An efficient approach based on multi-sources information to predict circRNA–disease associations using deep convolutional neural network

2019 ◽  
Vol 36 (13) ◽  
pp. 4038-4046 ◽  
Author(s):  
Lei Wang ◽  
Zhu-Hong You ◽  
Yu-An Huang ◽  
De-Shuang Huang ◽  
Keith C C Chan
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Deep Convolutional Neural Network ◽  
Computational Method ◽  
Supplementary Information ◽  
Small Scale ◽  
Svm Classifier ◽  
Source Information ◽  
Proposed Model ◽  
Disease Associations

Abstract Motivation Emerging evidence indicates that circular RNA (circRNA) plays a crucial role in human disease. Using circRNA as biomarker gives rise to a new perspective regarding our diagnosing of diseases and understanding of disease pathogenesis. However, detection of circRNA–disease associations by biological experiments alone is often blind, limited to small scale, high cost and time consuming. Therefore, there is an urgent need for reliable computational methods to rapidly infer the potential circRNA–disease associations on a large scale and to provide the most promising candidates for biological experiments. Results In this article, we propose an efficient computational method based on multi-source information combined with deep convolutional neural network (CNN) to predict circRNA–disease associations. The method first fuses multi-source information including disease semantic similarity, disease Gaussian interaction profile kernel similarity and circRNA Gaussian interaction profile kernel similarity, and then extracts its hidden deep feature through the CNN and finally sends them to the extreme learning machine classifier for prediction. The 5-fold cross-validation results show that the proposed method achieves 87.21% prediction accuracy with 88.50% sensitivity at the area under the curve of 86.67% on the CIRCR2Disease dataset. In comparison with the state-of-the-art SVM classifier and other feature extraction methods on the same dataset, the proposed model achieves the best results. In addition, we also obtained experimental support for prediction results by searching published literature. As a result, 7 of the top 15 circRNA–disease pairs with the highest scores were confirmed by literature. These results demonstrate that the proposed model is a suitable method for predicting circRNA–disease associations and can provide reliable candidates for biological experiments. Availability and implementation The source code and datasets explored in this work are available at https://github.com/look0012/circRNA-Disease-association. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data

2019 ◽  
Vol 35 (21) ◽  
pp. 4222-4228 ◽  
Author(s):  
Tong Liu ◽  
Zheng Wang
Keyword(s):  
Neural Network ◽  
High Resolution ◽  
Convolutional Neural Network ◽  
Mammalian Cells ◽  
Three Dimensional ◽  
Correlation Coefficients ◽  
Cell Types ◽  
Deep Convolutional Neural Network ◽  
Computational Method ◽  
Supplementary Information

Abstract Motivation High-resolution Hi-C data are indispensable for the studies of three-dimensional (3D) genome organization at kilobase level. However, generating high-resolution Hi-C data (e.g. 5 kb) by conducting Hi-C experiments needs millions of mammalian cells, which may eventually generate billions of paired-end reads with a high sequencing cost. Therefore, it will be important and helpful if we can enhance the resolutions of Hi-C data by computational methods. Results We developed a new computational method named HiCNN that used a 54-layer very deep convolutional neural network to enhance the resolutions of Hi-C data. The network contains both global and local residual learning with multiple speedup techniques included resulting in fast convergence. We used mean squared errors and Pearson’s correlation coefficients between real high-resolution and computationally predicted high-resolution Hi-C data to evaluate the method. The evaluation results show that HiCNN consistently outperforms HiCPlus, the only existing tool in the literature, when training and testing data are extracted from the same cell type (i.e. GM12878) and from two different cell types in the same or different species (i.e. GM12878 as training with K562 as testing, and GM12878 as training with CH12-LX as testing). We further found that the HiCNN-enhanced high-resolution Hi-C data are more consistent with real experimental high-resolution Hi-C data than HiCPlus-enhanced data in terms of indicating statistically significant interactions. Moreover, HiCNN can efficiently enhance low-resolution Hi-C data, which eventually helps recover two chromatin loops that were confirmed by 3D-FISH. Availability and implementation HiCNN is freely available at http://dna.cs.miami.edu/HiCNN/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Natural Disasters Intensity Analysis and Classification Based on Multispectral Images Using Multi-Layered Deep Convolutional Neural Network

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2648
Author(s):  
Muhammad Aamir ◽  
Tariq Ali ◽  
Muhammad Irfan ◽  
Ahmad Shaf ◽  
Muhammad Zeeshan Azam ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Natural Disasters ◽  
Deep Convolutional Neural Network ◽  
Multispectral Images ◽  
Learning Techniques ◽  
Proposed Model ◽  
Disaster Intensity ◽  
And Performance

Natural disasters not only disturb the human ecological system but also destroy the properties and critical infrastructures of human societies and even lead to permanent change in the ecosystem. Disaster can be caused by naturally occurring events such as earthquakes, cyclones, floods, and wildfires. Many deep learning techniques have been applied by various researchers to detect and classify natural disasters to overcome losses in ecosystems, but detection of natural disasters still faces issues due to the complex and imbalanced structures of images. To tackle this problem, we propose a multilayered deep convolutional neural network. The proposed model works in two blocks: Block-I convolutional neural network (B-I CNN), for detection and occurrence of disasters, and Block-II convolutional neural network (B-II CNN), for classification of natural disaster intensity types with different filters and parameters. The model is tested on 4428 natural images and performance is calculated and expressed as different statistical values: sensitivity (SE), 97.54%; specificity (SP), 98.22%; accuracy rate (AR), 99.92%; precision (PRE), 97.79%; and F1-score (F1), 97.97%. The overall accuracy for the whole model is 99.92%, which is competitive and comparable with state-of-the-art algorithms.

Identification of Tomato Leaf Disease Detection using Pretrained Deep Convolutional Neural Network Models

2020 ◽  
Vol 21 (4) ◽  
pp. 625-635
Author(s):  
Anandhakrishnan T ◽  
Jaisakthi S.M Murugaiyan
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Early Stage ◽  
Computing Time ◽  
Network Models ◽  
Deep Convolutional Neural Network ◽  
Neural Network Models ◽  
Leaf Disease ◽  
Proposed Model ◽  
Deep Cnn

In this paper, we proposed a plant leaf disease identification model based on a Pretrained deep convolutional neural network (Deep CNN). The Deep CNN model is trained using an open dataset with 10 different classes of tomato leaves We observed that overall architectures which can increase the best performance of the model. The proposed model was trained using different training epochs, batch sizes and dropouts. The Xception has attained maximum accuracy compare with all other approaches. After an extensive simulation, the proposed model achieves classification accuracy better. This accuracy of the proposed work is greater than the accuracy of all other Pretrained approaches. The proposed model is also tested with respect to its consistency and reliability. The set of data used for this work was collected from the plant village dataset, including sick and healthy images. Models for detection of plant disease should predict the disease quickly and accurately in the early stage itself so that a proper precautionary measures can be applied to avoid further spread of the diseases. So, to reduce the main issue about the leaf diseases, we can analyze distinct kinds of deep neural network architectures in this research. From the outcomes, Xception has a constantly improving more to enhance the accuracy by increasing the number of epochs, without any indications of overfitting and decreasein quality. And Xception also generated a fine 99.45% precision in less computing time.

Brain MRI Intelligent Diagnostic Using an Improved Deep Convolutional Neural Network

2021 ◽  
Vol 11 (3) ◽  
pp. 836-845
Author(s):  
Xiangsheng Zhang ◽  
Feng Pan ◽  
Leyuan Zhou
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Brain Tissue ◽  
Brain Mri ◽  
Deep Convolutional Neural Network ◽  
Brain Diseases ◽  
Support Vector ◽  
Svm Classifier ◽  
Intelligent Diagnosis ◽  
The Brain

The diagnosis of brain diseases based on magnetic resonance imaging (MRI) is a mainstream practice. In the course of practical treatment, medical personnel observe and analyze the changes in the size, position, and shape of various brain tissues in the brain MRI image, thereby judging whether the brain tissue has been diseased, and formulating the corresponding medical plan. The conclusion drawn after observing the image will be influenced by the subjective experience of the experts and is not objective. Therefore, it has become necessary to try to avoid subjective factors interfering with the diagnosis. This paper proposes an intelligent diagnosis model based on improved deep convolutional neural network (IDCNN). This model introduces integrated support vector machine (SVM) into IDCNN. During image segmentation, if IDCNN has problems such as irrational layer settings, too many parameters, etc., it will make its segmentation accuracy low. This study made a slight adjustment to the structure of IDCNN. First, adjust the number of convolution layers and down-sampling layers in the DCNN network structure, adjust the network’s activation function, and optimize the parameters to improve IDCNN’s non-linear expression ability. Then, use the integrated SVM classifier to replace the original Softmax classifier in IDCNN to improve its classification ability. The simulation experiment results tell that compared with the model before improvement and other classic classifiers, IDCNN improves segmentation results and promote the intelligent diagnosis of brain tissue.

An Optimized Approach for Intra-Class Fruit Classification Using Deep Convolutional Neural Network

2021 ◽  
pp. 2140014
Author(s):  
Rishipal Singh ◽  
Rajneesh Rani ◽  
Aman Kamboj
Keyword(s):  
Neural Network ◽  
Computer Vision ◽  
Convolutional Neural Network ◽  
State Of The Art ◽  
Deep Convolutional Neural Network ◽  
Classification Models ◽  
Proposed Model ◽  
Traditional Classification

Fruits classification is one of the influential applications of computer vision. Traditional classification models are trained by considering various features such as color, shape, texture, etc. These features are common for different varieties of the same fruit. Therefore, a new set of features is required to classify the fruits belonging to the same class. In this paper, we have proposed an optimized method to classify intra-class fruits using deep convolutional layers. The proposed architecture is capable of solving the challenges of a commercial tray-based system in the supermarket. As the research in intra-class classification is still in its infancy, there are challenges that have not been tackled. So, the proposed method is specifically designed to overcome the challenges related to intra-class fruits classification. The proposed method showcases an impressive performance for intra-class classification, which is achieved using a few parameters than the existing methods. The proposed model consists of Inception block, Residual connections and various other layers in very precise order. To validate its performance, the proposed method is compared with state-of-the-art models and performs best in terms of accuracy, loss, parameters, and depth.

Small Scale Targeted Face Detection using Deep Convolutional Neural Network

2021 ◽  
Author(s):  
Asedo Shektofik Ahmed ◽  
Hussein Abdumalik Ibrahim ◽  
B.Barani Sundaram ◽  
P. Karthika
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Face Detection ◽  
Deep Convolutional Neural Network ◽  
Small Scale

scholarly journals A Hybrid Deep Convolutional Neural Network Approach for Predicting the Traffic Congestion Index

2021 ◽  
Vol 33 (3) ◽  
pp. 373-385
Author(s):  
Duy Tran Quang ◽  
Sang Hoon Bae
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Traffic Congestion ◽  
Gradient Descent ◽  
Optimization Algorithms ◽  
Deep Convolutional Neural Network ◽  
Short Term ◽  
Probe Vehicles ◽  
Proposed Model ◽  
Congestion Index

Traffic congestion is one of the most important issues in large cities, and the overall travel speed is an important factor that reflects the traffic status on road networks. This study proposes a hybrid deep convolutional neural network (CNN) method that uses gradient descent optimization algorithms and pooling operations for predicting the short-term traffic congestion index in urban networks based on probe vehicles. First, the input data are collected by the probe vehicles to calculate the traffic congestion index (output label). Then, a CNN that uses gradient descent optimization algorithms and pooling operations is applied to enhance its performance. Finally, the proposed model is chosen on the basis of the R-squared (R2) and root mean square error (RMSE) values. In the best-case scenario, the proposed model achieved an R2 value of 98.7%. In addition, the experiments showed that the proposed model significantly outperforms other algorithms, namely the ordinary least squares (OLS), k-nearest neighbors (KNN), random forest (RF), recurrent neural network (RNN), artificial neural network (ANN), and convolutional long short-term memory (ConvLSTM), in predicting traffic congestion index. Furthermore, using the proposed method, the time-series changes in the traffic congestion status can be reliably visualized for the entire urban network.

scholarly journals Deep Convolutional Neural Network Based Extreme Learning Machine Image Classification

2021 ◽  
pp. 30-38
Author(s):  
G. D. Praveenkumar ◽  
Dr. R. Nagaraj
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Extreme Learning Machine ◽  
Deep Convolutional Neural Network ◽  
Computational Time ◽  
Machine Model ◽  
Proposed Model ◽  
Benchmark Datasets ◽  
Learning Machine ◽  
Elm Classifier

In this paper, we introduce a new deep convolutional neural network based extreme learning machine model for the classification task in order to improve the network's performance. The proposed model has two stages: first, the input images are fed into a convolutional neural network layer to extract deep-learned attributes, and then the input is classified using an ELM classifier. The proposed model achieves good recognition accuracy while reducing computational time on both the MNIST and CIFAR-10 benchmark datasets.

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