BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis

Weiting Gao; Xiangyu Gao; Wenjin Chen; David J. Foran; Yi Chen

doi:10.1007/978-981-97-2238-9_10

BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis

Weiting Gao, Xiangyu Gao, Wenjin Chen, David J. Foran, Yi Chen

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Biomarkers are critical in cancer diagnosis, prognosis, and treatment planning. However, this information is often buried in unstructured text form. In this paper, we make an analogy between Biomarker Information Extraction and Aspect-Based Sentiment Analysis. We propose a system, Biomarker and Result Extraction Model (BioReX). BioReX employs BERT post-training methods to augment the BioBERT model with domain-specific and task-specific knowledge for biomarker extraction. It uses syntactic-based and semantic-based attention to associate results to corresponding biomarkers. Evaluation demonstrates the effectiveness of the proposed approach.

Original language	English (US)
Title of host publication	Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings
Editors	De-Nian Yang, Xing Xie, Vincent S. Tseng, Jian Pei, Jen-Wei Huang, Jerry Chun-Wei Lin
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	129-141
Number of pages	13
ISBN (Print)	9789819722402
DOIs	https://doi.org/10.1007/978-981-97-2238-9_10
State	Published - 2024
Event	28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024 - Taipei, Taiwan, Province of China Duration: May 7 2024 → May 10 2024

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	14648 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024
Country/Territory	Taiwan, Province of China
City	Taipei
Period	5/7/24 → 5/10/24

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Keywords

Aspect-Based Sentiment Analysis
Attention Mechanism
Biomarker Extraction
Information Extraction
Large Language Model
Natural Language Processing

Access to Document

10.1007/978-981-97-2238-9_10

Cite this

Gao, W., Gao, X., Chen, W., Foran, D. J., & Chen, Y. (2024). BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis. In D.-N. Yang, X. Xie, V. S. Tseng, J. Pei, J.-W. Huang, & J. C.-W. Lin (Eds.), Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings (pp. 129-141). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 14648 LNAI). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-981-97-2238-9_10

Gao, Weiting ; Gao, Xiangyu ; Chen, Wenjin et al. / BioReX : Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis. Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings. editor / De-Nian Yang ; Xing Xie ; Vincent S. Tseng ; Jian Pei ; Jen-Wei Huang ; Jerry Chun-Wei Lin. Springer Science and Business Media Deutschland GmbH, 2024. pp. 129-141 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis",

abstract = "Biomarkers are critical in cancer diagnosis, prognosis, and treatment planning. However, this information is often buried in unstructured text form. In this paper, we make an analogy between Biomarker Information Extraction and Aspect-Based Sentiment Analysis. We propose a system, Biomarker and Result Extraction Model (BioReX). BioReX employs BERT post-training methods to augment the BioBERT model with domain-specific and task-specific knowledge for biomarker extraction. It uses syntactic-based and semantic-based attention to associate results to corresponding biomarkers. Evaluation demonstrates the effectiveness of the proposed approach.",

keywords = "Aspect-Based Sentiment Analysis, Attention Mechanism, Biomarker Extraction, Information Extraction, Large Language Model, Natural Language Processing",

author = "Weiting Gao and Xiangyu Gao and Wenjin Chen and Foran, {David J.} and Yi Chen",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.; 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024 ; Conference date: 07-05-2024 Through 10-05-2024",

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Gao, W, Gao, X, Chen, W, Foran, DJ & Chen, Y 2024, BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis. in D-N Yang, X Xie, VS Tseng, J Pei, J-W Huang & JC-W Lin (eds), Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 14648 LNAI, Springer Science and Business Media Deutschland GmbH, pp. 129-141, 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Taipei, Taiwan, Province of China, 5/7/24. https://doi.org/10.1007/978-981-97-2238-9_10

BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis. / Gao, Weiting; Gao, Xiangyu; Chen, Wenjin et al.
Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings. ed. / De-Nian Yang; Xing Xie; Vincent S. Tseng; Jian Pei; Jen-Wei Huang; Jerry Chun-Wei Lin. Springer Science and Business Media Deutschland GmbH, 2024. p. 129-141 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 14648 LNAI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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AU - Gao, Weiting

AU - Gao, Xiangyu

AU - Chen, Wenjin

AU - Foran, David J.

AU - Chen, Yi

N1 - Publisher Copyright: © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

PY - 2024

Y1 - 2024

N2 - Biomarkers are critical in cancer diagnosis, prognosis, and treatment planning. However, this information is often buried in unstructured text form. In this paper, we make an analogy between Biomarker Information Extraction and Aspect-Based Sentiment Analysis. We propose a system, Biomarker and Result Extraction Model (BioReX). BioReX employs BERT post-training methods to augment the BioBERT model with domain-specific and task-specific knowledge for biomarker extraction. It uses syntactic-based and semantic-based attention to associate results to corresponding biomarkers. Evaluation demonstrates the effectiveness of the proposed approach.

AB - Biomarkers are critical in cancer diagnosis, prognosis, and treatment planning. However, this information is often buried in unstructured text form. In this paper, we make an analogy between Biomarker Information Extraction and Aspect-Based Sentiment Analysis. We propose a system, Biomarker and Result Extraction Model (BioReX). BioReX employs BERT post-training methods to augment the BioBERT model with domain-specific and task-specific knowledge for biomarker extraction. It uses syntactic-based and semantic-based attention to associate results to corresponding biomarkers. Evaluation demonstrates the effectiveness of the proposed approach.

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SN - 9789819722402

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings

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PB - Springer Science and Business Media Deutschland GmbH

Y2 - 7 May 2024 through 10 May 2024

ER -

Gao W, Gao X, Chen W, Foran DJ, Chen Y. BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis. In Yang DN, Xie X, Tseng VS, Pei J, Huang JW, Lin JCW, editors, Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2024, Proceedings. Springer Science and Business Media Deutschland GmbH. 2024. p. 129-141. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-981-97-2238-9_10