Oct 24, 2018

Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and allow analysis of large datasets

BioRxiv : the Preprint Server for Biology
Anna C. BelkinaJennifer Snyder-Cappione


Accurate and comprehensive extraction of information from high-dimensional single cell datasets necessitates faithful visualizations to assess biological populations. A state-of-the-art algorithm for non-linear dimension reduction, t-SNE, requires multiple heuristics and fails to produce clear representations of datasets when millions of cells are projected. We developed opt-SNE, an automated toolkit for t-SNE parameter selection that utilizes Kullback-Liebler divergence evaluation in real time to tailor the early exaggeration and overall number of gradient descent iterations in a dataset-specific manner. The precise calibration of early exaggeration together with opt-SNE adjustment of gradient descent learning rate dramatically improves computation time and enables high-quality visualization of large cytometry and transcriptomics datasets, overcoming limitations of analysis tools with hard-coded parameters that often produce poorly resolved or misleading maps of fluorescent and mass cytometry data. In summary, opt-SNE enables superior data resolution in t-SNE space and thereby more accurate data interpretation.

  • References
  • Citations


  • We're still populating references for this paper, please check back later.
  • References
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Single-Cell Analysis
Fluorescent Dyes
Microtubule-Associated Proteins
MUTYH-Associate Polyposis
SGSM3 gene
Anatomical Space Structure
Fluorescent stain

About this Paper

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

The Journal of Immunology : Official Journal of the American Association of Immunologists
Yang ChengEvan W Newell
BioRxiv : the Preprint Server for Biology
Dmitry Kobak, Philipp Berens
BioRxiv : the Preprint Server for Biology
Miroslav KratochvilKarel Drbal
IEEE Transactions on Visualization and Computer Graphics
Shusen LiuValerio Pascucci
© 2020 Meta ULC. All rights reserved