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Elizabeth Louise Baker, Gefan Yang, Michael L. Severinsen, Christy Anna Hipsley, Stefan Sommer

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.

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Morten Akhøj, James Benn, Erlend Grong, Stefan Sommer, Xavier Pennec

In this paper we demonstrate how sub-Riemannian geometry can be used for manifold learning and surface reconstruction by combining local linear approximations of a point cloud to obtain lower dimensional bundles. Local approximations obtained by local PCAs are collected into a rank $k$ tangent subbundle on $\mathbb{R}^d$, $k<d$, which we call a principal subbundle. This determines a sub-Riemannian metric on $\mathbb{R}^d$. We show that sub-Riemannian geodesics with respect to this metric can successfully be applied to a number of important problems, such as: explicit construction of an approximating submanifold $M$, construction of a representation of the point-cloud in $\mathbb{R}^k$, and computation of distances between observations, taking the learned geometry into account. The reconstruction is guaranteed to equal the true submanifold in the limit case where tangent spaces are estimated exactly. Via simulations, we show that the framework is robust when applied to noisy data. Furthermore, the framework generalizes to observations on an a priori known Riemannian manifold.

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Lili Bao, Jiahao Lu, Shihui Ying, Stefan Sommer

In this paper, we propose a new approach to deformable image registration that captures sliding motions. The large deformation diffeomorphic metric mapping (LDDMM) registration method faces challenges in representing sliding motion since it per construction generates smooth warps. To address this issue, we extend LDDMM by incorporating both zeroth- and first-order momenta with a non-differentiable kernel. This allows to represent both discontinuous deformation at switching boundaries and diffeomorphic deformation in homogeneous regions. We provide a mathematical analysis of the proposed deformation model from the viewpoint of discontinuous systems. To evaluate our approach, we conduct experiments on both artificial images and the publicly available DIR-Lab 4DCT dataset. Results show the effectiveness of our approach in capturing plausible sliding motion.

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Francesco Santini, Jakob Wasserthal, Abramo Agosti, Xeni Deligianni, Kevin R. Keene, Hermien E. Kan, Stefan Sommer, Christoph Stuprich, Fengdan Wang, Claudia Weidensteiner, Giulia Manco, Matteo Paoletti, Valentina Mazzoli, Arjun Desai, Anna Pichiecchio

Semantic segmentation is a crucial step to extract quantitative information from medical (and, specifically, radiological) images to aid the diagnostic process, clinical follow-up. and to generate biomarkers for clinical research. In recent years, machine learning algorithms have become the primary tool for this task. However, its real-world performance is heavily reliant on the comprehensiveness of training data. Dafne is the first decentralized, collaborative solution that implements continuously evolving deep learning models exploiting the collective knowledge of the users of the system. In the Dafne workflow, the result of each automated segmentation is refined by the user through an integrated interface, so that the new information is used to continuously expand the training pool via federated incremental learning. The models deployed through Dafne are able to improve their performance over time and to generalize to data types not seen in the training sets, thus becoming a viable and practical solution for real-life medical segmentation tasks.

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Elizabeth Baker, Thomas Besnier, Stefan Sommer

Modelling randomness in shape data, for example, the evolution of shapes of organisms in biology, requires stochastic models of shapes. This paper presents a new stochastic shape model based on a description of shapes as functions in a Sobolev space. Using an explicit orthonormal basis as a reference frame for the noise, the model is independent of the parameterisation of the mesh. We define the stochastic model, explore its properties, and illustrate examples of stochastic shape evolutions using the resulting numerical framework.

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Gefan Yang, Stefan Sommer

We propose a novel denoising diffusion generative model for predicting nonlinear fluid fields named FluidDiff. By performing a diffusion process, the model is able to learn a complex representation of the high-dimensional dynamic system, and then Langevin sampling is used to generate predictions for the flow state under specified initial conditions. The model is trained with finite, discrete fluid simulation data. We demonstrate that our model has the capacity to model the distribution of simulated training data and that it gives accurate predictions on the test data. Without encoded prior knowledge of the underlying physical system, it shares competitive performance with other deep learning models for fluid prediction, which is promising for investigation on new computational fluid dynamics methods.

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Alexander Christgau, Alexis Arnaudon, Stefan Sommer

Models of stochastic image deformation allow study of time-continuous stochastic effects transforming images by deforming the image domain. Applications include longitudinal medical image analysis with both population trends and random subject specific variation. Focusing on a stochastic extension of the LDDMM models with evolutions governed by a stochastic EPDiff equation, we use moment approximations of the corresponding Ito diffusion to construct estimators for statistical inference in the full stochastic model. We show that this approach, when efficiently implemented with automatic differentiation tools, can successfully estimate parameters encoding the spatial correlation of the noise fields on the image

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Alexander Barbie, Niklas Pech, Wilhelm Hasselbring, Sascha Flögel, Frank Wenzhöfer, Michael Walter, Elena Shchekinova, Marc Busse, Matthias Türk, Michael Hofbauer, Stefan Sommer

During the research cruise AL547 with RV ALKOR (October 20-31, 2020), a collaborative underwater network of ocean observation systems was deployed in Boknis Eck (SW Baltic Sea, German exclusive economic zone (EEZ)) in the context of the project ARCHES (Autonomous Robotic Networks to Help Modern Societies). This network was realized via a Digital Twin Prototype approach. During that period different scenarios were executed to demonstrate the feasibility of Digital Twins in an extreme environment such as underwater. One of the scenarios showed the collaboration of stage IV Digital Twins with their physical counterparts on the seafloor. This way, we address the research question, whether Digital Twins represent a feasible approach to operate mobile ad hoc networks for ocean and coastal observation.

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Jakob Stolberg-Larsen, Stefan Sommer

Generative neural networks have a well recognized ability to estimate underlying manifold structure of high dimensional data. However, if a simply connected latent space is used, it is not possible to faithfully represent a manifold with non-trivial homotopy type. In this work we define the general class of Atlas Generative Models (AGMs), models with hybrid discrete-continuous latent space that estimate an atlas on the underlying data manifold together with a partition of unity on the data space. We identify existing examples of models from various popular generative paradigms that fit into this class. Due to the atlas interpretation, ideas from non-linear latent space analysis and statistics, e.g. geodesic interpolation, which has previously only been investigated for models with simply connected latent spaces, may be extended to the entire class of AGMs in a natural way. We exemplify this by generalizing an algorithm for graph based geodesic interpolation to the setting of AGMs, and verify its performance experimentally.

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Alexis Arnaudon, Frank van der Meulen, Moritz Schauer, Stefan Sommer

Stochastically evolving geometric systems are studied in geometric mechanics for modelling turbulence parts of multi-scale fluid flows and in shape analysis for stochastic evolutions of shapes of e.g. human organs. Recently introduced models involve stochastic differential equations that govern the dynamics of a diffusion process $X$. In applications $X$ is only partially observed at times $0$ and $T>0$. Conditional on these observations, interest lies in inferring parameters in the dynamics of the diffusion and reconstructing the path $(X_t,\, t\in [0,T])$. The latter problem is known as bridge simulation. We develop a general scheme for bridge sampling in the case of finite dimensional systems of shape landmarks and singular solutions in fluid dynamics. This scheme allows for subsequent statistical inference of properties of the fluid flow or the evolution of observed shapes. It covers stochastic landmark models for which no suitable simulation method has been proposed in the literature, that removes restrictions of earlier approaches, improves the handling of the nonlinearity of the configuration space leading to more effective sampling schemes and allows to generalise the common inexact matching scheme to the stochastic setting.

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