Topolow: Force-Directed Euclidean Embedding of Dissimilarity Data with Robustness Against Non-Metricity and Sparsity

TL;DR

Topolow is a robust, physics-inspired embedding method that accurately reconstructs Euclidean space from non-metric, sparse dissimilarity data without relying on gradients, outperforming standard MDS techniques.

Contribution

It introduces a gradient-free, stochastic optimization framework for embedding non-metric dissimilarities into Euclidean space, with proven robustness and improved accuracy.

Findings

Outperforms standard MDS in reconstructing sparse, non-Euclidean data

Robust against outliers and heterogenous errors

Does not require dissimilarities to be metric

Abstract

The problem of embedding a set of objects into a low-dimensional Euclidean space based on a matrix of pairwise dissimilarities is fundamental in data analysis, machine learning, and statistics. However, the assumptions of many standard analytical methods are violated when the input dissimilarities fail to satisfy metric or Euclidean axioms. We present the mathematical and statistical foundations of Topolow, a physics-inspired, gradient-free optimization framework for such embedding problems. Topolow is conceptually related to force-directed graph drawing algorithms but is fundamentally distinguished by its goal of quantitative metric reconstruction. It models objects as particles in a physical system, and its novel optimization scheme proceeds through sequential, stochastic pairwise interactions, which circumvents the need to compute a global gradient and provides robustness against convergence to local optima, especially for sparse data. Topolow maximizes the likelihood under a Laplace error model, robust to outliers and heterogeneous errors, and properly handles censored data. Crucially, Topolow does not require the input dissimilarities to be metric, making it a robust solution for embedding non-metric measurements into a valid Euclidean space, thereby enabling the use of standard analytical tools. We demonstrate the superior performance of Topolow compared to standard Multidimensional Scaling (MDS) methods in reconstructing the geometry of sparse and non-Euclidean data. This paper formalizes the algorithm, first introduced as Topolow in the context of antigenic mapping in (Arhami and Rohani, 2025) (open access), with emphasis on its metric embedding and mathematical properties for a broader audience. The general-purpose function Euclidify is available in the R package topolow.