Dimension reduction and clustering of single cell calcium spiking: Comparison of t-SNE and UMAP

Gare, S and Jana, S. and Giri, L (2021) Dimension reduction and clustering of single cell calcium spiking: Comparison of t-SNE and UMAP. In: 27th National Conference on Communications, NCC 2021, 27 July 2021 through 30 July 2021, Virtual, Kanpur.

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Abstract

Time-lapse fluorescent imaging of cytosolic calcium is used to detect cellular activity during preclinical experiments and drug screening studies. However, visualization and analysis of high dimension time series data remain challenging due to the presence of underlying heterogeneity. In this context, we propose t-distribution stochastic neighborhood embedding (t-SNE) and uniform manifold projection and approximation (UMAP) for visualization and analysis. Next, we show the density-based spatial clustering of applications with noise (DBSCAN) can be used to detect various spiking patterns present in calcium dose-response. The proposed framework combining t-SNE and DBSCAN was used to find repeating patterns, detect outliers, and label similar instances present in biological signaling.

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IITH Creators:

IITH Creators	ORCiD
Jana, Soumya	https://orcid.org/ 0000-0002-2049-2239
Giri, Lopamudra	http://orcid.org/0000-0002-2352-7919

Item Type:

Conference or Workshop Item (Paper)

Uncontrolled Keywords:

Clusterings, Density-based spatial clustering of applications with noise, Embeddings, Neighbourhood, Stochastics; T distribution; T-SNE; Time-series data; Uniform manifold projection and approximation, Visualization and analysis

Subjects:

Electrical Engineering
Chemical Engineering

Divisions:

Department of Electrical Engineering

Depositing User:

Mrs Haseena VKKM

Date Deposited:

09 Dec 2021 09:14

Last Modified:

22 Feb 2022 08:59

URI:

http://raiithold.iith.ac.in/id/eprint/9068