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• W3204653887 abstract "Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a significant increase in data collected from single-cell profilings, resulting in computational challenges to process these massive and complicated datasets. To address these challenges, deep learning (DL) is positioning as a competitive alternative for single-cell analyses besides the traditional machine learning approaches. Here we present a processing pipeline of single-cell RNA-seq data, survey a total of 25 DL algorithms and their applicability for a specific step in the processing pipeline. Specifically, we establish a unified mathematical representation of all variational autoencoder, autoencoder, and generative adversarial network models, compare the training strategies and loss functions for these models, and relate the loss functions of these models to specific objectives of the data processing step. Such presentation will allow readers to choose suitable algorithms for their particular objective at each step in the pipeline. We envision that this survey will serve as an important information portal for learning the application of DL for scRNA-seq analysis and inspire innovative use of DL to address a broader range of new challenges in emerging multi-omics and spatial single-cell sequencing." @default.
• W3204653887 created "2021-10-11" @default.
• W3204653887 creator A5008638025 @default.
• W3204653887 creator A5017681417 @default.
• W3204653887 creator A5024265492 @default.
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• W3204653887 creator A5046855484 @default.
• W3204653887 creator A5056745079 @default.
• W3204653887 creator A5057799604 @default.
• W3204653887 creator A5068887242 @default.
• W3204653887 creator A5073343116 @default.
• W3204653887 creator A5087249630 @default.
• W3204653887 date "2021-09-25" @default.
• W3204653887 modified "2023-09-26" @default.
• W3204653887 title "Deep learning tackles single-cell analysis A survey of deep learning for scRNA-seq analysis" @default.
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