scholarly journals scGAIN: Single Cell RNA-seq Data Imputation using Generative Adversarial Networks

2019 ◽  
Author(s):  
Mohamed K. Gunady ◽  
Jayaram Kancherla ◽  
Héctor Corrada Bravo ◽  
Soheil Feizi
Keyword(s):  
Single Cell ◽  
Real Data ◽  
Training Model ◽  
Generative Adversarial Networks ◽  
Data Imputation ◽  
Gene Expressions ◽  
Sharp Estimates ◽  
Adversarial Networks ◽  
Approximate Distribution ◽  
Cell Data

AbstractSingle cell RNA sequencing (scRNA-seq) provides a rich view into the heterogeneity underlying a cell population. However single-cell data are usually noisy and very sparse due to the presence of dropout genes. In this work we propose an approach to impute missing gene expressions in single cell data using generative adversarial networks (GANs). By learning an approximate distribution of the data, our approach, scGAIN, can impute dropouts in simulated and real single cell data. The work in this paper discusses how to adopt GAIN training model into the domain of imputing single cell data. Experiments show that scGAIN gives competitive results compared to the state-of-the-art approaches while showing superiority in various aspects in simulation and real data. Imputation by scGAIN successfully recovers the underlying clustering of different subpopulations, provides sharp estimates around true mean expressions and increase the correspondence with matched bulk RNAseq experiments.

scholarly journals RoCGAN: Robust Conditional GAN

2020 ◽  
Vol 128 (10-11) ◽  
pp. 2665-2683 ◽  
Author(s):  
Grigorios G. Chrysos ◽  
Jean Kossaifi ◽  
Stefanos Zafeiriou
Keyword(s):  
Large Scale ◽  
Real Data ◽  
Superior Performance ◽  
Target Space ◽  
Generative Adversarial Networks ◽  
Natural Scenes ◽  
Adversarial Networks ◽  
Target Manifold ◽  
The Face ◽  
Intense Noise

Abstract Conditional image generation lies at the heart of computer vision and conditional generative adversarial networks (cGAN) have recently become the method of choice for this task, owing to their superior performance. The focus so far has largely been on performance improvement, with little effort in making cGANs more robust to noise. However, the regression (of the generator) might lead to arbitrarily large errors in the output, which makes cGANs unreliable for real-world applications. In this work, we introduce a novel conditional GAN model, called RoCGAN, which leverages structure in the target space of the model to address the issue. Specifically, we augment the generator with an unsupervised pathway, which promotes the outputs of the generator to span the target manifold, even in the presence of intense noise. We prove that RoCGAN share similar theoretical properties as GAN and establish with both synthetic and real data the merits of our model. We perform a thorough experimental validation on large scale datasets for natural scenes and faces and observe that our model outperforms existing cGAN architectures by a large margin. We also empirically demonstrate the performance of our approach in the face of two types of noise (adversarial and Bernoulli).

scholarly journals Is Synthetic The New Real? Performance Analysis of Time Series Generation Techniques with Focus on Network Load Forecasting

2021 ◽  
Author(s):  
Muhammad Haris Naveed ◽  
Umair Hashmi ◽  
Nayab Tajved ◽  
Neha Sultan ◽  
Ali Imran
Keyword(s):  
Synthetic Data ◽  
Real Data ◽  
Generative Adversarial Networks ◽  
Data Set ◽  
Qualitative And Quantitative ◽  
Adversarial Networks ◽  
Network Load ◽  
Quantitative Metrics ◽  
Real Performance ◽  
Analysis Of Time Series

This paper explores whether Generative Adversarial Networks (GANs) can produce realistic network load data that can be utilized to train machine learning models in lieu of real data. In this regard, we evaluate the performance of three recent GAN architectures on the Telecom Italia data set across a set of qualitative and quantitative metrics. Our results show that GAN generated synthetic data is indeed similar to real data and forecasting models trained on this data achieve similar performance to those trained on real data.

scholarly journals A guide to trajectory inference and RNA velocity

2021 ◽  
Author(s):  
Philipp Weiler ◽  
Koen Van den Berge ◽  
Kelly Street ◽  
Simone Tiberi
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Time Derivative ◽  
Real Data ◽  
Use Case ◽  
Technological Developments ◽  
Inference Methods ◽  
Cell Data ◽  
Significant Attention ◽  
Gene Expression Levels

Technological developments have led to an explosion of high-throughput single cell data, which are revealing unprecedented perspectives on cell identity. Recently, significant attention has focused on investigating, from single-cell RNA-sequencing (scRNA-seq) data, cellular dynamic processes, such as cell differentiation, cell cycle and cell (de)activation. Trajectory inference methods estimate a trajectory, a collection of differentiation paths of a dynamic system, by ordering cells along the paths of such a dynamic process. While trajectory inference tools typically work with gene expression levels, common scRNA-seq protocols allow the identification and quantification of unspliced pre-mRNAs and mature spliced mRNAs, for each gene. By exploiting the abundance of unspliced and spliced mRNA, one can infer the RNA velocity of individual cells, i.e., the time derivative of the gene expression state of cells. Whereas traditional trajectory inference methods reconstruct cellular dynamics given a population of cells of varying maturity, RNA velocity relies on a dynamical model describing splicing dynamics. Here, we initially discuss conceptual and theoretical aspects of both approaches, then illustrate how they can be combined together, and finally present an example use-case on real data.

scholarly journals Generative adversarial networks for generating synthetic features for Wi-Fi signal quality

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260308
Author(s):  
Mauro Castelli ◽  
Luca Manzoni ◽  
Tatiane Espindola ◽  
Aleš Popovič ◽  
Andrea De Lorenzo
Keyword(s):  
Synthetic Data ◽  
Real Data ◽  
Generative Models ◽  
Generative Adversarial Networks ◽  
Signal Quality ◽  
Quality Service ◽  
High Quality ◽  
The Real ◽  
Adversarial Networks ◽  
High Quality Service

Wireless networks are among the fundamental technologies used to connect people. Considering the constant advancements in the field, telecommunication operators must guarantee a high-quality service to keep their customer portfolio. To ensure this high-quality service, it is common to establish partnerships with specialized technology companies that deliver software services in order to monitor the networks and identify faults and respective solutions. A common barrier faced by these specialized companies is the lack of data to develop and test their products. This paper investigates the use of generative adversarial networks (GANs), which are state-of-the-art generative models, for generating synthetic telecommunication data related to Wi-Fi signal quality. We developed, trained, and compared two of the most used GAN architectures: the Vanilla GAN and the Wasserstein GAN (WGAN). Both models presented satisfactory results and were able to generate synthetic data similar to the real ones. In particular, the distribution of the synthetic data overlaps the distribution of the real data for all of the considered features. Moreover, the considered generative models can reproduce the same associations observed for the synthetic features. We chose the WGAN as the final model, but both models are suitable for addressing the problem at hand.

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