Biomedical named entity recognition based on recurrent neural networks with different extended methods

2016 ◽  
Vol 16 (1) ◽  
pp. 17
Author(s):  
Degen Huang ◽  
Liuke Jin ◽  
Dingxin Song ◽  
Lishuang Li
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity ◽  
Biomedical Named Entity Recognition

Dataset-aware multi-task learning approaches for biomedical named entity recognition

2020 ◽  
Vol 36 (15) ◽  
pp. 4331-4338
Author(s):  
Mei Zuo ◽  
Yang Zhang
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Quality Data ◽  
Supplementary Information ◽  
Named Entity ◽  
Task Learning ◽  
Biomedical Named Entity Recognition

Abstract Motivation Named entity recognition is a critical and fundamental task for biomedical text mining. Recently, researchers have focused on exploiting deep neural networks for biomedical named entity recognition (Bio-NER). The performance of deep neural networks on a single dataset mostly depends on data quality and quantity while high-quality data tends to be limited in size. To alleviate task-specific data limitation, some studies explored the multi-task learning (MTL) for Bio-NER and achieved state-of-the-art performance. However, these MTL methods did not make full use of information from various datasets of Bio-NER. The performance of state-of-the-art MTL method was significantly limited by the number of training datasets. Results We propose two dataset-aware MTL approaches for Bio-NER which jointly train all models for numerous Bio-NER datasets, thus each of these models could discriminatively exploit information from all of related training datasets. Both of our two approaches achieve substantially better performance compared with the state-of-the-art MTL method on 14 out of 15 Bio-NER datasets. Furthermore, we implemented our approaches by incorporating Bio-NER and biomedical part-of-speech (POS) tagging datasets. The results verify Bio-NER and POS can significantly enhance one another. Availability and implementation Our source code is available at https://github.com/zmmzGitHub/MTL-BC-LBC-BioNER and all datasets are publicly available at https://github.com/cambridgeltl/MTL-Bioinformatics-2016. Supplementary information Supplementary data are available at Bioinformatics online.

R-BERT FOR RELATIONSHIP EXTRACTION ON RUSSIAN BUSINESS DOCUMENTS

2020 ◽  
Author(s):  
V. A. Korzun ◽  
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Shared Task ◽  
Named Entities ◽  
Named Entity ◽  
Relationship Extraction

This paper provides results of participation in the Russian Relation Extraction for Business shared task (RuREBus) within DialogueEvaluation 2020. Our team took the first place among 5 other teams in Relation Extraction with Named Entities task. The experiments showed that the best model is based on R-BERT model. R-BERT achieved significant result in comparison with models based on Convolutional or Recurrent Neural Networks on the SemEval-2010 task 8 relational dataset. In order to adapt this model to RuREBus task we also added some modifications like negative sampling. In addition, we have tested other models for Relation Extraction and Named Entity Recognition tasks.

scholarly journals Deep learning in clinical natural language processing: a methodical review

2019 ◽  
Vol 27 (3) ◽  
pp. 457-470 ◽  
Author(s):  
Stephen Wu ◽  
Kirk Roberts ◽  
Surabhi Datta ◽  
Jingcheng Du ◽  
Zongcheng Ji ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Computational Linguistics ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity

Abstract Objective This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research. Materials and Methods We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers. Results DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) and word2vec embeddings (74.1%) were the most popular methods; the information extraction tasks of text classification, named entity recognition, and relation extraction were dominant (89.2%). However, there was a “long tail” of other methods and specific tasks. Most contributions were methodological variants or applications, but 20.8% were new methods of some kind. The earliest adopters were in the NLP community, but the medical informatics community was the most prolific. Discussion Our analysis shows growing acceptance of deep learning as a baseline for NLP research, and of DL-based NLP in the medical community. A number of common associations were substantiated (eg, the preference of recurrent neural networks for sequence-labeling named entity recognition), while others were surprisingly nuanced (eg, the scarcity of French language clinical NLP with deep learning). Conclusion Deep learning has not yet fully penetrated clinical NLP and is growing rapidly. This review highlighted both the popular and unique trends in this active field.

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