Word embeddings and external resources for answer processing in biomedical factoid question answering

Biomedical question answering (QA) is a challenging task that has not been yet successfully solved, according to results on international benchmarks, such as BioASQ. Recent progress on deep neural networks has led to promising results in domain independent QA, but the lack of large datasets with biomedical question-answer pairs hinders their successful application to the domain of biomedicine. We propose a novel machine-learning based answer processing approach that exploits neural networks in an unsupervised way through word embeddings. Our approach first combines biomedical and general purpose tools to identify the candidate answers from a set of passages. Candidates are then represented using a combination of features based on both biomedical external resources and input textual sources, including features based on word embeddings. Candidates are then ranked based on the score given at the output of a binary classification model, trained from candidates extracted from a small number of questions, related passages and correct answer triplets from the BioASQ challenge. Our experimental results show that the use of word embeddings, combined with other features, improves the performance of answer processing in biomedical question answering. In addition, our results show that the use of several annotators improves the identification of answers in passages. Finally, our approach has participated in the last two versions (2017, 2018) of the BioASQ challenge achieving competitive results.