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.

Multidimensional scaling (MDS) is a widely used approach to representing high-dimensional, dependent data. MDS works by assigning each observation a location on a low-dimensional geometric manifold, with distance on the manifold representing similarity. We propose a Bayesian approach to multidimensional scaling when the low-dimensional manifold is hyperbolic. Using hyperbolic space facilitates representing tree-like structures common in many settings (e.g. text or genetic data with hierarchical structure). A Bayesian approach provides regularization that minimizes the impact of measurement error in the observed data and assesses uncertainty. We also propose a case-control likelihood approximation that allows for efficient sampling from the posterior distribution in larger data settings, reducing computational complexity from approximately $O(n^2)$ to $O(n)$. We evaluate the proposed method against state-of-the-art alternatives using simulations, canonical reference datasets, Indian village network data, and human gene expression data.

Visualizing and structuring pairwise dissimilarity data are difficult combinatorial op(cid:173) timization problems known as multidimensional scaling or pairwise data clustering. Algorithms for embedding dissimilarity data set in a Euclidian space, for clustering these data and for actively selecting data to support the clustering process are discussed in the maximum entropy framework. Active data selection provides a strategy to discover structure in a data set efficiently with partially unknown data.

Evidential clustering is an approach to clustering based on the use of Dempster-Shafer mass functions to represent cluster-membership uncertainty. In this paper, we introduce a neural-network based evidential clustering algorithm, called NN-EVCLUS, which learns a mapping from attribute vectors to mass functions, in such a way that more similar inputs are mapped to output mass functions with a lower degree of conflict. The neural network can be paired with a one-class support vector machine to make it robust to outliers and allow for novelty detection. The network is trained to minimize the discrepancy between dissimilarities and degrees of conflict for all or some object pairs. Additional terms can be added to the loss function to account for pairwise constraints or labeled data, which can also be used to adapt the metric. Comparative experiments show the superiority of N-EVCLUS over state-of-the-art evidential clustering algorithms for a range of unsupervised and constrained clustering tasks involving both attribute and dissimilarity data.

In numerous applicative contexts, data are too rich and too complex to be represented by numerical vectors. A general approach to extend machine learning and data mining techniques to such data is to really on a dissimilarity or on a kernel that measures how different or similar two objects are. This approach has been used to define several variants of the Self Organizing Map (SOM). This paper reviews those variants in using a common set of notations in order to outline differences and similarities between them.

In some applications and in order to address real world situations better, data may be more complex than simple vectors. In some examples, they can be known through their pairwise dissimilarities only. Several variants of the Self Organizing Map algorithm were introduced to generalize the original algorithm to this framework. Whereas median SOM is based on a rough representation of the prototypes, relational SOM allows representing these prototypes by a virtual combination of all elements in the data set. However, this latter approach suffers from two main drawbacks. First, its complexity can be large. Second, only a batch version of this algorithm has been studied so far and it often provides results having a bad topographic organization. In this article, an on-line version of relational SOM is described and justified. The algorithm is tested on several datasets, including categorical data and graphs, and compared with the batch version and with other SOM algorithms for non vector data.

We introduce in this paper a new way of optimizing the natural extension of the quantization error using in k-means clustering to dissimilarity data. The proposed method is based on hierarchical clustering analysis combined with multilevel heuristic refinement. The method is computationally efficient and achieves better quantization errors than the relational k-means.

Visualizing and structuring pairwise dissimilarity data are difficult combinatorial optimization problems known as multidimensional scaling or pairwise data clustering. Algorithms for embedding dissimilarity data set in a Euclidian space, for clustering these data and for actively selecting data to support the clustering process are discussed in the maximum entropy framework. Active data selection provides a strategy to discover structure in a data set efficiently with partially unknown data. 1 Introduction Grouping experimental data into compact clusters arises as a data analysis problem in psychology, linguistics, genetics and other experimental sciences. The data which are supposed to be clustered are either given by an explicit coordinate representation (central clustering) or, in the non-metric case, they are characterized by dissimilarity values for pairs of data points (pairwise clustering). In this paper we study algorithms (i) for embedding non-metric data in a D-dimensional Euclidian space, (ii) for simultaneous clustering and embedding of non-metric data, and (iii) for active data selection to determine a particular cluster structure with minimal number of data queries. All algorithms are derived from the maximum entropy principle (Hertz et al., 1991) which guarantees robust statistics (Tikochinsky et al., 1984).

Visualizing and structuring pairwise dissimilarity data are difficult combinatorial optimization problems known as multidimensional scaling or pairwise data clustering. Algorithms for embedding dissimilarity data set in a Euclidian space, for clustering these data and for actively selecting data to support the clustering process are discussed in the maximum entropy framework. Active data selection provides a strategy to discover structure in a data set efficiently with partially unknown data. 1 Introduction Grouping experimental data into compact clusters arises as a data analysis problem in psychology, linguistics, genetics and other experimental sciences. The data which are supposed to be clustered are either given by an explicit coordinate representation (central clustering) or, in the non-metric case, they are characterized by dissimilarity values for pairs of data points (pairwise clustering). In this paper we study algorithms (i) for embedding non-metric data in a D-dimensional Euclidian space, (ii) for simultaneous clustering and embedding of non-metric data, and (iii) for active data selection to determine a particular cluster structure with minimal number of data queries. All algorithms are derived from the maximum entropy principle (Hertz et al., 1991) which guarantees robust statistics (Tikochinsky et al., 1984).

Visualizing and structuring pairwise dissimilarity data are difficult combinatorial optimization problemsknown as multidimensional scaling or pairwise data clustering. Algorithms for embedding dissimilarity data set in a Euclidian space, for clustering these data and for actively selecting data to support the clustering process are discussed in the maximum entropy framework. Active data selection provides a strategy to discover structure in a data set efficiently with partially unknown data. 1 Introduction Grouping experimental data into compact clusters arises as a data analysis problem in psychology, linguistics,genetics and other experimental sciences. The data which are supposed to be clustered are either given by an explicit coordinate representation (central clustering) or, in the non-metric case, they are characterized by dissimilarity values for pairs of data points (pairwise clustering). In this paper we study algorithms (i) for embedding non-metric data in a D-dimensional Euclidian space, (ii) for simultaneous clustering and embedding of non-metric data, and (iii) for active data selection to determine a particular cluster structure with minimal number of data queries. All algorithms are derived from the maximum entropy principle (Hertz et al., 1991) which guarantees robust statistics (Tikochinsky et al., 1984).