arXiv subjects

Stefan Sommer

Publications and source records attributed to Stefan Sommer.

At least 19 recordsLinked to original sources

arXiv2026

Landmark shape spaces with induced metrics

We present a unification of Kendall's landmark shape spaces, where rigid motions are factored out and scale fixed on landmark configurations equipped with Euclidean geometry, with landmark configuration spaces carrying Riemannian metrics descending from right-invariant Sobolev metrics on the diffeomorphism group. The resulting new landmark shape spaces achieve the defining properties of both approaches: The regularity of the descending metric prevents landmarks from colliding, the metric is defined in the ambient space independent of the number of landmarks, local rigid transformations are preserved, global rigid motions are removed, and scale fixed. To achieve this, we define a particular Sobolev-type operator, the screened elasticity operator, whose null-space consists exactly of the rigid motions, we show how this operator descends to achieve the desired geometry, and we present approaches to solving matching problems and computing geodesics numerically. The resulting construction allows the use of landmark configuration spaces with sufficiently regular metrics in applications while retaining the shape invariances that are a hallmark of Kendall's shape spaces.

cs.CV↗

arXiv2026

Hyperiax and Phylogenetic Inference from Shape Data

Phylogenetic inference on high-dimensional morphological traits requires algorithms that account for both the nonlinear geometry of the shape data and the phylogenetic tree structure. The Backward Filtering Forward Guiding (BFFG) framework provides smoothing for nonlinear stochastic processes on trees and enables inference of parameters and ancestral states. As practical adoption has been limited by a lack of efficient implementations, we present Hyperiax, an open-source library for tree traversal algorithms and message passing using JAX, designed particularly to support operations needed for BFFG. Hyperiax enables efficient execution of operations on trees with large numbers of nodes and, coupled with the BFFG-specific operations, this allows efficient inference in both discrete-time and stochastic differential equation models. Concretely, we demonstrate that Hyperiax enables parameter inference and ancestral reconstruction for butterfly wing shapes represented by landmarks in two dimensions, and analyses of avian beaks from landmarks in three dimensions. Both cases demonstrate application of BFFG on two substantially larger phylogenetic trees with 850 and 696 nodes with higher resolution shape data (118 two-dimensional landmarks and 79 three-dimensional landmarks, specifically) than previously possible.

q-bio.PE↗

arXiv2026

Stochastic completeness for landmark space

We study stochastic completeness for landmark spaces equipped with Riemannian metrics induced by right-invariant metrics on subgroups of the diffeomorphism group of the shape domain. We extend a previous stochastic completeness result, which only covers the case of exactly two landmarks, to landmark spaces with any number of landmarks. This succeeds the characterization of geodesic completeness for landmark spaces with arbitrary numbers of landmarks, and thus finishes the completeness characterization for landmark spaces by covering the stochastic case. The proof makes use of Grigor'yan's volume growth criterion for stochastic completeness, which requires a suitable upper bound for the volume of growing geodesic balls. We obtain quantitative controls for geodesic balls in the landmark space by bounding both its Euclidean size and the rate at which pairwise landmark distances can approach zero. We then combine this with a lower bound on the minimal eigenvalue of the landmark cometric in terms of the Fourier transform of the kernel to yield volume growth bounds sufficient to prove stochastic completeness of landmark spaces for wide classes of kernels, including Matérn kernels.

math.PR↗

arXiv2026

Neural Backward Filtering Forward Guiding

Inference in nonlinear continuous stochastic processes on trees is challenging, particularly when observations are sparse and the topology is complex. Exact smoothing via Doob's $h$-transform is intractable for general nonlinear dynamics. We propose Neural Backward Filtering Forward Guiding (NBFFG), a unified framework for both discrete transitions and continuous diffusions. Our method constructs a variational posterior by leveraging a proxy linear-Gaussian process. This proxy process yields a closed-form backward filter that serves as a guide, steering the generative path toward high-likelihood regions. We then learn a neural residual to capture the non-linear discrepancies. This formulation allows for an unbiased pathwise subsampling scheme, reducing the training complexity from tree-size dependent to path-length dependent. Empirical results show that NBFFG outperforms baselines on synthetic benchmarks, and we demonstrate the method on a high-dimensional inference task in phylogenetic analysis with reconstruction of ancestral butterfly wing shapes.

stat.ML↗

arXiv2026

A Diffeomorphism Groupoid and Algebroid Framework for Discontinuous Image Registration

In this paper, we propose a novel mathematical framework for piecewise diffeomorphic image registration that involves discontinuous sliding motion using a diffeomorphism groupoid and algebroid approach. The traditional Large Deformation Diffeomorphic Metric Mapping (LDDMM) registration method builds on Lie groups, which assume continuity and smoothness in velocity fields, limiting its applicability in handling discontinuous sliding motion. To overcome this limitation, we extend the diffeomorphism Lie groups to a framework of discontinuous diffeomorphism Lie groupoids, allowing for discontinuities along sliding boundaries while maintaining diffeomorphism within homogeneous regions. We provide a rigorous analysis of the associated mathematical structures, including Lie algebroids and their duals, and derive specific Euler-Arnold equations to govern optimal flows for discontinuous deformations. Numerical tests are performed to validate the efficiency of the proposed approach.

math.GR↗

arXiv2026

Stochastics of shapes and Kunita flows

Stochastic processes of evolving shapes are used in applications including evolutionary biology, where morphology changes stochastically as a function of evolutionary processes. Due to the non-linear and often infinite-dimensional nature of shape spaces, the mathematical construction of suitable stochastic shape processes is far from immediate. We define and formalize properties that stochastic shape processes should ideally satisfy to be compatible with the shape structure, and we link this to Kunita flows that, when acting on shape spaces, induce stochastic processes that satisfy these criteria by their construction. We couple this with a survey of other relevant shape stochastic processes and show how bridge sampling techniques can be used to condition shape stochastic processes on observed data thereby allowing for statistical inference of parameters of the stochastic dynamics.

math.PR↗

arXiv2026

Most probable paths for developed processes

Optimal paths for the classical Onsager-Machlup function determining most probable paths between points on a manifold are only explicitly identified for specific processes, for example the Riemannian Brownian motion. This leaves out large classes of manifold-valued processes such as processes with parallel transported non-trivial diffusion matrix, processes with rank-deficient generator and sub-Riemannian processes, and push-forwards to quotient spaces. In this paper, we construct a general approach to definition and identification of most probable paths by measuring the Onsager-Machlup function on the anti-development of such processes. The construction encompasses large classes of manifold-valued process and results in explicit equation systems for the paths that we denote \emph{development most probable paths}. We define and derive these results and apply them to several cases of stochastic processes on Lie groups, homogeneous spaces, and landmark spaces appearing in shape analysis.

math.PR↗

arXiv2025

Parallel transport on matrix manifolds and Exponential Action

We express parallel transport for several common matrix Lie groups with a family of pseudo-Riemannian metrics in terms of matrix exponential and exponential actions. The metrics are constructed from a deformation of a bi-invariant metric and are naturally reductive. There is a similar picture for homogeneous spaces when taking quotients satisfying a general condition. In particular, for a Stiefel manifold of orthogonal matrices of size $n\times d$, we give an expression for parallel transport along a geodesic from time zero to $t$, that could be computed with time complexity of $O(n d^2)$ for small $t$, and of $O(td^3)$ for large $t$, contributing a step in a long-standing open problem in matrix manifolds. A similar result holds for {\it flag manifolds} with the canonical metric. We also show the parallel transport formulas for the {\it general linear group} and the {\it special orthogonal group} under these metrics.

math.NA↗

arXiv2025

Neural Guided Diffusion Bridges

We propose a novel method for simulating conditioned diffusion processes (diffusion bridges) in Euclidean spaces. By training a neural network to approximate bridge dynamics, our approach eliminates the need for computationally intensive Markov Chain Monte Carlo (MCMC) methods or score modeling. Compared to existing methods, it offers greater robustness across various diffusion specifications and conditioning scenarios. This applies in particular to rare events and multimodal distributions, which pose challenges for score-learning- and MCMC-based approaches. We introduce a flexible variational family, partially specified by a neural network, for approximating the diffusion bridge path measure. Once trained, it enables efficient sampling of independent bridges at a cost comparable to sampling the unconditioned (forward) process.

stat.ML↗

arXiv2025

Backward Filtering Forward Guiding

We develop a general methodological framework for probabilistic inference in discrete- and continuous-time stochastic processes evolving on directed acyclic graphs (DAGs). The process is observed only at the leaf nodes, and the challenge is to infer its full latent trajectory: a smoothing problem that arises in fields such as phylogenetics, epidemiology, and signal processing. Our approach combines a backward information filtering step, which constructs likelihood-informed potentials from observations, with a forward guiding step, where a tractable process is simulated under a change of measure constructed from these potentials. This Backward Filtering Forward Guiding (BFFG) scheme yields weighted samples from the posterior distribution over latent paths and is amenable to integration with MCMC and particle filtering methods. We demonstrate that BFFG applies to both discrete- and continuous-time models, enabling probabilistic inference in settings where standard transition densities are intractable or unavailable. Our framework opens avenues for incorporating structured stochastic dynamics into probabilistic programming. We numerically illustrate our approach for a branching diffusion process on a directed tree.

stat.ME↗

arXiv2025

Infinite-dimensional Diffusion Bridge Simulation via Operator Learning

The diffusion bridge, which is a diffusion process conditioned on hitting a specific state within a finite period, has found broad applications in various scientific and engineering fields. However, simulating diffusion bridges for modeling natural data can be challenging due to both the intractability of the drift term and continuous representations of the data. Although several methods are available to simulate finite-dimensional diffusion bridges, infinite-dimensional cases remain under explored. This paper presents a method that merges score matching techniques with operator learning, enabling a direct approach to learn the infinite-dimensional bridge and achieving a discretization equivariant bridge simulation. We conduct a series of experiments, ranging from synthetic examples with closed-form solutions to the stochastic nonlinear evolution of real-world biological shape data. Our method demonstrates high efficacy, particularly due to its ability to adapt to any resolution without extra training.

cs.LG↗

arXiv2025

Deep Anatomical Federated Network (Dafne): An open client-server framework for the continuous, collaborative improvement of deep learning-based medical image segmentation

Purpose: To present and evaluate Dafne (deep anatomical federated network), a freely available decentralized, collaborative deep learning system for the semantic segmentation of radiological images through federated incremental learning. Materials and Methods: Dafne is free software with a client-server architecture. The client side is an advanced user interface that applies the deep learning models stored on the server to the user's data and allows the user to check and refine the prediction. Incremental learning is then performed at the client's side and sent back to the server, where it is integrated into the root model. Dafne was evaluated locally, by assessing the performance gain across model generations on 38 MRI datasets of the lower legs, and through the analysis of real-world usage statistics (n = 639 use-cases). Results: Dafne demonstrated a statistically improvement in the accuracy of semantic segmentation over time (average increase of the Dice Similarity Coefficient by 0.007 points/generation on the local validation set, p < 0.001). Qualitatively, the models showed enhanced performance on various radiologic image types, including those not present in the initial training sets, indicating good model generalizability. Conclusion: Dafne showed improvement in segmentation quality over time, demonstrating potential for learning and generalization.

eess.IV↗

arXiv2025

Score matching for bridges without learning time-reversals

We propose a new algorithm for learning bridged diffusion processes using score-matching methods. Our method relies on reversing the dynamics of the forward process and using this to learn a score function, which, via Doob's $h$-transform, yields a bridged diffusion process; that is, a process conditioned on an endpoint. In contrast to prior methods, we learn the score term $\nabla_x \log p(t, x; T, y)$ directly, for given $t, y$, completely avoiding first learning a time-reversal. We compare the performance of our algorithm with existing methods and see that it outperforms using the (learned) time-reversals to learn the score term. The code can be found at https://github.com/libbylbaker/forward_bridge.

stat.ML↗

arXiv2025

Characterization of geodesic completeness for landmark space

We provide a full characterization of geodesic completeness for spaces of configurations of landmarks with smooth Riemannian metrics that satisfy a rotational and translation invariance and which are induced from metrics on subgroups of the diffeomorphism group for the shape domain. These spaces are widely used for applications in shape analysis, for example, for measuring shape changes in medical imaging and morphometrics in biology. For statistics of such data to be well-defined, it is imperative to know if geodesics exist for all times. We extend previously known sufficient conditions for geodesic completeness based on the regularity of the metric to give a full characterization for smooth Riemannian metrics with a rotational and translation invariance by means of an integrability criterion that involves only the behavior of the cometric kernel as landmarks approach collision. We further use the integrability criterion for geodesic completeness and previous work on stochastic completeness to construct a family of Riemannian landmark manifolds that are geodesically complete but stochastically incomplete.

math.DG↗

arXiv2025

Simulating conditioned diffusions on manifolds

To date, most methods for simulating conditioned diffusions are limited to the Euclidean setting. The conditioned process can be constructed using a change of measure known as Doob's $h$-transform. The specific type of conditioning depends on a function $h$ which is typically unknown in closed form. To resolve this, we extend the notion of guided processes to a manifold $M$, where one replaces $h$ by a function based on the heat kernel on $M$. We consider the case of a Brownian motion with drift, constructed using the frame bundle of $M$, conditioned to hit a point $x_T$ at time $T$. We prove equivalence of the laws of the conditioned process and the guided process with a tractable Radon-Nikodym derivative. Subsequently, we show how one can obtain guided processes on any manifold $N$ that is diffeomorphic to $M$ without assuming knowledge of the heat kernel on $N$. We illustrate our results with numerical simulations of guided processes and Bayesian parameter estimation based on discrete-time observations. For this, we consider both the torus and the Poincaré disk.

math.PR↗

arXiv2025

Score Matching Riemannian Diffusion Means

Estimating means on Riemannian manifolds is generally computationally expensive because the Riemannian distance function is not known in closed-form for most manifolds. To overcome this, we show that Riemannian diffusion means can be efficiently estimated using score matching with the gradient of Brownian motion transition densities using the same principle as in Riemannian diffusion models. Empirically, we show that this is more efficient than Monte Carlo simulation while retaining accuracy and is also applicable to learned manifolds. Our method, furthermore, extends to computing the Fréchet mean and the logarithmic map for general Riemannian manifolds. We illustrate the applicability of the estimation of diffusion mean by efficiently extending Euclidean algorithms to general Riemannian manifolds with a Riemannian $k$-means algorithm and maximum likelihood Riemannian regression.

stat.OT↗

arXiv2024

Parameter Inference via Differentiable Diffusion Bridge Importance Sampling

We introduce a methodology for performing parameter inference in high-dimensional, non-linear diffusion processes. We illustrate its applicability for obtaining insights into the evolution of and relationships between species, including ancestral state reconstruction. Estimation is performed by utilising score matching to approximate diffusion bridges, which are subsequently used in an importance sampler to estimate log-likelihoods. The entire setup is differentiable, allowing gradient ascent on approximated log-likelihoods. This allows both parameter inference and diffusion mean estimation. This novel, numerically stable, score matching-based parameter inference framework is presented and demonstrated on biological two- and three-dimensional morphometry data.

stat.ML↗

arXiv2024

Conditioning non-linear and infinite-dimensional diffusion processes

Generative diffusion models and many stochastic models in science and engineering naturally live in infinite dimensions before discretisation. To incorporate observed data for statistical and learning tasks, one needs to condition on observations. While recent work has treated conditioning linear processes in infinite dimensions, conditioning non-linear processes in infinite dimensions has not been explored. This paper conditions function valued stochastic processes without prior discretisation. To do so, we use an infinite-dimensional version of Girsanov's theorem to condition a function-valued stochastic process, leading to a stochastic differential equation (SDE) for the conditioned process involving the score. We apply this technique to do time series analysis for shapes of organisms in evolutionary biology, where we discretise via the Fourier basis and then learn the coefficients of the score function with score matching methods.

stat.ML↗