scholarly journals A topology-preserving dimensionality reduction method for single-cell RNA-seq data using graph autoencoder

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zixiang Luo ◽  
Chenyu Xu ◽  
Zhen Zhang ◽  
Wenfei Jin
Keyword(s):  
Dimensionality Reduction ◽  
Single Cell ◽  
Topological Structure ◽  
Reduction Method ◽  
Dimensional Space ◽  
Oriented Graph ◽  
Developmental Trajectory ◽  
Structure Information ◽  
Dimensionality Reduction Method ◽  
Cell Graph

AbstractDimensionality reduction is crucial for the visualization and interpretation of the high-dimensional single-cell RNA sequencing (scRNA-seq) data. However, preserving topological structure among cells to low dimensional space remains a challenge. Here, we present the single-cell graph autoencoder (scGAE), a dimensionality reduction method that preserves topological structure in scRNA-seq data. scGAE builds a cell graph and uses a multitask-oriented graph autoencoder to preserve topological structure information and feature information in scRNA-seq data simultaneously. We further extended scGAE for scRNA-seq data visualization, clustering, and trajectory inference. Analyses of simulated data showed that scGAE accurately reconstructs developmental trajectory and separates discrete cell clusters under different scenarios, outperforming recently developed deep learning methods. Furthermore, implementation of scGAE on empirical data showed scGAE provided novel insights into cell developmental lineages and preserved inter-cluster distances.

scholarly journals scGAE: topology-preserving dimensionality reduction for single-cell RNA-seq data using graph autoencoder

2021 ◽  
Author(s):  
Zixiang Luo ◽  
Chenyu Xu ◽  
Zhen Zhang ◽  
Wenfei Jin
Keyword(s):  
Dimensionality Reduction ◽  
Single Cell ◽  
Topological Structure ◽  
Dimensional Space ◽  
Simulated Data ◽  
Oriented Graph ◽  
Developmental Trajectory ◽  
Structure Information ◽  
Low Dimensional ◽  
Cell Graph

ABSTRACTDimensionality reduction is crucial for the visualization and interpretation of the high-dimensional single-cell RNA sequencing (scRNA-seq) data. However, preserving topological structure among cells to low dimensional space remains a challenge. Here, we present the single-cell graph autoencoder (scGAE), a dimensionality reduction method that preserves topological structure in scRNA-seq data. scGAE builds a cell graph and uses a multitask-oriented graph autoencoder to preserve topological structure information and feature information in scRNA-seq data simultaneously. We further extended scGAE for scRNA-seq data visualization, clustering, and trajectory inference. Analyses of simulated data showed that scGAE accurately reconstructs developmental trajectory and separates discrete cell clusters under different scenarios, outperforming recently developed deep learning methods. Furthermore, implementation of scGAE on empirical data showed scGAE provided novel insights into cell developmental lineages and preserved inter-cluster distances.

scholarly journals Commodity Price Recognition and Simulation of Image Recognition Technology Based on the Nonlinear Dimensionality Reduction Method

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Yongbin Liu ◽  
Jingjie Wang ◽  
Wei Bai
Keyword(s):  
Dimensionality Reduction ◽  
Image Recognition ◽  
Reduction Method ◽  
Dimensional Space ◽  
Recognition Rate ◽  
Commodity Price ◽  
High Dimensional ◽  
Nonlinear Dimensionality Reduction ◽  
Nonlinear Structure ◽  
Dimensionality Reduction Method

Dimensionality reduction of images with high-dimensional nonlinear structure is the key to improving the recognition rate. Although some traditional algorithms have achieved some results in the process of dimensionality reduction, they also expose their respective defects. In order to achieve the ideal effect of high-dimensional nonlinear image recognition, based on the analysis of the traditional dimensionality reduction algorithm and refining its advantages, an image recognition technology based on the nonlinear dimensionality reduction method is proposed. As an effective nonlinear feature extraction method, the nonlinear dimensionality reduction method can find the nonlinear structure of datasets and maintain the intrinsic structure of data. Applying the nonlinear dimensionality reduction method to image recognition is to divide the input image into blocks, take it as a dataset in high-dimensional space, reduce the dimension of its structure, and obtain the low-dimensional expression vector of its eigenstructure so that the problem of image recognition can be carried out in a lower dimension. Thus, the computational complexity can be reduced, the recognition accuracy can be improved, and it is convenient for further processing such as image recognition and search. The defects of traditional algorithms are solved, and the commodity price recognition and simulation experiments are carried out, which verifies the feasibility of image recognition technology based on the nonlinear dimensionality reduction method in commodity price recognition.

scholarly journals A model for spectroscopic food sample analysis using data sonification

2021 ◽  
Author(s):  
Hsein Kew
Keyword(s):  
Dimensionality Reduction ◽  
Classification Accuracy ◽  
Reduction Method ◽  
Real Life ◽  
Principal Component ◽  
Relevant Information ◽  
Analysis Model ◽  
Linear Discriminant ◽  
Audio Output ◽  
Dimensionality Reduction Method

AbstractIn this paper, we propose a method to generate an audio output based on spectroscopy data in order to discriminate two classes of data, based on the features of our spectral dataset. To do this, we first perform spectral pre-processing, and then extract features, followed by machine learning, for dimensionality reduction. The features are then mapped to the parameters of a sound synthesiser, as part of the audio processing, so as to generate audio samples in order to compute statistical results and identify important descriptors for the classification of the dataset. To optimise the process, we compare Amplitude Modulation (AM) and Frequency Modulation (FM) synthesis, as applied to two real-life datasets to evaluate the performance of sonification as a method for discriminating data. FM synthesis provides a higher subjective classification accuracy as compared with to AM synthesis. We then further compare the dimensionality reduction method of Principal Component Analysis (PCA) and Linear Discriminant Analysis in order to optimise our sonification algorithm. The results of classification accuracy using FM synthesis as the sound synthesiser and PCA as the dimensionality reduction method yields a mean classification accuracies of 93.81% and 88.57% for the coffee dataset and the fruit puree dataset respectively, and indicate that this spectroscopic analysis model is able to provide relevant information on the spectral data, and most importantly, is able to discriminate accurately between the two spectra and thus provides a complementary tool to supplement current methods.

scholarly journals Plant Leaf Recognition through Local Discriminative Tangent Space Alignment

2016 ◽  
Vol 2016 ◽  
pp. 1-5 ◽  
Author(s):  
Chuanlei Zhang ◽  
Shanwen Zhang ◽  
Weidong Fang
Keyword(s):  
Dimensionality Reduction ◽  
Manifold Learning ◽  
Tangent Space ◽  
Reduction Method ◽  
Plant Leaf ◽  
Local Patch ◽  
Dimensionality Reduction Method

Manifold learning based dimensionality reduction algorithms have been payed much attention in plant leaf recognition as the algorithms can select a subset of effective and efficient discriminative features in the leaf images. In this paper, a dimensionality reduction method based on local discriminative tangent space alignment (LDTSA) is introduced for plant leaf recognition based on leaf images. The proposed method can embrace part optimization and whole alignment and encapsulate the geometric and discriminative information into a local patch. The experiments on two plant leaf databases, ICL and Swedish plant leaf datasets, demonstrate the effectiveness and feasibility of the proposed method.

scholarly journals Fractional Wavelet-Based Generative Scattering Networks

2021 ◽  
Vol 15 ◽  
Author(s):  
Jiasong Wu ◽  
Xiang Qiu ◽  
Jing Zhang ◽  
Fuzhi Wu ◽  
Youyong Kong ◽  
...  
Keyword(s):  
Dimensionality Reduction ◽  
Reduction Method ◽  
Gaussian White Noise ◽  
Principal Component ◽  
Experimental Results ◽  
Generative Adversarial Networks ◽  
Image Generation ◽  
Adversarial Networks ◽  
Dimensionality Reduction Method

Generative adversarial networks and variational autoencoders (VAEs) provide impressive image generation from Gaussian white noise, but both are difficult to train, since they need a generator (or encoder) and a discriminator (or decoder) to be trained simultaneously, which can easily lead to unstable training. To solve or alleviate these synchronous training problems of generative adversarial networks (GANs) and VAEs, researchers recently proposed generative scattering networks (GSNs), which use wavelet scattering networks (ScatNets) as the encoder to obtain features (or ScatNet embeddings) and convolutional neural networks (CNNs) as the decoder to generate an image. The advantage of GSNs is that the parameters of ScatNets do not need to be learned, while the disadvantage of GSNs is that their ability to obtain representations of ScatNets is slightly weaker than that of CNNs. In addition, the dimensionality reduction method of principal component analysis (PCA) can easily lead to overfitting in the training of GSNs and, therefore, affect the quality of generated images in the testing process. To further improve the quality of generated images while keeping the advantages of GSNs, this study proposes generative fractional scattering networks (GFRSNs), which use more expressive fractional wavelet scattering networks (FrScatNets), instead of ScatNets as the encoder to obtain features (or FrScatNet embeddings) and use similar CNNs of GSNs as the decoder to generate an image. Additionally, this study develops a new dimensionality reduction method named feature-map fusion (FMF) instead of performing PCA to better retain the information of FrScatNets,; it also discusses the effect of image fusion on the quality of the generated image. The experimental results obtained on the CIFAR-10 and CelebA datasets show that the proposed GFRSNs can lead to better generated images than the original GSNs on testing datasets. The experimental results of the proposed GFRSNs with deep convolutional GAN (DCGAN), progressive GAN (PGAN), and CycleGAN are also given.

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