arXiv subjects

Willem Diepeveen

Publications and source records attributed to Willem Diepeveen.

15 recordsLinked to original sources

arXiv2026

Beyond Unimodal Bases: Pullback Geometry for Multimodal Data

Data-driven Riemannian geometry provides nonlinear interpolation and geometric representations of high-dimensional data. For these operations to be statistically meaningful, paths between observations should preferentially traverse high-likelihood regions. Existing scalable pullback constructions typically use a unimodal Gaussian latent distribution, assuming that the data reside close to a single manifold. For multimodal data, mapping separated modes or local structures into one Gaussian region can require substantial transport deformation and compromise the resulting geometry. We introduce a pullback geometry for data supported on mixtures of manifolds. Using a latent Gaussian mixture, we define its Riemannian metric as the matrix square of the responsibility-weighted expected component precision. The metric is smooth and positive definite and recovers the existing Gaussian construction in the single-component limit. For structured overlapping mixtures, we establish conditions under which the log-density is concave along geodesics, providing a formal connection between the proposed geometry and paths through high-likelihood regions, and derive the corresponding local curvature relations. We instantiate this geometry in a normalizing flow with adaptive mixture learning, allowing the number of active components to emerge from the data and supporting component-wise reconstruction and local effective-dimension estimation. Experiments on synthetic geometric data, a controlled multi-view image setting with a known reference trajectory, and MNIST show reduced transport distortion, competitive path support, close reference-trajectory recovery, and improved interpolation realism. These results extend scalable pullback geometry beyond datasets that reside close to a single manifold while retaining tractable and interpretable local structure.

cs.LG↗

arXiv2026

Iso-Riemannian Optimization on Learned Data Manifolds

We develop a theory of iso-Riemannian optimization for problems constrained to learned data manifolds, a setting in which classical Riemannian optimization - and Riemannian gradient descent in particular - can be poorly suited. That is, favorable Euclidean properties of an objective need not translate into geodesic convexity or L-smoothness, and the Riemannian gradient may provide an unsuitable search direction. We instead combine the manifold mappings induced by the iso-connection, whose geodesics have constant Euclidean speed, with the l2-projected Euclidean gradient, resulting in l2-projected gradient iso-Riemannian descent, in an attempt to alleviate these issues. We analyze this scheme from two complementary perspectives. First, we introduce iso-g-convexity and iso-L-smoothness, relate strong iso-g-convexity to a Polyak-Lojasiewicz-type condition, and establish general convergence guarantees. This function-based theory addresses the conditioning and search-direction issues that motivate our approach. Second, we introduce iso-monotonicity and iso-Lipschitzness for vector fields. However, while these notions yield analogous convergence results in one dimension and enable applications such as the computation of iso-Riemannian barycentres, the resulting theory need not extend meaningfully to higher dimensions. So unlike in the classical Levi-Civita setting, these function- and vector field-based perspectives need not be equivalent in the iso-Riemannian setting. Consequently, distinct extensions of classical Riemannian optimization lead to different assumptions and convergence guarantees. The theory developed here suggests that, for function optimization, the function-based perspective provides the more general, tractable and overall suitable framework, whereas the vector field perspective is naturally reserved for problems without a direct function-based formulation.

math.OC↗

arXiv2026

Riemannian AmbientFlow: Towards Simultaneous Manifold Learning and Generative Modeling from Corrupted Data

Modern generative modeling methods have demonstrated strong performance in learning complex data distributions from clean samples. In many scientific and imaging applications, however, clean samples are unavailable, and only noisy or linearly corrupted measurements can be observed. Moreover, latent structures, such as manifold geometries, present in the data are important to extract for further downstream scientific analysis. In this work, we introduce Riemannian AmbientFlow, a framework for simultaneously learning a probabilistic generative model and the underlying, nonlinear data manifold directly from corrupted observations. Building on the variational inference framework of AmbientFlow, our approach incorporates data-driven Riemannian geometry induced by normalizing flows, enabling the extraction of manifold structure through pullback metrics and Riemannian Autoencoders. We establish theoretical guarantees showing that, under appropriate geometric regularization and measurement conditions, the learned model recovers the underlying data distribution up to a controllable error and yields a smooth, bi-Lipschitz manifold parametrization. We further show that the resulting smooth decoder can serve as a principled generative prior for inverse problems with recovery guarantees. We empirically validate our approach on low-dimensional synthetic manifolds and on MNIST.

cs.LG↗

arXiv2026

Riemannian Archetypal Analysis: Interpretable non-linear data analysis on deformed star distributions

Classical archetypal analysis is appealing for its interpretability, but its linear geometry can limit performance on data with strongly non-linear structure; at the same time, existing neural extensions improve flexibility while often weakening the geometric meaning of archetypes and interpolations. In this work, we develop a Riemannian version of archetypal analysis based on data-driven pullback geometry for real-valued data, with the goal of combining the interpretability of classical archetypal analysis with the expressive power of modern non-linear models. We introduce a class of deformed star distributions together with associated pullback Riemannian geometry to provide a statistical interpretation of the resulting manifold mappings, define the Riemannian archetypal mapping (RAM) as a projection onto the manifold of geodesically convex combinations of archetypes, and propose a practical optimization scheme based on convex relaxation followed by non-convex refinement. We further propose a learning scheme that yields reasonable, albeit generally suboptimal, deformed star distributions from data. Experiments on synthetic examples and MNIST show that the resulting framework produces meaningful geodesics, useful denoising projections, and geometry-aware classifications, while also clarifying where current optimization limitations remain.

cs.LG↗

arXiv2026

Manifold Learning with Normalizing Flows: Towards Regularity, Expressivity and Iso-Riemannian Geometry

Modern machine learning increasingly leverages the insight that high-dimensional data often lie near low-dimensional, non-linear manifolds, an idea known as the manifold hypothesis. By explicitly modeling the geometric structure of data through learning Riemannian geometry algorithms can achieve improved performance and interpretability in tasks like clustering, dimensionality reduction, and interpolation. In particular, learned pullback geometry has recently undergone transformative developments that now make it scalable to learn and scalable to evaluate, which further opens the door for principled non-linear data analysis and interpretable machine learning. However, there are still steps to be taken when considering real-world multi-modal data. This work focuses on addressing distortions and modeling errors that can arise in the multi-modal setting and proposes to alleviate both challenges through isometrizing the learned Riemannian structure and balancing regularity and expressivity of the diffeomorphism parametrization. We showcase the effectiveness of the synergy of the proposed approaches in several numerical experiments with both synthetic and real data.

cs.LG↗

arXiv2025

Latent Diffeomorphic Dynamic Mode Decomposition

We present Latent Diffeomorphic Dynamic Mode Decomposition (LDDMD), a new data reduction approach for the analysis of non-linear systems that combines the interpretability of Dynamic Mode Decomposition (DMD) with the predictive power of Recurrent Neural Networks (RNNs). Notably, LDDMD maintains simplicity, which enhances interpretability, while effectively modeling and learning complex non-linear systems with memory, enabling accurate predictions. This is exemplified by its successful application in streamflow prediction.

cs.LG↗

arXiv2025

Pullback Flow Matching on Data Manifolds

We propose Pullback Flow Matching (PFM), a novel framework for generative modeling on data manifolds. Unlike existing methods that assume or learn restrictive closed-form manifold mappings for training Riemannian Flow Matching (RFM) models, PFM leverages pullback geometry and isometric learning to preserve the underlying manifold's geometry while enabling efficient generation and precise interpolation in latent space. This approach not only facilitates closed-form mappings on the data manifold but also allows for designable latent spaces, using assumed metrics on both data and latent manifolds. By enhancing isometric learning through Neural ODEs and proposing a scalable training objective, we achieve a latent space more suitable for interpolation, leading to improved manifold learning and generative performance. We demonstrate PFM's effectiveness through applications in synthetic data, protein dynamics and protein sequence data, generating novel proteins with specific properties. This method shows strong potential for drug discovery and materials science, where generating novel samples with specific properties is of great interest.

cs.LG↗

arXiv2025

Score-based Pullback Riemannian Geometry: Extracting the Data Manifold Geometry using Anisotropic Flows

Data-driven Riemannian geometry has emerged as a powerful tool for interpretable representation learning, offering improved efficiency in downstream tasks. Moving forward, it is crucial to balance cheap manifold mappings with efficient training algorithms. In this work, we integrate concepts from pullback Riemannian geometry and generative models to propose a framework for data-driven Riemannian geometry that is scalable in both geometry and learning: score-based pullback Riemannian geometry. Focusing on unimodal distributions as a first step, we propose a score-based Riemannian structure with closed-form geodesics that pass through the data probability density. With this structure, we construct a Riemannian autoencoder (RAE) with error bounds for discovering the correct data manifold dimension. This framework can naturally be used with anisotropic normalizing flows by adopting isometry regularization during training. Through numerical experiments on diverse datasets, including image data, we demonstrate that the proposed framework produces high-quality geodesics passing through the data support, reliably estimates the intrinsic dimension of the data manifold, and provides a global chart of the manifold. To the best of our knowledge, this is the first scalable framework for extracting the complete geometry of the data manifold.

cs.LG↗

arXiv2025

Curvature Corrected Nonnegative Manifold Data Factorization

Data with underlying nonlinear structure are collected across numerous application domains, necessitating new data processing and analysis methods adapted to nonlinear domain structure. Riemannanian manifolds present a rich environment in which to develop such tools, as manifold-valued data arise in a variety of scientific settings, and Riemannian geometry provides a solid theoretical grounding for geometric data analysis. Low-rank approximations, such as nonnegative matrix factorization (NMF), are the foundation of many Euclidean data analysis methods, so adaptations of these factorizations for manifold-valued data are important building blocks for further development of manifold data analysis. In this work, we propose curvature corrected nonnegative manifold data factorization (CC-NMDF) as a geometry-aware method for extracting interpretable factors from manifold-valued data, analogous to nonnegative matrix factorization. We develop an efficient iterative algorithm for computing CC-NMDF and demonstrate our method on real-world diffusion tensor magnetic resonance imaging data.

math.NA↗

arXiv2024

Pulling back symmetric Riemannian geometry for data analysis

Data sets tend to live in low-dimensional non-linear subspaces. Ideal data analysis tools for such data sets should therefore account for such non-linear geometry. The symmetric Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich mathematical structure to account for a wide range of non-linear geometries that has been shown to be able to capture the data geometry through empirical evidence from classical non-linear embedding. Second, many standard data analysis tools initially developed for data in Euclidean space can also be generalised efficiently to data on a symmetric Riemannian manifold. A conceptual challenge comes from the lack of guidelines for constructing a symmetric Riemannian structure on the data space itself and the lack of guidelines for modifying successful algorithms on symmetric Riemannian manifolds for data analysis to this setting. This work considers these challenges in the setting of pullback Riemannian geometry through a diffeomorphism. The first part of the paper characterises diffeomorphisms that result in proper, stable and efficient data analysis. The second part then uses these best practices to guide construction of such diffeomorphisms through deep learning. As a proof of concept, different types of pullback geometries -- among which the proposed construction -- are tested on several data analysis tasks and on several toy data sets. The numerical experiments confirm the predictions from theory, i.e., that the diffeomorphisms generating the pullback geometry need to map the data manifold into a geodesic subspace of the pulled back Riemannian manifold while preserving local isometry around the data manifold for proper, stable and efficient data analysis, and that pulling back positive curvature can be problematic in terms of stability.

math.DG↗

arXiv2023

Riemannian geometry for efficient analysis of protein dynamics data

An increasingly common viewpoint is that protein dynamics data sets reside in a non-linear subspace of low conformational energy. Ideal data analysis tools for such data sets should therefore account for such non-linear geometry. The Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich structure to account for a wide range of geometries that can be modelled after an energy landscape. Second, many standard data analysis tools initially developed for data in Euclidean space can also be generalised to data on a Riemannian manifold. In the context of protein dynamics, a conceptual challenge comes from the lack of a suitable smooth manifold and the lack of guidelines for constructing a smooth Riemannian structure based on an energy landscape. In addition, computational feasibility in computing geodesics and related mappings poses a major challenge. This work considers these challenges. The first part of the paper develops a novel local approximation technique for computing geodesics and related mappings on Riemannian manifolds in a computationally feasible manner. The second part constructs a smooth manifold of point clouds modulo rigid body group actions and a Riemannian structure that is based on an energy landscape for protein conformations. The resulting Riemannian geometry is tested on several data analysis tasks relevant for protein dynamics data. It performs exceptionally well on coarse-grained molecular dynamics simulated data. In particular, the geodesics with given start- and end-points approximately recover corresponding molecular dynamics trajectories for proteins that undergo relatively ordered transitions with medium sized deformations. The Riemannian protein geometry also gives physically realistic summary statistics and retrieves the underlying dimension even for large-sized deformations within seconds on a laptop.

q-bio.BM↗

arXiv2023

Curvature corrected tangent space-based approximation of manifold-valued data

When generalizing schemes for real-valued data approximation or decomposition to data living in Riemannian manifolds, tangent space-based schemes are very attractive for the simple reason that these spaces are linear. An open challenge is to do this in such a way that the generalized scheme is applicable to general Riemannian manifolds, is global-geometry aware and is computationally feasible. Existing schemes have been unable to account for all three of these key factors at the same time. In this work, we take a systematic approach to developing a framework that is able to account for all three factors. First, we will restrict ourselves to the -- still general -- class of symmetric Riemannian manifolds and show how curvature affects general manifold-valued tensor approximation schemes. Next, we show how the latter observations can be used in a general strategy for developing approximation schemes that are also global-geometry aware. Finally, having general applicability and global-geometry awareness taken into account we restrict ourselves once more in a case study on low-rank approximation. Here we show how computational feasibility can be achieved and propose the curvature-corrected truncated higher-order singular value decomposition (CC-tHOSVD), whose performance is subsequently tested in numerical experiments with both synthetic and real data living in symmetric Riemannian manifolds with both positive and negative curvature.

math.NA↗

arXiv2023

Regularising orientation estimation in Cryo-EM 3D map refinement through measure-based lifting over Riemannian manifolds

Motivated by the trade-off between noise-robustness and data-consistency for joint 3D map reconstruction and rotation estimation in single particle cryogenic-electron microscopy (Cryo-EM), we propose ellipsoidal support lifting (ESL), a measure-based lifting scheme for regularising and approximating the global minimiser of a smooth function over a Riemannian manifold. Under a uniqueness assumption on the minimiser we show several theoretical results, in particular well-posedness of the method and an error bound due to the induced bias with respect to the global minimiser. Additionally, we use the developed theory to integrate the measure-based lifting scheme into an alternating update method for joint homogeneous 3D map reconstruction and rotation estimation, where typically tens of thousands of manifold-valued minimisation problems have to be solved and where regularisation is necessary because of the high noise levels in the data. The joint recovery method is used to test both the theoretical predictions and algorithmic performance through numerical experiments with Cryo-EM data. In particular, the induced bias due to the regularising effect of ESL empirically estimates better rotations, i.e., rotations closer to the ground truth, than global optimisation would.

math.OC↗

arXiv2022

Spectral decomposition of atomic structures in heterogeneous cryo-EM

We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the macromolecule, taken from different viewing directions, and in the heterogeneous case, each image corresponds to a different conformation of the macromolecule. Under the assumption that the macromolecule can be modelled as a chain, or discrete curve (as it is for instance the case for a protein backbone with a single chain of amino-acids), we introduce a method to estimate the deformation of the atomic model with respect to a given conformation, which is assumed to be known a priori. Our method consists on estimating the torsion and bond angles of the atomic model in each conformation as a linear combination of the eigenfunctions of the Laplace operator in the manifold of conformations. These eigenfunctions can be approximated by means of a well-known technique in manifold learning, based on the construction of a graph Laplacian using the cryo-EM dataset. Finally, we test our approach with synthetic datasets, for which we recover the atomic model of two-dimensional and three-dimensional flexible structures from noisy tomographic projections.

eess.IV↗

arXiv2021

An Inexact Semi-smooth Newton Method on Riemannian Manifolds with Application to Duality-based Total Variation Denoising

We propose a higher-order method for solving non-smooth optimization problems on manifolds. In order to obtain superlinear convergence, we apply a Riemannian Semi-smooth Newton method to a non-smooth non-linear primal-dual optimality system based on a recent extension of Fenchel duality theory to Riemannian manifolds. We also propose an inexact version of the Riemannian Semi-smooth Newton method and prove conditions for local linear and superlinear convergence that hold independent of the sign of the curvature. Numerical experiments on l2-TV-like problems with dual regularization confirm superlinear convergence on manifolds with positive and negative curvature.

math.OC↗