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

Belkina, A.C., Ciccolella, C.O., Anno, R., et al.

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 develop opt-SNE, an automated toolkit for t-SNE parameter selection that utilizes Kullback-Leibler 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.

Citation

Belkina, A.C., Ciccolella, C.O., Anno, R., et al. "Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets" Nature Communications (2019): 5415