Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks

Abstract Background Protein post-translational modification (PTM) is a key issue to investigate the mechanism of protein’s function. With the rapid development of proteomics technology, a large amount of protein sequence data has been generated, which highlights the importance of the in-depth study and analysis of PTMs in proteins. Method We proposed a new multi-classification machine learning pipeline MultiLyGAN to identity seven types of lysine modified sites. Using eight different sequential and five structural construction methods, 1497 valid features were remained after the filtering by Pearson correlation coefficient. To solve the data imbalance problem, Conditional Generative Adversarial Network (CGAN) and Conditional Wasserstein Generative Adversarial Network (CWGAN), two influential deep generative methods were leveraged and compared to generate new samples for the types with fewer samples. Finally, random forest algorithm was utilized to predict seven categories. Results In the tenfold cross-validation, accuracy (Acc) and Matthews correlation coefficient (MCC) were 0.8589 and 0.8376, respectively. In the independent test, Acc and MCC were 0.8549 and 0.8330, respectively. The results indicated that CWGAN better solved the existing data imbalance and stabilized the training error. Alternatively, an accumulated feature importance analysis reported that CKSAAP, PWM and structural features were the three most important feature-encoding schemes. MultiLyGAN can be found at https://github.com/Lab-Xu/MultiLyGAN. Conclusions The CWGAN greatly improved the predictive performance in all experiments. Features derived from CKSAAP, PWM and structure schemes are the most informative and had the greatest contribution to the prediction of PTM.

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Generative Adversarial Networks-Based Semi-Supervised Automatic Modulation Recognition for Cognitive Radio Networks

Sensors ◽

10.3390/s18113913 ◽

2018 ◽

Vol 18 (11) ◽

pp. 3913 ◽

Cited By ~ 6

Author(s):

Mingxuan Li ◽

Ou Li ◽

Guangyi Liu ◽

Ce Zhang

Keyword(s):

Deep Learning ◽

Cognitive Radio ◽

Supervised Learning ◽

Rapid Development ◽

Generative Adversarial Networks ◽

Modulation Recognition ◽

Learning Methods ◽

Generative Adversarial Network ◽

Adversarial Network ◽

Automatic Modulation Recognition

With the recently explosive growth of deep learning, automatic modulation recognition has undergone rapid development. Most of the newly proposed methods are dependent on large numbers of labeled samples. We are committed to using fewer labeled samples to perform automatic modulation recognition in the cognitive radio domain. Here, a semi-supervised learning method based on adversarial training is proposed which is called signal classifier generative adversarial network. Most of the prior methods based on this technology involve computer vision applications. However, we improve the existing network structure of a generative adversarial network by adding the encoder network and a signal spatial transform module, allowing our framework to address radio signal processing tasks more efficiently. These two technical improvements effectively avoid nonconvergence and mode collapse problems caused by the complexity of the radio signals. The results of simulations show that compared with well-known deep learning methods, our method improves the classification accuracy on a synthetic radio frequency dataset by 0.1% to 12%. In addition, we verify the advantages of our method in a semi-supervised scenario and obtain a significant increase in accuracy compared with traditional semi-supervised learning methods.

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Application of an Improved DCGAN for Image GenerationApplication of an Improved DCGAN for Image Generation

10.21203/rs.3.rs-266104/v1 ◽

2021 ◽

Author(s):

Bingqi Liu ◽

Jiwei Lv ◽

Xinyue Fan ◽

Jie Luo ◽

Tianyi Zou

Keyword(s):

Rapid Development ◽

Activation Function ◽

Generative Adversarial Networks ◽

Generation Model ◽

Image Generation ◽

Generative Adversarial Network ◽

Research Areas ◽

Adversarial Network ◽

Fully Connected ◽

Initial Fraction

Abstract With the rapid development of deep learning, image generation technology has become one of the current hot research areas. A deep convolutional generative adversarial network (DCGAN) can better adapt to complex image distributions than other methods. In this paper, based on a traditional generative adversarial networks (GANs) image generation model, first, the fully connected layer of the DCGAN is further improved. To solve the problem of gradient disappearance in GANs, the activation functions of all layers of the discriminator are LeakyReLU functions, the output layer of the generator uses the Tanh activation function, and the other layers use ReLU. Second, the improved DCGAN model is verified on the MNIST dataset, and simple initial fraction (ISs) and complex initial fraction (ISc) indexes are established from the two aspects of image quality and image generation diversity, respectively. Finally, through a comparison of the two groups of experiments, it is found that the quality of images generated by the DCGAN model constructed in this paper is 2.02 higher than that of the GANs model, and the diversity of the images generated by the DCGAN is 1.55 higher than that of GANs. The results show that the improved DCGAN model can solve the problem of low-quality images being generated by the GANs and achieve good results.

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Fruit tree disease classification system using generative adversarial networks

International Journal of Electrical and Computer Engineering (IJECE) ◽

10.11591/ijece.v11i3.pp2508-2515 ◽

2021 ◽

Vol 11 (3) ◽

pp. 2508

Author(s):

Changsu Kim ◽

Hyesoo Lee ◽

Hoekyung Jung

Keyword(s):

Fruit Tree ◽

Disease Classification ◽

Generative Adversarial Networks ◽

Similar Amount ◽

Generative Adversarial Network ◽

Tree Disease ◽

Data Imbalance ◽

Imbalance Data ◽

Adversarial Network ◽

Adversarial Networks

Smart farm refers to a farm that can remotely and automatically maintain proper growth and management of crops and livestock by integrating technology with agriculture. Currently, smart farms are concentrated in the field of smart horticulture, and although spreading research is being conducted in limited spaces. In addition, it is difficult to obtain a sufficient amount of data to be used for learning, and there is a problem that data imbalance occurs because it is difficult to obtain a similar amount for each class. In this paper, we propose a method to amplify a small amount of data and to solve the problems of imbalance data by using a feature that can learn to mimic the data of a generative adversarial network. The proposed method can create dataset of various crops and also show high hit rate. Dataset generated from crops would be used to solve problems of data imbalance by learning.

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ORGANIC (1).pdf

10.26434/chemrxiv.5309668.v1 ◽

2017 ◽

Author(s):

Benjamin Sanchez-Lengeling ◽

Carlos Outeiral ◽

Gabriel L. Guimaraes ◽

Alan Aspuru-Guzik

Keyword(s):

Machine Learning ◽

Learning Community ◽

Chemical Species ◽

Material Design ◽

Organic Photovoltaic ◽

Generative Adversarial Networks ◽

Generative Adversarial Network ◽

Adversarial Network ◽

Adversarial Networks ◽

Photovoltaic Material

Molecular discovery seeks to generate chemical species tailored to very specific needs. In this paper, we present ORGANIC, a framework based on Objective-Reinforced Generative Adversarial Networks (ORGAN), capable of producing a distribution over molecular space that matches with a certain set of desirable metrics. This methodology combines two successful techniques from the machine learning community: a Generative Adversarial Network (GAN), to create non-repetitive sensible molecular species, and Reinforcement Learning (RL), to bias this generative distribution towards certain attributes. We explore several applications, from optimization of random physicochemical properties to candidates for drug discovery and organic photovoltaic material design.

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Restoring Raindrops Using Attentive Generative Adversarial Networks

Applied Sciences ◽

10.3390/app11157034 ◽

2021 ◽

Vol 11 (15) ◽

pp. 7034

Author(s):

Hee-Deok Yang

Keyword(s):

Weather Conditions ◽

Recurrent Network ◽

Generative Adversarial Networks ◽

Navigation Systems ◽

Vision Systems ◽

Generative Adversarial Network ◽

Network Layers ◽

Adversarial Network ◽

Adversarial Networks ◽

Outdoor Vision

Artificial intelligence technologies and vision systems are used in various devices, such as automotive navigation systems, object-tracking systems, and intelligent closed-circuit televisions. In particular, outdoor vision systems have been applied across numerous fields of analysis. Despite their widespread use, current systems work well under good weather conditions. They cannot account for inclement conditions, such as rain, fog, mist, and snow. Images captured under inclement conditions degrade the performance of vision systems. Vision systems need to detect, recognize, and remove noise because of rain, snow, and mist to boost the performance of the algorithms employed in image processing. Several studies have targeted the removal of noise resulting from inclement conditions. We focused on eliminating the effects of raindrops on images captured with outdoor vision systems in which the camera was exposed to rain. An attentive generative adversarial network (ATTGAN) was used to remove raindrops from the images. This network was composed of two parts: an attentive-recurrent network and a contextual autoencoder. The ATTGAN generated an attention map to detect rain droplets. A de-rained image was generated by increasing the number of attentive-recurrent network layers. We increased the number of visual attentive-recurrent network layers in order to prevent gradient sparsity so that the entire generation was more stable against the network without preventing the network from converging. The experimental results confirmed that the extended ATTGAN could effectively remove various types of raindrops from images.

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Stochastic Restoration of Heavily Compressed Musical Audio Using Generative Adversarial Networks

Electronics ◽

10.3390/electronics10111349 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1349

Author(s):

Stefan Lattner ◽

Javier Nistal

Keyword(s):

Data Storage ◽

Audio Signal ◽

Human Perception ◽

Generative Adversarial Networks ◽

Audio Signals ◽

Generative Adversarial Network ◽

Adversarial Network ◽

Extensive Evaluation ◽

Listening Tests ◽

Musical Audio

Lossy audio codecs compress (and decompress) digital audio streams by removing information that tends to be inaudible in human perception. Under high compression rates, such codecs may introduce a variety of impairments in the audio signal. Many works have tackled the problem of audio enhancement and compression artifact removal using deep-learning techniques. However, only a few works tackle the restoration of heavily compressed audio signals in the musical domain. In such a scenario, there is no unique solution for the restoration of the original signal. Therefore, in this study, we test a stochastic generator of a Generative Adversarial Network (GAN) architecture for this task. Such a stochastic generator, conditioned on highly compressed musical audio signals, could one day generate outputs indistinguishable from high-quality releases. Therefore, the present study may yield insights into more efficient musical data storage and transmission. We train stochastic and deterministic generators on MP3-compressed audio signals with 16, 32, and 64 kbit/s. We perform an extensive evaluation of the different experiments utilizing objective metrics and listening tests. We find that the models can improve the quality of the audio signals over the MP3 versions for 16 and 32 kbit/s and that the stochastic generators are capable of generating outputs that are closer to the original signals than those of the deterministic generators.

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Remote Sensing Image Dataset Expansion Based on Generative Adversarial Networks with Modified Shuffle Attention

Sensors ◽

10.3390/s21144867 ◽

2021 ◽

Vol 21 (14) ◽

pp. 4867

Author(s):

Lu Chen ◽

Hongjun Wang ◽

Xianghao Meng

Keyword(s):

Remote Sensing ◽

Neural Networks ◽

Image Processing ◽

Remote Sensing Image ◽

Generative Adversarial Networks ◽

Generative Adversarial Network ◽

Evaluation Indexes ◽

Adversarial Network ◽

Remote Sensing Image Processing ◽

Data Expansion

With the development of science and technology, neural networks, as an effective tool in image processing, play an important role in gradual remote-sensing image-processing. However, the training of neural networks requires a large sample database. Therefore, expanding datasets with limited samples has gradually become a research hotspot. The emergence of the generative adversarial network (GAN) provides new ideas for data expansion. Traditional GANs either require a large number of input data, or lack detail in the pictures generated. In this paper, we modify a shuffle attention network and introduce it into GAN to generate higher quality pictures with limited inputs. In addition, we improved the existing resize method and proposed an equal stretch resize method to solve the problem of image distortion caused by different input sizes. In the experiment, we also embed the newly proposed coordinate attention (CA) module into the backbone network as a control test. Qualitative indexes and six quantitative evaluation indexes were used to evaluate the experimental results, which show that, compared with other GANs used for picture generation, the modified Shuffle Attention GAN proposed in this paper can generate more refined and high-quality diversified aircraft pictures with more detailed features of the object under limited datasets.

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Enhanced network optimized generative adversarial network for image enhancement

Multimedia Tools and Applications ◽

10.1007/s11042-020-10310-z ◽

2021 ◽

Author(s):

Lingyu Yan ◽

Jiarun Fu ◽

Chunzhi Wang ◽

Zhiwei Ye ◽

Hongwei Chen ◽

...

Keyword(s):

Image Enhancement ◽

Image Recognition ◽

Generative Adversarial Networks ◽

Low Light ◽

Generative Adversarial Network ◽

Adversarial Network ◽

Adversarial Networks ◽

Enhancement Method ◽

New Space ◽

Traditional Image

AbstractWith the development of image recognition technology, face, body shape, and other factors have been widely used as identification labels, which provide a lot of convenience for our daily life. However, image recognition has much higher requirements for image conditions than traditional identification methods like a password. Therefore, image enhancement plays an important role in the process of image analysis for images with noise, among which the image of low-light is the top priority of our research. In this paper, a low-light image enhancement method based on the enhanced network module optimized Generative Adversarial Networks(GAN) is proposed. The proposed method first applied the enhancement network to input the image into the generator to generate a similar image in the new space, Then constructed a loss function and minimized it to train the discriminator, which is used to compare the image generated by the generator with the real image. We implemented the proposed method on two image datasets (DPED, LOL), and compared it with both the traditional image enhancement method and the deep learning approach. Experiments showed that our proposed network enhanced images have higher PNSR and SSIM, the overall perception of relatively good quality, demonstrating the effectiveness of the method in the aspect of low illumination image enhancement.

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CDL-GAN: Contrastive Distance Learning Generative Adversarial Network for Image Generation

Applied Sciences ◽

10.3390/app11041380 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1380

Author(s):

Yingbo Zhou ◽

Pengcheng Zhao ◽

Weiqin Tong ◽

Yongxin Zhu

Keyword(s):

Distance Learning ◽

Feature Learning ◽

Image Synthesis ◽

Image Feature ◽

Generative Adversarial Networks ◽

Image Generation ◽

Generative Adversarial Network ◽

Feature Representations ◽

Adversarial Network ◽

Public Datasets

While Generative Adversarial Networks (GANs) have shown promising performance in image generation, they suffer from numerous issues such as mode collapse and training instability. To stabilize GAN training and improve image synthesis quality with diversity, we propose a simple yet effective approach as Contrastive Distance Learning GAN (CDL-GAN) in this paper. Specifically, we add Consistent Contrastive Distance (CoCD) and Characteristic Contrastive Distance (ChCD) into a principled framework to improve GAN performance. The CoCD explicitly maximizes the ratio of the distance between generated images and the increment between noise vectors to strengthen image feature learning for the generator. The ChCD measures the sampling distance of the encoded images in Euler space to boost feature representations for the discriminator. We model the framework by employing Siamese Network as a module into GANs without any modification on the backbone. Both qualitative and quantitative experiments conducted on three public datasets demonstrate the effectiveness of our method.

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Continuous missing data imputation with incomplete dataset by generative adversarial networks–based unsupervised learning for long-term bridge health monitoring

Structural Health Monitoring ◽

10.1177/14759217211021942 ◽

2021 ◽

pp. 147592172110219

Author(s):

Huachen Jiang ◽

Chunfeng Wan ◽

Kang Yang ◽

Youliang Ding ◽

Songtao Xue

Keyword(s):

Missing Data ◽

Health Monitoring ◽

Signal Transmission ◽

Imputation Accuracy ◽

Generative Adversarial Networks ◽

Data Imputation ◽

Sensor Failure ◽

Generative Adversarial Network ◽

Missing Data Imputation ◽

Adversarial Network

Wireless sensors are the key components of structural health monitoring systems. During the signal transmission, sensor failure is inevitable, among which, data loss is the most common type. Missing data problem poses a huge challenge to the consequent damage detection and condition assessment, and therefore, great importance should be attached. Conventional missing data imputation basically adopts the correlation-based method, especially for strain monitoring data. However, such methods often require delicate model selection, and the correlations for vehicle-induced strains are much harder to be captured compared with temperature-induced strains. In this article, a novel data-driven generative adversarial network (GAN) for imputing missing strain response is proposed. As opposed to traditional ways where correlations for inter-strains are explicitly modeled, the proposed method directly imputes the missing data considering the spatial–temporal relationships with other strain sensors based on the remaining observed data. Furthermore, the intact and complete dataset is not even necessary during the training process, which shows another great superiority over the model-based imputation method. The proposed method is implemented and verified on a real concrete bridge. In order to demonstrate the applicability and robustness of the GAN, imputation for single and multiple sensors is studied. Results show the proposed method provides an excellent performance of imputation accuracy and efficiency.

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