Related papers: DR-SNE: Density-Regularized Stochastic Neighbor Em…
Molecular simulation trajectories represent high-dimensional data. Such data can be visualized by methods of dimensionality reduction. Non-linear dimensionality reduction methods are likely to be more efficient than linear ones due to the…
This work considers large-data asymptotics for t-distributed stochastic neighbor embedding (tSNE), a widely-used non-linear dimension reduction algorithm. We identify an appropriate continuum limit of the tSNE objective function, which can…
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…
In deep neural nets, lower level embedding layers account for a large portion of the total number of parameters. Tikhonov regularization, graph-based regularization, and hard parameter sharing are approaches that introduce explicit biases…
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…
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…
While high-dimensional embedding vectors are being increasingly employed in various tasks like Retrieval-Augmented Generation and Recommendation Systems, popular dimensionality reduction (DR) methods such as PCA and UMAP have rarely been…
Parametric embedding methods such as parametric t-SNE (pt-SNE) have been widely adopted for data visualization and out-of-sample data embedding without further computationally expensive optimization or approximation. However, the…
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.…
We present S+t-SNE, an adaptation of the t-SNE algorithm designed to handle infinite data streams. The core idea behind S+t-SNE is to update the t-SNE embedding incrementally as new data arrives, ensuring scalability and adaptability to…
Stochastic neighbor embedding (SNE) methods $t$-SNE, UMAP are two most popular dimensionality reduction methods for data visualization. Contrastive learning, especially self-supervised contrastive learning (SSCL), has showed great success…
T-SNE is a well-known approach to embedding high-dimensional data and has been widely used in data visualization. The basic assumption of t-SNE is that the data are non-constrained in the Euclidean space and the local proximity can be…
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…
Data features and class probabilities are two main perspectives when, e.g., evaluating model results and identifying problematic items. Class probabilities represent the likelihood that each instance belongs to a particular class, which can…
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,…
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…
Unsupervised machine learning has recently gained much attention in the field of molecular dynamics (MD). Particularly, dimensionality reduction techniques have been regularly employed to analyze large volumes of high-dimensional MD data to…
The t-distributed Stochastic Neighbor Embedding (tSNE) algorithm has become in recent years one of the most used and insightful techniques for the exploratory data analysis of high-dimensional data. tSNE reveals clusters of high-dimensional…
The vast majority of Dimensionality Reduction (DR) techniques rely on second-order statistics to define their optimization objective. Even though this provides adequate results in most cases, it comes with several shortcomings. The methods…
Contrastive learning, especially self-supervised contrastive learning (SSCL), has achieved great success in extracting powerful features from unlabeled data. In this work, we contribute to the theoretical understanding of SSCL and uncover…