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.

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 HiCNN2: Enhancing the Resolution of Hi-C Data Using an Ensemble of Convolutional Neural Networks

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 862
Author(s):  
Tong Liu ◽  
Zheng Wang
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
High Resolution ◽  
Convolutional Neural Network ◽  
Mean Squared Error ◽  
Correlation Coefficients ◽  
Chromatin Interactions ◽  
Squared Error ◽  
Genome Wide

We present a deep-learning package named HiCNN2 to learn the mapping between low-resolution and high-resolution Hi-C (a technique for capturing genome-wide chromatin interactions) data, which can enhance the resolution of Hi-C interaction matrices. The HiCNN2 package includes three methods each with a different deep learning architecture: HiCNN2-1 is based on one single convolutional neural network (ConvNet); HiCNN2-2 consists of an ensemble of two different ConvNets; and HiCNN2-3 is an ensemble of three different ConvNets. Our evaluation results indicate that HiCNN2-enhanced high-resolution Hi-C data achieve smaller mean squared error and higher Pearson’s correlation coefficients with experimental high-resolution Hi-C data compared with existing methods HiCPlus and HiCNN. Moreover, all of the three HiCNN2 methods can recover more significant interactions detected by Fit-Hi-C compared to HiCPlus and HiCNN. Based on our evaluation results, we would recommend using HiCNN2-1 and HiCNN2-3 if recovering more significant interactions from Hi-C data is of interest, and HiCNN2-2 and HiCNN if the goal is to achieve higher reproducibility scores between the enhanced Hi-C matrix and the real high-resolution Hi-C matrix.

scholarly journals Road Extraction from High-Resolution Remote Sensing Imagery Using Deep Learning

2018 ◽  
Vol 10 (9) ◽  
pp. 1461 ◽  
Author(s):  
Yongyang Xu ◽  
Zhong Xie ◽  
Yaxing Feng ◽  
Zhanlong Chen
Keyword(s):  
Neural Network ◽  
Remote Sensing ◽  
Deep Learning ◽  
High Resolution ◽  
Convolutional Neural Network ◽  
Road Network ◽  
Deep Convolutional Neural Network ◽  
Road Extraction ◽  
Remote Sensing Imagery ◽  
The Road

The road network plays an important role in the modern traffic system; as development occurs, the road structure changes frequently. Owing to the advancements in the field of high-resolution remote sensing, and the success of semantic segmentation success using deep learning in computer version, extracting the road network from high-resolution remote sensing imagery is becoming increasingly popular, and has become a new tool to update the geospatial database. Considering that the training dataset of the deep convolutional neural network will be clipped to a fixed size, which lead to the roads run through each sample, and that different kinds of road types have different widths, this work provides a segmentation model that was designed based on densely connected convolutional networks (DenseNet) and introduces the local and global attention units. The aim of this work is to propose a novel road extraction method that can efficiently extract the road network from remote sensing imagery with local and global information. A dataset from Google Earth was used to validate the method, and experiments showed that the proposed deep convolutional neural network can extract the road network accurately and effectively. This method also achieves a harmonic mean of precision and recall higher than other machine learning and deep learning methods.

scholarly journals Identification and Diagnosis of Cerebral Stroke through Deep Convolutional Neural Network-Based Multimodal MRI Images

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Yanyan Pan ◽  
Huiping Zhang ◽  
Jinsuo Yang ◽  
Jing Guo ◽  
Zhiguo Yang ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Automatic Segmentation ◽  
Three Dimensional ◽  
Deep Convolutional Neural Network ◽  
Cerebral Stroke ◽  
Good Convergence ◽  
Segmentation Accuracy ◽  
Multimodal Mri ◽  
Magnetic Resonance Imaging Mri

This study aimed to explore the application value of multimodal magnetic resonance imaging (MRI) images based on the deep convolutional neural network (Conv.Net) in the diagnosis of strokes. Specifically, four automatic segmentation algorithms were proposed to segment multimodal MRI images of stroke patients. The segmentation effects were evaluated factoring into DICE, accuracy, sensitivity, and segmentation distance coefficient. It was found that although two-dimensional (2D) full convolutional neural network-based segmentation algorithm can locate and segment the lesion, its accuracy was low; the three-dimensional one exhibited higher accuracy, with various objective indicators improved, and the segmentation accuracy of the training set and the test set was 0.93 and 0.79, respectively, meeting the needs of automatic diagnosis. The asymmetric 3D residual U-Net network had good convergence and high segmentation accuracy, and the 3D deep residual network proposed on its basis had good segmentation coefficients, which can not only ensure segmentation accuracy but also avoid network degradation problems. In conclusion, the Conv.Net model can accurately segment the foci of patients with ischemic stroke and is suggested in clinic.

scholarly journals A Deep Convolutional Neural Network to Detect the Existence of Geospatial Elements in High-Resolution Aerial Imagery

Proceedings ◽  
2019 ◽  
Vol 19 (1) ◽  
pp. 17 ◽  
Author(s):  
Calimanut-Ionut Cira ◽  
Ramón Alcarria ◽  
Miguel-Ángel Manso-Callejo ◽  
Francisco Serradilla
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Object Recognition ◽  
High Resolution ◽  
Convolutional Neural Network ◽  
Road Network ◽  
Deep Convolutional Neural Network ◽  
Aerial Imagery ◽  
Learning Techniques

This paper tackles the problem of object recognition in high-resolution aerial imagery and addresses the application of Deep Learning techniques to solve a challenge related to detecting the existence of geospatial elements (road network) in the available cartographic support. This challenge is addressed by building a convolutional neural network (CNN) trained to detect roads in high resolution aerial orthophotos divided in tiles (256 × 256 pixels) using manually labelled data.

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