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Accumulated studies have discovered that circular RNAs (CircRNAs) are closely related to many complex human diseases. Due to this close relationship, CircRNAs can be used as good biomarkers for disease diagnosis and therapeutic targets for treatments. However, the number of experimentally verified circRNA-disease associations are still fewer and also conducting wet-lab experiments are constrained by the small scale and cost of time and labour. Therefore, effective computational methods are required to predict associations between circRNAs and diseases which will be promising candidates for small scale biological and clinical experiments. In this paper, we propose novel computational models based on Graph Convolution Networks (GCN) for the potential circRNA-disease association prediction. Currently most of the existing prediction methods use shallow learning algorithms. Instead, the proposed models combine the strengths of deep learning and graphs for the computation. First, they integrate multi-source similarity information into the association network. Next, models predict potential associations using graph convolution which explore this important relational knowledge of that network structure. Two circRNA-disease association prediction models, GCN based Node Classification (GCN-NC) and GCN based Link Prediction (GCN-LP) are introduced in this work and they demonstrate promising results in various experiments and outperforms other existing methods. Further, a case study proves that some of the predicted results of the novel computational models were confirmed by published literature and all top results could be verified using gene-gene interaction networks.

The field of neuroimaging can greatly benefit from building machine learning models to detect and predict diseases, and discover novel biomarkers, but much of the data collected at various organizations and research centers is unable to be shared due to privacy or regulatory concerns (especially for clinical data or rare disorders). In addition, aggregating data across multiple large studies results in a huge amount of duplicated technical debt and the resources required can be challenging or impossible for an individual site to build. Training on the data distributed across organizations can result in models that generalize much better than models trained on data from any of organizations alone. While there are approaches for decentralized sharing, these often do not provide the highest possible guarantees of sample privacy that only cryptography can provide. In addition, such approaches are often focused on probabilistic solutions. In this paper, we propose an approach that leverages the potential of datasets spread among a number of data collecting organizations by performing joint analyses in a secure and deterministic manner when only encrypted data is shared and manipulated. The approach is based on secure multiparty computation which refers to cryptographic protocols that enable distributed computation of a function over distributed inputs without revealing additional information about the inputs. It enables multiple organizations to train machine learning models on their joint data and apply the trained models to encrypted data without revealing their sensitive data to the other parties. In our proposed approach, organizations (or sites) securely collaborate to build a machine learning model as it would have been trained on the aggregated data of all the organizations combined. Importantly, the approach does not require a trusted party (i.e. aggregator), each contributing site plays an equal role in the process, and no site can learn individual data of any other site. We demonstrate effectiveness of the proposed approach, in a range of empirical evaluations using different machine learning algorithms including logistic regression and convolutional neural network models on human structural and functional magnetic resonance imaging datasets.

Graphs can be used to effectively represent complex data structures. Learning these irregular data in graphs is challenging and still suffers from shallow learning. Applying deep learning on graphs has demonstrated good performance in many applications including social analysis, bioinformatics etc. Message passing graph convolution network is a powerful method which has expressive power to learn graph structures. Meanwhile, circular ribonucleic acid (circRNA) is a type of non-coding RNA which plays a critical role in human diseases. Identifying the associations between circRNAs and diseases is important for diagnosis and treatment of complex diseases. However, there are limited number of known associations between them and conducting biological experiments to identify new associations is time consuming and expensive. As a result, there is a need of building efficient and feasible computation methods to predict potential circRNA-disease associations. In this paper, we propose a novel graph convolution network framework to learn features from a graph built with multi-source similarity information to predict circRNA-disease associations. First we use multi-source information of circRNA similarity, disease and circRNA Gaussian Interaction Profile (GIP) kernel similarity to extract the features using first graph convolution. Then we predict disease associations for each circRNA with a second graph convolution. Proposed framework with five-fold cross validation on various experiments shows promising results in predicting circRNA-disease association and outperforms other existing methods.