Sequence tagging for biomedical extractive question answering

• Published in: Bioinformatics Vol. 38; no. 15; pp. 3794 - 3801
• Main Authors: Yoon, Wonjin, Jackson, Richard, Lagerberg, Aron, Kang, Jaewoo
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 02.08.2022
• Subjects: Computational Biology; Original Papers; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btac397

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 article, 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 7b and 8b list-type questions outperformed the best-performing existing models without requiring post-processing steps. Availability and implementation 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.