Biomedical Named Entity Recognition via Knowledge Guidance and Question Answering

2021 ◽  
Vol 2 (4) ◽  
pp. 1-24
Author(s):  
Pratyay Banerjee ◽  
Kuntal Kumar Pal ◽  
Murthy Devarakonda ◽  
Chitta Baral
Keyword(s):  
Question Answering ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Neural Models ◽  
Named Entity ◽  
Input Text ◽  
The Impact ◽  
Biomedical Named Entity Recognition ◽  
Entity Class

In this work, we formulated the named entity recognition (NER) task as a multi-answer knowledge guided question-answer task (KGQA) and showed that the knowledge guidance helps to achieve state-of-the-art results for 11 of 18 biomedical NER datasets. We prepended five different knowledge contexts—entity types, questions, definitions, and examples—to the input text and trained and tested BERT-based neural models on such input sequences from a combined dataset of the 18 different datasets. This novel formulation of the task (a) improved named entity recognition and illustrated the impact of different knowledge contexts, (b) reduced system confusion by limiting prediction to a single entity-class for each input token (i.e., B , I , O only) compared to multiple entity-classes in traditional NER (i.e., B entity 1, B entity 2, I entity 1, I , O ), (c) made detection of nested entities easier, and (d) enabled the models to jointly learn NER-specific features from a large number of datasets. We performed extensive experiments of this KGQA formulation on the biomedical datasets, and through the experiments, we showed when knowledge improved named entity recognition. We analyzed the effect of the task formulation, the impact of the different knowledge contexts, the multi-task aspect of the generic format, and the generalization ability of KGQA. We also probed the model to better understand the key contributors for these improvements.

Towards corpus and model: Hierarchical structured-attention-based features for Indonesian named entity recognition

2021 ◽  
pp. 1-12
Author(s):  
Yingwen Fu ◽  
Nankai Lin ◽  
Xiaotian Lin ◽  
Shengyi Jiang
Keyword(s):  
Language Processing ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Language Models ◽  
Neural Models ◽  
Performance Models ◽  
Named Entity ◽  
High Resource ◽  
Benchmark Datasets

Named entity recognition (NER) is fundamental to natural language processing (NLP). Most state-of-the-art researches on NER are based on pre-trained language models (PLMs) or classic neural models. However, these researches are mainly oriented to high-resource languages such as English. While for Indonesian, related resources (both in dataset and technology) are not yet well-developed. Besides, affix is an important word composition for Indonesian language, indicating the essentiality of character and token features for token-wise Indonesian NLP tasks. However, features extracted by currently top-performance models are insufficient. Aiming at Indonesian NER task, in this paper, we build an Indonesian NER dataset (IDNER) comprising over 50 thousand sentences (over 670 thousand tokens) to alleviate the shortage of labeled resources in Indonesian. Furthermore, we construct a hierarchical structured-attention-based model (HSA) for Indonesian NER to extract sequence features from different perspectives. Specifically, we use an enhanced convolutional structure as well as an enhanced attention structure to extract deeper features from characters and tokens. Experimental results show that HSA establishes competitive performance on IDNER and three benchmark datasets.

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 Domain-Transferable Method for Named Entity Recognition Task

2020 ◽  
Author(s):  
Vladislav Mikhailov ◽  
Tatiana Shavrina
Keyword(s):  
Language Processing ◽  
Question Answering ◽  
Named Entity Recognition ◽  
Recognition Task ◽  
Entity Recognition ◽  
Neural Models ◽  
Named Entities ◽  
Named Entity ◽  
Domain Specific ◽  
Human Effort

Named Entity Recognition (NER) is a fundamental task in the fields of natural language processing and information extraction. NER has been widely used as a standalone tool or an essential component in a variety of applications such as question answering, dialogue assistants and knowledge graphs development. However, training reliable NER models requires a large amount of labelled data which is expensive to obtain, particularly in specialized domains. This paper describes a method to learn a domain-specific NER model for an arbitrary set of named entities when domain-specific supervision is not available. We assume that the supervision can be obtained with no human effort, and neural models can learn from each other. The code, data and models are publicly available.

HUNER: improving biomedical NER with pretraining

2019 ◽  
Vol 36 (1) ◽  
pp. 295-302 ◽  
Author(s):  
Leon Weber ◽  
Jannes Münchmeyer ◽  
Tim Rocktäschel ◽  
Maryam Habibi ◽  
Ulf Leser
Keyword(s):  
Deep Neural Networks ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
The State ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Supplementary Information ◽  
Named Entity ◽  
Training Development ◽  
The Impact

Abstract Motivation Several recent studies showed that the application of deep neural networks advanced the state-of-the-art in named entity recognition (NER), including biomedical NER. However, the impact on performance and the robustness of improvements crucially depends on the availability of sufficiently large training corpora, which is a problem in the biomedical domain with its often rather small gold standard corpora. Results We evaluate different methods for alleviating the data sparsity problem by pretraining a deep neural network (LSTM-CRF), followed by a rather short fine-tuning phase focusing on a particular corpus. Experiments were performed using 34 different corpora covering five different biomedical entity types, yielding an average increase in F1-score of ∼2 pp compared to learning without pretraining. We experimented both with supervised and semi-supervised pretraining, leading to interesting insights into the precision/recall trade-off. Based on our results, we created the stand-alone NER tool HUNER incorporating fully trained models for five entity types. On the independent CRAFT corpus, which was not used for creating HUNER, it outperforms the state-of-the-art tools GNormPlus and tmChem by 5–13 pp on the entity types chemicals, species and genes. Availability and implementation HUNER is freely available at https://hu-ner.github.io. HUNER comes in containers, making it easy to install and use, and it can be applied off-the-shelf to arbitrary texts. We also provide an integrated tool for obtaining and converting all 34 corpora used in our evaluation, including fixed training, development and test splits to enable fair comparisons in the future. Supplementary information Supplementary data are available at Bioinformatics online.

Joined Type Length Encoding for Nested Named Entity Recognition

2022 ◽  
Vol 21 (3) ◽  
pp. 1-23
Author(s):  
Mohammad Sadegh Sheikhaei ◽  
Hasan Zafari ◽  
Yuan Tian
Keyword(s):  
State Of The Art ◽  
Named Entity Recognition ◽  
Ensemble Method ◽  
Entity Recognition ◽  
Neural Models ◽  
Named Entities ◽  
Layer Sequence ◽  
Named Entity ◽  
The Ensemble Method ◽  
Single Sequence

In this article, we propose a new encoding scheme for named entity recognition (NER) called Joined Type-Length encoding (JoinedTL). Unlike most existing named entity encoding schemes, which focus on flat entities, JoinedTL can label nested named entities in a single sequence. JoinedTL uses a packed encoding to represent both type and span of a named entity, which not only results in less tagged tokens compared to existing encoding schemes, but also enables it to support nested NER. We evaluate the effectiveness of JoinedTL for nested NER on three nested NER datasets: GENIA in English, GermEval in German, and PerNest, our newly created nested NER dataset in Persian. We apply CharLSTM+WordLSTM+CRF, a three-layer sequence tagging model on three datasets encoded using JoinedTL and two existing nested NE encoding schemes, i.e., JoinedBIO and JoinedBILOU. Our experiment results show that CharLSTM+WordLSTM+CRF trained with JoinedTL encoded datasets can achieve competitive F1 scores as the ones trained with datasets encoded by two other encodings, but with 27%–48% less tagged tokens. To leverage the power of three different encodings, i.e., JoinedTL, JoinedBIO, and JoinedBILOU, we propose an encoding-based ensemble method for nested NER. Evaluation results show that the ensemble method achieves higher F1 scores on all datasets than the three models each trained using one of the three encodings. By using nested NE encodings including JoinedTL with CharLSTM+WordLSTM+CRF, we establish new state-of-the-art performance with an F1 score of 83.7 on PerNest, 74.9 on GENIA, and 70.5 on GermEval, surpassing two recent neural models specially designed for nested NER.

scholarly journals We are not ready yet: limitations of transfer learning for Disease Named Entity Recognition

2021 ◽  
Author(s):  
Lisa Langnickel ◽  
Juliane Fluck
Keyword(s):  
Transfer Learning ◽  
Language Processing ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Clinical Applications ◽  
Entity Recognition ◽  
Data Sets ◽  
Named Entity ◽  
Current State ◽  
Biomedical Named Entity Recognition

Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer learning-based methods, BERT models are used in a variety of biomedical and clinical applications. For the available data sets, these models show excellent results - partly exceeding the inter-annotator agreements. However, biomedical named entity recognition applied on COVID-19 preprints shows a performance drop compared to the results on available test data. The question arises how well trained models are able to predict on completely new data, i.e. to generalize. Based on the example of disease named entity recognition, we investigate the robustness of different machine learning-based methods - thereof transfer learning - and show that current state-of-the-art methods work well for a given training and the corresponding test set but experience a significant lack of generalization when applying to new data. We therefore argue that there is a need for larger annotated data sets for training and testing.

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 Improving deep learning method for biomedical named entity recognition by using entity definition information

2021 ◽  
Vol 22 (S1) ◽  
Author(s):  
Ying Xiong ◽  
Shuai Chen ◽  
Buzhou Tang ◽  
Qingcai Chen ◽  
Xiaolong Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
The State ◽  
Entity Recognition ◽  
Biomedical Text ◽  
Learning Methods ◽  
Named Entity ◽  
Sequence Labeling ◽  
Biomedical Named Entity Recognition

Abstract Background Biomedical named entity recognition (NER) is a fundamental task of biomedical text mining that finds the boundaries of entity mentions in biomedical text and determines their entity type. To accelerate the development of biomedical NER techniques in Spanish, the PharmaCoNER organizers launched a competition to recognize pharmacological substances, compounds, and proteins. Biomedical NER is usually recognized as a sequence labeling task, and almost all state-of-the-art sequence labeling methods ignore the meaning of different entity types. In this paper, we investigate some methods to introduce the meaning of entity types in deep learning methods for biomedical NER and apply them to the PharmaCoNER 2019 challenge. The meaning of each entity type is represented by its definition information. Material and method We investigate how to use entity definition information in the following two methods: (1) SQuad-style machine reading comprehension (MRC) methods that treat entity definition information as query and biomedical text as context and predict answer spans as entities. (2) Span-level one-pass (SOne) methods that predict entity spans of one type by one type and introduce entity type meaning, which is represented by entity definition information. All models are trained and tested on the PharmaCoNER 2019 corpus, and their performance is evaluated by strict micro-average precision, recall, and F1-score. Results Entity definition information brings improvements to both SQuad-style MRC and SOne methods by about 0.003 in micro-averaged F1-score. The SQuad-style MRC model using entity definition information as query achieves the best performance with a micro-averaged precision of 0.9225, a recall of 0.9050, and an F1-score of 0.9137, respectively. It outperforms the best model of the PharmaCoNER 2019 challenge by 0.0032 in F1-score. Compared with the state-of-the-art model without using manually-crafted features, our model obtains a 1% improvement in F1-score, which is significant. These results indicate that entity definition information is useful for deep learning methods on biomedical NER. Conclusion Our entity definition information enhanced models achieve the state-of-the-art micro-average F1 score of 0.9137, which implies that entity definition information has a positive impact on biomedical NER detection. In the future, we will explore more entity definition information from knowledge graph.

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