Question-Driven Summarization of Answers to Consumer Health Questions

Automatic summarization of natural language is a widely studied area in computer science, one that is broadly applicable to anyone who routinely needs to understand large quantities of information. For example, in the medical domain, recent developments in deep learning approaches to automatic summarization have the potential to make health information more easily accessible to patients and consumers. However, to evaluate the quality of automatically generated summaries of health information, gold-standard, human generated summaries are required. Using answers provided by the National Library of Medicine's consumer health question answering system, we present the MEDIQA Answer Summarization dataset, the first summarization collection containing question-driven summaries of answers to consumer health questions. This dataset can be used to evaluate single or multi-document summaries generated by algorithms using extractive or abstractive approaches. In order to benchmark the dataset, we include results of baseline and state-of-the-art deep learning summarization models, demonstrating that this dataset can be used to effectively evaluate question-driven machine-generated summaries and promote further machine learning research in medical question answering.

Bridging the Knowledge Gap: Enhancing Question Answering with World and Domain Knowledge

In this paper we present OSCAR (Ontology-based Semantic Composition Augmented Regularization), a method for injecting task-agnostic knowledge from an Ontology or knowledge graph into a neural network during pretraining. We evaluated the impact of including OSCAR when pretraining BERT with Wikipedia articles by measuring the performance when fine-tuning on two question answering tasks involving world knowledge and causal reasoning and one requiring domain (healthcare) knowledge and obtained 33:3%, 18:6%, and 4% improved accuracy compared to pretraining BERT without OSCAR and obtaining new state-of-the-art results on two of the tasks.

Understanding Spatial Language in Radiology: Representation Framework, Annotation, and Spatial Relation Extraction from Chest X-ray Reports using Deep Learning

We define a representation framework for extracting spatial information from radiology reports (Rad-SpRL). We annotated a total of 2000 chest X-ray reports with 4 spatial roles corresponding to the common radiology entities. Our focus is on extracting detailed information of a radiologist's interpretation containing a radiographic finding, its anatomical location, corresponding probable diagnoses, as well as associated hedging terms. For this, we propose a deep learning-based natural language processing (NLP) method involving both word and character-level encodings. Specifically, we utilize a bidirectional long short-term memory (Bi-LSTM) conditional random field (CRF) model for extracting the spatial roles. The model achieved average F1 measures of 90.28 and 94.61 for extracting the Trajector and Landmark roles respectively whereas the performance was moderate for Diagnosis and Hedge roles with average F1 of 71.47 and 73.27 respectively. The corpus will soon be made available upon request.

A Question-Entailment Approach to Question Answering

One of the challenges in large-scale information retrieval (IR) is to develop fine-grained and domain-specific methods to answer natural language questions. Despite the availability of numerous sources and datasets for answer retrieval, Question Answering (QA) remains a challenging problem due to the difficulty of the question understanding and answer extraction tasks. One of the promising tracks investigated in QA is to map new questions to formerly answered questions that are `similar'. In this paper, we propose a novel QA approach based on Recognizing Question Entailment (RQE) and we describe the QA system and resources that we built and evaluated on real medical questions. First, we compare machine learning and deep learning methods for RQE using different kinds of datasets, including textual inference, question similarity and entailment in both the open and clinical domains. Second, we combine IR models with the best RQE method to select entailed questions and rank the retrieved answers. To study the end-to-end QA approach, we built the MedQuAD collection of 47,457 question-answer pairs from trusted medical sources, that we introduce and share in the scope of this paper. Following the evaluation process used in TREC 2017 LiveQA, we find that our approach exceeds the best results of the medical task with a 29.8% increase over the best official score. The evaluation results also support the relevance of question entailment for QA and highlight the effectiveness of combining IR and RQE for future QA efforts. Our findings also show that relying on a restricted set of reliable answer sources can bring a substantial improvement in medical QA.

Learning to Read Chest X-Rays: Recurrent Neural Cascade Model for Automated Image Annotation

Despite the recent advances in automatically describing image contents, their applications have been mostly limited to image caption datasets containing natural images (e.g., Flickr 30k, MSCOCO). In this paper, we present a deep learning model to efficiently detect a disease from an image and annotate its contexts (e.g., location, severity and the affected organs). We employ a publicly available radiology dataset of chest x-rays and their reports, and use its image annotations to mine disease names to train convolutional neural networks (CNNs). In doing so, we adopt various regularization techniques to circumvent the large normal-vs-diseased cases bias. Recurrent neural networks (RNNs) are then trained to describe the contexts of a detected disease, based on the deep CNN features. Moreover, we introduce a novel approach to use the weights of the already trained pair of CNN/RNN on the domain-specific image/text dataset, to infer the joint image/text contexts for composite image labeling. Significantly improved image annotation results are demonstrated using the recurrent neural cascade model by taking the joint image/text contexts into account.