Related papers: t-SNE Exaggerates Clusters, Provably
Visualizing high-dimensional data is essential for understanding biomedical data and deep learning models. Neighbor embedding methods, such as t-SNE and UMAP, are widely used but can introduce misleading visual artifacts. We find that the…
Dimensionality reduction techniques are essential for visualizing and analyzing high-dimensional biological sequencing data. t-distributed Stochastic Neighbor Embedding (t-SNE) is widely used for this purpose, traditionally employing the…
Most existing graph visualization methods based on dimension reduction are limited to relatively small graphs due to performance issues. In this work, we propose a novel dimension reduction method for graph visualization, called…
The clustering and visualisation of high-dimensional data is a ubiquitous task in modern data science. Popular techniques include nonlinear dimensionality reduction methods like t-SNE or UMAP. These methods face the `scale-problem' of…
A first line of attack in exploratory data analysis is data visualization, i.e., generating a 2-dimensional representation of data that makes clusters of similar points visually identifiable. Standard Johnson-Lindenstrauss dimensionality…
This paper presents a new insight into improving the performance of Stochastic Neighbour Embedding (t-SNE) by using Isolation kernel instead of Gaussian kernel. Isolation kernel outperforms Gaussian kernel in two aspects. First, the use of…
t-SNE has gained popularity as a dimension reduction technique, especially for visualizing data. It is well-known that all dimension reduction techniques may lose important features of the data. We provide a mathematical framework for…
Progressive Visual Analytics aims at improving the interactivity in existing analytics techniques by means of visualization as well as interaction with intermediate results. One key method for data analysis is dimensionality reduction, for…
t-SNE is one of the most commonly used force-based nonlinear dimensionality reduction methods. This paper has two contributions: the first is forceful colorings, an idea that is also applicable to other force-based methods (UMAP,…
An increasing number of multi-view data are being published by studies in several fields. This type of data corresponds to multiple data-views, each representing a different aspect of the same set of samples. We have recently proposed…
Nearest neighbor (k-NN) graphs are widely used in machine learning and data mining applications, and our aim is to better understand what they reveal about the cluster structure of the unknown underlying distribution of points. Moreover, is…
Embedding and visualizing large-scale high-dimensional data in a two-dimensional space is an important problem since such visualization can reveal deep insights out of complex data. Most of the existing embedding approaches, however, run on…
Subspace clustering refers to the problem of clustering high-dimensional data points into a union of low-dimensional linear subspaces, where the number of subspaces, their dimensions and orientations are all unknown. In this paper, we…
Previous statistical approaches to hierarchical clustering for social network analysis all construct an "ultrametric" hierarchy. While the assumption of ultrametricity has been discussed and studied in the phylogenetics literature, it has…
Neighbour embeddings (NE) allow the representation of high dimensional datasets into lower dimensional spaces and are often used in data visualisation. In practice, accelerated approximations are employed to handle very large datasets.…
Neighbor embedding methods $t$-SNE and UMAP are the de facto standard for visualizing high-dimensional datasets. Motivated from entirely different viewpoints, their loss functions appear to be unrelated. In practice, they yield strongly…
Multidimensional scaling is a statistical process that aims to embed high dimensional data into a lower-dimensional space; this process is often used for the purpose of data visualisation. Common multidimensional scaling algorithms tend to…
We use graphical methods to probe neural nets that classify images. Plots of t-SNE outputs at successive layers in a network reveal increasingly organized arrangement of the data points. They can also reveal how a network can diminish or…
t-distributed stochastic neighbor embedding (t-SNE) is a well-established visualization method for complex high-dimensional data. However, the original t-SNE method is nonparametric, stochastic, and often cannot well prevserve the global…
Misuses of t-SNE and UMAP in visual analytics have become increasingly common. For example, although t-SNE and UMAP projections often do not faithfully reflect the original distances between clusters, practitioners frequently use them to…