Bogomolny, Bohigas and Schmit (BBS) found that the spectrum of the pairwise distance matrix on N points sampled from a smooth d-dimensional manifold encodes a signature of the underlying geometry. We develop I-BBS (Inference-BBS), a coordinate-free method that identifies a low-dimensional latent sub-manifold embedded in a high-dimensional ambient distance matrix alone, without accessing an ambient high-dimensional vector space. It therefore applies even when that space is only partly observable or undefined. We model the ambient embedding by two classes of generative noise, model-based and model-free. The noise mixes the latent signal with off-manifold components, so the eigenvalues reorganise collectively and the latent geometry cannot be read off eigenvalue by eigenvalue. We recover it instead from two integer-stable signatures that survive the noise: the multiplicity of the top non-Perron multiplet, which fixes $d$, and a parameter-free law for how the multiplet positions shrink as the noise grows. On synthetic spheres $S^1$, $S^2$ and $S^3$ these integer signatures are far more stable under noise than the continuous spectral slope, and a blind test recovers both the manifold and the noise model from a single distance matrix. Applications to neural-network representations and to the dynamic training regime are developed in two companion papers.

Trees and the associated shortest-path tree metrics provide a powerful framework for representing hierarchical and combinatorial structures in data. Given an arbitrary metric space, its deviation from a tree metric can be quantified by Gromov's δhyperbolicity. Nonetheless, designing algorithms that bridge an arbitrary metric to its closest tree metric is still a vivid subject of interest, as most common approaches are either heuristical and lack guarantees, or perform moderately well. In this work, we introduce a novel differentiable optimization framework, coined DELTAZERO, that solves this problem. Our method leverages a smooth surrogate for Gromov's δ-hyperbolicity which enables a gradient-based optimization, with a tractable complexity. The corresponding optimization procedure is derived from a problem with better worst case guarantees than existing bounds, and is justified statistically. Experiments on synthetic and real-world datasets demonstrate that our method consistently achieves state-of-the-art distortion.

The Johnson-Lindenstrauss (JL) lemma is a cornerstone of dimensionality reduction in Euclidean space, but its applicability to non-Euclidean data has remained limited. This paper extends the JL lemma beyond Euclidean geometry to handle general dissimilarity matrices that are prevalent in real-world applications. We present two complementary approaches: First, we show the JL transform can be applied to vectors in pseudo-Euclidean space with signature (p,q), providing theoretical guarantees that depend on the ratio of the (p,q)norm and Euclidean norm of two vectors, measuring the deviation from Euclidean geometry. Second, we prove that any symmetric hollow dissimilarity matrix can be represented as a matrix of generalized power distances, with an additional parameter representing the uncertainty level within the data. In this representation, applying the JL transform yields multiplicative approximation with a controlled additive error term proportional to the deviation from Euclidean geometry. Our theoretical results provide fine-grained performance analysis based on the degree to which the input data deviates from Euclidean geometry, making practical and meaningful reduction in dimensionality accessible to a wider class of data.

Federated clustering (FC) aims to discover global cluster structures across decentralized clients without sharing raw data, making privacy preservation a fundamental requirement. There are two critical challenges: (1) privacy leakage during collaboration, and (2) robustness degradation due to aggregation of proxy information from non-independent and identically distributed (Non-IID) local data, leading to inaccurate or inconsistent global clustering. Existing solutions typically rely on model-specific local proxies, which are sensitive to data heterogeneity and inherit inductive biases from their centralized counterparts, thus limiting robustness and generality. We propose Omni Federated Clustering (OmniFC), a unified and modelagnostic framework. Leveraging Lagrange coded computing, our method enables clients to share only encoded data, allowing exact reconstruction of the global distance matrix--a fundamental representation of sample relationships--without leaking private information, even under client collusion. This construction is naturally resilient to Non-IID data distributions. This approach decouples FC from model-specific proxies, providing a unified extension mechanism applicable to diverse centralized clustering methods. Theoretical analysis confirms both reconstruction fidelity and privacy guarantees, while comprehensive experiments demonstrate OmniFC's superior robustness, effectiveness, and generality across various benchmarks compared to state-of-the-art methods.

The shape of objects is an important source of visual information in a wide range of applications. One of the core challenges of shape quantification is to ensure that the extracted measurements remain invariant to transformations that preserve an object's intrinsic geometry, such as changing its size, orientation, and position in the image. In this work, we introduce ShapeEmbed, a self-supervised representation learning framework designed to encode the contour of objects in 2D images, represented as a Euclidean distance matrix, into a shape descriptor that is invariant to translation, scaling, rotation, reflection, and point indexing. Our approach overcomes the limitations of traditional shape descriptors while improving upon existing state-of-the-art autoencoder-based approaches. We demonstrate that the descriptors learned by our framework outperform their competitors in shape classification tasks on natural and biological images. We envision our approach to be of particular relevance to biological imaging applications.

Topological Data Analysis (TDA) offers a principled, intrinsic lens for comparing neural representations. However, existing paired topological divergences (e.g., RTD) are limited by heuristic asymmetry and, more critically, unbounded scores that depend on sample size, hindering reliable cross-scenario benchmarking. To address these challenges, we develop a unified topological toolkit serving two complementary needs: fine-grained structural diagnosis and robust, standardized evaluation. First, we complete the RTD framework by introducing Symmetric Representation Topology Divergence (SRTD) and its efficient variant SRTD-lite. Beyond resolving the theoretical asymmetry of prior variants, SRTD consolidates diagnostic information into a single, comprehensive cross-barcode signature. This allows for precise localization of structural discrepancies and serves as an effective optimization objective without the overhead of dual directional computations. Second, to enable reliable benchmarking across heterogeneous settings, we propose Normalized Topological Similarity (NTS). By measuring the rank correlation of hierarchical merge orders, NTS yields a scale-invariant metric bounded between -1 and 1, effectively overcoming the scale and sample-dependence of unnormalized divergences. Experiments across synthetic and real-world deep learning settings demonstrate that our toolkit captures functional shifts in CNNs missed by geometric measures and robustly maps LLM genealogy even under distance saturation, offering a rigorous, topology-aware perspective that complements measures like CKA.

Spectral clustering has gained popularity for clustering non-convex data due to its simplicity and effectiveness. It is essential to construct a similarity graph using a high-quality affinity measure that models the local neighborhood relations among the data samples. However, incomplete data can lead to inaccurate affinity measures, resulting in degraded clustering performance. To address these issues, we propose an imputation-free framework with two novel approaches to improve spectral clustering on incomplete data. Firstly, we introduce a new kernel correction method that enhances the quality of the kernel matrix estimated on incomplete data with a theoretical guarantee, benefiting classical spectral clustering on pre-defined kernels. Secondly, we develop a series of affinity learning methods that equip the selfexpressive framework with ℓp-norm to construct an intrinsic affinity matrix with an adaptive extension. Our methods outperform existing data imputation and distance calibration techniques on benchmark datasets, offering a promising solution to spectral clustering on incomplete data in various real-world applications.

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.