scholarly journals MB-GAN: Microbiome Simulation via Generative Adversarial Network

2019 ◽  
Author(s):  
Ruichen Rong ◽  
Shuang Jiang ◽  
Lin Xu ◽  
Guanghua Xiao ◽  
Yang Xie ◽  
...  
Keyword(s):  
Learning Community ◽  
Association Studies ◽  
Complex Structure ◽  
Simulated Data ◽  
Real Data ◽  
Original Data ◽  
Generative Adversarial Network ◽  
Methodology Development ◽  
Adversarial Network ◽  
Microbiome Data

AbstractSimulation is a critical component of experimental design and evaluation of analysis methods in microbiome association studies. However, statistically modeling the microbiome data is challenging since that the complex structure in the real data is difficult to be fully represented by statistical models. To address this challenge, we designed a novel simulation framework for microbiome data using a generative adversarial network (GAN), called MB-GAN, by utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from a given dataset and compute simulated datasets that are indistinguishable from it. When MB-GAN was applied to a case-control microbiome study of 396 samples, we demonstrated that the simulated data and the original data had similar first-order and second-order properties, including sparsity, diversities, and taxa-taxa correlations. These advantages are suitable for further microbiome methodology development where high fidelity microbiome data are needed.

scholarly journals MB-GAN: Microbiome Simulation via Generative Adversarial Network

GigaScience ◽  
2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Ruichen Rong ◽  
Shuang Jiang ◽  
Lin Xu ◽  
Guanghua Xiao ◽  
Yang Xie ◽  
...  
Keyword(s):  
Learning Community ◽  
Association Studies ◽  
Human Microbiome ◽  
Simulated Data ◽  
Original Data ◽  
Generative Adversarial Network ◽  
Methodology Development ◽  
Adversarial Network ◽  
Microbiome Data ◽  
Analytical Tools

Abstract Background Trillions of microbes inhabit the human body and have a profound effect on human health. The recent development of metagenome-wide association studies and other quantitative analysis methods accelerate the discovery of the associations between human microbiome and diseases. To assess the strengths and limitations of these analytical tools, simulating realistic microbiome datasets is critically important. However, simulating the real microbiome data is challenging because it is difficult to model their correlation structure using explicit statistical models. Results To address the challenge of simulating realistic microbiome data, we designed a novel simulation framework termed MB-GAN, by using a generative adversarial network (GAN) and utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from them. In practice, MB-GAN showed the following advantages. First, MB-GAN avoids explicit statistical modeling assumptions, and it only requires real datasets as inputs. Second, unlike the traditional GANs, MB-GAN is easily applicable and can converge efficiently. Conclusions By applying MB-GAN to a case-control gut microbiome study of 396 samples, we demonstrated that the simulated data and the original data had similar first-order and second-order properties, including sparsity, diversities, and taxa-taxa correlations. These advantages are suitable for further microbiome methodology development where high-fidelity microbiome data are needed.

scholarly journals Separating Chinese Character from Noisy Background Using GAN

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Bin Huang ◽  
Jiaqi Lin ◽  
Jinming Liu ◽  
Jie Chen ◽  
Jiemin Zhang ◽  
...  
Keyword(s):  
Character Recognition ◽  
Optical Character Recognition ◽  
Complex Structure ◽  
Real Data ◽  
Semantic Segmentation ◽  
Chinese Characters ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Basic Network ◽  
Noisy Background

Separating printed or handwritten characters from a noisy background is valuable for many applications including test paper autoscoring. The complex structure of Chinese characters makes it difficult to obtain the goal because of easy loss of fine details and overall structure in reconstructed characters. This paper proposes a method for separating Chinese characters based on generative adversarial network (GAN). We used ESRGAN as the basic network structure and applied dilated convolution and a novel loss function that improve the quality of reconstructed characters. Four popular Chinese fonts (Hei, Song, Kai, and Imitation Song) on real data collection were tested, and the proposed design was compared with other semantic segmentation approaches. The experimental results showed that the proposed method effectively separates Chinese characters from noisy background. In particular, our methods achieve better results in terms of Intersection over Union (IoU) and optical character recognition (OCR) accuracy.

scholarly journals Automatic Inference of Demographic Parameters Using Generative Adversarial Networks

2020 ◽  
Author(s):  
Zhanpeng Wang ◽  
Jiaping Wang ◽  
Michael Kourakos ◽  
Nhung Hoang ◽  
Hyong Hark Lee ◽  
...  
Keyword(s):  
Synthetic Data ◽  
Simulated Data ◽  
Real Data ◽  
Simulation Software ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Isolation With Migration ◽  
Adversarial Network ◽  
Novel Approach ◽  
Input Parameters

AbstractPopulation genetics relies heavily on simulated data for validation, inference, and intuition. In particular, since real data is always limited, simulated data is crucial for training machine learning methods. Simulation software can accurately model evolutionary processes, but requires many hand-selected input parameters. As a result, simulated data often fails to mirror the properties of real genetic data, which limits the scope of methods that rely on it. In this work, we develop a novel approach to estimating parameters in population genetic models that automatically adapts to data from any population. Our method is based on a generative adversarial network that gradually learns to generate realistic synthetic data. We demonstrate that our method is able to recover input parameters in a simulated isolation-with-migration model. We then apply our method to human data from the 1000 Genomes Project, and show that we can accurately recapitulate the features of real data.

scholarly journals Decentralized Learning with Virtual Patients for Medical Diagnosis of Diabetes

2021 ◽  
Vol 2 (4) ◽  
Author(s):  
Yuta Takahashi ◽  
Han-ten Chang ◽  
Akie Nakai ◽  
Rina Kagawa ◽  
Hiroyasu Ando ◽  
...  
Keyword(s):  
Machine Learning ◽  
Linear Method ◽  
Real Data ◽  
Original Data ◽  
Medical Data ◽  
Generative Adversarial Network ◽  
Trade Off ◽  
Distributed Information ◽  
Adversarial Network ◽  
Data Collaboration

AbstractMachine learning, applied to medical data, can uncover new knowledge and support medical practices. However, analyzing medical data by machine learning methods presents a trade-off between accuracy and privacy. To overcome the trade-off, we apply the data collaboration analysis method to medical data. This method using artificial dummy data enables analysis to compare distributed information without using the original data. The purpose of our experiment is to identify patients diagnosed with diabetes mellitus (DM), using 29,802 instances of real data obtained from the University of Tsukuba Hospital between 01/03/2013 and 30/09/2018. The whole data is divided into a number of datasets to simulate different hospitals. We propose the following improvements for the data collaboration analysis. (1) Making the dummy data which has a reality and (2) using non-linear reconverting functions into the comparable space. Both can be realized using the generative adversarial network (GAN) and Node2Vec, respectively. The improvement effects of dummy data with GAN scores more than 10% over the effects of dummy data with random numbers. Furthermore, the improvement effect of the re-conversion by Node2Vec with GAN anchor data scores about 20% higher than the linear method with random dummy data. Our results reveal that the data collaboration method with appropriate modifications, depending on data type, improves analysis performance.

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 Penalized partial least squares for pleiotropy

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Camilo Broc ◽  
Therese Truong ◽  
Benoit Liquet
Keyword(s):  
Least Squares ◽  
Partial Least Squares ◽  
Association Studies ◽  
A Priori ◽  
Simulated Data ◽  
Real Data ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Multiple Traits ◽  
Application Fields

Abstract Background The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting these cross-phenotype genetic associations could help to identify and understand common biological mechanisms underlying some diseases. Common approaches test the association between genetic variants and multiple traits at the SNP level. In this paper, we propose a novel gene- and a pathway-level approach in the case where several independent GWAS on independent traits are available. The method is based on a generalization of the sparse group Partial Least Squares (sgPLS) to take into account groups of variables, and a Lasso penalization that links all independent data sets. This method, called joint-sgPLS, is able to convincingly detect signal at the variable level and at the group level. Results Our method has the advantage to propose a global readable model while coping with the architecture of data. It can outperform traditional methods and provides a wider insight in terms of a priori information. We compared the performance of the proposed method to other benchmark methods on simulated data and gave an example of application on real data with the aim to highlight common susceptibility variants to breast and thyroid cancers. Conclusion The joint-sgPLS shows interesting properties for detecting a signal. As an extension of the PLS, the method is suited for data with a large number of variables. The choice of Lasso penalization copes with architectures of groups of variables and observations sets. Furthermore, although the method has been applied to a genetic study, its formulation is adapted to any data with high number of variables and an exposed a priori architecture in other application fields.

scholarly journals Data Augmentation Using Generative Adversarial Network for Automatic Machine Fault Detection Based on Vibration Signals

2021 ◽  
Vol 11 (5) ◽  
pp. 2166
Author(s):  
Van Bui ◽  
Tung Lam Pham ◽  
Huy Nguyen ◽  
Yeong Min Jang
Keyword(s):  
Fault Detection ◽  
Data Augmentation ◽  
Model Performance ◽  
Original Data ◽  
Fault Classification ◽  
Training Process ◽  
Generative Adversarial Network ◽  
Data Set ◽  
Adversarial Network ◽  
Machine Fault

In the last decade, predictive maintenance has attracted a lot of attention in industrial factories because of its wide use of the Internet of Things and artificial intelligence algorithms for data management. However, in the early phases where the abnormal and faulty machines rarely appeared in factories, there were limited sets of machine fault samples. With limited fault samples, it is difficult to perform a training process for fault classification due to the imbalance of input data. Therefore, data augmentation was required to increase the accuracy of the learning model. However, there were limited methods to generate and evaluate the data applied for data analysis. In this paper, we introduce a method of using the generative adversarial network as the fault signal augmentation method to enrich the dataset. The enhanced data set could increase the accuracy of the machine fault detection model in the training process. We also performed fault detection using a variety of preprocessing approaches and classified the models to evaluate the similarities between the generated data and authentic data. The generated fault data has high similarity with the original data and it significantly improves the accuracy of the model. The accuracy of fault machine detection reaches 99.41% with 20% original fault machine data set and 93.1% with 0% original fault machine data set (only use generate data only). Based on this, we concluded that the generated data could be used to mix with original data and improve the model performance.

scholarly journals 1D conditional generative adversarial network for spectrum-to-spectrum translation of simulated chemical reflectance signatures

2021 ◽  
Author(s):  
Cara Murphy ◽  
John Kerekes
Keyword(s):  
Classification Accuracy ◽  
Domain Adaptation ◽  
Real Data ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Average Classification Accuracy ◽  
Adversarial Network ◽  
Chemical Residues ◽  
Reflectance Data

The classification of trace chemical residues through active spectroscopic sensing is challenging due to the lack of physics-based models that can accurately predict spectra. To overcome this challenge, we leveraged the field of domain adaptation to translate data from the simulated to the measured domain for training a classifier. We developed the first 1D conditional generative adversarial network (GAN) to perform spectrum-to-spectrum translation of reflectance signatures. We applied the 1D conditional GAN to a library of simulated spectra and quantified the improvement in classification accuracy on real data using the translated spectra for training the classifier. Using the GAN-translated library, the average classification accuracy increased from 0.622 to 0.723 on real chemical reflectance data, including data from chemicals not included in the GAN training set.

scholarly journals JANE: Jointly Adversarial Network Embedding

2020 ◽  
Author(s):  
Liang Yang ◽  
Yuexue Wang ◽  
Junhua Gu ◽  
Chuan Wang ◽  
Xiaochun Cao ◽  
...  
Keyword(s):  
Link Prediction ◽  
Real Data ◽  
Semantic Space ◽  
Network Embedding ◽  
Generative Adversarial Network ◽  
Adversarial Learning ◽  
Adversarial Network ◽  
Node Clustering ◽  
Topology Information ◽  
Embedding Methods

Motivated by the capability of Generative Adversarial Network on exploring the latent semantic space and capturing semantic variations in the data distribution, adversarial learning has been adopted in network embedding to improve the robustness. However, this important ability is lost in existing adversarially regularized network embedding methods, because their embedding results are directly compared to the samples drawn from perturbation (Gaussian) distribution without any rectification from real data. To overcome this vital issue, a novel Joint Adversarial Network Embedding (JANE) framework is proposed to jointly distinguish the real and fake combinations of the embeddings, topology information and node features. JANE contains three pluggable components, Embedding module, Generator module and Discriminator module. The overall objective function of JANE is defined in a min-max form, which can be optimized via alternating stochastic gradient. Extensive experiments demonstrate the remarkable superiority of the proposed JANE on link prediction (3% gains in both AUC and AP) and node clustering (5% gain in F1 score).

Sound Field Reconstruction in Rooms with Deep Generative Models

2021 ◽  
Vol 263 (5) ◽  
pp. 1527-1538
Author(s):  
Xenofon Karakonstantis ◽  
Efren Fernandez Grande
Keyword(s):  
Plane Waves ◽  
Sound Field ◽  
Real Data ◽  
Generative Models ◽  
Random Wave ◽  
Generative Adversarial Network ◽  
Underlying Distribution ◽  
Adversarial Network ◽  
Reconstruction Methods ◽  
Free Region

The characterization of Room Impulse Responses (RIR) over an extended region in a room by means of measurements requires dense spatial with many microphones. This can often become intractable and time consuming in practice. Well established reconstruction methods such as plane wave regression show that the sound field in a room can be reconstructed from sparsely distributed measurements. However, these reconstructions usually rely on assuming physical sparsity (i.e. few waves compose the sound field) or trait in the measured sound field, making the models less generalizable and problem specific. In this paper we introduce a method to reconstruct a sound field in an enclosure with the use of a Generative Adversarial Network (GAN), which s new variants of the data distributions that it is trained upon. The goal of the proposed GAN model is to estimate the underlying distribution of plane waves in any source free region, and map these distributions from a stochastic, latent representation. A GAN is trained on a large number of synthesized sound fields represented by a random wave field and then tested on both simulated and real data sets, of lightly damped and reverberant rooms.

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