Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification

Network biology has been successfully used to help reveal complex mechanisms of disease, especially cancer. On the other hand, network biology requires in-depth knowledge to construct disease-specific networks, but our current knowledge is very limited even with the recent advances in human cancer biology. Deep learning has shown a great potential to address the difficult situation like this. However, deep learning technologies conventionally use grid-like structured data, thus application of deep learning technologies to the classification of human disease subtypes is yet to be explored. Recently, graph based deep learning techniques have emerged, which becomes an opportunity to leverage analyses in network biology. In this paper, we proposed a hybrid model, which integrates two key components 1) graph convolution neural network (graph CNN) and 2) relation network (RN). We utilize graph CNN as a component to learn expression patterns of cooperative gene community, and RN as a component to learn associations between learned patterns. The proposed model is applied to the PAM50 breast cancer subtype classification task, the standard breast cancer subtype classification of clinical utility. In experiments of both subtype classification and patient survival analysis, our proposed method achieved significantly better performances than existing methods. We believe that this work is an important starting point to realize the upcoming personalized medicine.Comment: 8 pages, To be published in proceeding of IJCAI 201

The Control Fallacy: Why OA Out-Innovates the Alternative

This article examines the relationship between Open Access to the scholarly literature and innovation. It traces the ideas of "end to end" network principles in the Internet and the World Wide Web and applies them to the scholarly biomedical literature. And the article argues for the importance of relieving not just price barriers but permission barriers

A Survey of Natural Language Generation

This paper offers a comprehensive review of the research on Natural Language Generation (NLG) over the past two decades, especially in relation to data-to-text generation and text-to-text generation deep learning methods, as well as new applications of NLG technology. This survey aims to (a) give the latest synthesis of deep learning research on the NLG core tasks, as well as the architectures adopted in the field; (b) detail meticulously and comprehensively various NLG tasks and datasets, and draw attention to the challenges in NLG evaluation, focusing on different evaluation methods and their relationships; (c) highlight some future emphasis and relatively recent research issues that arise due to the increasing synergy between NLG and other artificial intelligence areas, such as computer vision, text and computational creativity.Comment: Accepted by ACM Computing Survey (CSUR) 202