TransGCN: a semi-supervised graph convolution network-based framework to infer protein translocations in spatio-temporal proteomics.

Protein subcellular localization (PSL) is very important in order to understand its functions, and its movement between subcellular niches within cells plays fundamental roles in biological process regulation. Mass spectrometry-based spatio-temporal proteomics technologies can help provide new insights of protein translocation, but bring the challenge in identifying reliable protein translocation events due to the noise interference and insufficient data mining. We propose a semi-supervised graph convolution network (GCN)-based framework termed TransGCN that infers protein translocation events from spatio-temporal proteomics. Based on expanded multiple distance features and joint graph representations of proteins, TransGCN utilizes the semi-supervised GCN to enable effective knowledge transfer from proteins with known PSLs for predicting protein localization and translocation. Our results demonstrate that TransGCN outperforms current state-of-the-art methods in identifying protein translocations, especially in coping with batch effects. It also exhibited excellent predictive accuracy in PSL prediction. TransGCN is freely available on GitHub at https://github.com/XuejiangGuo/TransGCN.

Predicting miRNA-disease associations based on lncRNA-miRNA interactions and graph convolution networks.

Increasing studies have proved that microRNAs (miRNAs) are critical biomarkers in the development of human complex diseases. Identifying disease-related miRNAs is beneficial to disease prevention, diagnosis and remedy. Based on the assumption that similar miRNAs tend to associate with similar diseases, various computational methods have been developed to predict novel miRNA-disease associations (MDAs). However, selecting proper features for similarity calculation is a challenging task because of data deficiencies in biomedical science. In this study, we propose a deep learning-based computational method named MAGCN to predict potential MDAs without using any similarity measurements. Our method predicts novel MDAs based on known lncRNA-miRNA interactions via graph convolution networks with multichannel attention mechanism and convolutional neural network combiner. Extensive experiments show that the average area under the receiver operating characteristic values obtained by our method under 2-fold, 5-fold and 10-fold cross-validations are 0.8994, 0.9032 and 0.9044, respectively. When compared with five state-of-the-art methods, MAGCN shows improvement in terms of prediction accuracy. In addition, we conduct case studies on three diseases to discover their related miRNAs, and find that all the top 50 predictions for all the three diseases have been supported by established databases. The comprehensive results demonstrate that our method is a reliable tool in detecting new disease-related miRNAs.

AdaPPI: identification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network.

Identifying unknown protein functional modules, such as protein complexes and biological pathways, from protein-protein interaction (PPI) networks, provides biologists with an opportunity to efficiently understand cellular function and organization. Finding complex nonlinear relationships in underlying functional modules may involve a long-chain of PPI and pose great challenges in a PPI network with an unevenly sparse and dense node distribution. To overcome these challenges, we propose AdaPPI, an adaptive convolution graph network in PPI networks to predict protein functional modules. We first suggest an attributed graph node presentation algorithm. It can effectively integrate protein gene ontology attributes and network topology, and adaptively aggregates low- or high-order graph structural information according to the node distribution by considering graph node smoothness. Based on the obtained node representations, core cliques and expansion algorithms are applied to find functional modules in PPI networks. Comprehensive performance evaluations and case studies indicate that the framework significantly outperforms state-of-the-art methods. We also presented potential functional modules based on their confidence.

Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks.

MOTIVATION: Recent advances in spatially resolved transcriptomics (ST) technologies enable the measurement of gene expression profiles while preserving cellular spatial context. Linking gene expression of cells with their spatial distribution is essential for better understanding of tissue microenvironment and biological progress. However, effectively combining gene expression data with spatial information to identify spatial domains remains challenging. RESULTS: To deal with the above issue, in this paper, we propose a novel unsupervised learning framework named STMGCN for identifying spatial domains using multi-view graph convolution networks (MGCNs). Specifically, to fully exploit spatial information, we first construct multiple neighbor graphs (views) with different similarity measures based on the spatial coordinates. Then, STMGCN learns multiple view-specific embeddings by combining gene expressions with each neighbor graph through graph convolution networks. Finally, to capture the importance of different graphs, we further introduce an attention mechanism to adaptively fuse view-specific embeddings and thus derive the final spot embedding. STMGCN allows for the effective utilization of spatial context to enhance the expressive power of the latent embeddings with multiple graph convolutions. We apply STMGCN on two simulation datasets and five real spatial transcriptomics datasets with different resolutions across distinct platforms. The experimental results demonstrate that STMGCN obtains competitive results in spatial domain identification compared with five state-of-the-art methods, including spatial and non-spatial alternatives. Besides, STMGCN can detect spatially variable genes with enriched expression patterns in the identified domains. Overall, STMGCN is a powerful and efficient computational framework for identifying spatial domains in spatial transcriptomics data.

Multipattern graph convolutional network-based autism spectrum disorder identification.

The early diagnosis of autism spectrum disorder (ASD) has been extensively facilitated through the utilization of resting-state fMRI (rs-fMRI). With rs-fMRI, the functional brain network (FBN) has gained much attention in diagnosing ASD. As a promising strategy, graph convolutional networks (GCN) provide an attractive approach to simultaneously extract FBN features and facilitate ASD identification, thus replacing the manual feature extraction from FBN. Previous GCN studies primarily emphasized the exploration of topological simultaneously connection weights of the estimated FBNs while only focusing on the single connection pattern. However, this approach fails to exploit the potential complementary information offered by different connection patterns of FBNs, thereby inherently limiting the performance. To enhance the diagnostic performance, we propose a multipattern graph convolution network (MPGCN) that integrates multiple connection patterns to improve the accuracy of ASD diagnosis. As an initial endeavor, we endeavored to integrate information from multiple connection patterns by incorporating multiple graph convolution modules. The effectiveness of the MPGCN approach is evaluated by analyzing rs-fMRI scans from a cohort of 92 subjects sourced from the publicly accessible Autism Brain Imaging Data Exchange database. Notably, the experiment demonstrates that our model achieves an accuracy of 91.1% and an area under ROC curve score of 0.9742. The implementation codes are available at https://github.com/immutableJackz/MPGCN.

BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution.

MOTIVATION: Understanding chemical-gene interactions (CGIs) is crucial for screening drugs. Wet experiments are usually costly and laborious, which limits relevant studies to a small scale. On the contrary, computational studies enable efficient in-silico exploration. For the CGI prediction problem, a common method is to perform systematic analyses on a heterogeneous network involving various biomedical entities. Recently, graph neural networks become popular in the field of relation prediction. However, the inherent heterogeneous complexity of biological interaction networks and the massive amount of data pose enormous challenges. This paper aims to develop a data-driven model that is capable of learning latent information from the interaction network and making correct predictions. RESULTS: We developed BioNet, a deep biological networkmodel with a graph encoder-decoder architecture. The graph encoder utilizes graph convolution to learn latent information embedded in complex interactions among chemicals, genes, diseases and biological pathways. The learning process is featured by two consecutive steps. Then, embedded information learnt by the encoder is then employed to make multi-type interaction predictions between chemicals and genes with a tensor decomposition decoder based on the RESCAL algorithm. BioNet includes 79 325 entities as nodes, and 34 005 501 relations as edges. To train such a massive deep graph model, BioNet introduces a parallel training algorithm utilizing multiple Graphics Processing Unit (GPUs). The evaluation experiments indicated that BioNet exhibits outstanding prediction performance with a best area under Receiver Operating Characteristic (ROC) curve of 0.952, which significantly surpasses state-of-theart methods. For further validation, top predicted CGIs of cancer and COVID-19 by BioNet were verified by external curated data and published literature.

MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.

Circular RNA (circRNA) is closely involved in physiological and pathological processes of many diseases. Discovering the associations between circRNAs and diseases is of great significance. Due to the high-cost to verify the circRNA-disease associations by wet-lab experiments, computational approaches for predicting the associations become a promising research direction. In this paper, we propose a method, MDGF-MCEC, based on multi-view dual attention graph convolution network (GCN) with cooperative ensemble learning to predict circRNA-disease associations. First, MDGF-MCEC constructs two disease relation graphs and two circRNA relation graphs based on different similarities. Then, the relation graphs are fed into a multi-view GCN for representation learning. In order to learn high discriminative features, a dual-attention mechanism is introduced to adjust the contribution weights, at both channel level and spatial level, of different features. Based on the learned embedding features of diseases and circRNAs, nine different feature combinations between diseases and circRNAs are treated as new multi-view data. Finally, we construct a multi-view cooperative ensemble classifier to predict the associations between circRNAs and diseases. Experiments conducted on the CircR2Disease database demonstrate that the proposed MDGF-MCEC model achieves a high area under curve of 0.9744 and outperforms the state-of-the-art methods. Promising results are also obtained from experiments on the circ2Disease and circRNADisease databases. Furthermore, the predicted associated circRNAs for hepatocellular carcinoma and gastric cancer are supported by the literature. The code and dataset of this study are available at https://github.com/ABard0/MDGF-MCEC.

iGRLCDA: identifying circRNA-disease association based on graph representation learning.

While the technologies of ribonucleic acid-sequence (RNA-seq) and transcript assembly analysis have continued to improve, a novel topology of RNA transcript was uncovered in the last decade and is called circular RNA (circRNA). Recently, researchers have revealed that they compete with messenger RNA (mRNA) and long noncoding for combining with microRNA in gene regulation. Therefore, circRNA was assumed to be associated with complex disease and discovering the relationship between them would contribute to medical research. However, the work of identifying the association between circRNA and disease in vitro takes a long time and usually without direction. During these years, more and more associations were verified by experiments. Hence, we proposed a computational method named identifying circRNA-disease association based on graph representation learning (iGRLCDA) for the prediction of the potential association of circRNA and disease, which utilized a deep learning model of graph convolution network (GCN) and graph factorization (GF). In detail, iGRLCDA first derived the hidden feature of known associations between circRNA and disease using the Gaussian interaction profile (GIP) kernel combined with disease semantic information to form a numeric descriptor. After that, it further used the deep learning model of GCN and GF to extract hidden features from the descriptor. Finally, the random forest classifier is introduced to identify the potential circRNA-disease association. The five-fold cross-validation of iGRLCDA shows strong competitiveness in comparison with other excellent prediction models at the gold standard data and achieved an average area under the receiver operating characteristic curve of 0.9289 and an area under the precision-recall curve of 0.9377. On reviewing the prediction results from the relevant literature, 22 of the top 30 predicted circRNA-disease associations were noted in recent published papers. These exceptional results make us believe that iGRLCDA can provide reliable circRNA-disease associations for medical research and reduce the blindness of wet-lab experiments.

Arrhythmia detection by the graph convolution network and a proposed structure for communication between cardiac leads.

One of the most common causes of death worldwide is heart disease, including arrhythmia. Today, sciences such as artificial intelligence and medical statistics are looking for methods and models for correct and automatic diagnosis of cardiac arrhythmia. In pursuit of increasing the accuracy of automated methods, many studies have been conducted. However, in none of the previous articles, the relationship and structure between the heart leads have not been included in the model. It seems that the structure of ECG data can help develop the accuracy of arrhythmia detection. Therefore, in this study, a new structure of Electrocardiogram (ECG) data was introduced, and the Graph Convolution Network (GCN), which has the possibility of learning the structure, was used to develop the accuracy of cardiac arrhythmia diagnosis. Considering the relationship between the heart leads and clusters based on different ECG poles, a new structure was introduced. In this structure, the Mutual Information(MI) index was used to evaluate the relationship between the leads, and weight was given based on the poles of the leads. Weighted Mutual Information (WMI) matrices (new structure) were formed by R software. Finally, the 15-layer GCN network was adjusted by this structure and the arrhythmia of people was detected and classified by it. To evaluate the performance of the proposed new network, sensitivity, precision, specificity, accuracy, and confusion matrix indices were used. Also, the accuracy of GCN networks was compared by three different structures, including WMI, MI, and Identity. Chapman's 12-lead ECG Dataset was used in this study. The results showed that the values of sensitivity, precision, specificity, and accuracy of the GCN-WMI network with 15 intermediate layers were equal to 98.74%, 99.08%, 99.97% & 99.82%, respectively. This new proposed network was more accurate than the Graph Convolution Network-Mutual Information (GCN-MI) with an accuracy equal to 99.71% and GCN-Id with an accuracy equal to 92.68%. Therefore, utilizing this network, the types of arrhythmia were recognized and classified. Also, the new network proposed by the Graph Convolution Network-Weighted Mutual Information (GCN-WMI) was more accurate than those conducted in other studies on the same data set (Chapman). Based on the obtained results, the structure proposed in this study increased the accuracy of cardiac arrhythmia diagnosis and classification on the Chapman data set. Achieving such accuracy for arrhythmia diagnosis is a great achievement in clinical sciences.

A Rotating Machinery Fault Diagnosis Method Based on Dynamic Graph Convolution Network and Hard Threshold Denoising.

With the development of precision sensing instruments and data storage devices, the fusion of multi-sensor data in gearbox fault diagnosis has attracted much attention. However, existing methods have difficulty in capturing the local temporal dependencies of multi-sensor monitoring information, and the inescapable noise severely decreases the accuracy of multi-sensor information fusion diagnosis. To address these issues, this paper proposes a fault diagnosis method based on dynamic graph convolutional neural networks and hard threshold denoising. Firstly, considering that the relationships between monitoring data from different sensors change over time, a dynamic graph structure is adopted to model the temporal dependencies of multi-sensor data, and, further, a graph convolutional neural network is constructed to achieve the interaction and feature extraction of temporal information from multi-sensor data. Secondly, to avoid the influence of noise in practical engineering, a hard threshold denoising strategy is designed, and a learnable hard threshold denoising layer is embedded into the graph neural network. Experimental fault datasets from two typical gearbox fault test benches under environmental noise are used to verify the effectiveness of the proposed method in gearbox fault diagnosis. The experimental results show that the proposed DDGCN method achieves an average diagnostic accuracy of up to 99.7% under different levels of environmental noise, demonstrating good noise resistance.

Deformation Estimation of Textureless Objects from a Single Image.

Deformations introduced during the production of plastic components degrade the accuracy of their 3D geometric information, a critical aspect of object inspection processes. This phenomenon is prevalent among primary plastic products from manufacturers. This work proposes a solution for the deformation estimation of textureless plastic objects using only a single RGB image. This solution encompasses a unique image dataset of five deformed parts, a novel method for generating mesh labels, sequential deformation, and a training model based on graph convolution. The proposed sequential deformation method outperforms the prevalent chamfer distance algorithm in generating precise mesh labels. The training model projects object vertices into features extracted from the input image, and then, predicts vertex location offsets based on the projected features. The predicted meshes using these offsets achieve a sub-millimeter accuracy on synthetic images and approximately 2.0 mm on real images.

A 3D Point Cloud Classification Method Based on Adaptive Graph Convolution and Global Attention.

In recent years, there has been significant growth in the ubiquity and popularity of three-dimensional (3D) point clouds, with an increasing focus on the classification of 3D point clouds. To extract richer features from point clouds, many researchers have turned their attention to various point set regions and channels within irregular point clouds. However, this approach has limited capability in attending to crucial regions of interest in 3D point clouds and may overlook valuable information from neighboring features during feature aggregation. Therefore, this paper proposes a novel 3D point cloud classification method based on global attention and adaptive graph convolution (Att-AdaptNet). The method consists of two main branches: the first branch computes attention masks for each point, while the second branch employs adaptive graph convolution to extract global features from the point set. It dynamically learns features based on point interactions, generating adaptive kernels to effectively and precisely capture diverse relationships among points from different semantic parts. Experimental results demonstrate that the proposed model achieves 93.8% in overall accuracy and 90.8% in average accuracy on the ModeNet40 dataset.

GCN-Based LSTM Autoencoder with Self-Attention for Bearing Fault Diagnosis.

The manufacturing industry has been operating within a constantly evolving technological environment, underscoring the importance of maintaining the efficiency and reliability of manufacturing processes. Motor-related failures, especially bearing defects, are common and serious issues in manufacturing processes. Bearings provide accurate and smooth movements and play essential roles in mechanical equipment with shafts. Given their importance, bearing failure diagnosis has been extensively studied. However, the imbalance in failure data and the complexity of time series data make diagnosis challenging. Conventional AI models (convolutional neural networks (CNNs), long short-term memory (LSTM), support vector machine (SVM), and extreme gradient boosting (XGBoost)) face limitations in diagnosing such failures. To address this problem, this paper proposes a bearing failure diagnosis model using a graph convolution network (GCN)-based LSTM autoencoder with self-attention. The model was trained on data extracted from the Case Western Reserve University (CWRU) dataset and a fault simulator testbed. The proposed model achieved 97.3% accuracy on the CWRU dataset and 99.9% accuracy on the fault simulator dataset.

A Dual-Branch Fusion of a Graph Convolutional Network and a Convolutional Neural Network for Hyperspectral Image Classification.

Semi-supervised graph convolutional networks (SSGCNs) have been proven to be effective in hyperspectral image classification (HSIC). However, limited training data and spectral uncertainty restrict the classification performance, and the computational demands of a graph convolution network (GCN) present challenges for real-time applications. To overcome these issues, a dual-branch fusion of a GCN and convolutional neural network (DFGCN) is proposed for HSIC tasks. The GCN branch uses an adaptive multi-scale superpixel segmentation method to build fusion adjacency matrices at various scales, which improves the graph convolution efficiency and node representations. Additionally, a spectral feature enhancement module (SFEM) enhances the transmission of crucial channel information between the two graph convolutions. Meanwhile, the CNN branch uses a convolutional network with an attention mechanism to focus on detailed features of local areas. By combining the multi-scale superpixel features from the GCN branch and the local pixel features from the CNN branch, this method leverages complementary features to fully learn rich spatial-spectral information. Our experimental results demonstrate that the proposed method outperforms existing advanced approaches in terms of classification efficiency and accuracy across three benchmark data sets.

Graph Adaptive Attention Network with Cross-Entropy.

Non-Euclidean data, such as social networks and citation relationships between documents, have node and structural information. The Graph Convolutional Network (GCN) can automatically learn node features and association information between nodes. The core ideology of the Graph Convolutional Network is to aggregate node information by using edge information, thereby generating a new node feature. In updating node features, there are two core influencing factors. One is the number of neighboring nodes of the central node; the other is the contribution of the neighboring nodes to the central node. Due to the previous GCN methods not simultaneously considering the numbers and different contributions of neighboring nodes to the central node, we design the adaptive attention mechanism (AAM). To further enhance the representational capability of the model, we utilize Multi-Head Graph Convolution (MHGC). Finally, we adopt the cross-entropy (CE) loss function to describe the difference between the predicted results of node categories and the ground truth (GT). Combined with backpropagation, this ultimately achieves accurate node classification. Based on the AAM, MHGC, and CE, we contrive the novel Graph Adaptive Attention Network (GAAN). The experiments show that classification accuracy achieves outstanding performances on Cora, Citeseer, and Pubmed datasets.

A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder.

BACKGROUND: Autism spectrum disorder (ASD) is a serious developmental disorder of the brain. Recently, various deep learning methods based on functional magnetic resonance imaging (fMRI) data have been developed for the classification of ASD. Among them, graph neural networks, which generalize deep neural network models to graph structured data, have shown great advantages. However, in graph neural methods, because the graphs constructed are homogeneous, the phenotype information of the subjects cannot be fully utilized. This affects the improvement of the classification performance. METHODS: To fully utilize the phenotype information, this paper proposes a heterogeneous graph convolutional attention network (HCAN) model to classify ASD. By combining an attention mechanism and a heterogeneous graph convolutional network, important aggregated features can be extracted in the HCAN. The model consists of a multilayer HCAN feature extractor and a multilayer perceptron (MLP) classifier. First, a heterogeneous population graph was constructed based on the fMRI and phenotypic data. Then, a multilayer HCAN is used to mine graph-based features from the heterogeneous graph. Finally, the extracted features are fed into an MLP for the final classification. RESULTS: The proposed method is assessed on the autism brain imaging data exchange (ABIDE) repository. In total, 871 subjects in the ABIDE I dataset are used for the classification task. The best classification accuracy of 82.9% is achieved. Compared to the other methods using exactly the same subjects in the literature, the proposed method achieves superior performance to the best reported result. CONCLUSIONS: The proposed method can effectively integrate heterogeneous graph convolutional networks with a semantic attention mechanism so that the phenotype features of the subjects can be fully utilized. Moreover, it shows great potential in the diagnosis of brain functional disorders with fMRI data.

Predicting potential microbe-disease associations based on auto-encoder and graph convolution network.

The increasing body of research has consistently demonstrated the intricate correlation between the human microbiome and human well-being. Microbes can impact the efficacy and toxicity of drugs through various pathways, as well as influence the occurrence and metastasis of tumors. In clinical practice, it is crucial to elucidate the association between microbes and diseases. Although traditional biological experiments accurately identify this association, they are time-consuming, expensive, and susceptible to experimental conditions. Consequently, conducting extensive biological experiments to screen potential microbe-disease associations becomes challenging. The computational methods can solve the above problems well, but the previous computational methods still have the problems of low utilization of node features and the prediction accuracy needs to be improved. To address this issue, we propose the DAEGCNDF model predicting potential associations between microbes and diseases. Our model calculates four similar features for each microbe and disease. These features are fused to obtain a comprehensive feature matrix representing microbes and diseases. Our model first uses the graph convolutional network module to extract low-rank features with graph information of microbes and diseases, and then uses a deep sparse Auto-Encoder to extract high-rank features of microbe-disease pairs, after which the low-rank and high-rank features are spliced to improve the utilization of node features. Finally, Deep Forest was used for microbe-disease potential relationship prediction. The experimental results show that combining low-rank and high-rank features helps to improve the model performance and Deep Forest has better classification performance than the baseline model.

Identification of epileptic networks with graph convolutional network incorporating oscillatory activities and evoked synaptic responses.

Stereoelectroencephalography (SEEG) offers unique neural data from in-depth brain structures with fine temporal resolutions to better investigate the origin of epileptic brain activities. Although oscillatory patterns from different frequency bands and functional connectivity computed from the SEEG datasets are employed to study the epileptic zones, direct electrical stimulation-evoked electrophysiological recordings of synaptic responses, namely cortical-cortical evoked potentials (CCEPs), from the same SEEG electrodes are not explored for the localization of epileptic zones. Here we proposed a two-stream model with unsupervised learning and graph convolutional network tailored to the SEEG and CCEP datasets in individual patients to perform localization of epileptic zones. We compared our localization results with the clinically marked electrode sites determined for surgical resections. Our model had good classification capability when compared to other state-of-the-art methods. Furthermore, based on our prediction results we performed group-level brain-area mapping analysis for temporal, frontal and parietal epilepsy patients and found that epileptic and non-epileptic brain networks were distinct in patients with different types of focal epilepsy. Our unsupervised data-driven model provides personalized localization analysis for the epileptic zones. The epileptic and non-epileptic brain areas disclosed by the prediction model provide novel insights into the network-level pathological characteristics of epilepsy.

Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method.

Accurate predictions of druggability and bioactivities of compounds are desirable to reduce the high cost and time of drug discovery. After more than five decades of continuing developments, quantitative structure-activity relationship (QSAR) methods have been established as indispensable tools that facilitate fast, reliable and affordable assessments of physicochemical and biological properties of compounds in drug-discovery programs. Currently, there are mainly two types of QSAR methods, descriptor-based methods and graph-based methods. The former is developed based on predefined molecular descriptors, whereas the latter is developed based on simple atomic and bond information. In this study, we presented a simple but highly efficient modeling method by combining molecular graphs and molecular descriptors as the input of a modified graph neural network, called hyperbolic relational graph convolution network plus (HRGCN+). The evaluation results show that HRGCN+ achieves state-of-the-art performance on 11 drug-discovery-related datasets. We also explored the impact of the addition of traditional molecular descriptors on the predictions of graph-based methods, and found that the addition of molecular descriptors can indeed boost the predictive power of graph-based methods. The results also highlight the strong anti-noise capability of our method. In addition, our method provides a way to interpret models at both the atom and descriptor levels, which can help medicinal chemists extract hidden information from complex datasets. We also offer an HRGCN+'s online prediction service at https://quantum.tencent.com/hrgcn/.

Predicting CircRNA disease associations using novel node classification and link prediction models on Graph Convolutional Networks.

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.