A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

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Biomedical named entity recognition and linking datasets: survey and our recent development

Briefings in Bioinformatics ◽

10.1093/bib/bbaa054 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2219-2238 ◽

Cited By ~ 2

Author(s):

Ming-Siang Huang ◽

Po-Ting Lai ◽

Pei-Yen Lin ◽

Yu-Ting You ◽

Richard Tzong-Han Tsai ◽

...

Keyword(s):

Language Processing ◽

Protein Interaction ◽

Named Entity Recognition ◽

Paper Analysis ◽

Biomedical Literature ◽

Entity Recognition ◽

Supplementary Information ◽

Protein Protein Interaction ◽

Named Entity ◽

Biomedical Named Entity Recognition

Abstract Natural language processing (NLP) is widely applied in biological domains to retrieve information from publications. Systems to address numerous applications exist, such as biomedical named entity recognition (BNER), named entity normalization (NEN) and protein–protein interaction extraction (PPIE). High-quality datasets can assist the development of robust and reliable systems; however, due to the endless applications and evolving techniques, the annotations of benchmark datasets may become outdated and inappropriate. In this study, we first review commonlyused BNER datasets and their potential annotation problems such as inconsistency and low portability. Then, we introduce a revised version of the JNLPBA dataset that solves potential problems in the original and use state-of-the-art named entity recognition systems to evaluate its portability to different kinds of biomedical literature, including protein–protein interaction and biology events. Lastly, we introduce an ensembled biomedical entity dataset (EBED) by extending the revised JNLPBA dataset with PubMed Central full-text paragraphs, figure captions and patent abstracts. This EBED is a multi-task dataset that covers annotations including gene, disease and chemical entities. In total, it contains 85000 entity mentions, 25000 entity mentions with database identifiers and 5000 attribute tags. To demonstrate the usage of the EBED, we review the BNER track from the AI CUP Biomedical Paper Analysis challenge. Availability: The revised JNLPBA dataset is available at https://iasl-btm.iis.sinica.edu.tw/BNER/Content/Re vised_JNLPBA.zip. The EBED dataset is available at https://iasl-btm.iis.sinica.edu.tw/BNER/Content/AICUP _EBED_dataset.rar. Contact: Email: [email protected], Tel. 886-3-4227151 ext. 35203, Fax: 886-3-422-2681 Email: [email protected], Tel. 886-2-2788-3799 ext. 2211, Fax: 886-2-2782-4814 Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.

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SCIENTIFIC NAMED ENTITY RECOGNITION WITH THE HELP OF MODERN METHODS

Bulletin Series of Physics & Mathematical Sciences ◽

10.51889/2021-3.1728-7901.11 ◽

2021 ◽

Vol 75 (3) ◽

pp. 94-99

Author(s):

A.M. Yelenov ◽

◽

A.B. Jaxylykova ◽

Keyword(s):

Machine Learning ◽

Language Processing ◽

Named Entity Recognition ◽

Recognition Task ◽

Entity Recognition ◽

Support Vector ◽

Scientific Article ◽

Natural Languages ◽

Named Entity ◽

Learning Area

This research focuses on a comparative study of the Named Entity Recognition task for scientific article texts. Natural language processing could be considered as one of the cornerstones in the machine learning area which devotes its attention to the problems connected with the understanding of different natural languages and linguistic analysis. It was already shown that current deep learning techniques have a good performance and accuracy in such areas as image recognition, pattern recognition, computer vision, that could mean that such technology probably would be successful in the neuro-linguistic programming area too and lead to a dramatic increase on the research interest on this topic. For a very long time, quite trivial algorithms have been used in this area, such as support vector machines or various types of regression, basic encoding on text data was also used, which did not provide high results. The following dataset was used to process the experiment models: Dataset Scientific Entity Relation Core. The algorithms used were Long short-term memory, Random Forest Classifier with Conditional Random Fields, and Named-entity recognition with Bidirectional Encoder Representations from Transformers. In the findings, the metrics scores of all models were compared to each other to make a comparison. This research is devoted to the processing of scientific articles, concerning the machine learning area, because the subject is not investigated on enough properly level.The consideration of this task can help machines to understand natural languages better, so that they can solve other neuro-linguistic programming tasks better, enhancing scores in common sense.

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Enhancing the Performance of Telugu Named Entity Recognition Using Gazetteer Features

Information ◽

10.3390/info11020082 ◽

2020 ◽

Vol 11 (2) ◽

pp. 82

Author(s):

SaiKiranmai Gorla ◽

Lalita Bhanu Murthy Neti ◽

Aruna Malapati

Keyword(s):

Language Processing ◽

Conditional Random Field ◽

Named Entity Recognition ◽

Entity Recognition ◽

Limited Resources ◽

Support Vector ◽

Named Entity ◽

Word Level ◽

Asian Languages ◽

Better Than

Named entity recognition (NER) is a fundamental step for many natural language processing tasks and hence enhancing the performance of NER models is always appreciated. With limited resources being available, NER for South-East Asian languages like Telugu is quite a challenging problem. This paper attempts to improve the NER performance for Telugu using gazetteer-related features, which are automatically generated using Wikipedia pages. We make use of these gazetteer features along with other well-known features like contextual, word-level, and corpus features to build NER models. NER models are developed using three well-known classifiers—conditional random field (CRF), support vector machine (SVM), and margin infused relaxed algorithms (MIRA). The gazetteer features are shown to improve the performance, and theMIRA-based NER model fared better than its counterparts SVM and CRF.

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COST-SENSITIVE STRUCTURED PERCEPTRON INCORPORATING CATEGORY HIERARCHY FOR NAMED ENTITY RECOGNITION

Journal of Information and Communication Technology ◽

10.32890/jict.14.2015.8153 ◽

2015 ◽

Author(s):

Shohei Higashiyama ◽

Blondel Mathieu ◽

Kazuhiro Seki ◽

Kuniaki Uehara

Keyword(s):

Cost Function ◽

Language Processing ◽

Named Entity Recognition ◽

Entity Recognition ◽

Superior Performance ◽

Support Vector ◽

Named Entity ◽

Vector Machines ◽

Representative Work ◽

Correct Category

Named Entity Recognition (NER) is a fundamental natural language processing task for the identifi cation and classifi cation of expressions into predefi ned categories, such as person and organization. Existing NER systems usually target about 10 categories and do not incorporate analysis of category relations. However, categories often belong naturally to some predefi ned hierarchy. In such cases, the distance between categories in the hierarchy becomes a rich source of information that can be exploited. This is intuitively useful particularly when the categories are numerous. On that account, this paper proposes an NER approach that can leverage category hierarchy information by introducing, in the structured perceptron framework, a cost function more strongly penalizing category predictions that are more distant from the correct category in the hierarchy. Experimental results on the GENIA biomedical text corpus indicate the effectiveness of the proposed approach as compared with the case where no cost function is utilized. In addition, the proposed approach demonstrates the superior performance over a representative work using multi-class support vector machines on the same corpus. A possible direction to further improve the proposed approach is to investigate more elaborate cost functions than a simple additive cost adopted in this work.

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Named Entity Recognition for Code Mixed Social Media Sentences

International Journal of Software Science and Computational Intelligence ◽

10.4018/ijssci.2021040102 ◽

2021 ◽

Vol 13 (2) ◽

pp. 23-36

Author(s):

Yashvardhan Sharma ◽

Rupal Bhargava ◽

Bapiraju Vamsi Tadikonda

Keyword(s):

Social Media ◽

Language Processing ◽

Short Term Memory ◽

Named Entity Recognition ◽

Entity Recognition ◽

Machine Learning Techniques ◽

Support Vector ◽

Internet Applications ◽

Named Entity ◽

Code Mixing

With the increase of internet applications and social media platforms there has been an increase in the informal way of text communication. People belonging to different regions tend to mix their regional language with English on social media text. This has been the trend with many multilingual nations now and is commonly known as code mixing. In code mixing, multiple languages are used within a statement. The problem of named entity recognition (NER) is a well-researched topic in natural language processing (NLP), but the present NER systems tend to perform inefficiently on code-mixed text. This paper proposes three approaches to improve named entity recognizers for handling code-mixing. The first approach is based on machine learning techniques such as support vector machines and other tree-based classifiers. The second approach is based on neural networks and the third approach uses long short-term memory (LSTM) architecture to solve the problem.

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Named entity recognition in Bengali and Hindi using support vector machine

Lingvisticae Investigationes ◽

10.1075/li.34.1.02ekb ◽

2011 ◽

Vol 34 (1) ◽

pp. 35-67 ◽

Cited By ~ 9

Author(s):

Asif Ekbal ◽

Sivaji Bandyopadhyay

Keyword(s):

Support Vector Machine ◽

Language Processing ◽

Question Answering ◽

Contextual Information ◽

Named Entity Recognition ◽

Standard Test ◽

Entity Recognition ◽

Support Vector ◽

Named Entity ◽

Question Answering Systems

Named Entity Recognition (NER) aims to classify each word of a document into predefined target named entity (NE) classes and is nowadays considered to be fundamental for many Natural Language Processing (NLP) tasks such as information retrieval, machine translation, information extraction, question answering systems and others. This paper reports about the development of a NER system for Bengali and Hindi using Support Vector Machine (SVM). We have used the annotated corpora of 122,467 tokens of Bengali and 502,974 tokens of Hindi tagged with the twelve different NE classes, defined as part of the IJCNLP-08 NER Shared Task for South and South East Asian Languages (SSEAL). An appropriate tag conversion routine has been developed in order to convert the data into the forms tagged with the four NE tags, namely Person name, Location name, Organization name and Miscellaneous name. The system makes use of the different contextual information of the words along with the variety of orthographic word-level features that are helpful in predicting the different NE classes. The system has been tested with the gold standard test sets of 35K, and 38K tokens for Bengali, and Hindi, respectively. Evaluation results have demonstrated the overall recall, precision, and f-score values of 85.11%, 81.74%, and 83.39%, respectively, for Bengali and 82.76%, 77.81%, and 80.21%, respectively, for Hindi. Statistical analysis, ANOVA is performed to show that the improvement in the performance with the use of language dependent features is statistically significant over the language independent features for Bengali and Hindi both.

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An Annotated Corpus of Crime-Related Portuguese Documents for NLP and Machine Learning Processing

Data ◽

10.3390/data6070071 ◽

2021 ◽

Vol 6 (7) ◽

pp. 71

Author(s):

Gonçalo Carnaz ◽

Mário Antunes ◽

Vitor Beires Nogueira

Keyword(s):

Machine Learning ◽

Language Processing ◽

Named Entity Recognition ◽

Entity Recognition ◽

Automatic Identification ◽

Named Entities ◽

Related Data ◽

Named Entity ◽

Chain Of Custody ◽

Evidence Collection

Criminal investigations collect and analyze the facts related to a crime, from which the investigators can deduce evidence to be used in court. It is a multidisciplinary and applied science, which includes interviews, interrogations, evidence collection, preservation of the chain of custody, and other methods and techniques of investigation. These techniques produce both digital and paper documents that have to be carefully analyzed to identify correlations and interactions among suspects, places, license plates, and other entities that are mentioned in the investigation. The computerized processing of these documents is a helping hand to the criminal investigation, as it allows the automatic identification of entities and their relations, being some of which difficult to identify manually. There exists a wide set of dedicated tools, but they have a major limitation: they are unable to process criminal reports in the Portuguese language, as an annotated corpus for that purpose does not exist. This paper presents an annotated corpus, composed of a collection of anonymized crime-related documents, which were extracted from official and open sources. The dataset was produced as the result of an exploratory initiative to collect crime-related data from websites and conditioned-access police reports. The dataset was evaluated and a mean precision of 0.808, recall of 0.722, and F1-score of 0.733 were obtained with the classification of the annotated named-entities present in the crime-related documents. This corpus can be employed to benchmark Machine Learning (ML) and Natural Language Processing (NLP) methods and tools to detect and correlate entities in the documents. Some examples are sentence detection, named-entity recognition, and identification of terms related to the criminal domain.

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

Journal of Intelligent & Fuzzy Systems ◽

10.3233/jifs-202286 ◽

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.

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Obtaining Knowledge in Pathology Reports Through a Natural Language Processing Approach With Classification, Named-Entity Recognition, and Relation-Extraction Heuristics

JCO Clinical Cancer Informatics ◽

10.1200/cci.19.00008 ◽

2019 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Tomasz Oliwa ◽

Steven B. Maron ◽

Leah M. Chase ◽

Samantha Lomnicki ◽

Daniel V.T. Catenacci ◽

...

Keyword(s):

Machine Learning ◽

Natural Language Processing ◽

Natural Language ◽

Language Processing ◽

Named Entity Recognition ◽

Entity Recognition ◽

Classification Model ◽

Supervised Machine Learning ◽

Named Entity ◽

Pathology Reports

PURPOSE Robust institutional tumor banks depend on continuous sample curation or else subsequent biopsy or resection specimens are overlooked after initial enrollment. Curation automation is hindered by semistructured free-text clinical pathology notes, which complicate data abstraction. Our motivation is to develop a natural language processing method that dynamically identifies existing pathology specimen elements necessary for locating specimens for future use in a manner that can be re-implemented by other institutions. PATIENTS AND METHODS Pathology reports from patients with gastroesophageal cancer enrolled in The University of Chicago GI oncology tumor bank were used to train and validate a novel composite natural language processing-based pipeline with a supervised machine learning classification step to separate notes into internal (primary review) and external (consultation) reports; a named-entity recognition step to obtain label (accession number), location, date, and sublabels (block identifiers); and a results proofreading step. RESULTS We analyzed 188 pathology reports, including 82 internal reports and 106 external consult reports, and successfully extracted named entities grouped as sample information (label, date, location). Our approach identified up to 24 additional unique samples in external consult notes that could have been overlooked. Our classification model obtained 100% accuracy on the basis of 10-fold cross-validation. Precision, recall, and F1 for class-specific named-entity recognition models show strong performance. CONCLUSION Through a combination of natural language processing and machine learning, we devised a re-implementable and automated approach that can accurately extract specimen attributes from semistructured pathology notes to dynamically populate a tumor registry.

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

Information ◽

10.3390/info11020079 ◽

2020 ◽

Vol 11 (2) ◽

pp. 79 ◽

Cited By ~ 2

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.

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