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BACKGROUND Research on disease-disease association, like comorbidity and complication, provides important insights into disease treatment and drug discovery, and a large body of literature has been published in the field. However, using current search tools, it is not easy for researchers to retrieve information on the latest disease association findings. For one thing, comorbidity and complication keywords pull up large numbers of PubMed studies. Secondly, disease is not highlighted in search results. Third, disease-disease association (DDA) is not identified, as currently no DDA extraction dataset or tools are available. OBJECTIVE Since there are no available disease-disease association extraction (DDAE) datasets or tools, we aim to develop (1) a DDAE dataset and (2) a neural network model for extracting DDAs from literature. METHODS In this study, we formulate DDAE as a supervised machine learning classification problem. To develop the system, we first build a DDAE dataset. We then employ two machine-learning models, support vector machine (SVM) and convolutional neural network (CNN), to extract DDAs. Furthermore, we evaluate the effect of using the output layer as features of the SVM-based model. Finally, we implement large margin context-aware convolutional neural network (LC-CNN) architecture to integrate context features and CNN through the large margin function. RESULTS Our DDAE dataset consists of 521 PubMed abstracts. Experiment results show that the SVM-based approach achieves an F1-measure of 80.32%, which is higher than the CNN-based approach (73.32%). Using the output layer of CNN as a feature for SVM does not further improve the performance of SVM. However, our LC-CNN achieves the highest F1-measure of 84.18%, and demonstrates combining the hinge loss function of SVM with CNN into a single NN architecture outperforms other approaches. CONCLUSIONS To facilitate the development of text-mining research for DDAE, we develop the first publicly available DDAE dataset consisting of disease mentions, MeSH IDs and relation annotations. We develop different conventional ML models and NN architectures, and evaluate their effects on our DDAE dataset. To further improve DDAE performance, we propose an LC-CNN model for DDAE that outperforms other approaches. |
