Yoon W, Jackson R, Lagerberg A, Kang J. Sequence Tagging For Biomedical Extractive Question Answering.
Bioinformatics 2022;
38:3794-3801. [PMID:
35713500 PMCID:
PMC9344839 DOI:
10.1093/bioinformatics/btac397]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/01/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION
Current studies in extractive question answering (EQA) have modeled the single-span extraction setting, where a single answer span is a label to predict for a given question-passage pair. This setting is natural for general domain EQA as the majority of the questions in the general domain can be answered with a single span. Following general domain EQA models, current biomedical EQA (BioEQA) models utilize the single-span extraction setting with post-processing steps.
RESULTS
In this paper, we investigate the question distribution across the general and biomedical domains and discover biomedical questions are more likely to require list-type answers (multiple answers) than factoid-type answers (single answer). This necessitates the models capable of producing multiple answers for a question. Based on this preliminary study, we propose a sequence tagging approach for BioEQA, which is a multi-span extraction setting. Our approach directly tackles questions with a variable number of phrases as their answer and can learn to decide the number of answers for a question from training data. Our experimental results on the BioASQ 7 b and 8 b list-type questions outperformed the best-performing existing models without requiring post-processing steps.
AVAILABILITY
Source codes and resources are freely available for download at https://github.com/dmis-lab/SeqTagQA.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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