arXiv subjects

Caroline Moosmüller

Publications and source records attributed to Caroline Moosmüller.

16 recordsLinked to original sources

arXiv2026

A Unified Geometric Framework for Developmental Analysis of Spatial Transcriptomic Data

High-throughput single-cell and spatial transcriptomic technologies provide high-resolution snapshots of heterogeneous cellular states, but their destructive nature prevents repeated measurements of the same cells over time. Consequently, temporal and spatial dynamics must be inferred from independently sampled, unaligned cell populations, making it challenging to reconstruct developmental trajectories. Optimal transport (OT) offers a geometric framework for aligning cell populations and inferring developmental trajectories, but many existing approaches focus on modeling the evolution of distributions of cells in gene expression space rather than the relational structure encoded by gene expression networks. To address this limitation, we introduce a geometric framework for analyzing the spatiotemporal evolution of gene expression networks through embeddings in Gromov--Wasserstein (GW) space. By representing each developmental stage as a graph combining gene expression and spatial proximity, our approach enables comparisons of network structure across time, continuous interpolation between developmental stages via GW geodesics, and quantification of network-level changes using Ollivier-Ricci curvature. We evaluate our framework on a spatiotemporal transcriptomic \textit{Drosophila} dataset and show that GW geodesic interpolations reproduce main trends in curvature dynamics observed in empirical gene expression networks. Agreement with higher-order Co-Optimal Transport (COOT) distances, which jointly represent spatial and temporal information, further validates the framework and suggests that hypernetwork representations successfully record salient biological changes across time. In general, our approach provides a unified geometric approach to study dynamically evolving biological networks.

stat.ML↗

arXiv2026

Wasserstein Mahalanobis Distances for Recovering Latent Geometry

The Mahalanobis distance is a fundamental covariance-adapted metric for multivariate data and plays a central role in recovering latent geometry from nonlinear observations. We extend this principle from vector-valued data to probability measures by introducing a Wasserstein Mahalanobis distance. Our construction replaces Euclidean displacement vectors with optimal transport displacement fields and local covariance matrices with covariance operators defined on Wasserstein tangent spaces. We show that this construction inherits the geometry-recovery property underlying nonlinear independent component analysis. In particular, for Gaussian measures with common covariance transformed by a smooth nonlinear pushforward, the proposed Wasserstein Mahalanobis distance approximates the classical Mahalanobis distance between the transformed latent means. The correspondence is exact for affine transformations and holds up to controlled higher-order error terms for general smooth transformations. These results establish a distribution-valued analog of classical Mahalanobis geometry and provide theoretical support for covariance-adapted learning directly in Wasserstein space. Numerical experiments confirm the theoretical predictions and demonstrate accurate recovery of latent geometric structure.

math.OC↗

arXiv2025

Adaptive Multimodal Protein Plug-and-Play with Diffusion-Based Priors

In an inverse problem, the goal is to recover an unknown parameter (e.g., an image) that has typically undergone some lossy or noisy transformation during measurement. Recently, deep generative models, particularly diffusion models, have emerged as powerful priors for protein structure generation. However, integrating noisy experimental data from multiple sources to guide these models remains a significant challenge. Existing methods often require precise knowledge of experimental noise levels and manually tuned weights for each data modality. In this work, we introduce Adam-PnP, a Plug-and-Play framework that guides a pre-trained protein diffusion model using gradients from multiple, heterogeneous experimental sources. Our framework features an adaptive noise estimation scheme and a dynamic modality weighting mechanism integrated into the diffusion process, which reduce the need for manual hyperparameter tuning. Experiments on complex reconstruction tasks demonstrate significantly improved accuracy using Adam-PnP.

cs.LG↗

arXiv2025

Manifold learning in Wasserstein space

This paper aims at building the theoretical foundations for manifold learning algorithms in the space of absolutely continuous probability measures $\mathcal{P}_{\mathrm{a.c.}}(Ω)$ with $Ω$ a compact and convex subset of $\mathbb{R}^d$, metrized with the Wasserstein-2 distance $\mathbb{W}$. We begin by introducing a construction of submanifolds $Λ$ in $\mathcal{P}_{\mathrm{a.c.}}(Ω)$ equipped with metric $\mathbb{W}_Λ$, the geodesic restriction of $\mathbb{W}$ to $Λ$. In contrast to other constructions, these submanifolds are not necessarily flat, but still allow for local linearizations in a similar fashion to Riemannian submanifolds of $\mathbb{R}^d$. We then show how the latent manifold structure of $(Λ,\mathbb{W}_Λ)$ can be learned from samples $\{λ_i\}_{i=1}^N$ of $Λ$ and pairwise extrinsic Wasserstein distances $\mathbb{W}$ on $\mathcal{P}_{\mathrm{a.c.}}(Ω)$ only. In particular, we show that the metric space $(Λ,\mathbb{W}_Λ)$ can be asymptotically recovered in the sense of Gromov--Wasserstein from a graph with nodes $\{λ_i\}_{i=1}^N$ and edge weights $W(λ_i,λ_j)$. In addition, we demonstrate how the tangent space at a sample $λ$ can be asymptotically recovered via spectral analysis of a suitable ``covariance operator'' using optimal transport maps from $λ$ to sufficiently close and diverse samples $\{λ_i\}_{i=1}^N$. The paper closes with some explicit constructions of submanifolds $Λ$ and numerical examples on the recovery of tangent spaces through spectral analysis.

stat.ML↗

arXiv2025

Efficient Trajectory Inference in Wasserstein Space Using Consecutive Averaging

Capturing data from dynamic processes through cross-sectional measurements is seen in many fields, such as computational biology. Trajectory inference deals with the challenge of reconstructing continuous processes from such observations. In this work, we propose methods for B-spline approximation and interpolation of point clouds through consecutive averaging that is intrinsic to the Wasserstein space. Combining subdivision schemes with optimal transport-based geodesic, our methods carry out trajectory inference at a chosen level of precision and smoothness, and can automatically handle scenarios where particles undergo division over time. We prove linear convergence rates and rigorously evaluate our method on cell data characterized by bifurcations, merges, and trajectory splitting scenarios like $supercells$, comparing its performance against state-of-the-art trajectory inference and interpolation methods. The results not only underscore the effectiveness of our method in inferring trajectories but also highlight the benefit of performing interpolation and approximation that respect the inherent geometric properties of the data.

cs.LG↗

arXiv2024

Point Cloud Classification via Deep Set Linearized Optimal Transport

We introduce Deep Set Linearized Optimal Transport, an algorithm designed for the efficient simultaneous embedding of point clouds into an $L^2-$space. This embedding preserves specific low-dimensional structures within the Wasserstein space while constructing a classifier to distinguish between various classes of point clouds. Our approach is motivated by the observation that $L^2-$distances between optimal transport maps for distinct point clouds, originating from a shared fixed reference distribution, provide an approximation of the Wasserstein-2 distance between these point clouds, under certain assumptions. To learn approximations of these transport maps, we employ input convex neural networks (ICNNs) and establish that, under specific conditions, Euclidean distances between samples from these ICNNs closely mirror Wasserstein-2 distances between the true distributions. Additionally, we train a discriminator network that attaches weights these samples and creates a permutation invariant classifier to differentiate between different classes of point clouds. We showcase the advantages of our algorithm over the standard deep set approach through experiments on a flow cytometry dataset with a limited number of labeled point clouds.

cs.LG↗

arXiv2023

Linearized Wasserstein dimensionality reduction with approximation guarantees

We introduce LOT Wassmap, a computationally feasible algorithm to uncover low-dimensional structures in the Wasserstein space. The algorithm is motivated by the observation that many datasets are naturally interpreted as probability measures rather than points in $\mathbb{R}^n$, and that finding low-dimensional descriptions of such datasets requires manifold learning algorithms in the Wasserstein space. Most available algorithms are based on computing the pairwise Wasserstein distance matrix, which can be computationally challenging for large datasets in high dimensions. Our algorithm leverages approximation schemes such as Sinkhorn distances and linearized optimal transport to speed-up computations, and in particular, avoids computing a pairwise distance matrix. We provide guarantees on the embedding quality under such approximations, including when explicit descriptions of the probability measures are not available and one must deal with finite samples instead. Experiments demonstrate that LOT Wassmap attains correct embeddings and that the quality improves with increased sample size. We also show how LOT Wassmap significantly reduces the computational cost when compared to algorithms that depend on pairwise distance computations.

cs.LG↗

arXiv2022

Supervised learning of sheared distributions using linearized optimal transport

In this paper we study supervised learning tasks on the space of probability measures. We approach this problem by embedding the space of probability measures into $L^2$ spaces using the optimal transport framework. In the embedding spaces, regular machine learning techniques are used to achieve linear separability. This idea has proved successful in applications and when the classes to be separated are generated by shifts and scalings of a fixed measure. This paper extends the class of elementary transformations suitable for the framework to families of shearings, describing conditions under which two classes of sheared distributions can be linearly separated. We furthermore give necessary bounds on the transformations to achieve a pre-specified separation level, and show how multiple embeddings can be used to allow for larger families of transformations. We demonstrate our results on image classification tasks.

math.ST↗

arXiv2021

Hermite multiwavelets for manifold-valued data

In this paper we present a construction of interpolatory Hermite multiwavelets for functions that take values in nonlinear geometries such as Riemannian manifolds or Lie groups. We rely on the strong connection between wavelets and subdivision schemes to define a prediction-correction approach based on Hermite subdivision schemes that operate on manifold-valued data. The main result concerns the decay of the wavelet coefficients: We show that our manifold-valued construction essentially admits the same coefficient decay as linear Hermite wavelets, which also generalizes results on manifold-valued scalar wavelets.

math.NA↗

arXiv2021

Linear Optimal Transport Embedding: Provable Wasserstein classification for certain rigid transformations and perturbations

Discriminating between distributions is an important problem in a number of scientific fields. This motivated the introduction of Linear Optimal Transportation (LOT), which embeds the space of distributions into an $L^2$-space. The transform is defined by computing the optimal transport of each distribution to a fixed reference distribution, and has a number of benefits when it comes to speed of computation and to determining classification boundaries. In this paper, we characterize a number of settings in which LOT embeds families of distributions into a space in which they are linearly separable. This is true in arbitrary dimension, and for families of distributions generated through perturbations of shifts and scalings of a fixed distribution.We also prove conditions under which the $L^2$ distance of the LOT embedding between two distributions in arbitrary dimension is nearly isometric to Wasserstein-2 distance between those distributions. This is of significant computational benefit, as one must only compute $N$ optimal transport maps to define the $N^2$ pairwise distances between $N$ distributions. We demonstrate the benefits of LOT on a number of distribution classification problems.

stat.ML↗

arXiv2020

Polynomial overreproduction by Hermite subdivision operators, and $p$-Cauchy numbers

We study the case of Hermite subdivision operators satisfying a spectral condition of order greater than their size. We show that this can be characterized by operator factorizations involving Taylor operators and difference factorizations of a rank one vector scheme. Giving explicit expressions for the factorization operators, we put into evidence that the factorization only depends on the order of the spectral condition but not on the polynomials that define it. We further show that the derivation of these operators is based on an interplay between Stirling numbers and $p$-Cauchy numbers (or generalized Gregory coefficients).

math.NA↗

arXiv2019

A geometric approach to the transport of discontinuous densities

Different observations of a relation between inputs ("sources") and outputs ("targets") are often reported in terms of histograms (discretizations of the source and the target densities). Transporting these densities to each other provides insight regarding the underlying relation. In (forward) uncertainty quantification, one typically studies how the distribution of inputs to a system affects the distribution of the system responses. Here, we focus on the identification of the system (the transport map) itself, once the input and output distributions are determined, and suggest a modification of current practice by including data from what we call "an observation process". We hypothesize that there exists a smooth manifold underlying the relation; the sources and the targets are then partial observations (possibly projections) of this manifold. Knowledge of such a manifold implies knowledge of the relation, and thus of "the right" transport between source and target observations. When the source-target observations are not bijective (when the manifold is not the graph of a function over both observation spaces, either because folds over them give rise to density singularities, or because it marginalizes over several observables), recovery of the manifold is obscured. Using ideas from attractor reconstruction in dynamical systems, we demonstrate how additional information in the form of short histories of an observation process can help us recover the underlying manifold. The types of additional information employed and the relation to optimal transport based solely on density observations is illustrated and discussed, along with limitations in the recovery of the true underlying relation.

physics.data-an↗

arXiv2019

Stirling numbers and Gregory coefficients for the factorization of Hermite subdivision operators

In this paper we present a factorization framework for Hermite subdivision schemes refining function values and first derivatives, which satisfy a spectral condition of high order. In particular we show that spectral order $d$ allows for $d$ factorizations of the subdivision operator with respect to the Gregory operators: A new sequence of operators we define using Stirling numbers and Gregory coefficients. We further prove that the $d$-th factorization provides a ``convergence from contractivity'' method for showing $C^d$-convergence of the associated Hermite subdivision scheme. The power of our factorization framework lies in the reduction of computational effort for large $d$: In order to prove $C^d$-convergence, up to now, $d$ factorization steps were needed, while our method requires only one step, independently of $d$. Furthermore, in this paper, we show by an example that the spectral condition is not equivalent to the reproduction of polynomials.

math.NA↗

arXiv2018

A note on spectral properties of Hermite subdivision operators

In this paper we study the connection between the spectral condition of an Hermite subdivision operator and polynomial reproduction properties of the associated subdivision scheme. While it is known that in general the spectral condition does not imply the reproduction of polynomials, we here prove that a special spectral condition (defined by shifted monomials) is actually equivalent to the reproduction of polynomials. We further put into evidence that the sum rule of order $\ell>d$ associated with an Hermite subdivision operator of order $d$ does not imply that the spectral condition of order $\ell$ is satisfied, while it is known that these two concepts are equivalent in the case $\ell=d$.

math.NA↗

arXiv2018

Increasing the smoothness of vector and Hermite subdivision schemes

In this paper we suggest a method for transforming a vector subdivision scheme generating $C^{\ell}$ limits to another such scheme of the same dimension, generating $C^{\ell+1}$ limits. In scalar subdivision, it is well known that a scheme generating $C^{\ell}$ limit curves can be transformed to a new scheme producing $C^{\ell+1}$ limit curves by multiplying the scheme's symbol with the smoothing factor $\tfrac{z+1}{2}$. We extend this approach to vector and Hermite subdivision schemes, by manipulating symbols. The algorithms presented in this paper allow to construct vector (Hermite) subdivision schemes of arbitrarily high regularity from a convergent vector scheme (from a Hermite scheme whose Taylor scheme is convergent with limit functions of vanishing first component).

math.NA↗

arXiv2018

Level-dependent interpolatory Hermite subdivision schemes and wavelets

We study many properties of level-dependent Hermite subdivision, focusing on schemes preserving polynomial and exponential data. We specifically consider interpolatory schemes, which give rise to level-dependent multiresolution analyses through a prediction-correction approach. A result on the decay of the associated multiwavelet coefficients, corresponding to a uniformly continuous and differentiable function, is derived. It makes use of the approximation of any such function with a generalized Taylor formula expressed in terms of polynomials and exponentials.

math.NA↗