scholarly journals Evaluation of UMAP as an alternative to t-SNE for single-cell data

2018 ◽  
Author(s):  
Etienne Becht ◽  
Charles-Antoine Dutertre ◽  
Immanuel W. H. Kwok ◽  
Lai Guan Ng ◽  
Florent Ginhoux ◽  
...  
Keyword(s):  
Dimensionality Reduction ◽  
Single Cell ◽  
Rna Sequencing ◽  
Reduction Technique ◽  
High Dimensional ◽  
The Past ◽  
Dimensionality Reduction Technique ◽  
Single Cell Rna Sequencing ◽  
Linear Dimensionality Reduction ◽  
Cell Data

AbstractUniform Manifold Approximation and Projection (UMAP) is a recently-published non-linear dimensionality reduction technique. Another such algorithm, t-SNE, has been the default method for such task in the past years. Herein we comment on the usefulness of UMAP high-dimensional cytometry and single-cell RNA sequencing, notably highlighting faster runtime and consistency, meaningful organization of cell clusters and preservation of continuums in UMAP compared to t-SNE.

scholarly journals Untangling biological factors influencing trajectory inference from single cell data

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Mohammed Charrout ◽  
Marcel J T Reinders ◽  
Ahmed Mahfouz
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Rna Sequencing ◽  
The Past ◽  
Single Cell Rna Sequencing ◽  
Sources Of Variation ◽  
Biological Sources ◽  
Cellular Identity ◽  
Cell Data ◽  
Transcriptional State

Abstract Advances in single-cell RNA sequencing over the past decade has shifted the discussion of cell identity toward the transcriptional state of the cell. While the incredible resolution provided by single-cell RNA sequencing has led to great advances in unraveling tissue heterogeneity and inferring cell differentiation dynamics, it raises the question of which sources of variation are important for determining cellular identity. Here we show that confounding biological sources of variation, most notably the cell cycle, can distort the inference of differentiation trajectories. We show that by factorizing single cell data into distinct sources of variation, we can select a relevant set of factors that constitute the core regulators for trajectory inference, while filtering out confounding sources of variation (e.g. cell cycle) which can perturb the inferred trajectory. Script are available publicly on https://github.com/mochar/cell_variation.

scholarly journals Dimensionality Reduction by Weighted Connections between Neighborhoods

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Fuding Xie ◽  
Yutao Fan ◽  
Ming Zhou
Keyword(s):  
Dimensionality Reduction ◽  
Dimensional Space ◽  
High Dimensional Data ◽  
Reduction Technique ◽  
Experimental Results ◽  
High Dimensional ◽  
Reduced Dimensionality ◽  
Dimensionality Reduction Technique ◽  
Low Dimensionality ◽  
Local Topology

Dimensionality reduction is the transformation of high-dimensional data into a meaningful representation of reduced dimensionality. This paper introduces a dimensionality reduction technique by weighted connections between neighborhoods to improveK-Isomap method, attempting to preserve perfectly the relationships between neighborhoods in the process of dimensionality reduction. The validity of the proposal is tested by three typical examples which are widely employed in the algorithms based on manifold. The experimental results show that the local topology nature of dataset is preserved well while transforming dataset in high-dimensional space into a new dataset in low-dimensionality by the proposed method.

scholarly journals Single-Cell Manifold Preserving Feature Selection (SCMER)

2020 ◽  
Author(s):  
Ken Chen ◽  
Shaoheng Liang ◽  
Vakul Mohanty ◽  
Jinzhuang Dou ◽  
Miao Qi ◽  
...  
Keyword(s):  
Dimensionality Reduction ◽  
Single Cell ◽  
Cost Effective ◽  
High Dimensional ◽  
Compact Set ◽  
Cell Lineages ◽  
Molecular Features ◽  
Unsupervised Approach ◽  
Cell Data ◽  
Common Cell

Abstract A key challenge in studying organisms and diseases is to detect rare molecular programs and rare cell populations (RCPs) that drive development, differentiation, and transformation. Molecular features such as genes and proteins defining RCPs are often unknown and difficult to detect from unenriched single-cell data, using conventional dimensionality reduction and clustering-based approaches. Here, we propose a novel unsupervised approach, named SCMER, which performs UMAP style dimensionality reduction via selecting a compact set of molecular features with definitive meanings. We applied SCMER in the context of hematopoiesis, lymphogenesis, tumorigenesis, and drug resistance and response. We found that SCMER can identify non-redundant features that sensitively delineate both common cell lineages and rare cellular states ignored by current approaches. SCMER can be widely used for discovering novel molecular features in a high dimensional dataset, designing targeted, cost-effective assays for clinical applications, and facilitating multi-modality integration.

scholarly journals Computational Methods for Single-Cell RNA Sequencing

2020 ◽  
Vol 3 (1) ◽  
pp. 339-364 ◽  
Author(s):  
Brian Hie ◽  
Joshua Peters ◽  
Sarah K. Nyquist ◽  
Alex K. Shalek ◽  
Bonnie Berger ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Computational Methods ◽  
Analytical Methods ◽  
High Dimensional ◽  
Computational Tools ◽  
Single Cell Rna Sequencing ◽  
Selection Of

Single-cell RNA sequencing (scRNA-seq) has provided a high-dimensional catalog of millions of cells across species and diseases. These data have spurred the development of hundreds of computational tools to derive novel biological insights. Here, we outline the components of scRNA-seq analytical pipelines and the computational methods that underlie these steps. We describe available methods, highlight well-executed benchmarking studies, and identify opportunities for additional benchmarking studies and computational methods. As the biochemical approaches for single-cell omics advance, we propose coupled development of robust analytical pipelines suited for the challenges that new data present and principled selection of analytical methods that are suited for the biological questions to be addressed.

scholarly journals Explaining three-dimensional dimensionality reduction plots

2015 ◽  
Vol 15 (2) ◽  
pp. 154-172 ◽  
Author(s):  
Danilo B Coimbra ◽  
Rafael M Martins ◽  
Tácito TAT Neves ◽  
Alexandru C Telea ◽  
Fernando V Paulovich
Keyword(s):  
Dimensionality Reduction ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Original Data ◽  
Reduction Technique ◽  
High Dimensional ◽  
Dimensionality Reduction Technique ◽  
Visualization Techniques ◽  
High Dimensional Datasets ◽  
Three Dimensional Space

Understanding three-dimensional projections created by dimensionality reduction from high-variate datasets is very challenging. In particular, classical three-dimensional scatterplots used to display such projections do not explicitly show the relations between the projected points, the viewpoint used to visualize the projection, and the original data variables. To explore and explain such relations, we propose a set of interactive visualization techniques. First, we adapt and enhance biplots to show the data variables in the projected three-dimensional space. Next, we use a set of interactive bar chart legends to show variables that are visible from a given viewpoint and also assist users to select an optimal viewpoint to examine a desired set of variables. Finally, we propose an interactive viewpoint legend that provides an overview of the information visible in a given three-dimensional projection from all possible viewpoints. Our techniques are simple to implement and can be applied to any dimensionality reduction technique. We demonstrate our techniques on the exploration of several real-world high-dimensional datasets.

scholarly journals Implication of specific retinal cell-type involvement and gene expression changes in AMD progression using integrative analysis of single-cell and bulk RNA-seq profiling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yafei Lyu ◽  
Randy Zauhar ◽  
Nicholas Dana ◽  
Christianne E. Strang ◽  
Jian Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Age Related Macular Degeneration ◽  
Specific Gene ◽  
Cell Type ◽  
Adult Human ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific ◽  
Cell Data

AbstractAge‐related macular degeneration (AMD) is a blinding eye disease with no unifying theme for its etiology. We used single-cell RNA sequencing to analyze the transcriptomes of ~ 93,000 cells from the macula and peripheral retina from two adult human donors and bulk RNA sequencing from fifteen adult human donors with and without AMD. Analysis of our single-cell data identified 267 cell-type-specific genes. Comparison of macula and peripheral retinal regions found no cell-type differences but did identify 50 differentially expressed genes (DEGs) with about 1/3 expressed in cones. Integration of our single-cell data with bulk RNA sequencing data from normal and AMD donors showed compositional changes more pronounced in macula in rods, microglia, endothelium, Müller glia, and astrocytes in the transition from normal to advanced AMD. KEGG pathway analysis of our normal vs. advanced AMD eyes identified enrichment in complement and coagulation pathways, antigen presentation, tissue remodeling, and signaling pathways including PI3K-Akt, NOD-like, Toll-like, and Rap1. These results showcase the use of single-cell RNA sequencing to infer cell-type compositional and cell-type-specific gene expression changes in intact bulk tissue and provide a foundation for investigating molecular mechanisms of retinal disease that lead to new therapeutic targets.

scholarly journals Semi-Supervised Non-Linear Dimensionality Reduction Technique for Sentiment Analysis Classification

2019 ◽  
Vol 8 (9) ◽  
pp. 1721-1725
Keyword(s):  
Dimensionality Reduction ◽  
Sentiment Analysis ◽  
Reduction Technique ◽  
Sentiment Classification ◽  
Random Subspace ◽  
Wide Scope ◽  
Dimensionality Reduction Technique ◽  
Non Linear ◽  
Linear Dimensionality Reduction ◽  
The Web

With the quick development in data advances, client created substance, for example, reviews, ratings, recommendations can be advantageously posted on the web, which have powered enthusiasm for sentiment classification. The quantity of records accessible on both online and offline is expanding drastically. Sentiment Classification has a wide scope of utilizations in review related sites. In this paper, we present our investigations about some exploration paper in this field and exhibited our plan to distinguish the sentiment extremity of a given content as positive or negative by lessening the documents dimension, through utilizing semi-supervised non-linear dimensionality decrease technique. For Sentiment Classification, Random Subspace strategy is utilized. For exploratory assessment, openly accessible sentiment datasets can be utilized to check the adequacy of the proposed technique.

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