Abstract: This paper describes our submission to the 2017 BioASQ challenge. We participated in Task B, Phase B which is concerned with biomedical question answering (QA). We focus on factoid and list question, using an extractive QA model, that is, we restrict our system to output substrings of the provided text snippets. At the core of our system, we use FastQA, a state-of-the-art neural QA system. We extended it with biomedical word embeddings and changed its answer layer to be able to answer list questions in addition to factoid questions. We pre-trained the model on a large-scale open-domain QA dataset, SQuAD, and then fine-tuned the parameters on the BioASQ training set. With our approach, we achieve state-of-the-art results on factoid questions and competitive results on list questions.

Introduction: BioASQ is a semantic indexing, question answering (QA) and information extraction challenge BIBREF0 . We participated in Task B of the challenge which is concerned with biomedical QA. More specifically, our system participated in Task B, Phase B: Given a question and gold-standard snippets (i.e., pieces of text that contain the answer(s) to the question), the system is asked to return a list of answer candidates. The fifth BioASQ challenge is taking place at the time of writing. Five batches of 100 questions each were released every two weeks. Participating systems have 24 hours to submit their results. At the time of writing, all batches had been released. The questions are categorized into different question types: factoid, list, summary and yes/no. Our work concentrates on answering factoid and list questions. For factoid questions, the system's responses are interpreted as a ranked list of answer candidates. They are evaluated using mean-reciprocal rank (MRR). For list questions, the system's responses are interpreted as a set of answers to the list question. Precision and recall are computed by comparing the given answers to the gold-standard answers. F1 score, i.e., the harmonic mean of precision and recall, is used as the official evaluation measure . Most existing biomedical QA systems employ a traditional QA pipeline, similar in structure to the baseline system by weissenborn2013answering. They consist of several discrete steps, e.g., named-entity recognition, question classification, and candidate answer scoring. These systems require a large amount of resources and feature engineering that is specific to the biomedical domain. For example, OAQA BIBREF1 , which has been very successful in last year's challenge, uses a biomedical parser, entity tagger and a thesaurus to retrieve synonyms. Our system, on the other hand, is based on a neural network QA architecture that is trained end-to-end on the target task. We build upon FastQA BIBREF2 , an extractive factoid QA system which achieves state-of-the-art results on QA benchmarks that provide large amounts of training data. For example, SQuAD BIBREF3 provides a dataset of $\approx 100,000$ questions on Wikipedia articles. Our approach is to train FastQA (with some extensions) on the SQuAD dataset and then fine-tune the model parameters on the BioASQ training set. Note that by using an extractive QA network as our central component, we restrict our system's responses to substrings in the provided snippets. This also implies that the network will not be able to answer yes/no questions. We do, however, generalize the FastQA output layer in order to be able to answer list questions in addition to factoid questions.

Question: Are answers in this dataset guaranteed to be substrings of the text? If not, what is the coverage of answers being substrings?
Answer: No, the answers can also be summaries or yes/no.