Proceedings ArticleDOI
Classification of PBMC cell types using scRNAseq, ANN, and incremental learning
Jiahui Zhong,Razin A. Shaikh,Haoguo Wu,Xin Lin,Zhiwei Cao,Lou Chitkushev,Guang Lan Zhang,Derin B. Keskin,Vladimir Brusic +8 more
- pp 1351-1355
TLDR
In this article, the authors used artificial neural networks (ANN) to assess the ability of ANN to classify main blood mononuclear cells (PBMC) cell types, and the overall prediction accuracy reached 93% in 4-class classification.Abstract:
Single cell transcriptomics (SCT) technology reveals gene expression of individual cells. Peripheral blood mononuclear cells (PBMC) are important diagnostic targets in immunology. In this study, we obtained and standardized 27 SCT data sets, derived from healthy PBMC samples using 10x SCT. We used artificial neural networks (ANN) to assess the ability of ANN to classify main PBMC cell types. Incremental learning by the gradual addition of new data sets to ANN training improved classification. The overall prediction accuracy of the final step of incremental learning reached 93% in 4-class classification.read more
Citations
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Posted ContentDOI
Artificial Neural Networks for classification of single cell gene expression
Jiahui Zhong,Minjie Lyu,Huan Jin,Zhiwei Cao,Lou Chitkushev,Guang Lan Zhang,Derin B. Keskin,Vladimir Brusic +7 more
TL;DR: In this article, a supervised ML method that deploys artificial neural networks (ANN) for 5-class classification of healthy peripheral blood mononuclear cells (PBMC) from multiple diverse studies is described.
Posted ContentDOI
Prediction of therapy outcomes of CLL using gene expression intensity, clustering, and ANN classification of single cell transcriptomes
TL;DR: In this paper, the authors applied five analytical tools for the study of single cell gene expression in CLL course of therapy, including the analysis of gene expression distributions: median, interquartile ranges, and percentage above quality control (QC) threshold; hierarchical clustering applied to all cells within individual single cell data sets; and artificial neural network (ANN) for classification of healthy peripheral blood mononuclear cell (PBMC) subtypes.
Book ChapterDOI
Protocol for Classification Single-Cell PBMC Types from Pathological Samples Using Supervised Machine Learning.
TL;DR: In this paper , a protocol that uses supervised machine learning (ML) methods with SCT data for the classification of peripheral blood mononuclear cells (PBMC) cell types in samples representing pathological states is described.
References
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Book ChapterDOI
The Gene Expression Omnibus Database.
Emily Clough,Tanya Barrett +1 more
TL;DR: This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data.
Journal ArticleDOI
Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken,Fabian J. Theis +1 more
TL;DR: The steps of a typical single‐cell RNA‐seq analysis, including pre‐processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell‐ and gene‐level downstream analysis, are detailed.
Journal ArticleDOI
Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson,Valentine Svensson,Roser Vento-Tormo,Sarah A. Teichmann,Sarah A. Teichmann +4 more
TL;DR: In this paper, the authors highlight the key technological developments that have enabled the growth in the data obtained from single-cell RNA-seq experiments, and highlight the advantages of using large numbers of cells.
Journal ArticleDOI
Beyond bulk: a review of single cell transcriptomics methodologies and applications
TL;DR: This review overviews fundamental sample preparation and data analysis processes of scRNA-seq and provides a comparative perspective for analyzing and visualizing these data.
Book ChapterDOI
Peripheral Blood Mononuclear Cells
TL;DR: Human peripheral blood mononuclear cells (PBMCs) are used to investigate the effect of food bioactives on various immune cells to investigate effects of bioactive components.
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