scholarly journals HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps

2020 ◽  
Author(s):  
Michael C. Dimmick ◽  
Leo J. Lee ◽  
Brendan J. Frey
Keyword(s):  
High Resolution ◽  
Super Resolution ◽  
Cell Types ◽  
Supplementary Information ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
High Resolution Data ◽  
Contact Maps ◽  
Adversarial Network ◽  
And Function

AbstractMotivationHi-C data has enabled the genome-wide study of chromatin folding and architecture, and has led to important discoveries in the structure and function of chromatin conformation. Here, high resolution data plays a particularly important role as many chromatin substructures such as Topologically Associating Domains (TADs) and chromatin loops cannot be adequately studied with low resolution contact maps. However, the high sequencing costs associated with the generation of high resolution Hi-C data has become an experimental barrier. Data driven machine learning models, which allow low resolution Hi-C data to be computationally enhanced, offer a promising avenue to address this challenge.ResultsBy carefully examining the properties of Hi-C maps and integrating various recent advances in deep learning, we developed a Hi-C Super-Resolution (HiCSR) framework capable of accurately recovering the fine details, textures, and substructures found in high resolution contact maps. This was achieved using a novel loss function tailored to the Hi-C enhancement problem which optimizes for an adversarial loss from a Generative Adversarial Network (GAN), a feature reconstruction loss derived from the latent representation of a denoising autoencoder, and a pixel-wise loss. Not only can the resulting framework generate enhanced Hi-C maps more visually similar to the original high resolution maps, it also excels on a suite of reproducibility metrics produced by members of the ENCODE Consortium compared to existing approaches, including HiCPlus, HiCNN, hicGAN and DeepHiC. Finally, we demonstrate that HiCSR is capable of enhancing Hi-C data across sequencing depth, cell types, and species, recovering biologically significant contact domain boundaries.AvailabilityWe make our implementation available for download at: https://github.com/PSI-Lab/[email protected] informationAvailable Online

scholarly journals Upsampling Real-Time, Low-Resolution CCTV Videos Using Generative Adversarial Networks

Electronics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1312
Author(s):  
Debapriya Hazra ◽  
Yung-Cheol Byun
Keyword(s):  
High Resolution ◽  
Real Time ◽  
Super Resolution ◽  
Poor Quality ◽  
Generative Adversarial Networks ◽  
Temporal Consistency ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Benchmark Datasets

Video super-resolution has become an emerging topic in the field of machine learning. The generative adversarial network is a framework that is widely used to develop solutions for low-resolution videos. Video surveillance using closed-circuit television (CCTV) is significant in every field, all over the world. A common problem with CCTV videos is sudden video loss or poor quality. In this paper, we propose a generative adversarial network that implements spatio-temporal generators and discriminators to enhance real-time low-resolution CCTV videos to high-resolution. The proposed model considers both foreground and background motion of a CCTV video and effectively models the spatial and temporal consistency from low-resolution video frames to generate high-resolution videos. Quantitative and qualitative experiments on benchmark datasets, including Kinetics-700, UCF101, HMDB51 and IITH_Helmet2, showed that our model outperforms the existing GAN models for video super-resolution.

scholarly journals Super-Resolution Enhancement Method Based on Generative Adversarial Network for Integral Imaging Microscopy

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 2164
Author(s):  
Md. Shahinur Alam ◽  
Ki-Chul Kwon ◽  
Munkh-Uchral Erdenebat ◽  
Mohammed Y. Abbass ◽  
Md. Ashraful Alam ◽  
...  
Keyword(s):  
High Resolution ◽  
Resolution Enhancement ◽  
Three Dimensional ◽  
Super Resolution ◽  
Input Image ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Microscopic Object ◽  
Integral Imaging ◽  
Adversarial Network

The integral imaging microscopy system provides a three-dimensional visualization of a microscopic object. However, it has a low-resolution problem due to the fundamental limitation of the F-number (the aperture stops) by using micro lens array (MLA) and a poor illumination environment. In this paper, a generative adversarial network (GAN)-based super-resolution algorithm is proposed to enhance the resolution where the directional view image is directly fed as input. In a GAN network, the generator regresses the high-resolution output from the low-resolution input image, whereas the discriminator distinguishes between the original and generated image. In the generator part, we use consecutive residual blocks with the content loss to retrieve the photo-realistic original image. It can restore the edges and enhance the resolution by ×2, ×4, and even ×8 times without seriously hampering the image quality. The model is tested with a variety of low-resolution microscopic sample images and successfully generates high-resolution directional view images with better illumination. The quantitative analysis shows that the proposed model performs better for microscopic images than the existing algorithms.

scholarly journals A GENERATIVE ADVERSARIAL NETWORK APPROACH FOR SUPER-RESOLUTION OF SENTINEL-2 SATELLITE IMAGES

2020 ◽  
Vol XLIII-B1-2020 ◽  
pp. 9-14
Author(s):  
F. Pineda ◽  
V. Ayma ◽  
C. Beltran
Keyword(s):  
High Resolution ◽  
Satellite Images ◽  
Resolution Enhancement ◽  
Super Resolution ◽  
Structural Similarity ◽  
Generative Adversarial Network ◽  
Acceptable Result ◽  
Adversarial Network ◽  
High Resolution Satellite Images ◽  
Sentinel 2

Abstract. High-resolution satellite images have always been in high demand due to the greater detail and precision they offer, as well as the wide scope of the fields in which they could be applied; however, satellites in operation offering very high-resolution (VHR) images has experienced an important increase, but they remain as a smaller proportion against existing lower resolution (HR) satellites. Recent models of convolutional neural networks (CNN) are very suitable for applications with image processing, like resolution enhancement of images; but in order to obtain an acceptable result, it is important, not only to define the kind of CNN architecture but the reference set of images to train the model. Our work proposes an alternative to improve the spatial resolution of HR images obtained by Sentinel-2 satellite by using the VHR images from PeruSat1, a peruvian satellite, which serve as the reference for the super-resolution approach implementation based on a Generative Adversarial Network (GAN) model, as an alternative for obtaining VHR images. The VHR PeruSat-1 image dataset is used for the training process of the network. The results obtained were analyzed considering the Peak Signal to Noise Ratios (PSNR) and the Structural Similarity (SSIM). Finally, some visual outcomes, over a given testing dataset, are presented so the performance of the model could be analyzed as well.

scholarly journals Fast and accurate learned multiresolution dynamical downscaling for precipitation

2021 ◽  
Author(s):  
Jiali Wang ◽  
Zhengchun Liu ◽  
Ian Foster ◽  
Won Chang ◽  
Rajkumar Kettimuthu ◽  
...  
Keyword(s):  
Neural Network ◽  
High Resolution ◽  
Dynamical Downscaling ◽  
Computational Cost ◽  
Super Resolution ◽  
Ground Truth ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Spatial And Temporal Distributions ◽  
Data Variability

Abstract. This study develops a neural network-based approach for emulating high-resolution modeled precipitation data with comparable statistical properties but at greatly reduced computational cost. The key idea is to use combination of low- and high- resolution simulations to train a neural network to map from the former to the latter. Specifically, we define two types of CNNs, one that stacks variables directly and one that encodes each variable before stacking, and we train each CNN type both with a conventional loss function, such as mean square error (MSE), and with a conditional generative adversarial network (CGAN), for a total of four CNN variants.We compare the four new CNN-derived high-resolution precipitation results with precipitation generated from original high resolution simulations, a bilinear interpolater and the state-of-the-art CNN-based super-resolution (SR) technique. Results show that the SR technique produces results similar to those of the bilinear interpolator with smoother spatial and temporal distributions and smaller data variabilities and extremes than the high resolution simulations. While the new CNNs trained by MSE generate better results over some regions than the interpolator and SR technique do, their predictions are still not as close as ground truth. The CNNs trained by CGAN generate more realistic and physically reasonable results, better capturing not only data variability in time and space but also extremes such as intense and long-lasting storms. The new proposed CNN-based downscaling approach can downscale precipitation from 50 km to 12 km in 14 min for 30 years once the network is trained (training takes 4 hours using 1 GPU), while the conventional dynamical downscaling would take 1 months using 600 CPU cores to generate simulations at the resolution of 12 km over contiguous United States.

scholarly journals Deep feature extraction of single-cell transcriptomes by generative adversarial network

2020 ◽  
Author(s):  
Mojtaba Bahrami ◽  
Malosree Maitra ◽  
Corina Nagy ◽  
Gustavo Turecki ◽  
Hamid R Rabiee ◽  
...  
Keyword(s):  
Single Cell ◽  
Expression Patterns ◽  
Cell Types ◽  
Individual Variability ◽  
Superior Performance ◽  
Supplementary Information ◽  
Specific Gene ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Deep Feature Extraction

Abstract Motivation Single-cell RNA-sequencing (scRNA-seq) offers the opportunity to dissect heterogeneous cellular compositions and interrogate the cell-type-specific gene expression patterns across diverse conditions. However, batch effects such as laboratory conditions and individual-variability hinder their usage in cross-condition designs. Results Here, we present a single-cell Generative Adversarial Network (scGAN) to simultaneously acquire patterns from raw data while minimizing the confounding effect driven by technical artifacts or other factors inherent to the data. Specifically, scGAN models the data likelihood of the raw scRNA-seq counts by projecting each cell onto a latent embedding. Meanwhile, scGAN attempts to minimize the correlation between the latent embeddings and the batch labels across all cells. We demonstrate scGAN on three public scRNA-seq datasets and show that our method confers superior performance over the state-of-the-art methods in forming clusters of known cell types and identifying known psychiatric genes that are associated with major depressive disorder. Availabilityand implementation The scGAN code and the information for the public scRNA-seq datasets are available at https://github.com/li-lab-mcgill/singlecell-deepfeature. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Extreme Low-Resolution Activity Recognition Using a Super-Resolution-Oriented Generative Adversarial Network

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 670
Author(s):  
Mingzheng Hou ◽  
Song Liu ◽  
Jiliu Zhou ◽  
Yi Zhang ◽  
Ziliang Feng
Keyword(s):  
Activity Recognition ◽  
Large Scale ◽  
Super Resolution ◽  
General Activity ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Video Clips ◽  
Adversarial Network ◽  
Efficient Recognition ◽  
Low Resolution Images

Activity recognition is a fundamental and crucial task in computer vision. Impressive results have been achieved for activity recognition in high-resolution videos, but for extreme low-resolution videos, which capture the action information at a distance and are vital for preserving privacy, the performance of activity recognition algorithms is far from satisfactory. The reason is that extreme low-resolution (e.g., 12 × 16 pixels) images lack adequate scene and appearance information, which is needed for efficient recognition. To address this problem, we propose a super-resolution-driven generative adversarial network for activity recognition. To fully take advantage of the latent information in low-resolution images, a powerful network module is employed to super-resolve the extremely low-resolution images with a large scale factor. Then, a general activity recognition network is applied to analyze the super-resolved video clips. Extensive experiments on two public benchmarks were conducted to evaluate the effectiveness of our proposed method. The results demonstrate that our method outperforms several state-of-the-art low-resolution activity recognition approaches.

scholarly journals Low Resolution Face Recognition Using Generative Adversarial Network (GAN)

2020 ◽  
Author(s):  
Howard Martin ◽  
Suharjito
Keyword(s):  
Face Recognition ◽  
Super Resolution ◽  
Image Data ◽  
Face Image ◽  
Image Resolution ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Resolution Image ◽  
Surveillance Camera ◽  
Adversarial Network

Abstract Face recognition has a lot of use on smartphone authentication, finding people, etc. Nowadays, face recognition with a constrained environment has achieved very good performance on accuracy. However, the accuracy of existing face recognition methods will gradually decrease when using a dataset with an unconstrained environment. Face image with an unconstrained environment is usually taken from a surveillance camera. In general, surveillance cameras will be placed on the corner of a room or even on the street. So, the image resolution will be low. Low-resolution image will cause the face very hard to be recognized and the accuracy will eventually decrease. That is the main reason why increasing the accuracy of the Low-Resolution Face Recognition (LRFR) problem is still challenging. This research aimed to solve the Low-Resolution Face Recognition (LRFR) problem. The datasets are YouTube Faces Database (YTF) and Labelled Faces in The Wild (LFW). In this research, face image resolution would be decreased using bicubic linear and became the low-resolution image data. Then super resolution methods as the preprocessing step would increase the image resolution. Super resolution methods used in this research are Super resolution GAN (SRGAN) [1] and Enhanced Super resolution GAN (ESRGAN) [2]. These methods would be compared to reach a better accuracy on solving LRFR problem. After increased the image resolution, the image would be recognized using FaceNet. This research concluded that using super resolution as the preprocessing step for LRFR problem has achieved a higher accuracy compared to [3]. The highest accuracy achieved by using ESRGAN as the preprocessing and FaceNet for face recognition with accuracy of 98.96 % and Validation rate 96.757 %.

scholarly journals Unpaired Remote Sensing Image Super-Resolution with Multi-Stage Aggregation Networks

2021 ◽  
Vol 13 (16) ◽  
pp. 3167
Author(s):  
Lize Zhang ◽  
Wen Lu ◽  
Yuanfei Huang ◽  
Xiaopeng Sun ◽  
Hongyi Zhang
Keyword(s):  
Remote Sensing ◽  
Super Resolution ◽  
Perceptual Content ◽  
Remote Sensing Images ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Imaging Device ◽  
Adversarial Network ◽  
Multi Stage ◽  
Image Super Resolution

Mainstream image super-resolution (SR) methods are generally based on paired training samples. As the high-resolution (HR) remote sensing images are difficult to collect with a limited imaging device, most of the existing remote sensing super-resolution methods try to down-sample the collected original images to generate an auxiliary low-resolution (LR) image and form a paired pseudo HR-LR dataset for training. However, the distribution of the generated LR images is generally inconsistent with the real images due to the limitation of remote sensing imaging devices. In this paper, we propose a perceptually unpaired super-resolution method by constructing a multi-stage aggregation network (MSAN). The optimization of the network depends on consistency losses. In particular, the first phase is to preserve the contents of the super-resolved results, by constraining the content consistency between the down-scaled SR results and the low-quality low-resolution inputs. The second stage minimizes perceptual feature loss between the current result and LR input to constrain perceptual-content consistency. The final phase employs the generative adversarial network (GAN) to adding photo-realistic textures by constraining perceptual-distribution consistency. Numerous experiments on synthetic remote sensing datasets and real remote sensing images show that our method obtains more plausible results than other SR methods quantitatively and qualitatively. The PSNR of our network is 0.06dB higher than the SOTA method—HAN on the UC Merced test set with complex degradation.

scholarly journals Target Detection Method for Low-Resolution Remote Sensing Image Based on ESRGAN and ReDet

Photonics ◽  
2021 ◽  
Vol 8 (10) ◽  
pp. 431
Author(s):  
Yuwu Wang ◽  
Guobing Sun ◽  
Shengwei Guo
Keyword(s):  
Remote Sensing ◽  
Target Detection ◽  
Detection Method ◽  
Recognition Rate ◽  
Super Resolution ◽  
Remote Sensing Image ◽  
Remote Sensing Images ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Adversarial Network

With the widespread use of remote sensing images, low-resolution target detection in remote sensing images has become a hot research topic in the field of computer vision. In this paper, we propose a Target Detection on Super-Resolution Reconstruction (TDoSR) method to solve the problem of low target recognition rates in low-resolution remote sensing images under foggy conditions. The TDoSR method uses the Enhanced Super-Resolution Generative Adversarial Network (ESRGAN) to perform defogging and super-resolution reconstruction of foggy low-resolution remote sensing images. In the target detection part, the Rotation Equivariant Detector (ReDet) algorithm, which has a higher recognition rate at this stage, is used to identify and classify various types of targets. While a large number of experiments have been carried out on the remote sensing image dataset DOTA-v1.5, the results of this paper suggest that the proposed method achieves good results in the target detection of low-resolution foggy remote sensing images. The principal result of this paper demonstrates that the recognition rate of the TDoSR method increases by roughly 20% when compared with low-resolution foggy remote sensing images.

Super-resolution in Structural Geological Models.

2021 ◽  
Author(s):  
Mustaeen Ur Rehman Qazi ◽  
Florian Wellmann
Keyword(s):  
High Resolution ◽  
Structural Model ◽  
Mean Squared Error ◽  
Super Resolution ◽  
Generative Adversarial Networks ◽  
Low Resolution ◽  
Generative Adversarial Network ◽  
Data Set ◽  
Adversarial Networks ◽  
Geological Models

<p>Structural geological models are often calculated on a specific spatial resolution – for example in the form of grid representations, or when surfaces are extracted from implicit fields. However, the structural inventory in these models is limited by the underlying mathematical formulations. It is therefore logical that, above a certain resolution, no additional information is added to the representation.</p><p>We evaluate here if Deep Neural Networks can be trained to obtain a high-resolution representation based on a low-resolution structural model, at different levels of resolution. More specifically, we test the use of state-of-the-art Generative Adversarial Networks (GAN’s) for image superresolution in the context of 2-D geological model sections. These techniques aim to learn the hidden structure or information in high resolution image data set and then reproduce highly detailed and super resolved image from its low resolution counterpart. We propose the use of Generative Adversarial Networks GANS for super resolution of geological images and 2D geological models represented as images. In this work a generative adversarial network called SRGAN has been used which uses a perceptual loss function consisting of an adversarial loss, mean squared error loss and content loss for photo realistic image super resolution. First results are promising, but challenges remain due to the different interpretation of color in images for which these GAN’s are typically used, whereas we are mostly interested in structures.</p>

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