scholarly journals Dual Convolutional Neural Network Based Method for Predicting Disease-Related miRNAs

2018 ◽  
Vol 19 (12) ◽  
pp. 3732 ◽  
Author(s):  
Ping Xuan ◽  
Yihua Dong ◽  
Yahong Guo ◽  
Tiangang Zhang ◽  
Yong Liu
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Feature Representation ◽  
The Novel ◽  
Disease Networks ◽  
Novel Mirna ◽  
Deep Feature ◽  
Disease Associations ◽  
The Right ◽  
New Framework

Identification of disease-related microRNAs (disease miRNAs) is helpful for understanding and exploring the etiology and pathogenesis of diseases. Most of recent methods predict disease miRNAs by integrating the similarities and associations of miRNAs and diseases. However, these methods fail to learn the deep features of the miRNA similarities, the disease similarities, and the miRNA–disease associations. We propose a dual convolutional neural network-based method for predicting candidate disease miRNAs and refer to it as CNNDMP. CNNDMP not only exploits the similarities and associations of miRNAs and diseases, but also captures the topology structures of the miRNA and disease networks. An embedding layer is constructed by combining the biological premises about the miRNA–disease associations. A new framework based on the dual convolutional neural network is presented for extracting the deep feature representation of associations. The left part of the framework focuses on integrating the original similarities and associations of miRNAs and diseases. The novel miRNA and disease similarities which contain the topology structures are obtained by random walks on the miRNA and disease networks, and their deep features are learned by the right part of the framework. CNNDMP achieves the superior prediction performance than several state-of-the-art methods during the cross-validation process. Case studies on breast cancer, colorectal cancer and lung cancer further demonstrate CNNDMP’s powerful ability of discovering potential disease miRNAs.

scholarly journals Graph Convolutional Network and Convolutional Neural Network Based Method for Predicting lncRNA-Disease Associations

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 1012 ◽  
Author(s):  
Xuan ◽  
Pan ◽  
Zhang ◽  
Liu ◽  
Sun
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Heterogeneous Network ◽  
Heterogeneous Data ◽  
Superior Performance ◽  
Convolutional Network ◽  
Topological Information ◽  
Disease Pair ◽  
Disease Associations ◽  
The Right

Aberrant expressions of long non-coding RNAs (lncRNAs) are often associated with diseases and identification of disease-related lncRNAs is helpful for elucidating complex pathogenesis. Recent methods for predicting associations between lncRNAs and diseases integrate their pertinent heterogeneous data. However, they failed to deeply integrate topological information of heterogeneous network comprising lncRNAs, diseases, and miRNAs. We proposed a novel method based on the graph convolutional network and convolutional neural network, referred to as GCNLDA, to infer disease-related lncRNA candidates. The heterogeneous network containing the lncRNA, disease, and miRNA nodes, is constructed firstly. The embedding matrix of a lncRNA-disease node pair was constructed according to various biological premises about lncRNAs, diseases, and miRNAs. A new framework based on a graph convolutional network and a convolutional neural network was developed to learn network and local representations of the lncRNA-disease pair. On the left side of the framework, the autoencoder based on graph convolution deeply integrated topological information within the heterogeneous lncRNA-disease-miRNA network. Moreover, as different node features have discriminative contributions to the association prediction, an attention mechanism at node feature level is constructed. The left side learnt the network representation of the lncRNA-disease pair. The convolutional neural networks on the right side of the framework learnt the local representation of the lncRNA-disease pair by focusing on the similarities, associations, and interactions that are only related to the pair. Compared to several state-of-the-art prediction methods, GCNLDA had superior performance. Case studies on stomach cancer, osteosarcoma, and lung cancer confirmed that GCNLDA effectively discovers the potential lncRNA-disease associations.

Deep Feature Representation with Stacked Sparse Auto-Encoder and Convolutional Neural Network for Hyperspectral Imaging-Based Detection of Cucumber Defects

2018 ◽  
Vol 61 (2) ◽  
pp. 425-436 ◽  
Author(s):  
Ziyi Liu ◽  
Yong He ◽  
Haiyan Cen ◽  
Renfu Lu
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Hyperspectral Imaging ◽  
Defect Detection ◽  
Hyperspectral Image ◽  
Imaging System ◽  
Feature Representation ◽  
Inspection System ◽  
Deep Feature ◽  
Pickling Cucumbers

Abstract. It is challenging to achieve rapid and accurate processing of large amounts of hyperspectral image data. This research was aimed to develop a novel classification method by employing deep feature representation with the stacked sparse auto-encoder (SSAE) and the SSAE combined with convolutional neural network (CNN-SSAE) learning for hyperspectral imaging-based defect detection of pickling cucumbers. Hyperspectral images of normal and defective pickling cucumbers were acquired using a hyperspectral imaging system running at two conveyor speeds of 85 and 165 mm s-1. An SSAE model was developed to learn the feature representation from the preprocessed data and to perform five-class (normal, watery, split/hollow, shrivel, and surface defect) classification. To deal with a more complicated task for different types of surface defects (i.e., dirt/sand and gouge/rot classes) in six-class classification, a CNN-SSAE system was developed. The results showed that the CNN-SSAE system improved the classification performance, compared with the SSAE, with overall accuracies of 91.1% and 88.3% for six-class classification at the two conveyor speeds. Additionally, the average running time of the CNN-SSAE system for each sample was less than 14 ms, showing considerable potential for application in an automated on-line inspection system for cucumber sorting and grading. Keywords: Convolutional neural network, Defect detection, Hyperspectral imaging, Pickling cucumber, Representation learning, Stacked sparse auto-encoder.

scholarly journals Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit

Molecules ◽  
2019 ◽  
Vol 24 (15) ◽  
pp. 2712 ◽  
Author(s):  
Ping Xuan ◽  
Lianfeng Zhao ◽  
Tiangang Zhang ◽  
Yilin Ye ◽  
Yan Zhang
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Prediction Models ◽  
Auxiliary Information ◽  
Path Information ◽  
Path Representation ◽  
Disease Pair ◽  
Disease Associations ◽  
The Right ◽  
Gated Recurrent Unit

Predicting novel uses for drugs using their chemical, pharmacological, and indication information contributes to minimizing costs and development periods. Most previous prediction methods focused on integrating the similarity and association information of drugs and diseases. However, they tended to construct shallow prediction models to predict drug-associated diseases, which make deeply integrating the information difficult. Further, path information between drugs and diseases is important auxiliary information for association prediction, while it is not deeply integrated. We present a deep learning-based method, CGARDP, for predicting drug-related candidate disease indications. CGARDP establishes a feature matrix by exploiting a variety of biological premises related to drugs and diseases. A novel model based on convolutional neural network (CNN) and gated recurrent unit (GRU) is constructed to learn the local and path representations for a drug-disease pair. The CNN-based framework on the left of the model learns the local representation of the drug-disease pair from their feature matrix. As the different paths have discriminative contributions to the drug-disease association prediction, we construct an attention mechanism at the path level to learn the informative paths. In the right part, a GRU-based framework learns the path representation based on path information between the drug and the disease. Cross-validation results indicate that CGARDP performs better than several state-of-the-art methods. Further, CGARDP retrieves more real drug-disease associations in the top part of the prediction result that are of concern to biologists. Case studies on five drugs demonstrate that CGARDP can discover potential drug-related disease indications.

scholarly journals LDAPred: A Method Based on Information Flow Propagation and a Convolutional Neural Network for the Prediction of Disease-Associated lncRNAs

2019 ◽  
Vol 20 (18) ◽  
pp. 4458 ◽  
Author(s):  
Ping Xuan ◽  
Lan Jia ◽  
Tiangang Zhang ◽  
Nan Sheng ◽  
Xiaokun Li ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Information Flow ◽  
Topological Structure ◽  
Molecular Mechanisms ◽  
Disease Diagnosis ◽  
Structure Information ◽  
Disease Associations ◽  
The Right ◽  
Flow Propagation

Long non-coding RNAs (lncRNAs) play a crucial role in the pathogenesis and development of complex diseases. Predicting potential lncRNA–disease associations can improve our understanding of the molecular mechanisms of human diseases and help identify biomarkers for disease diagnosis, treatment, and prevention. Previous research methods have mostly integrated the similarity and association information of lncRNAs and diseases, without considering the topological structure information among these nodes, which is important for predicting lncRNA–disease associations. We propose a method based on information flow propagation and convolutional neural networks, called LDAPred, to predict disease-related lncRNAs. LDAPred not only integrates the similarities, associations, and interactions among lncRNAs, diseases, and miRNAs, but also exploits the topological structures formed by them. In this study, we construct a dual convolutional neural network-based framework that comprises the left and right sides. The embedding layer on the left side is established by utilizing lncRNA, miRNA, and disease-related biological premises. On the right side of the frame, multiple types of similarity, association, and interaction relationships among lncRNAs, diseases, and miRNAs are calculated based on information flow propagation on the bi-layer networks, such as the lncRNA–disease network. They contain the network topological structure and they are learned by the right side of the framework. The experimental results based on five-fold cross-validation indicate that LDAPred performs better than several state-of-the-art methods. Case studies on breast cancer, colon cancer, and osteosarcoma further demonstrate LDAPred’s ability to discover potential lncRNA–disease associations.

scholarly journals Multisite Autism Spectrum Disorder Classification Using Convolutional Neural Network Classifier and Individual Morphological Brain Networks

2021 ◽  
Vol 14 ◽  
Author(s):  
Jingjing Gao ◽  
Mingren Chen ◽  
Yuanyuan Li ◽  
Yachun Gao ◽  
Yanling Li ◽  
...  
Keyword(s):  
Neural Network ◽  
Autism Spectrum Disorder ◽  
Convolutional Neural Network ◽  
Structural Mri ◽  
Autism Spectrum ◽  
Brain Network ◽  
Spectrum Disorder ◽  
Structural Covariance ◽  
Almost All ◽  
New Framework

Autism spectrum disorder (ASD) is a range of neurodevelopmental disorders with behavioral and cognitive impairment and brings huge burdens to the patients’ families and the society. To accurately identify patients with ASD from typical controls is important for early detection and early intervention. However, almost all the current existing classification methods for ASD based on structural MRI (sMRI) mainly utilize the independent local morphological features and do not consider the covariance patterns of these features between regions. In this study, by combining the convolutional neural network (CNN) and individual structural covariance network, we proposed a new framework to classify ASD patients with sMRI data from the ABIDE consortium. Moreover, gradient-weighted class activation mapping (Grad-CAM) was applied to characterize the weight of features contributing to the classification. The experimental results showed that our proposed method outperforms the currently used methods for classifying ASD patients with the ABIDE data and achieves a high classification accuracy of 71.8% across different sites. Furthermore, the discriminative features were found to be mainly located in the prefrontal cortex and cerebellum, which may be the early biomarkers for the diagnosis of ASD. Our study demonstrated that CNN is an effective tool to build the framework for the diagnosis of ASD with individual structural covariance brain network.

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