scholarly journals LSH-GAN: in-silico generation of cells for small sample high dimensional scRNA-seq data

2021 ◽  
Author(s):  
Snehalika Lall ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Gene Selection ◽  
Fundamental Problem ◽  
Small Sample ◽  
Locality Sensitive Hashing ◽  
Training Procedure ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Cell Clustering ◽  
Standard Procedures ◽  
Downstream Analysis

Abstract A fundamental problem of downstream analysis of scRNA-seq data is the unavailability of enough cell samples compare to the feature size. This is mostly due to the budgetary constraint of single cell experiments or simply because of the small number of available patient samples. Here, we present an improved version of generative adversarial network (GAN) called LSH-GAN to address this issue by producing new realistic cell samples. We update the training procedure of the generator of GAN using locality sensitive hashing which speeds up the sample generation, thus maintains the feasibility of applying the standard procedures of downstream analysis. LSH-GAN outperforms the benchmarks for realistic generation of quality cell samples. Experimental results show that generated samples of LSH-GAN improves the performance of the downstream analysis such as feature (gene) selection and cell clustering.

scholarly journals Generating realistic cell samples for gene selection in scRNA-seq data: A novel generative framework

2021 ◽  
Author(s):  
Snehalika Lall ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Gene Selection ◽  
Small Sample Size ◽  
Small Sample ◽  
Locality Sensitive Hashing ◽  
High Dimensional ◽  
Training Procedure ◽  
Generative Adversarial Network ◽  
Selection Procedures ◽  
Adversarial Network ◽  
Cell Clustering

AbstractHigh dimensional, small sample size (HDSS) scRNA-seq data presents a challenge to the gene selection task in single cell. Conventional gene selection techniques are unstable and less reliable due to the fewer number of available samples which affects cell clustering and annotation. Here, we present an improved version of generative adversarial network (GAN) called LSH-GAN to address this issue by producing new realistic samples and combining this with the original scRNA-seq data. We update the training procedure of the generator of GAN using locality sensitive hashing which speeds up the sample generation, thus maintains the feasibility of applying gene selection procedures in high dimension scRNA-seq data. Experimental results show a significant improvement in the performance of benchmark feature (gene) selection techniques on generated samples of one synthetic and four HDSS scRNA-seq data. Comprehensive simulation study ensures the applicability of the model in the feature (gene) selection domain of HDSS scRNA-seq data.AvailabilityThe corresponding software is available at https://github.com/Snehalikalall/LSH-GAN

scholarly journals sc-REnF: An Entropy Guided Robust Feature Selection for Single-Cell RNA-seq Data

2021 ◽  
Author(s):  
Snehalika Lall ◽  
Abhik Ghosh ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Small Sample ◽  
Rna Seq ◽  
Homogeneous Grouping ◽  
Cell Clustering ◽  
Selection For ◽  
Downstream Analysis ◽  
Cell Data

Abstract Annotation of cells in single-cell clustering requires a homogeneous grouping of cell populations. Since single cell data is susceptible to technical noise, the quality of genes selected prior to clustering is of crucial importance in the preliminary steps of downstream analysis. Therefore, interest in robust gene selection has gained considerable attention in recent years. We introduce sc-REnF, (robust entropy based feature (gene) selection method), aiming to leverage the advantages of Rényi and Tsallis> entropies in gene selection for single cell clustering. Experiments demonstrate that with tuned parameter (q), Rényi and Tsallis entropies select genes that improved the clustering results significantly, over the other competing methods. sc-REnF can capture relevancy and redundancy among the features of noisy data extremely well due to its robust objective function. Moreover, the selected features/genes can able to clusters the unknown cells with a high accuracy. Finally, sc-REnF yields good clustering performance in small sample, large feature scRNA-seq data.

scholarly journals sc-REnF:An entropy guided robust feature selection for clustering of single-cell rna-seq data

2020 ◽  
Author(s):  
Snehalika Lall ◽  
Abhik Ghosh ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Rna Seq ◽  
Technical Noise ◽  
Marker Selection ◽  
Cell Clustering ◽  
Typing Methods ◽  
Original Application ◽  
Downstream Analysis ◽  
Cell Typing

ABSTRACTMany single-cell typing methods require pure clustering of cells, which is susceptible towards the technical noise, and heavily dependent on high quality informative genes selected in the preliminary steps of downstream analysis. Techniques for gene selection in single-cell RNA sequencing (scRNA-seq) data are seemingly simple which casts problems with respect to the resolution of (sub-)types detection, marker selection and ultimately impacts towards cell annotation. We introduce sc-REnF, a novel and robust entropy based feature (gene) selection method, which leverages the landmark advantage of ‘Renyi’ and ‘Tsallis’ entropy achieved in their original application, in single cell clustering. Thereby, gene selection is robust and less sensitive towards the technical noise present in the data, producing a pure clustering of cells, beyond classifying independent and unknown sample with utmost accuracy. The corresponding software is available at: https://github.com/Snehalikalall/sc-REnF

scholarly journals Learning to Transfer: Unsupervised Domain Translation via Meta-Learning

2020 ◽  
Vol 34 (07) ◽  
pp. 11507-11514
Author(s):  
Jianxin Lin ◽  
Yijun Wang ◽  
Zhibo Chen ◽  
Tianyu He
Keyword(s):  
Learning Experiences ◽  
Training Data ◽  
Training Procedure ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Training Samples ◽  
Meta Learning ◽  
Translation Methods ◽  
Meta Optimization ◽  
Dual Translation

Unsupervised domain translation has recently achieved impressive performance with Generative Adversarial Network (GAN) and sufficient (unpaired) training data. However, existing domain translation frameworks form in a disposable way where the learning experiences are ignored and the obtained model cannot be adapted to a new coming domain. In this work, we take on unsupervised domain translation problems from a meta-learning perspective. We propose a model called Meta-Translation GAN (MT-GAN) to find good initialization of translation models. In the meta-training procedure, MT-GAN is explicitly trained with a primary translation task and a synthesized dual translation task. A cycle-consistency meta-optimization objective is designed to ensure the generalization ability. We demonstrate effectiveness of our model on ten diverse two-domain translation tasks and multiple face identity translation tasks. We show that our proposed approach significantly outperforms the existing domain translation methods when each domain contains no more than ten training samples.

Speech Emotion Recognition on Small Sample Learning by Hybrid WGAN-LSTM Networks

2021 ◽  
Author(s):  
Cunwei Sun ◽  
Luping Ji ◽  
Hailing Zhong
Keyword(s):  
Emotion Recognition ◽  
Language Processing ◽  
Short Term Memory ◽  
Small Sample ◽  
New Method ◽  
Small Samples ◽  
Speech Emotion Recognition ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
In Series

The speech emotion recognition based on the deep networks on small samples is often a very challenging problem in natural language processing. The massive parameters of a deep network are much difficult to be trained reliably on small-quantity speech samples. Aiming at this problem, we propose a new method through the systematical cooperation of Generative Adversarial Network (GAN) and Long Short Term Memory (LSTM). In this method, it utilizes the adversarial training of GAN’s generator and discriminator on speech spectrogram images to implement sufficient sample augmentation. A six-layer convolution neural network (CNN), followed in series by a two-layer LSTM, is designed to extract features from speech spectrograms. For accelerating the training of networks, the parameters of discriminator are transferred to our feature extractor. By the sample augmentation, a well-trained feature extraction network and an efficient classifier could be achieved. The tests and comparisons on two publicly available datasets, i.e., EMO-DB and IEMOCAP, show that our new method is effective, and it is often superior to some state-of-the-art methods.

scholarly journals Single Image De-Raining Using Spinning Detail Perceptual Generative Adversarial Networks

2020 ◽  
Vol 24 (7) ◽  
pp. 811-819
Author(s):  
Kaizheng Chen ◽  
◽  
Yaping Dai ◽  
Zhiyang Jia ◽  
Kaoru Hirota
Keyword(s):  
Generative Adversarial Networks ◽  
Perceptual Quality ◽  
Training Procedure ◽  
Single Image ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Adversarial Networks ◽  
Real World Datasets ◽  
High Level

In this paper, Spinning Detail Perceptual Generative Adversarial Networks (SDP-GAN) is proposed for single image de-raining. The proposed method adopts the Generative Adversarial Network (GAN) framework and consists of two following networks: the rain streaks generative network G and the discriminative network D. To reduce the background interference, we propose a rain streaks generative network which not only focuses on the high frequency detail map of rainy image, but also directly reduces the mapping range from input to output. To further improve the perceptual quality of generated images, we modify the perceptual loss by extracting high-level features from discriminative network D, rather than pre-trained networks. Furthermore, we introduce a new training procedure based on the notion of self spinning to improve the final de-raining performance. Extensive experiments on the synthetic and real-world datasets demonstrate that the proposed method achieves significant improvements over the recent state-of-the-art methods.

scholarly journals AWGAN: A Powerful Batch Correction Model for scRNA-seq Data

2021 ◽  
Author(s):  
Tianyu Liu ◽  
Yuge Wang ◽  
Hong-yu Zhao
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Batch Effects ◽  
Generative Adversarial Network ◽  
Correction Model ◽  
Batch Correction ◽  
Learning Framework ◽  
Adversarial Network ◽  
Genomics Research ◽  
Downstream Analysis

With the advancement of technology, we can generate and access large-scale, high dimensional and diverse genomics data, especially through single-cell RNA sequencing (scRNA-seq). However, integrative downstream analysis from multiple scRNA-seq datasets remains challenging due to batch effects. In this paper, we focus on scRNA-seq data integration and propose a new deep learning framework based on Wasserstein Generative Adversarial Network (WGAN) combined with an attention mechanism to reduce the differences among batches. We also discuss the limitations of the existing methods and demonstrate the advantages of our new model from both theoretical and practical aspects, advocating the use of deep learning in genomics research.

scholarly journals Tomographic reconstruction with a generative adversarial network

2020 ◽  
Vol 27 (2) ◽  
pp. 486-493 ◽  
Author(s):  
Xiaogang Yang ◽  
Maik Kahnt ◽  
Dennis Brückner ◽  
Andreas Schropp ◽  
Yakub Fam ◽  
...  
Keyword(s):  
Phase Retrieval ◽  
Learning Algorithm ◽  
Tomographic Reconstruction ◽  
Training Data ◽  
Training Procedure ◽  
Contrast Imaging ◽  
Generative Adversarial Network ◽  
Data Set ◽  
Adversarial Network ◽  
Deep Learning Algorithm

This paper presents a deep learning algorithm for tomographic reconstruction (GANrec). The algorithm uses a generative adversarial network (GAN) to solve the inverse of the Radon transform directly. It works for independent sinograms without additional training steps. The GAN has been developed to fit the input sinogram with the model sinogram generated from the predicted reconstruction. Good quality reconstructions can be obtained during the minimization of the fitting errors. The reconstruction is a self-training procedure based on the physics model, instead of on training data. The algorithm showed significant improvements in the reconstruction accuracy, especially for missing-wedge tomography acquired at less than 180° rotational range. It was also validated by reconstructing a missing-wedge X-ray ptychographic tomography (PXCT) data set of a macroporous zeolite particle, for which only 51 projections over 70° could be collected. The GANrec recovered the 3D pore structure with reasonable quality for further analysis. This reconstruction concept can work universally for most of the ill-posed inverse problems if the forward model is well defined, such as phase retrieval of in-line phase-contrast imaging.

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