scholarly journals Generative Adversarial Learning of Protein Tertiary Structures

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1209
Author(s):  
Taseef Rahman ◽  
Yuanqi Du ◽  
Liang Zhao ◽  
Amarda Shehu
Keyword(s):  
Protein Molecule ◽  
Generative Models ◽  
Generative Adversarial Networks ◽  
Tertiary Structures ◽  
Adversarial Learning ◽  
Good Balance ◽  
Physiological Conditions ◽  
Adversarial Networks ◽  
Protein Molecules

Protein molecules are inherently dynamic and modulate their interactions with different molecular partners by accessing different tertiary structures under physiological conditions. Elucidating such structures remains challenging. Current momentum in deep learning and the powerful performance of generative adversarial networks (GANs) in complex domains, such as computer vision, inspires us to investigate GANs on their ability to generate physically-realistic protein tertiary structures. The analysis presented here shows that several GAN models fail to capture complex, distal structural patterns present in protein tertiary structures. The study additionally reveals that mechanisms touted as effective in stabilizing the training of a GAN model are not all effective, and that performance based on loss alone may be orthogonal to performance based on the quality of generated datasets. A novel contribution in this study is the demonstration that Wasserstein GAN strikes a good balance and manages to capture both local and distal patterns, thus presenting a first step towards more powerful deep generative models for exploring a possibly very diverse set of structures supporting diverse activities of a protein molecule in the cell.

scholarly journals Image-Adaptive GAN Based Reconstruction

2020 ◽  
Vol 34 (04) ◽  
pp. 3121-3129 ◽  
Author(s):  
Shady Abu Hussein ◽  
Tom Tirer ◽  
Raja Giryes
Keyword(s):  
Inverse Problems ◽  
Compressed Sensing ◽  
Super Resolution ◽  
Generative Models ◽  
Generative Adversarial Networks ◽  
Adversarial Networks ◽  
Image Super Resolution ◽  
Human Faces

In the recent years, there has been a significant improvement in the quality of samples produced by (deep) generative models such as variational auto-encoders and generative adversarial networks. However, the representation capabilities of these methods still do not capture the full distribution for complex classes of images, such as human faces. This deficiency has been clearly observed in previous works that use pre-trained generative models to solve imaging inverse problems. In this paper, we suggest to mitigate the limited representation capabilities of generators by making them image-adaptive and enforcing compliance of the restoration with the observations via back-projections. We empirically demonstrate the advantages of our proposed approach for image super-resolution and compressed sensing.

scholarly journals Improvement of Learning Stability of Generative Adversarial Network Using Variational Learning

2020 ◽  
Vol 10 (13) ◽  
pp. 4528
Author(s):  
Je-Yeol Lee ◽  
Sang-Il Choi 
Keyword(s):  
Generative Models ◽  
Learning Processes ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Adversarial Networks ◽  
Secondary Network ◽  
Variational Autoencoder ◽  
Variational Learning

In this paper, we propose a new network model using variational learning to improve the learning stability of generative adversarial networks (GAN). The proposed method can be easily applied to improve the learning stability of GAN-based models that were developed for various purposes, given that the variational autoencoder (VAE) is used as a secondary network while the basic GAN structure is maintained. When the gradient of the generator vanishes in the learning process of GAN, the proposed method receives gradient information from the decoder of the VAE that maintains gradient stably, so that the learning processes of the generator and discriminator are not halted. The experimental results of the MNIST and the CelebA datasets verify that the proposed method improves the learning stability of the networks by overcoming the vanishing gradient problem of the generator, and maintains the excellent data quality of the conventional GAN-based generative models.

Generative Adversarial Networks (GANs)

2021 ◽  
Vol 54 (3) ◽  
pp. 1-42
Author(s):  
Divya Saxena ◽  
Jiannong Cao
Keyword(s):  
Optimization Technique ◽  
Generative Models ◽  
Generative Adversarial Networks ◽  
Network Architectures ◽  
Research Directions ◽  
Research Issues ◽  
Design And Optimization ◽  
Adversarial Networks ◽  
Comprehensive Survey ◽  
Selection Of

Generative Adversarial Networks (GANs) is a novel class of deep generative models that has recently gained significant attention. GANs learn complex and high-dimensional distributions implicitly over images, audio, and data. However, there exist major challenges in training of GANs, i.e., mode collapse, non-convergence, and instability, due to inappropriate design of network architectre, use of objective function, and selection of optimization algorithm. Recently, to address these challenges, several solutions for better design and optimization of GANs have been investigated based on techniques of re-engineered network architectures, new objective functions, and alternative optimization algorithms. To the best of our knowledge, there is no existing survey that has particularly focused on the broad and systematic developments of these solutions. In this study, we perform a comprehensive survey of the advancements in GANs design and optimization solutions proposed to handle GANs challenges. We first identify key research issues within each design and optimization technique and then propose a new taxonomy to structure solutions by key research issues. In accordance with the taxonomy, we provide a detailed discussion on different GANs variants proposed within each solution and their relationships. Finally, based on the insights gained, we present promising research directions in this rapidly growing field.

Towards Accuracy Enhancement of Age Group Classification Using Generative Adversarial Networks

2021 ◽  
pp. 1-17
Author(s):  
Khaled ELKarazle ◽  
Valliappan Raman ◽  
Patrick Then
Keyword(s):  
Age Estimation ◽  
Super Resolution ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Adversarial Networks ◽  
Original Dataset ◽  
Age Group Classification ◽  
Facial Images

Age estimation models can be employed in many applications, including soft biometrics, content access control, targeted advertising, and many more. However, as some facial images are taken in unrestrained conditions, the quality relegates, which results in the loss of several essential ageing features. This study investigates how introducing a new layer of data processing based on a super-resolution generative adversarial network (SRGAN) model can influence the accuracy of age estimation by enhancing the quality of both the training and testing samples. Additionally, we introduce a novel convolutional neural network (CNN) classifier to distinguish between several age classes. We train one of our classifiers on a reconstructed version of the original dataset and compare its performance with an identical classifier trained on the original version of the same dataset. Our findings reveal that the classifier which trains on the reconstructed dataset produces better classification accuracy, opening the door for more research into building data-centric machine learning systems.

scholarly journals Conditional Wasserstein Generative Adversarial Networks for Fast Detector Simulation

2021 ◽  
Vol 251 ◽  
pp. 03055
Author(s):  
John Blue ◽  
Braden Kronheim ◽  
Michelle Kuchera ◽  
Raghuram Ramanujan
Keyword(s):  
High Energy Physics ◽  
High Energy ◽  
Generative Models ◽  
Generative Adversarial Networks ◽  
Detector Response ◽  
Event Simulation ◽  
Simulation Process ◽  
Adversarial Networks ◽  
Wide Range ◽  
Detector Simulation

Detector simulation in high energy physics experiments is a key yet computationally expensive step in the event simulation process. There has been much recent interest in using deep generative models as a faster alternative to the full Monte Carlo simulation process in situations in which the utmost accuracy is not necessary. In this work we investigate the use of conditional Wasserstein Generative Adversarial Networks to simulate both hadronization and the detector response to jets. Our model takes the 4-momenta of jets formed from partons post-showering and pre-hadronization as inputs and predicts the 4-momenta of the corresponding reconstructed jet. Our model is trained on fully simulated tt events using the publicly available GEANT-based simulation of the CMS Collaboration. We demonstrate that the model produces accurate conditional reconstructed jet transverse momentum (pT) distributions over a wide range of pT for the input parton jet. Our model takes only a fraction of the time necessary for conventional detector simulation methods, running on a CPU in less than a millisecond per event.

scholarly journals Fractional Wavelet-Based Generative Scattering Networks

2021 ◽  
Vol 15 ◽  
Author(s):  
Jiasong Wu ◽  
Xiang Qiu ◽  
Jing Zhang ◽  
Fuzhi Wu ◽  
Youyong Kong ◽  
...  
Keyword(s):  
Dimensionality Reduction ◽  
Reduction Method ◽  
Gaussian White Noise ◽  
Principal Component ◽  
Experimental Results ◽  
Generative Adversarial Networks ◽  
Image Generation ◽  
Adversarial Networks ◽  
Dimensionality Reduction Method

Generative adversarial networks and variational autoencoders (VAEs) provide impressive image generation from Gaussian white noise, but both are difficult to train, since they need a generator (or encoder) and a discriminator (or decoder) to be trained simultaneously, which can easily lead to unstable training. To solve or alleviate these synchronous training problems of generative adversarial networks (GANs) and VAEs, researchers recently proposed generative scattering networks (GSNs), which use wavelet scattering networks (ScatNets) as the encoder to obtain features (or ScatNet embeddings) and convolutional neural networks (CNNs) as the decoder to generate an image. The advantage of GSNs is that the parameters of ScatNets do not need to be learned, while the disadvantage of GSNs is that their ability to obtain representations of ScatNets is slightly weaker than that of CNNs. In addition, the dimensionality reduction method of principal component analysis (PCA) can easily lead to overfitting in the training of GSNs and, therefore, affect the quality of generated images in the testing process. To further improve the quality of generated images while keeping the advantages of GSNs, this study proposes generative fractional scattering networks (GFRSNs), which use more expressive fractional wavelet scattering networks (FrScatNets), instead of ScatNets as the encoder to obtain features (or FrScatNet embeddings) and use similar CNNs of GSNs as the decoder to generate an image. Additionally, this study develops a new dimensionality reduction method named feature-map fusion (FMF) instead of performing PCA to better retain the information of FrScatNets,; it also discusses the effect of image fusion on the quality of the generated image. The experimental results obtained on the CIFAR-10 and CelebA datasets show that the proposed GFRSNs can lead to better generated images than the original GSNs on testing datasets. The experimental results of the proposed GFRSNs with deep convolutional GAN (DCGAN), progressive GAN (PGAN), and CycleGAN are also given.

scholarly journals Multi-Turn Chatbot Based on Query-Context Attentions and Dual Wasserstein Generative Adversarial Networks

2019 ◽  
Vol 9 (18) ◽  
pp. 3908 ◽  
Author(s):  
Jintae Kim ◽  
Shinhyeok Oh ◽  
Oh-Woog Kwon ◽  
Harksoo Kim
Keyword(s):  
Performance Measures ◽  
State Of The Art ◽  
Attention Mechanism ◽  
Generative Adversarial Networks ◽  
Training Method ◽  
Adversarial Networks ◽  
Proposed Model ◽  
Previous State ◽  
Vector Representations

To generate proper responses to user queries, multi-turn chatbot models should selectively consider dialogue histories. However, previous chatbot models have simply concatenated or averaged vector representations of all previous utterances without considering contextual importance. To mitigate this problem, we propose a multi-turn chatbot model in which previous utterances participate in response generation using different weights. The proposed model calculates the contextual importance of previous utterances by using an attention mechanism. In addition, we propose a training method that uses two types of Wasserstein generative adversarial networks to improve the quality of responses. In experiments with the DailyDialog dataset, the proposed model outperformed the previous state-of-the-art models based on various performance measures.

scholarly journals A Novel Method for the Deblurring of Photogrammetric Images Using Conditional Generative Adversarial Networks

2020 ◽  
Vol 12 (16) ◽  
pp. 2586 ◽  
Author(s):  
Pawel Burdziakowski
Keyword(s):  
Point Clouds ◽  
Aerial Images ◽  
Generative Adversarial Networks ◽  
Camera Motion ◽  
Data Set ◽  
Adversarial Networks ◽  
Blur Kernel ◽  
Almost All ◽  
Blurred Images

The visual data acquisition from small unmanned aerial vehicles (UAVs) may encounter a situation in which blur appears on the images. Image blurring caused by camera motion during exposure significantly impacts the images interpretation quality and consequently the quality of photogrammetric products. On blurred images, it is difficult to visually locate ground control points, and the number of identified feature points decreases rapidly together with an increasing blur kernel. The nature of blur can be non-uniform, which makes it hard to forecast for traditional deblurring methods. Due to the above, the author of this publication concluded that the neural methods developed in recent years were able to eliminate blur on UAV images with an unpredictable or highly variable blur nature. In this research, a new, rapid method based on generative adversarial networks (GANs) was applied for deblurring. A data set for neural network training was developed based on real aerial images collected over the last few years. More than 20 full sets of photogrammetric products were developed, including point clouds, orthoimages and digital surface models. The sets were generated from both blurred and deblurred images using the presented method. The results presented in the publication show that the method for improving blurred photo quality significantly contributed to an improvement in the general quality of typical photogrammetric products. The geometric accuracy of the products generated from deblurred photos was maintained despite the rising blur kernel. The quality of textures and input photos was increased. This research proves that the developed method based on neural networks can be used for deblur, even in highly blurred images, and it significantly increases the final geometric quality of the photogrammetric products. In practical cases, it will be possible to implement an additional feature in the photogrammetric software, which will eliminate unwanted blur and allow one to use almost all blurred images in the modelling process.

scholarly journals Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2228
Author(s):  
Ahmed Bin Zaman ◽  
Parastoo Kamranfar ◽  
Carlotta Domeniconi ◽  
Amarda Shehu
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
De Novo ◽  
Source Code ◽  
Protein Molecule ◽  
Biologically Active ◽  
Major Drawback ◽  
Tertiary Structures ◽  
Active Structure

Controlling the quality of tertiary structures computed for a protein molecule remains a central challenge in de-novo protein structure prediction. The rule of thumb is to generate as many structures as can be afforded, effectively acknowledging that having more structures increases the likelihood that some will reside near the sought biologically-active structure. A major drawback with this approach is that computing a large number of structures imposes time and space costs. In this paper, we propose a novel clustering-based approach which we demonstrate to significantly reduce an ensemble of generated structures without sacrificing quality. Evaluations are related on both benchmark and CASP target proteins. Structure ensembles subjected to the proposed approach and the source code of the proposed approach are publicly-available at the links provided in Section 1.

scholarly journals Reconstruction of Generative Adversarial Networks in Cross Modal Image Generation with Canonical Polyadic Decomposition

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Ruixin Ma ◽  
Junying Lou ◽  
Peng Li ◽  
Jing Gao
Keyword(s):  
Mobile Terminal ◽  
Experimental Results ◽  
Generative Adversarial Networks ◽  
Image Generation ◽  
Adversarial Networks ◽  
Speed Up ◽  
Canonical Polyadic Decomposition

Generating pictures from text is an interesting, classic, and challenging task. Benefited from the development of generative adversarial networks (GAN), the generation quality of this task has been greatly improved. Many excellent cross modal GAN models have been put forward. These models add extensive layers and constraints to get impressive generation pictures. However, complexity and computation of existing cross modal GANs are too high to be deployed in mobile terminal. To solve this problem, this paper designs a compact cross modal GAN based on canonical polyadic decomposition. We replace an original convolution layer with three small convolution layers and use an autoencoder to stabilize and speed up training. The experimental results show that our model achieves 20% times of compression in both parameters and FLOPs without loss of quality on generated images.

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