BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis
Document Type
Conference Proceeding
Publication Date
1-1-2024
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.
Identifier
85193621639 (Scopus)
ISBN
[9789819722402]
Publication Title
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
External Full Text Location
https://doi.org/10.1007/978-981-97-2238-9_10
e-ISSN
16113349
ISSN
03029743
First Page
129
Last Page
141
Volume
14648 LNAI
Grant
UL1TR003017
Fund Ref
Leir Foundation
Recommended Citation
Gao, Weiting; Gao, Xiangyu; Chen, Wenjin; Foran, David J.; and Chen, Yi, "BioReX: Biomarker Information Extraction Inspired by Aspect-Based Sentiment Analysis" (2024). Faculty Publications. 998.
https://digitalcommons.njit.edu/fac_pubs/998
