# Uncertainty-aware t-distributed Stochastic Neighbor Embedding for Single-cell RNA-seq Data

arXiv: https://arxiv.org/abs/2410.00473 · HTML: https://mlsanity.com/paper/2410.00473/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 3 of its 19 references that are in the map.
- First posted on arXiv 1 Oct 2024.

## Builds on (most cited first, 3 of 3)

- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Theoretical Foundations of t-SNE for Visualizing High-Dimensional Clustered Data](https://mlsanity.com/paper/2105.07536/) (2021)
- [Laplacian Eigenmaps from Sparse, Noisy Similarity Measurements](https://mlsanity.com/paper/1603.03972/) (2016)

## Abstract (arXiv)

Nonlinear data visualization using t-distributed stochastic neighbor embedding (t-SNE) enables the representation of complex single-cell transcriptomic landscapes in two or three dimensions to depict biological populations accurately. However, t-SNE often fails to account for uncertainties in the original dataset, leading to misleading visualizations where cell subsets with noise appear indistinguishable. To address these challenges, we introduce uncertainty-aware t-SNE (Ut-SNE), a noise-defending visualization tool tailored for uncertain single-cell RNA-seq data. By creating a probabilistic representation for each sample, Our Ut-SNE accurately incorporates noise about transcriptomic variability into the visual interpretation of single-cell RNA sequencing data, revealing significant uncertainties in transcriptomic variability. Through various examples, we showcase the practical value of Ut-SNE and underscore the significance of incorporating uncertainty awareness into data visualization practices. This versatile uncertainty-aware visualization tool can be easily adapted to other scientific domains beyond single-cell RNA sequencing, making them valuable resources for high-dimensional data analysis.