Model-Based Learning of Latent Euclidean Embedding from Relational Data

Learning low-dimensional representations from multi-view relational data is challenging when underlying geometries differ across views. We propose Bary-GWMDS, a Gromov-Wasserstein-based method that operates directly on distance matrices to learn a consensus embedding preserving shared relational structure. By leveraging intrinsic distances, the approach naturally handles nonlinear distortions across views. We also introduce Mean-GWMDS-C, a clustering-oriented formulation that averages distance matrices and learns reduced-support representations via a consensus Gromov-Wasserstein transport. Experiments on synthetic and real-world datasets show that the proposed framework yields stable and geometrically meaningful embeddings.

We study the problem of recovering a globally consistent Euclidean embedding of data, given only a local distance graph and propose a method that optimally represents these distances. The method operates solely on a neighborhood graph weighted by pairwise distances, without requiring any prior vector representation of the data. The embedding is obtained by solving a variational problem that matches local, on-graph distances to the Euclidean metric, induced by the differentials of the embedding functions. The resulting Euler-Lagrange equations are derived in a coordinate-free form, enabling direct evaluation of all operators from the distance graph alone. Though non-linear and missing an explicit expression for their non-linearity, these equations are shown to be resolved as an iteratively updated sparse linear problem. The main contributions of the proposed approach are (a) the derivation of the functional equations governing the optimal Euclidean embedding in the continuum, (b) a representation-free formulation that requires only a neighborhood distance graph and no feature vectors and (c) an estimation procedure based exclusively on local graph operations. We experimentally evaluate the resulting non-parametric algorithm on synthetic manifolds and real datasets, demonstrating consistent preservation of local metric structure and neighboring relations, while approximating the global isometric embedding.

Latent space models are widely used for analyzing high-dimensional discrete data matrices, such as patient-feature matrices in electronic health records (EHRs), by capturing complex dependence structures through low-dimensional embeddings. However, estimation becomes challenging in the imbalanced regime, where one matrix dimension is much larger than the other. In EHR applications, cohort sizes are often limited by disease prevalence or data availability, whereas the feature space remains extremely large due to the breadth of medical coding system. Motivated by the increasing availability of external semantic embeddings, such as pre-trained embeddings of clinical concepts in EHRs, we propose a knowledge-embedded latent projection model that leverages semantic side information to regularize representation learning. Specifically, we model column embeddings as smooth functions of semantic embeddings via a mapping in a reproducing kernel Hilbert space. We develop a computationally efficient two-step estimation procedure that combines semantically guided subspace construction via kernel principal component analysis with scalable projected gradient descent. We establish estimation error bounds that characterize the trade-off between statistical error and approximation error induced by the kernel projection. Furthermore, we provide local convergence guarantees for our non-convex optimization procedure. Extensive simulation studies and a real-world EHR application demonstrate the effectiveness of the proposed method.