219235

Nested Biomedical Named Entity Recognition

Article

Last updated: 03 Jan 2025

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Tags

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Abstract

Named entity recognition has been regarded as an important task in natural language processing. Extracting biomedical entities such as RNAs, DNAs, cell lines, proteins, and cell types has been recognized as a challenging task. Most of the existing research focuses on the extraction of flat named entities only and ignores the nested entities. Nested entities, on the other hand, are commonly used in real world biomedical applications due to their ability to represent semantic meaning of the named entity. This paper proposes an approach to improve the performance of nested biomedical named entity recognition by using a combination of diverse types of features namely morphological, orthographical, context, part of speech and word representation features while using Structured Support Vector Machine as a machine learning technique. The results obtained from the proposed approach were compared with those from popular benchmark approaches. The popular dataset “Genia" is utilized to evaluate the proposed approach which achieved Recall, Precision and F1-Measure of 84.033%, 85.946 %, and 84.113% respectively.

DOI

10.21608/ijicis.2022.104170.1134

Keywords

Machine Learning, Nested Entities, classification

Authors

First Name

Lobna

Last Name

Mady

MiddleName

Ahmed

Affiliation

Department of Information Systems, Faculty of Computer and Information Sciences, Ain shams Univ.

Email

lobna.mady@cis.asu.edu.eg

City

Cairo

Orcid

-

First Name

yasmine

Last Name

afify

MiddleName

A

Affiliation

Department of Information Systems, Faculty of Computer and Information Sciences, Ain shams Univ.

Email

yasmine.afify@cis.asu.edu.eg

City

Cairo

Orcid

0000-000106400-8472

First Name

Nagwa

Last Name

Badr

MiddleName

-

Affiliation

Department of Information Systems, Faculty of Computer and Information Sciences, Ain Shams University, Cairo, 11566, Egypt

Email

nagwabadr@cis.asu.edu.eg

City

-

Orcid

0000-0002-5382-1385

Volume

22

Article Issue

1

Related Issue

31259

Issue Date

2022-02-01

Receive Date

2021-11-03

Publish Date

2022-02-01

Page Start

98

Page End

107

Print ISSN

1687-109X

Online ISSN

2535-1710

Link

https://ijicis.journals.ekb.eg/article_219235.html

Detail API

https://ijicis.journals.ekb.eg/service?article_code=219235

Order

8

Type

Original Article

Type Code

494

Publication Type

Journal

Publication Title

International Journal of Intelligent Computing and Information Sciences

Publication Link

https://ijicis.journals.ekb.eg/

MainTitle

Nested Biomedical Named Entity Recognition

Details

Type

Article

Created At

22 Jan 2023