Related papers: Stop Misusing t-SNE and UMAP for Visual Analytics

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…

Cluster visualization is an essential task for nonlinear dimensionality reduction as a data analysis tool. It is often believed that Student t-Distributed Stochastic Neighbor Embedding (t-SNE) can show clusters for well clusterable data,…

Stochastic Neighbor Embedding (SNE) algorithms like UMAP and tSNE often produce visualizations that do not preserve the geometry of noisy and high dimensional data. In particular, they can spuriously separate connected components of the…

Dimensionality reduction (DR) techniques are essential for visually analyzing high-dimensional data. However, visual analytics using DR often face unreliability, stemming from factors such as inherent distortions in DR projections. This…

Projection algorithms such as t-SNE or UMAP are useful for the visualization of high dimensional data, but depend on hyperparameters which must be tuned carefully. Unfortunately, iteratively recomputing projections to find the optimal…

Dimensionality reduction methods, also known as projections, are frequently used for exploring multidimensional data in machine learning, data science, and information visualization. Among these, t-SNE and its variants have become very…

This paper presents a comprehensive comparative analysis of prominent clustering algorithms K-means, DBSCAN, and Spectral Clustering on high-dimensional datasets. We introduce a novel evaluation framework that assesses clustering…

$t$-SNE is an embedding method that the data science community has widely Two interesting characteristics of t-SNE are the structure preservation property and the answer to the crowding problem, where all neighbors in high dimensional space…

Malicious software are categorized into families based on their static and dynamic characteristics, infection methods, and nature of threat. Visual exploration of malware instances and families in a low dimensional space helps in giving a…

Conditional t-SNE (ct-SNE) is a recent extension to t-SNE that allows removal of known cluster information from the embedding, to obtain a visualization revealing structure beyond label information. This is useful, for example, when one…

The goal of dimension reduction tools is to construct a low-dimensional representation of high-dimensional data. These tools are employed for a variety of reasons such as noise reduction, visualization, and to lower computational costs.…

Most popular dimension reduction (DR) methods like t-SNE and UMAP are based on minimizing a cost between input and latent pairwise similarities. Though widely used, these approaches lack clear probabilistic foundations to enable a full…

When visualizing a high-dimensional dataset, dimension reduction techniques are commonly employed which provide a single 2-dimensional view of the data. We describe ENS-t-SNE: an algorithm for Embedding Neighborhoods Simultaneously that…

This paper shows that dimensionality reduction methods such as UMAP and t-SNE, can be approximately recast as MAP inference methods corresponding to a model introduced in Ravuri et al. (2023), that describes the graph Laplacian (an estimate…

Central to the widespread use of t-distributed stochastic neighbor embedding (t-SNE) is the conviction that it produces visualizations whose structure roughly matches that of the input. To the contrary, we prove that (1) the strength of the…

Dimensionality reduction methods such as t-SNE are designed to preserve local neighborhood structure but do not explicitly account for how probability mass is distributed, often leading to distortions of data density. We reformulate…

Two-dimensional data maps can visually reveal information about the relations between data instances. Popular techniques to construct data maps are t-SNE and UMAP. The resulting point-based visualizations, though, provide information only…

With the recent surge in big data analytics for hyper-dimensional data there is a renewed interest in dimensionality reduction techniques for machine learning applications. In order for these methods to improve performance gains and…

Dimensionality reduction methods such as UMAP and t-SNE are central tools for visualising high-dimensional data, but their local-neighborhood objectives can preserve sampling noise while distorting global topology. We show that standard…

With the increasing availability of high-dimensional data, analysts often rely on exploratory data analysis to understand complex data sets. A key approach to exploring such data is dimensionality reduction, which embeds high-dimensional…