Named Entity ◽  
Corpus Construction

Constructing a knowledge graph of geological hazards literature can facilitate the reuse of geological hazards literature and provide a reference for geological hazard governance. Named entity recognition (NER), as a core technology for constructing a geological hazard knowledge graph, has to face the challenges that named entities in geological hazard literature are diverse in form, ambiguous in semantics, and uncertain in context. This can introduce difficulties in designing practical features during the NER classification. To address the above problem, this paper proposes a deep learning-based NER model; namely, the deep, multi-branch BiGRU-CRF model, which combines a multi-branch bidirectional gated recurrent unit (BiGRU) layer and a conditional random field (CRF) model. In an end-to-end and supervised process, the proposed model automatically learns and transforms features by a multi-branch bidirectional GRU layer and enhances the output with a CRF layer. Besides the deep, multi-branch BiGRU-CRF model, we also proposed a pattern-based corpus construction method to construct the corpus needed for the deep, multi-branch BiGRU-CRF model. Experimental results indicated the proposed deep, multi-branch BiGRU-CRF model outperformed state-of-the-art models. The proposed deep, multi-branch BiGRU-CRF model constructed a large-scale geological hazard literature knowledge graph containing 34,457 entities nodes and 84,561 relations.

Sign in / Sign up

Export Citation Format

Share Document