scholarly journals Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learning

2018 ◽  
Author(s):  
Xuan Wang ◽  
Yu Zhang ◽  
Xiang Ren ◽  
Yuhao Zhang ◽  
Marinka Zitnik ◽  
...  
Keyword(s):  
State Of The Art ◽  
Named Entity Recognition ◽  
Network Models ◽  
Training Data ◽  
Entity Recognition ◽  
Neural Network Models ◽  
Named Entity ◽  
Task Learning ◽  
Level Information ◽  
Biomedical Named Entity Recognition

AbstractMotivationState-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for BioNER to free experts from manual feature engineering, the performance remains limited by the available training data for each entity type.ResultsWe propose a multi-task learning framework for BioNER to collectively use the training data of different types of entities and improve the performance on each of them. In experiments on 15 benchmark BioNER datasets, our multi-task model achieves substantially better performance compared with state-of-the-art BioNER systems and baseline neural sequence labeling models. Further analysis shows that the large performance gains come from sharing character- and word-level information among relevant biomedical entities across differently labeled corpora.AvailabilityOur source code is available at https://github.com/yuzhimanhua/[email protected], [email protected].

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.

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.

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 Coreference Aware Representation Learning for Neural Named Entity Recognition

2019 ◽  
Author(s):  
Zeyu Dai ◽  
Hongliang Fei ◽  
Ping Li
Keyword(s):  
Neural Network ◽  
State Of The Art ◽  
Structural Information ◽  
Named Entity Recognition ◽  
Network Models ◽  
Third Party ◽  
Entity Recognition ◽  
Neural Network Models ◽  
Named Entity ◽  
Art Performance

Recent neural network models have achieved state-of-the-art performance on the task of named entity recognition (NER). However, previous neural network models typically treat the input sentences as a linear sequence of words but ignore rich structural information, such as the coreference relations among non-adjacent words, phrases or entities. In this paper, we propose a novel approach to learn coreference-aware word representations for the NER task at the document level. In particular, we enrich the well-known neural architecture ``CNN-BiLSTM-CRF'' with a coreference layer on top of the BiLSTM layer to incorporate coreferential relations. Furthermore, we introduce the coreference regularization to ensure the coreferential entities to share similar representations and consistent predictions within the same coreference cluster. Our proposed model achieves new state-of-the-art performance on two NER benchmarks: CoNLL-2003 and OntoNotes v5.0. More importantly, we demonstrate that our framework does not rely on gold coreference knowledge, and can still work well even when the coreferential relations are generated by a third-party toolkit.

scholarly journals InferNER: an attentive model leveraging the sentence-level information for Named Entity Recognition in Microblogs

2021 ◽  
Vol 34 (1) ◽  
Author(s):  
Moemmur Shahzad ◽  
Ayesha Amin ◽  
Diego Esteves ◽  
Axel-Cyrille Ngonga Ngomo
Keyword(s):  
Social Media ◽  
Visual Information ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity ◽  
Current State ◽  
Sentence Level ◽  
Level Information ◽  
External Sources

We investigate the problem of named entity recognition in the user-generated text such as social media posts. This task is rendered particularly difficult by the restricted length and limited grammatical coherence of this data type. Current state-of-the-art approaches rely on external sources such as gazetteers to alleviate some of these restrictions. We present a neural model able to outperform state of the art on this task without recurring to gazetteers or similar external sources of information. Our approach relies on word-, character-, and sentence-level information for NER in short-text. Social media posts like tweets often have associated images that may provide auxiliary context relevant to understand these texts. Hence, we also incorporate visual information and introduce an attention component which computes attention weight probabilities over textual and text-relevant visual contexts separately. Our model outperforms the current state of the art on various NER datasets. On WNUT 2016 and 2017, our model achieved 53.48\% and 50.52\% F1 score, respectively. With Multimodal model, our system also outperforms the current SOTA with an F1 score of 74\% on the multimodal dataset. Our evaluation further suggests that our model also goes beyond the current state-of-the-art on newswire data, hence corroborating its suitability for various NER tasks.

scholarly journals A Hierarchical Multi-Task Approach for Learning Embeddings from Semantic Tasks

2019 ◽  
Vol 33 ◽  
pp. 6949-6956 ◽  
Author(s):  
Victor Sanh ◽  
Thomas Wolf ◽  
Sebastian Ruder
Keyword(s):  
Language Processing ◽  
Semantic Information ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Inductive Bias ◽  
Named Entity ◽  
Task Learning ◽  
Hidden States

Much effort has been devoted to evaluate whether multi-task learning can be leveraged to learn rich representations that can be used in various Natural Language Processing (NLP) down-stream applications. However, there is still a lack of understanding of the settings in which multi-task learning has a significant effect. In this work, we introduce a hierarchical model trained in a multi-task learning setup on a set of carefully selected semantic tasks. The model is trained in a hierarchical fashion to introduce an inductive bias by supervising a set of low level tasks at the bottom layers of the model and more complex tasks at the top layers of the model. This model achieves state-of-the-art results on a number of tasks, namely Named Entity Recognition, Entity Mention Detection and Relation Extraction without hand-engineered features or external NLP tools like syntactic parsers. The hierarchical training supervision induces a set of shared semantic representations at lower layers of the model. We show that as we move from the bottom to the top layers of the model, the hidden states of the layers tend to represent more complex semantic information.

An Experimental Study of Hybrid Machine Learning Models for Extracting Named Entities

10.29007/dp5m ◽  
2019 ◽  
Author(s):  
Lei Jiang ◽  
Elena Bolshakova
Keyword(s):  
Neural Network ◽  
Conditional Random Fields ◽  
Named Entity Recognition ◽  
Network Models ◽  
Entity Recognition ◽  
Neural Network Models ◽  
Named Entities ◽  
Hybrid Neural Network ◽  
Named Entity ◽  
Two Hybrid

The paper describes two hybrid neural network models for named entity recognition (NER) in texts, as well as results of experiments with them. The first model, namely Bi-LSTM-CRF, is known and used for NER, while the other model named Gated-CNN- CRF is proposed in this work. It combines convolutional neural network (CNN), gated linear units, and conditional random fields (CRF). Both models were tested for NER on three different language datasets, for English, Russian, and Chinese. All resulted scores of precision, recall and F1-measure for both models are close to the state-of-the-art for NER, and for the English dataset CoNLL-2003, Gated-CNN-CRF model achieves 92.66 of F1-measure, outperforming the known result.

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