Can MDS rival with t-SNE by using the symmetric Kullback-Leibler divergence\\ across neighborhoods as a pseudo-distance?

Local methods of dimensionality reduction like neighborhood embedding (NE) and t-SNE in particular outperform older global approaches such as stress-based multi-dimensional scaling (MDS).Stochastic neighborhoods are less sensitive than distances to statistical variations between spaces with strongly different dimensionalities, making a match across them very difficult.Here, we take inspiration from those stochastic neighborhoods in order to devise a pseudo-distance that is less prone to concentration than the Euclidean distance.For two points in the high-dimensional data space, it is defined as the symmetrized Kullback-Leibler divergence across the (stochastic) neighborhoods of the two points (SKLAN).Plugging the SKLAN in a method of stress-based MDS, we compare quantitatively t-SNE, MDS with all Euclidean distances, and MDS with SKLAN & Euclidean distances on several data sets.The results show that SKLAN allows MDS to perform competitively with t-SNE.

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Published
2025-01-01
DOI
https://doi.org/10.14428/esann/2025.es2025-174
Primary Topic
Complex Systems and Time Series Analysis
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article
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article

Can MDS rival with t-SNE by using the symmetric Kullback-Leibler divergence\\ across neighborhoods as a pseudo-distance?

Michel Verleysen, P Merveille, Pierre Lambert, John Chi‐Kin Lee et al.
Complex Systems and Time Series Analysis
article

Can MDS rival with t-SNE by using the symmetric Kullback-Leibler divergence\\ across neighborhoods as a pseudo-distance?

Michel Verleysen, P Merveille, Pierre Lambert, John Chi‐Kin Lee, Dounia Mulders, Cyril de Bodt, Edouard Couplet, Ludovic Journaux
article en

Abstract

Local methods of dimensionality reduction like neighborhood embedding (NE) and t-SNE in particular outperform older global approaches such as stress-based multi-dimensional scaling (MDS).Stochastic neighborhoods are less sensitive than distances to statistical variations between spaces with strongly different dimensionalities, making a match across them very difficult.Here, we take inspiration from those stochastic neighborhoods in order to devise a pseudo-distance that is less prone to concentration than the Euclidean distance.For two points in the high-dimensional data space, it is defined as the symmetrized Kullback-Leibler divergence across the (stochastic) neighborhoods of the two points (SKLAN).Plugging the SKLAN in a method of stress-based MDS, we compare quantitatively t-SNE, MDS with all Euclidean distances, and MDS with SKLAN & Euclidean distances on several data sets.The results show that SKLAN allows MDS to perform competitively with t-SNE.

Institut Agro Dijon (FR), Laboratoire d'Informatique de Bourgogne (FR)
Reduced inequalities
Openalex Percentile: Top 89%
Complex Systems and Time Series Analysis
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Can MDS rival with t-SNE by using the symmetric Kullback-Leibler divergence\\ across neighborhoods as a pseudo-distance? — Michel Verleysen, P Merveille, et al. · (2025) | TGRS Research Map | TGRS