Sequence tagging for biomedical extractive question answering
arXiv:2104.07535 · doi:10.1093/bioinformatics/btac397
Abstract
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. 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. Source codes and resources are freely available for download at https://github.com/dmis-lab/SeqTagQA
Published as "advanced access". Bioinformatics (2022). Supplementary data are available at Bioinformatics online
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- BoolQ: Exploring the Surprising Difficulty of Natural Yes/No Questions
- Overview of BioASQ 2020: The eighth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering
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- Pre-trained Language Models in Biomedical Domain: A Systematic Survey
- Advancing Italian Biomedical Information Extraction with Transformers-based Models: Methodological Insights and Multicenter Practical Application
- Development of an Extractive Clinical Question Answering Dataset with Multi-Answer and Multi-Focus Questions