scholarly journals Leveraging high-throughput screening data and conditional generative adversarial networks to advance predictive toxicology

2020 ◽  
Author(s):  
Adrian J. Green ◽  
Martin J. Mohlenkamp ◽  
Jhuma Das ◽  
Meenal Chaudhari ◽  
Lisa Truong ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Chemical Structure ◽  
Structural Information ◽  
Generative Adversarial Networks ◽  
Toxicity Data ◽  
Generative Adversarial Network ◽  
Structure Information ◽  
Adversarial Network

AbstractThere are currently 85,000 chemicals registered with the Environmental Protection Agency (EPA) under the Toxic Substances Control Act, but only a small fraction have measured toxicological data. To address this gap, high-throughput screening (HTS) methods are vital. As part of one such HTS effort, embryonic zebrafish were used to examine a suite of morphological and mortality endpoints at six concentrations from over 1,000 unique chemicals found in the ToxCast library (phase 1 and 2). We hypothesized that by using a conditional Generative Adversarial Network (cGAN) and leveraging this large set of toxicity data, plus chemical structure information, we could efficiently predict toxic outcomes of untested chemicals. CAS numbers for each chemical were used to generate textual files containing three-dimensional structural information for each chemical. Utilizing a novel method in this space, we converted the 3D structural information into a weighted set of points while retaining all information about the structure. In vivo toxicity and chemical data were used to train two neural network generators. The first used regression (Go-ZT) while the second utilized cGAN architecture (GAN-ZT) to train a generator to produce toxicity data. Our results showed that both Go-ZT and GAN-ZT models produce similar results, but the cGAN achieved a higher sensitivity (SE) value of 85.7% vs 71.4%. Conversely, Go-ZT attained higher specificity (SP), positive predictive value (PPV), and Kappa results of 67.3%, 23.4%, and 0.21 compared to 24.5%, 14.0%, and 0.03 for the cGAN, respectively. By combining both Go-ZT and GAN-ZT, our consensus model improved the SP, PPV, and Kappa, to 75.5%, 25.0%, and 0.211, respectively, resulting in an area under the receiver operating characteristic (AUROC) of 0.663. Considering their potential use as prescreening tools, these models could provide in vivo toxicity predictions and insight into untested areas of the chemical space to prioritize compounds for HT testing.SummaryA conditional Generative Adversarial Network (cGAN) can leverage a large chemical set of experimental toxicity data plus chemical structure information to predict the toxicity of untested compounds.

scholarly journals Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology

2021 ◽  
Vol 17 (7) ◽  
pp. e1009135
Author(s):  
Adrian J. Green ◽  
Martin J. Mohlenkamp ◽  
Jhuma Das ◽  
Meenal Chaudhari ◽  
Lisa Truong ◽  
...  
Keyword(s):  
Neural Networks ◽  
High Throughput ◽  
Environmental Protection Agency ◽  
High Throughput Screening ◽  
Deep Neural Networks ◽  
Generative Adversarial Networks ◽  
Support Vector ◽  
Large Set ◽  
Toxicity Data

There are currently 85,000 chemicals registered with the Environmental Protection Agency (EPA) under the Toxic Substances Control Act, but only a small fraction have measured toxicological data. To address this gap, high-throughput screening (HTS) and computational methods are vital. As part of one such HTS effort, embryonic zebrafish were used to examine a suite of morphological and mortality endpoints at six concentrations from over 1,000 unique chemicals found in the ToxCast library (phase 1 and 2). We hypothesized that by using a conditional generative adversarial network (cGAN) or deep neural networks (DNN), and leveraging this large set of toxicity data we could efficiently predict toxic outcomes of untested chemicals. Utilizing a novel method in this space, we converted the 3D structural information into a weighted set of points while retaining all information about the structure. In vivo toxicity and chemical data were used to train two neural network generators. The first was a DNN (Go-ZT) while the second utilized cGAN architecture (GAN-ZT) to train generators to produce toxicity data. Our results showed that Go-ZT significantly outperformed the cGAN, support vector machine, random forest and multilayer perceptron models in cross-validation, and when tested against an external test dataset. By combining both Go-ZT and GAN-ZT, our consensus model improved the SE, SP, PPV, and Kappa, to 71.4%, 95.9%, 71.4% and 0.673, respectively, resulting in an area under the receiver operating characteristic (AUROC) of 0.837. Considering their potential use as prescreening tools, these models could provide in vivo toxicity predictions and insight into the hundreds of thousands of untested chemicals to prioritize compounds for HT testing.

scholarly journals SEGAN: Structure-Enhanced Generative Adversarial Network for Compressed Sensing MRI Reconstruction

2019 ◽  
Vol 33 ◽  
pp. 1012-1019 ◽  
Author(s):  
Zhongnian Li ◽  
Tao Zhang ◽  
Peng Wan ◽  
Daoqiang Zhang
Keyword(s):  
Compressed Sensing ◽  
Multiple Scale ◽  
Global Scale ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Structure Information ◽  
Adversarial Network ◽  
Adversarial Networks ◽  
Mri Reconstruction ◽  
Convolution Filters

Generative Adversarial Networks (GANs) are powerful tools for reconstructing Compressed Sensing Magnetic Resonance Imaging (CS-MRI). However most recent works lack exploration of structure information of MRI images that is crucial for clinical diagnosis. To tackle this problem, we propose the Structure-Enhanced GAN (SEGAN) that aims at restoring structure information at both local and global scale. SEGAN defines a new structure regularization called Patch Correlation Regularization (PCR) which allows for efficient extraction of structure information. In addition, to further enhance the ability to uncover structure information, we propose a novel generator SU-Net by incorporating multiple-scale convolution filters into each layer. Besides, we theoretically analyze the convergence of stochastic factors contained in training process. Experimental results show that SEGAN is able to learn target structure information and achieves state-of-theart performance for CS-MRI reconstruction.

ORGANIC (1).pdf

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.

scholarly journals Restoring Raindrops Using Attentive Generative Adversarial Networks

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.

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

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yingxi Yang ◽  
Hui Wang ◽  
Wen Li ◽  
Xiaobo Wang ◽  
Shizhao Wei ◽  
...  
Keyword(s):  
Correlation Coefficient ◽  
Sequence Data ◽  
Rapid Development ◽  
Pearson Correlation ◽  
Structural Features ◽  
Generative Adversarial Networks ◽  
Post Translational Modification ◽  
Generative Adversarial Network ◽  
Data Imbalance ◽  
Adversarial Network

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.

scholarly journals High-throughput screening and rational design of biofunctionalized surfaces with optimized biocompatibility and antimicrobial activity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhou Fang ◽  
Junjian Chen ◽  
Ye Zhu ◽  
Guansong Hu ◽  
Haoqian Xin ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
High Throughput ◽  
High Throughput Screening ◽  
Rational Design ◽  
Click Reaction ◽  
Reaction Times ◽  
Great Promise ◽  
Biomaterial Surfaces

AbstractPeptides are widely used for surface modification to develop improved implants, such as cell adhesion RGD peptide and antimicrobial peptide (AMP). However, it is a daunting challenge to identify an optimized condition with the two peptides showing their intended activities and the parameters for reaching such a condition. Herein, we develop a high-throughput strategy, preparing titanium (Ti) surfaces with a gradient in peptide density by click reaction as a platform, to screen the positions with desired functions. Such positions are corresponding to optimized molecular parameters (peptide densities/ratios) and associated preparation parameters (reaction times/reactant concentrations). These parameters are then extracted to prepare nongradient mono- and dual-peptide functionalized Ti surfaces with desired biocompatibility or/and antimicrobial activity in vitro and in vivo. We also demonstrate this strategy could be extended to other materials. Here, we show that the high-throughput versatile strategy holds great promise for rational design and preparation of functional biomaterial surfaces.

scholarly journals Stochastic Restoration of Heavily Compressed Musical Audio Using Generative Adversarial Networks

Electronics ◽  
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.

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

Sensors ◽  
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.

scholarly journals Enhanced network optimized generative adversarial network for image enhancement

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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