scholarly journals Creating Training Data for Scientific Named Entity Recognition with Minimal Human Effort

2019 ◽  
pp. 398-411 ◽  
Author(s):  
Roselyne B. Tchoua ◽  
Aswathy Ajith ◽  
Zhi Hong ◽  
Logan T. Ward ◽  
Kyle Chard ◽  
...  
Keyword(s):  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entity ◽  
Human Effort

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 Named Entity Recognition for a Low Resource Language

2019 ◽  
Vol 8 (3) ◽  
pp. 587-590
Keyword(s):  
Machine Learning ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Linguistic Knowledge ◽  
Rule Based ◽  
Low Resource ◽  
Named Entity ◽  
The North ◽  
Rule Based Approach

Kokborok named entity recognition using the rules based approach is being studied in this paper. Named entity recognition is one of the applications of natural language processing. It is considered a subtask for information extraction. Named entity recognition is the means of identifying the named entity for some specific task. We have studied the named entity recognition system for the Kokborok language. Kokborok is the official language of the state of Tripura situated in the north eastern part of India. It is also widely spoken in other part of the north eastern state of India and adjoining areas of Bangladesh. The named entities are like the name of person, organization, location etc. Named entity recognitions are studied using the machine learning approach, rule based approach or the hybrid approach combining the machine learning and rule based approaches. Rule based named entity recognitions are influence by the linguistic knowledge of the language. Machine learning approach requires a large number of training data. Kokborok being a low resource language has very limited number of training data. The rule based approach requires linguistic rules and the results are not depended on the size of data available. We have framed a heuristic rules for identifying the named entity based on linguistic knowledge of the language. An encouraging result is obtained after we test our data with the rule based approach. We also tried to study and frame the rules for the counting system in Kokborok in this paper. The rule based approach to named entity recognition is found suitable for low resource language with limited digital work and absence of named entity tagged data. We have framed a suitable algorithm using the rules for solving the named entity recognition task for obtaining a desirable result.

scholarly journals Named Entity Recognition (NER) for Tibetan and Mongolian Newspapers

2021 ◽  
Author(s):  
Robert Barnett ◽  
Christian Faggionato ◽  
Marieke Meelen ◽  
Sargai Yunshaab ◽  
Tsering Samdrup ◽  
...  
Keyword(s):  
Gold Standard ◽  
Named Entity Recognition ◽  
The State ◽  
Training Data ◽  
Entity Recognition ◽  
People's Republic Of China ◽  
Republic Of China ◽  
Named Entity ◽  
Policy Analysts ◽  
Standard Training

Modern Tibetan and Vertical (Traditional) Mongolian are scripts used by c.11m people, mostly within the People’s Republic of China. In terms of publicly available tools for NLP, these languages and their scripts are extremely low-resourced and under-researched. We set out firstly to survey the state of NLP for these languages, and secondly to facilitate research by historians and policy analysts working on Tibetan newspapers. Their primary need is to be able to carry out Named Entity Recognition (NER) in Modern Tibetan, a script which has no word or sentence boundaries and for which no segmenters have been developed. Working on LightTag, an online tagger using character-based modelling, we were able to produce gold-standard training data for NER for use with Modern Tibetan.

scholarly journals NER for Tibetan and Mongolian Newspapers

2021 ◽  
Author(s):  
Robert Barnett ◽  
Christian Faggionato ◽  
Marieke Meelen ◽  
Sargai Yunshaab ◽  
Tsering Samdrup ◽  
...  
Keyword(s):  
Gold Standard ◽  
Named Entity Recognition ◽  
The State ◽  
Training Data ◽  
Entity Recognition ◽  
People's Republic Of China ◽  
Republic Of China ◽  
Named Entity ◽  
Policy Analysts ◽  
Standard Training

Modern Tibetan and Vertical (Traditional) Mongolian are scripts used by c.11m people, mostly within the People’s Republic of China. In terms of publicly available tools for NLP, these languages and their scripts are extremely low-resourced and under-researched. We set out firstly to survey the state of NLP for these languages, and secondly to facilitate research by historians and policy analysts working on Tibetan newspapers. Their primary need is to be able to carry out Named Entity Recognition (NER) in Modern Tibetan, a script which has no word or sentence boundaries and for which no segmenters have been developed. Working on LightTag, an online tagger using character-based modelling, we were able to produce gold-standard training data for NER for use with Modern Tibetan.

scholarly journals A pre-training and self-training approach for biomedical named entity recognition

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246310
Author(s):  
Shang Gao ◽  
Olivera Kotevska ◽  
Alexandre Sorokine ◽  
J. Blair Christian
Keyword(s):  
Transfer Learning ◽  
Question Answering ◽  
Named Entity Recognition ◽  
Model Performance ◽  
Training Data ◽  
Entity Recognition ◽  
Literature Mining ◽  
Unified Medical Language System ◽  
Named Entity ◽  
Training Approach

Named entity recognition (NER) is a key component of many scientific literature mining tasks, such as information retrieval, information extraction, and question answering; however, many modern approaches require large amounts of labeled training data in order to be effective. This severely limits the effectiveness of NER models in applications where expert annotations are difficult and expensive to obtain. In this work, we explore the effectiveness of transfer learning and semi-supervised self-training to improve the performance of NER models in biomedical settings with very limited labeled data (250-2000 labeled samples). We first pre-train a BiLSTM-CRF and a BERT model on a very large general biomedical NER corpus such as MedMentions or Semantic Medline, and then we fine-tune the model on a more specific target NER task that has very limited training data; finally, we apply semi-supervised self-training using unlabeled data to further boost model performance. We show that in NER tasks that focus on common biomedical entity types such as those in the Unified Medical Language System (UMLS), combining transfer learning with self-training enables a NER model such as a BiLSTM-CRF or BERT to obtain similar performance with the same model trained on 3x-8x the amount of labeled data. We further show that our approach can also boost performance in a low-resource application where entities types are more rare and not specifically covered in UMLS.

scholarly journals Reference ontology and database annotation of the COVID-19 Open Research Dataset (CORD-19)

2020 ◽  
Author(s):  
Oliver Giles ◽  
Rachael Huntley ◽  
Anneli Karlsson ◽  
Jane Lomax ◽  
James Malone
Keyword(s):  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entity ◽  
Open Research ◽  
Reference Ontology ◽  
Downstream Analysis ◽  
Biological Entities ◽  
Scientific Questions ◽  
Virus Strains

AbstractThe COVID-19 Open Research Dataset (CORD-19) was released in March 2020 to allow the machine learning and wider research community to develop techniques to answer scientific questions on COVID-19. The dataset consists of a large collection of scientific literature, including over 100,000 full text papers. Annotating training data to normalise variability in biological entities can improve the performance of downstream analysis and interpretation. To facilitate and enhance the use of the CORD-19 data in these applications, in late March 2020 we performed a comprehensive annotation process using named entity recognition tool, TERMite, along with a number of large reference ontologies and vocabularies including domains of genes, proteins, drugs and virus strains. The additional annotation has identified and tagged over 45 million entities within the corpus made up of 62,746 unique biomedical entities. The latest updated version of the annotated data, as well as older versions, is made openly available under GPL-2.0 License for the community to use at: https://github.com/SciBiteLabs/CORD19

scholarly journals Combining the NER-OCR methods to improve information retrieval efficiency in the Indonesian posters

2020 ◽  
Vol 8 (4) ◽  
pp. 263-269
Author(s):  
Ahmad Syarif Rosidy ◽  
Tubagus Mohammad Akhriza ◽  
Mochammad Husni
Keyword(s):  
Information Retrieval ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Time Efficiency ◽  
Named Entity ◽  
Retrieval Efficiency ◽  
Information Retrieval Methods

Event organizers in Indonesia often use websites to disseminate information about these events through digital posters. However, manually processing for transferring information from posters to websites is constrained by time efficiency, given the increasing number of posters uploaded. Also, information retrieval methods, such as Named Entity Recognition (NER) for Indonesian posters, are still rarely discussed in the literature. In contrast, the NER method application to Indonesian corpus is challenged by accuracy improvement because Indonesian is a low-resource language that causes a lack of corpus availability as a reference. This study proposes a solution to improve the efficiency of information extraction time from digital posters. The proposed solution is a combination of the NER method with the Optical Character Recognition (OCR) method to recognize text on posters developed with the support of relevant training data corpus to improve accuracy. The experimental results show that the system can increase time efficiency by 94 % with 82-92 % accuracy for several extracted information entities from 50 testing digital posters.

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