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BEGIN:VEVENT
UID:20260428T120000@shape-analysis
SUMMARY:Shape Sem. - Mark Gillespie
DTSTART;TZID=Europe/Paris:20260428T120000
DTEND;TZID=Europe/Paris:20260428T140000
LOCATION:TBA.
DESCRIPTION:Mark Gillespie (INRIA Saclay)  - TBA - TBA
END:VEVENT

BEGIN:VEVENT
UID:20260407T120000@shape-analysis
SUMMARY:Shape Sem. - Cyprien Plateau Holleville
DTSTART;TZID=Europe/Paris:20260407T120000
DTEND;TZID=Europe/Paris:20260407T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Paul Erdős room (A115) for the presentation at 1.30pm.
DESCRIPTION:Cyprien Plateau Holleville (Inria Saclay, Parma team)  - Efficient computation of geometry for structural analysis of large molecular systems - The Solvent-Excluded Surface (SES) is an essential representation of molecules which is massively used in molecular modeling and drug discovery since it represents the interacting surface between molecules. Based on its properties, it supports the visualization of both large scale shapes and details of molecules. While several methods targeted its computation, the ability to process large molecular structures to address the introduction of big complex analysis while leveraging the massively parallel architecture of GPUs has remained a challenge. This is mostly caused by the need for consequent memory allocation or by the complexity of the parallelization of its processing. In this paper, we leverage the last theoretical advances made for the depiction of the SES to provide fast analytical computation with low impact on memory. We show that our method is able to compute the complete surface while handling large molecular complexes with competitive computation time costs compared to previous works.
END:VEVENT

BEGIN:VEVENT
UID:20260317T120000@shape-analysis
SUMMARY:Shape Sem. - Barbara Gris
DTSTART;TZID=Europe/Paris:20260317T120000
DTEND;TZID=Europe/Paris:20260317T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309 (between towers 15 and 16, on the 3rd floor), at noon for the lunch buffet and at 1.30pm for the presentation.
DESCRIPTION:Barbara Gris (CNRS, LJLL)  - Constrained deformations for shape registration - an introduction the the Imodal library - One of the goals of shape analysis is to model and characterise shape evolution. We focus on methods where this evolution is modeled by the action of a time-dependent diffeomorphism, which is characterised by its time-derivatives: vector fields. Reconstructing the evolution of a shape from observations then amounts to determining an optimal path of vector fields whose flow of diffeomorphisms deforms the initial shape in accordance with the observations. However, if the space of considered vector fields is not constrained, optimal paths may be inaccurate from a modeling point of view. To overcome this problem, the notion of deformation module allows to incorporate prior information from the data into the set of considered deformations and the associated metric. I will present this generic framework as well as the Python library IMODAL, which allows to perform registration using such structured deformations.
END:VEVENT

BEGIN:VEVENT
UID:20260217T120000@shape-analysis
SUMMARY:Shape Sem. - Johannes Hertrich
DTSTART;TZID=Europe/Paris:20260217T120000
DTEND;TZID=Europe/Paris:20260217T140000
LOCATION:the seminar room ("Salle du conseil - Turing space") of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Johannes Hertrich (ENS Paris)  - Numerical Methods for Kernel Slicing - Kernels are key in machine learning for modeling interactions. Unfortunately, brute-force computation of the related kernel sums scales quadratically with the number of samples. Recent Fourier-slicing methods lead to an improved linear complexity, provided that the kernel can be sliced and its Fourier coefficients are known. To obtain these coefficients, we view the slicing relation as an inverse problem and present two algorithms for their recovery. Extensive numerical experiments demonstrate the speed and accuracy of our methods.
END:VEVENT

BEGIN:VEVENT
UID:20260127T120000@shape-analysis
SUMMARY:Shape Sem. - François-Xavier Vialard
DTSTART;TZID=Europe/Paris:20260127T120000
DTEND;TZID=Europe/Paris:20260127T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309 (between towers 15 and 16, on the 3rd floor), at noon for the lunch buffet and at 1.30pm for the presentation.
DESCRIPTION:François-Xavier Vialard (Université Gustave Eiffel)  - A discussion of the minus distance kernel - Methods based on the Gaussian kernel are popular in machine learning and imaging sciences. But over the last decade, several works have highlighted the "minus distance" kernel $k(x,y) = -\|x-y\|$ as a better baseline in many settings: this formula does not rely on a scale parameter, can be implemented efficiently via random 1D projections and defines a gradient flow with global convergence properties. It induces the well-known "Energy Distance" in statistics and "thin plate splines" model for 3D shape registration. On the other hand, technical difficulties arise when one must consider the splitting of particle masses or distributions with varying total masses. So is the "minus distance" kernel ready for widespread use in shape analysis? To answer this question, we will begin with a 20-minute presentation by François-Xavier Vialard, followed by an open discussion moderated by Joan Glaunès.
END:VEVENT

BEGIN:VEVENT
UID:20260106T120000@shape-analysis
SUMMARY:Shape Sem. - Antoine Diez
DTSTART;TZID=Europe/Paris:20260106T120000
DTEND;TZID=Europe/Paris:20260106T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Paul Erdős room (A115) for the presentation at 1.30pm.
DESCRIPTION:Antoine Diez (RIKEN, iTHEMS)  - Multicellular simulations with shape and volume constraints using optimal transport - Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these constraints lead to macroscopic self-organized structures is a fundamental question in e.g. developmental biology. To this end, various types of computational models have been developed. Here, we introduce a new framework based on optimal transport theory to model particle systems with arbitrary dynamical shapes and deformability properties. Our method builds upon the pioneering work of Brenier on incompressible fluids and its recent applications to materials science. It lets us specify the shapes and volumes of individual cells and supports a wide range of interaction mechanisms, while automatically taking care of the volume exclusion constraint at an affordable numerical cost. We showcase the versatility of this approach by reproducing several classical systems in computational biology. Our Python code is freely available at https://iceshot.readthedocs.io
END:VEVENT

BEGIN:VEVENT
UID:20251209T120000@shape-analysis
SUMMARY:Shape Sem. - Guillaume Houry
DTSTART;TZID=Europe/Paris:20251209T120000
DTEND;TZID=Europe/Paris:20251209T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Paul Erdős room (A115) for the presentation at 1.30pm.
DESCRIPTION:Guillaume Houry (INRIA Paris, HeKA team)  - Untangling vascular trees for surgery and interventional radiology - The diffusion of minimally invasive, endovascular interventions motivates the development of visualization methods for complex vascular networks. We propose a planar representation of blood vessel trees which preserves the properties that are most relevant to catheter navigation: topology, length and curvature. Taking as input a three-dimensional digital angiography, our algorithm produces a faithful two-dimensional map of the patient's vessels within a few seconds. To this end, we propose optimized implementations of standard morphological filters and a new recursive embedding algorithm that preserves the global orientation of the vascular network. We showcase our method on peroperative images of the brain, pelvic and knee artery networks. On the clinical side, our method simplifies the choice of devices prior to and during the intervention. This lowers the risk of failure during navigation or device deployment and may help to reduce the gap between expert and common intervention centers. From a research perspective, our method simulates the cadaveric display of artery trees from anatomical dissections. This opens the door to large population studies on the branching patterns and tortuosity of fine human blood vessels. Our code is released under the permissive MIT license as part of the scikit-shapes Python library.
END:VEVENT

BEGIN:VEVENT
UID:20251118T120000@shape-analysis
SUMMARY:Shape Sem. - Sylvain Arguillère
DTSTART;TZID=Europe/Paris:20251118T120000
DTEND;TZID=Europe/Paris:20251118T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the Café Circus restaurant (204 rue de Tolbiac) at noon for lunch, and in the Paul Erdős room (A115) for the presentation at 1.30pm.
DESCRIPTION:Sylvain Arguillère (CNRS, Laboratoire Paul Painlevé)  - Reparametrization invariance in geometric deep learning and applications to human body and face deformation - Sylvain will present his work on shape autoencoders and interpolations in latent spaces.
END:VEVENT

BEGIN:VEVENT
UID:20251028T120000@shape-analysis
SUMMARY:Shape Sem. - Nathan Kessler
DTSTART;TZID=Europe/Paris:20251028T120000
DTEND;TZID=Europe/Paris:20251028T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Anita Borg room (A116) for the presentation at 1pm.
DESCRIPTION:Nathan Kessler (Centre Borelli, ENS Paris-Saclay)  - Normalizing Diffusion Kernels with Optimal Transport - Smoothing a signal based on local neighborhoods is a core operation in machine learning and geometry processing. On well-structured domains such as vector spaces and manifolds, the Laplace operator derived from differential geometry offers a principled approach to smoothing via heat diffusion, with strong theoretical guarantees. However, constructing such Laplacians requires a carefully defined domain structure, which is not always available. Most practitioners thus rely on simple convolution kernels and message-passing layers, which are biased against the boundaries of the domain. We bridge this gap by introducing a broad class of smoothing operators, derived from general similarity or adjacency matrices, and demonstrate that they can be normalized into diffusion-like operators that inherit desirable properties from Laplacians. Our approach relies on a symmetric variant of the Sinkhorn algorithm, which rescales positive smoothing operators to match the structural behavior of heat diffusion. This construction enables Laplacian-like smoothing and processing of irregular data such as point clouds, sparse voxel grids or mixture of Gaussians. We show that the resulting operators not only approximate heat diffusion but also retain spectral information from the Laplacian itself, with applications to shape analysis and matching.
END:VEVENT

BEGIN:VEVENT
UID:20250930T120000@shape-analysis
SUMMARY:Shape Sem. - Jean-Marc Mercier and Max Aguirre
DTSTART;TZID=Europe/Paris:20250930T120000
DTEND;TZID=Europe/Paris:20250930T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Paul Erdős room (A115) for the presentation at 1pm.
DESCRIPTION:Jean-Marc Mercier and Max Aguirre (MPG-Partners)  - Reproducing kernel methods for machine learning, PDEs, and statistics with Python - This monograph offers an introduction to a collection of numerical algorithms implemented in the library CodPy (an acronym that stands for the Curse Of Dimensionality in PYthon), which has found widespread applications across various areas, including machine learning, statistics, and computational physics. We develop here a strategy based on the theory of reproducing kernel Hilbert spaces (RKHS) and the theory of optimal transport. Initially designed for mathematical finance, this library has since been enhanced and broadened to be applicable to problems arising in engineering and industry. In order to present the general principles and techniques employed in CodPy and its applications, we have structured this monograph into two main parts. First of all, we focus on the fundamental principles of kernel-based representations of data and solutions, also that the presentation therein is supplemented with illustrative examples only. Next, we discuss the application of these principles to many classes of concrete problems, spanning from the numerical approximation of partial differential equations to (supervised, unsupervised) machine learning, extending to generative methods with a focus on stochastic aspects.
END:VEVENT

BEGIN:VEVENT
UID:20250916T120000@shape-analysis
SUMMARY:Shape Sem. - Benjamin Charlier
DTSTART;TZID=Europe/Paris:20250916T120000
DTEND;TZID=Europe/Paris:20250916T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the Café Circus restaurant (204 rue de Tolbiac) at noon for lunch, and in the Paul Erdős room (A115) for the presentation at 1.30pm.
DESCRIPTION:Benjamin Charlier (INRAE)  - Representing and Mapping 3D Imaging and Spatial-omics Data Simultaneously Across Scales with Image-Varifold - Advancements in imaging and molecular techniques enable the collection of subcellular-scale data. Diversity in measured features, resolution, and physical scope of capture across technologies and experimental protocols pose numerous challenges to integrating data with reference coordinate systems and across scales.      This presentation describes a collection of technologies, using LDDMM (non rigid deformation) and varifold-based distance (to compare data), that we have developed for mapping data across scales and modalities, such as genes to tissues (2D or 3D).     The dedicated `xmodmap` python package include (i) an explicit censored data representation for the partial matching problem mapping whole brains to subsampled subvolumes, (ii) a multi, scale-space optimization technology for generating resampling grids optimized to represent spatial geometry at fixed complexities, and (iii) mutual-information based functional feature selection.      Finally, we will discuss practical strategies for managing peta-scale data, including tiling, sharding (multi-GPU processing), and multi-scale approaches.
END:VEVENT

BEGIN:VEVENT
UID:20250617T120000@shape-analysis
SUMMARY:Shape Sem. - Anton François
DTSTART;TZID=Europe/Paris:20250617T120000
DTEND;TZID=Europe/Paris:20250617T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Paul Erdős room (A115) for the presentation at 1pm.
DESCRIPTION:Anton François (ENS Paris-Saclay)  - Longitudinal MRI registration -- Implementing metamorphoses on the simplex with a focus on GPU-memory optimisation - In this presentation, we will discuss my post-doctoral project, which aims to perform longitudinal registration of brains with glioblastomas on MRI images with values in the simplex - seen as probability vectors. We will begin by describing the metamorphoses on the simplex and their implementation using the Fisher-Rao metric. We will also detail the optimisation work required to perform these calculations on images of adequate resolution. Our approach includes the use of Torch checkpoints as well as a review of the L-BFGS algorithm. Finally, as a perspective, we will discuss a data-driven strategy to achieve these registrations on these specific data.
END:VEVENT

BEGIN:VEVENT
UID:20250520T120000@shape-analysis
SUMMARY:Shape Sem. - Rayane Mouhli
DTSTART;TZID=Europe/Paris:20250520T120000
DTEND;TZID=Europe/Paris:20250520T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the Café Circus restaurant (204 rue de Tolbiac) for lunch, and in the Grace Hopper room (B601) for the presentation at 1.30pm.
DESCRIPTION:Rayane Mouhli (Université Paris Cité and Sorbonne Université)  - Decorrelation of vector fields with speed of varifolds - To perform a registration task, various types of diffeomorphic deformations can be combined to leverage their intrinsic properties (e.g., scales, linearity) or to incorporate prior knowledge (e.g., modules). To have a better interpretability of the model and to prevent the overlapping of the two types of deformations, their action on a shape have to be as "orthogonal" as possible. We introduce a quantification of the correlation between two deformations as the difference of the speeds of a varifold associated to a shape in the direction of both vector fields representing the two deformations.
END:VEVENT

BEGIN:VEVENT
UID:20250326T120000@shape-analysis
SUMMARY:Shape Sem. - Olivier Couture
DTSTART;TZID=Europe/Paris:20250326T120000
DTEND;TZID=Europe/Paris:20250326T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Grace Hopper room (B601) for the presentation.
DESCRIPTION:Olivier Couture (CNRS, Sorbonne University)  - Volumetric ultrasound localization microscopy - Ultrasound imaging is a widely used medical technique sensitive to blood flow. However, it is limited by a classic tradeoff between penetration and resolution. In particular, brain imaging and ultrasound angiography are compromised by the skull, which attenuates the acoustic waves, especially those that could provide submillimeter details. Ultrasound localization microscopy (ULM) is a technique that provides very high-resolution depth imaging in tissues. It relies on clinical contrast agents, called microbubbles, which are isolated and localized at the micrometer scale in ultrasound images. Tracking their trajectories can provide blood speeds in the microcirculation. This technique has been demonstrated in the brain (Errico et al. Nature 2015), as well as in the kidney, tumors, peripheral vessels and lymph nodes, in both humans and animals (see the review in Couture et al. IEEE UFFC 2018, Christensen-Jeffries et al. UMB 2020 or Song et al. "Super-resolution ultrasound microvascular imaging: Is it ready for clinical use?" 2023). During this presentation, we will describe recent advances in ULM. In particular, we will show the three-dimensional reconstruction of the rat brain hemodynamics at the micrometer scale. A full-brain angiography at this scale will also be presented. We will discuss its application for the differentiation of strokes and its transfer to the clinical domain through intermediate experiments on the sheep brain and two-dimensional ULM with clinical ultrasound devices. All these developments aim to create a new imaging tool for stroke patients in intensive care, potentially reducing treatment time for ischemic patients. We will also describe recent developments in kidney imaging, where ULM offers new perspectives on the functional units of the organ, namely the nephron and its glomeruli, in both humans and animals. In the future, ULM could enable depth angiography at a scale currently only achievable through invasive modalities.
END:VEVENT

BEGIN:VEVENT
UID:20250304T120000@shape-analysis
SUMMARY:Shape Sem. - Clément Zanolli
DTSTART;TZID=Europe/Paris:20250304T120000
DTEND;TZID=Europe/Paris:20250304T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the Café Circus restaurant (204 rue de Tolbiac) for lunch, and in the Ruth Margaret Davis room (B402) for the presentation.
DESCRIPTION:Clément Zanolli (Laboratory PACEA, University of Bordeaux, CNRS)  - How the evolution of 3D imaging methods helps us to understand hominin evolution - Since the 19th century, the study of human evolution has mostly been based on the study of morphological variation observed in the fossil record. The use of "classic" paleoanthropological approaches using linear measurements and visual descriptions has now moved to the three-dimensional quantification of size and shape thanks to the development of virtual imaging approaches. Since the first use of X-ray microtomography on a hominin tooth in 2004, the field of virtual paleoanthropology has successfully grown and has become state-of-the-art for the study of the external and internal structure of fossil teeth and bones. In parallel, geometric morphometric approaches became a standard method to finely characterize morphological variation and, coupled with statistical methods, improve our understanding of hominin evolution. This presentation will show a few examples of application of 3D imaging techniques that contributed to resolving scientific questions related to hominin diversity and their evolutionary trajectories.
END:VEVENT

BEGIN:VEVENT
UID:20250219T120000@shape-analysis
SUMMARY:Shape Sem. - Maxime Taverne
DTSTART;TZID=Europe/Paris:20250219T120000
DTEND;TZID=Europe/Paris:20250219T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Grace Hopper room (B601) for the presentation.
DESCRIPTION:Maxime Taverne (APHP, Necker Enfants Malades, Craniofacial Growth and Form lab)  - Geometric morphometrics, from anthropology to clinical care - Maxime will present an overview of his research on the statistics of anatomical shapes, from lizard forearms to human skulls.
END:VEVENT

BEGIN:VEVENT
UID:20250129T120000@shape-analysis
SUMMARY:Shape Sem. - Pascal Romon
DTSTART;TZID=Europe/Paris:20250129T120000
DTEND;TZID=Europe/Paris:20250129T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the cafeteria on the 3rd floor for lunch, and in the Maryam Mirzakhani room (B302) for the presentation.
DESCRIPTION:Pascal Romon (Université Paris-Est Marne-la-Vallée - LAMA)  - Lightweight curvature estimation on point clouds with randomized corrected curvature measures - The estimation of differential quantities on oriented point cloud is a classical step for many geometry processing tasks in computer graphics and vision. Even if many solutions exist to estimate such quantities, they usually fail at satisfying both a stable estimation with theoretical guarantee, and the efficiency of the associated algorithm. Relying on the notion of corrected curvature measures designed for surfaces, the method introduced in this paper meets both requirements. Given a point of interest and a few nearest neighbours, our method estimates the whole curvature tensor information by generating random triangles within these neighbours and normalising the corrected curvature measures by the corrected area measure. We provide a stability theorem showing that our pointwise curvatures are accurate and convergent, provided the noise in position and normal information has a variance smaller than the radius of neighbourhood. Experiments and comparisons with the state-of-the-art confirm that our approach is more accurate and much faster than alternatives. The method is fully parallelizable, requires only one nearest neighbour request per point of computation, and is trivial to implement.
END:VEVENT

BEGIN:VEVENT
UID:20250108T120000@shape-analysis
SUMMARY:Shape Sem. - Siwan Boufadène
DTSTART;TZID=Europe/Paris:20250108T120000
DTEND;TZID=Europe/Paris:20250108T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the Leonhard Euler room (A303bis) behind the cafeteria.
DESCRIPTION:Siwan Boufadène (Université Gustave Eiffel, LIGM)  - On the global convergence of Wasserstein gradient flow of the Coulomb discrepancy - In this work, we study the Wasserstein gradient flow of the Riesz energy defined on the space of probability measures. The Riesz kernels define a quadratic functional on the space of measure which is not in general geodesically convex in the Wasserstein geometry, therefore one cannot conclude to global convergence of the Wasserstein gradient flow using standard arguments. Our main result is the exponential convergence of the flow to the minimizer on a closed Riemannian manifold under the condition that the logarithm of the source and target measures are Hölder continuous. To this goal, we first prove that the Polyak-Lojasiewicz inequality is satisfied for sufficiently regular solutions. The key regularity result is the global in-time existence of Hölder solutions if the initial and target data are Hölder continuous, proven either in Euclidean space or on a closed Riemannian manifold. For general measures, we prove using flow interchange techniques that there is no local minima other than the global one for the Coulomb kernel. In fact, we prove that a Lagrangian critical point of the functional for the Coulomb (or Energy distance) kernel is equal to the target everywhere except on singular sets with empty interior. In addition, singular enough measures cannot be critical points. [Link to the preprint.](https://hal.science/hal-04282762v1)
END:VEVENT

BEGIN:VEVENT
UID:20241218T120000@shape-analysis
SUMMARY:Shape Sem. - Julien Tierny
DTSTART;TZID=Europe/Paris:20241218T120000
DTEND;TZID=Europe/Paris:20241218T140000
LOCATION:the new Inria Paris centre (48 rue Barrault), in the Emmy Noether room (A002) on the ground floor behind the auditorium.
DESCRIPTION:Julien Tierny (CNRS, Sorbonne University, École Polytechnique)  - Topological analysis of massive datasets - Topological Data Analysis (TDA) is a recent area of computer science that focuses on discovering intrinsic structures hidden in data. Based on sound mathematical foundations such as Morse theory and Persistent Homology, TDA enables the robust extraction of the main features of a dataset into stable, concise, and multi-scale descriptors that facilitate data analysis and interpretation. In this talk, I will give an intuitive overview of the main tools used in TDA, and I will illustrate their application in a concrete use-case in computational fluid dynamics. This talk will be illustrated with results produced with the "Topology ToolKit" (TTK), an open-source library (BSD license) that we develop with collaborators to showcase our research. Tutorials for re-producing these experiments are available on the [TTK website](https://topology-tool-kit.github.io/).
END:VEVENT

BEGIN:VEVENT
UID:20241127T120000@shape-analysis
SUMMARY:Shape Sem. - Josua Sassen
DTSTART;TZID=Europe/Paris:20241127T120000
DTEND;TZID=Europe/Paris:20241127T140000
LOCATION:the seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Josua Sassen (École Normale Supérieure Paris-Saclay)  - Repulsive Shells - This paper develops a shape space framework for collision-aware geometric modeling, where basic geometric operations automatically avoid interpenetration. Shape spaces are a powerful tool for surface modeling, shape analysis, nonrigid motion planning, and animation, but past formulations permit nonphysical intersections. Our framework augments an existing shape space using a repulsive energy such that collision avoidance becomes a first-class property, encoded in the Riemannian metric itself. In turn, tasks like intersection-free shape interpolation or motion extrapolation amount to simply computing geodesic paths via standard numerical algorithms. To make optimization practical, we develop an adaptive collision penalty that prevents mesh self-intersection, and converges to a meaningful limit energy under refinement. The final algorithms apply to any category of shape, and do not require a dataset of examples, training, rigging, nor any other prior information. For instance, to interpolate between two shapes we need only a single pair of meshes with the same connectivity. We evaluate our method on a variety of challenging examples from modeling and animation. [Project page.](https://www.cs.cmu.edu/~kmcrane/Projects/RepulsiveShells/index.html)
END:VEVENT

BEGIN:VEVENT
UID:20241106T120000@shape-analysis
SUMMARY:Shape Sem. - Jean Feydy
DTSTART;TZID=Europe/Paris:20241106T120000
DTEND;TZID=Europe/Paris:20241106T140000
LOCATION:the seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Jean Feydy (Inria Paris, HeKA team)  - Producing great 3D figures with minimal effort - This will be a tutorial on the rendering of 3D data for scientific publications. We will start from simple practical questions: how to load a 3D mesh, a vector field, a volumetric image. Then, I will explain how to go from "plain" to "gorgeous" graphics with shadows, textures, animations or physical material models. Finally, I will discuss some advanced tricks to improve the legibility of complex 3D shapes such as brain vessel trees or volumetric CT scans. I will rely on the Visualization ToolKit, a stable and versatile engine that can be used interactively with [Paraview](https://www.paraview.org/download/) and as a substitute for Matplotlib with [PyVista](https://docs.pyvista.org/) and [Vedo](https://vedo.embl.es/).
END:VEVENT

BEGIN:VEVENT
UID:20241016T120000@shape-analysis
SUMMARY:Shape Sem. - Thérèse E. Malliavin
DTSTART;TZID=Europe/Paris:20241016T120000
DTEND;TZID=Europe/Paris:20241016T140000
LOCATION:the Turing room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Thérèse E. Malliavin (CNRS, Laboratoire de Physique et Chimie Théoriques at the University of Lorraine)  - Harnessing geometric information for calculating protein structures and exploring conformational space of disordered proteins - Structural bioinformatics plays an increasingly important role in the prediction and calculation of biopolymer structures, leading to a better definition of their function. In addition, intrinsically disordered proteins (IDP) and intrinsically disordered regions (IDR) are at the center of numerous regulation and control pathways in the cell, and attract consequently extreme interest nowadays in structural biology. The optimization problem that arises for protein structure determination is more complex for such objects as the convergence criterion is more difficult to set up and the size of the conformational space is a obstacle to exhaustive exploration. The threading-augmented interval Branch-and-Prune (TAiBP), based on a reformulation of the Distance Geometry Problem (DGP), provides a theoretical frame for the fast generation of protein conformations, avoiding the combinatorial explosion of the Branch-and-Prune approach due to exponential complexity. ([1](https://link.springer.com/article/10.1007/s10898-018-0635-0), [2](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00215)) The TAiBP pipeline was applied to a several disordered proteins ([3](https://www.nature.com/articles/s41598-021-96370-z), [4](https://www.nature.com/articles/s41598-022-21648-9), [5](https://link.springer.com/chapter/10.1007/978-3-031-38299-4_55)) and a Gaussian mixture approach RamaMix has been developed for the quantification of IDP conformations from the global distributions of backbone torsion angles. The presentation will be oriented to propose possible connections of the structural bioinformatics to the use of methods coming from optimal transport approaches.
END:VEVENT

BEGIN:VEVENT
UID:20240925T120000@shape-analysis
SUMMARY:Shape Sem. - Thomas Pierron
DTSTART;TZID=Europe/Paris:20240925T120000
DTEND;TZID=Europe/Paris:20240925T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309 (between towers 15 and 16, on the 3rd floor).
DESCRIPTION:Thomas Pierron (ENS Paris-Saclay, Centre Borelli)  - A right-invariant setting for large deformations model, and applications to matching problems - This talk will be divided in two parts. First we will study the extension of LDDMM framework to continuous actions of right half-Lie groups equipped with a right invariant sub-Riemannian metric. This generalizes work from Arguillere on the sub-Riemannian geometry of Sobolev diffeomorphisms and their applications to shape analysis. In particular, it allows to introduce news co-adjoint variables and study new dynamics. We will discuss on some optimization problems that this  framework raises with some examples of half-Lie group actions
END:VEVENT

BEGIN:VEVENT
UID:20240911T120000@shape-analysis
SUMMARY:Shape Sem. - Gautam Pai
DTSTART;TZID=Europe/Paris:20240911T120000
DTEND;TZID=Europe/Paris:20240911T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309 (between towers 15 and 16, on the 3rd floor).
DESCRIPTION:Gautam Pai (Eindhoven University of Technology)  - Optimal Transport on the Lie Group of Roto-Translations - The roto-translation group SE(2) has been of active interest in image analysis due to methods that lift the image data to multi-orientation representations defined in this Lie group. This has led to impactful applications of crossing-preserving flows for image de-noising, geodesic tracking, and roto-translation equivariant deep learning.  In this talk, I will enumerate a computational framework for optimal transportation over Lie groups, with a special focus on SE(2). I will describe several theoretical aspects such as the non-optimality of group actions as transport maps, invariance and equivariance of optimal transport, and the quality of the entropic-regularized optimal transport plan using geodesic distance approximations. Finally, I will illustrate a Sinkhorn-like algorithm that can be efficiently implemented using fast and accurate distance approximations of the Lie group and GPU-friendly group convolutions. We report advancements with the experiments on 1) 2D shape/image barycenters, 2) interpolation of planar orientation fields, and 3) Wasserstein gradient flows on SE(2). We observe that our framework of lifting images to SE(2) and optimal transport with left-invariant anisotropic metrics leads to equivariant transport along dominant contours and salient line structures in the image and leads to meaningful interpolations compared to their counterparts on R^2. [Link to the preprint.](https://arxiv.org/abs/2402.15322)
END:VEVENT

BEGIN:VEVENT
UID:20240703T120000@shape-analysis
SUMMARY:Shape Sem. - Open discussion
DTSTART;TZID=Europe/Paris:20240703T120000
DTEND;TZID=Europe/Paris:20240703T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309.
DESCRIPTION:Open discussion (collective)  - Optimization in shape analysis - For this end-of-year seminar, we will have an open discussion around optimization methods for shape analysis, built around small presentations.
END:VEVENT

BEGIN:VEVENT
UID:20240619T120000@shape-analysis
SUMMARY:Shape Sem. - Philippe Moireau
DTSTART;TZID=Europe/Paris:20240619T120000
DTEND;TZID=Europe/Paris:20240619T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.101.
DESCRIPTION:Philippe Moireau (Inria Saclay and École Polytechnique, MΞDISIM team)  - Data assimilation in shape spaces - Data assimilation aims to couple dynamic models of physical systems with available measurements in order to propose a case-specific, true digital twin of the observed physics. This field, originally developed in the 1970s for accurate predictions in environmental sciences, is now being extended to various fields, including engineering and life sciences. In this talk, we propose to adapt classical data assimilation formulations to deal with shape data defined in adapted space manifolds. We will present configurations where the state space in which the dynamics lives is a space manifold, or configurations where the partial observations are defined in a manifold, so that we can adapt our strategy to all cases of shape data assimilation. Finally, our approach will be illustrated by the assimilation of models taken from environmental sciences - in particular wildfire models - or from life sciences - in particular cardiovascular models.
END:VEVENT

BEGIN:VEVENT
UID:20240515T120000@shape-analysis
SUMMARY:Shape Sem. - Bruno Lévy
DTSTART;TZID=Europe/Paris:20240515T120000
DTEND;TZID=Europe/Paris:20240515T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-25.328: between towers 15 and 25, on the 3rd floor.
DESCRIPTION:Bruno Lévy (Inria Saclay, ParMA team)  - A Lagrangian method for fluids with free boundaries - In this presentation, I'll describe a numerical simulation method for free-surface fluids. I will start by giving an intuitive understanding of the physical phenomena involved in fluid dynamics, pressure, viscosity and surface tension. Then I will detail the numerical simulation method, based on the Gallouet-Mérigot numerical scheme, that describes the fluid as a set of cells, that can deform, but that keep a constant volume, and that follow the motion of the fluid (Lagrangian method). The constant volume constraint takes the form of a partial semi-discrete optimal transport. I will present the geometric and numerical aspects of this optimal transport problem.
END:VEVENT

BEGIN:VEVENT
UID:20240410T120000@shape-analysis
SUMMARY:Shape Sem. - Josua Sassen
DTSTART;TZID=Europe/Paris:20240410T120000
DTEND;TZID=Europe/Paris:20240410T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309: between towers 15 and 16, on the 3rd floor.
DESCRIPTION:Josua Sassen (École Normale Supérieure Paris-Saclay)  - Shape optimization problems on discrete surfaces - Josua will present his work on surface segmentation and design with applications to architecture, mechanical engineering and graphics.
END:VEVENT

BEGIN:VEVENT
UID:20240320T120000@shape-analysis
SUMMARY:Shape Sem. - Robin Magnet
DTSTART;TZID=Europe/Paris:20240320T120000
DTEND;TZID=Europe/Paris:20240320T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.105 for lunch at noon, 15-16.413 for the talk at 1pm.
DESCRIPTION:Robin Magnet (GeoVic team, LIX, Ecole Polytechnique)  - Non-rigid shape matching with intrinsic methods - Robin will present his work on functional maps, including his [pyFM](https://github.com/RobinMagnet/pyFM) library.
END:VEVENT

BEGIN:VEVENT
UID:20240228T120000@shape-analysis
SUMMARY:Shape Sem. - Louis Pujol
DTSTART;TZID=Europe/Paris:20240228T120000
DTEND;TZID=Europe/Paris:20240228T140000
LOCATION:the seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Louis Pujol (Université Paris-Cité, HeKA team)  - scikit-shapes, a transparent package for statistical shape analysis - Louis will present the first (beta) release of the [scikit-shapes](https://github.com/scikit-shapes/scikit-shapes/) library. The talk will be followed by an informal lab session - feel free to bring your laptop! Links: [tutorial](https://louis-pujol.github.io/scikit-shapes-tutorial/index.html), [GitHub](https://github.com/scikit-shapes/scikit-shapes), [documentation](https://scikit-shapes.github.io/scikit-shapes/), [one-page gallery](https://github.com/Louis-Pujol/one-page-gallery-pyvista).
END:VEVENT

BEGIN:VEVENT
UID:20240207T120000@shape-analysis
SUMMARY:Shape Sem. - Slavica Jonic
DTSTART;TZID=Europe/Paris:20240207T120000
DTEND;TZID=Europe/Paris:20240207T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309: between towers 15 and 16, on the 3rd floor.
DESCRIPTION:Slavica Jonic (IMPMC – UMR 7590 CNRS, Sorbonne University)  - From cryo electron microscopy data to continuous conformational landscapes of biomolecules - The elucidation of different conformations of biomolecular complexes is the key for understanding the molecular mechanisms behind the biological functions of the complexes and the key to novel drug discovery. Single particle analysis (SPA) is a data collection and analysis technique of cryo electron microscopy (cryo-EM) that allows 3D reconstruction of multiple conformations of purified biomolecular complexes from their 2D images. Another cryo-EM technique is cryo electron tomography (cryo-ET), which allows obtaining multiple conformations of the complexes in their cellular environment. Currently, one of the most important and challenging open problems in the cryo-EM field is how to obtain the entire, continuous conformational landscapes of the biomolecules from the data. Consequently, since a few years, methods development to solve this problem has been a very active research area. My group is developing such methods, by combining image processing, molecular dynamics simulations, and deep learning approaches. These methods are made available publicly via our open-source, ContinuousFlex software package, which can be run as a plugin of the broadly used Scipion software package. In this talk, I will present some of our most important achievements regarding this work.
END:VEVENT

BEGIN:VEVENT
UID:20240117T120000@shape-analysis
SUMMARY:Shape Sem. - Fleur Gaudfernau
DTSTART;TZID=Europe/Paris:20240117T120000
DTEND;TZID=Europe/Paris:20240117T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-25.328: between towers 15 and 25, on the 3rd floor.
DESCRIPTION:Fleur Gaudfernau (Université de Paris, HeKA team)  - Multiscale optimisation for shape registration - Fleur will present her PhD thesis work, done under the supervision of Stéphanie Allassonnière and Erwan Le Pennec.
END:VEVENT

BEGIN:VEVENT
UID:20231220T120000@shape-analysis
SUMMARY:Shape Sem. - Elodie Maignant
DTSTART;TZID=Europe/Paris:20231220T120000
DTEND;TZID=Europe/Paris:20231220T140000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309: between towers 15 and 16, on the 3rd floor.
DESCRIPTION:Elodie Maignant (Inria Sophia and École Normale Supérieure Paris-Saclay)  - Intrinsic methods for manifold-valued data - Elodie will present her PhD thesis work, done under the supervision of Xavier Pennec and Alain Trouvé.
END:VEVENT

BEGIN:VEVENT
UID:20231206T100000@shape-analysis
SUMMARY:Shape Sem. - Barbara Gris
DTSTART;TZID=Europe/Paris:20231206T100000
DTEND;TZID=Europe/Paris:20231206T120000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309: between towers 15 and 16, on the 3rd floor.
DESCRIPTION:Barbara Gris (CNRS, Laboratoire Jacques-Louis Lions)  - Constrained diffeomorphometry in computational anatomy. - Barbara will present an optimal control framework to perform statistical shape analysis with plausible biological priors.
END:VEVENT

BEGIN:VEVENT
UID:20231206T090000@shape-analysis
SUMMARY:Shape Sem. - Jean Feydy
DTSTART;TZID=Europe/Paris:20231206T090000
DTEND;TZID=Europe/Paris:20231206T100000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-16.309: between towers 15 and 16, on the 3rd floor.
DESCRIPTION:Jean Feydy (Inria Paris, HeKA team)  - Optimal transport with 3D shapes. - Jean will present modern optimal transport algorithms, articulating the difference between simple, solved problems in dimension 2 or 3 and NP-hard problems in high dimension.
END:VEVENT

BEGIN:VEVENT
UID:20231129T123000@shape-analysis
SUMMARY:Shape Sem. - Josua Sassen
DTSTART;TZID=Europe/Paris:20231129T123000
DTEND;TZID=Europe/Paris:20231129T143000
LOCATION:[Jussieu](https://sciences.sorbonne-universite.fr/vie-de-campus-sciences/accueil-vie-pratique/plan-du-campus) - room 15-25.328: between towers 15 and 25, on the 3rd floor.
DESCRIPTION:Josua Sassen (École Normale Supérieure Paris-Saclay)  - Some numerical methods for computer graphics and geometric design - Josua is starting a PostDoc in Paris and will introduce himself with a collection of results from his work in Bonn.
END:VEVENT

BEGIN:VEVENT
UID:20231108T120000@shape-analysis
SUMMARY:Shape Sem. - Théo Dumont
DTSTART;TZID=Europe/Paris:20231108T120000
DTEND;TZID=Europe/Paris:20231108T140000
LOCATION:Seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Théo Dumont (Université Gustave Eiffel)  - The geometry of optimal transport (and Gromov-Wasserstein) - Théo will present new results on the structure of the Wasserstein and Gromov-Wasserstein metrics.
END:VEVENT

BEGIN:VEVENT
UID:20231011T120000@shape-analysis
SUMMARY:Shape Sem. - Louis Pujol and others
DTSTART;TZID=Europe/Paris:20231011T120000
DTEND;TZID=Europe/Paris:20231011T140000
LOCATION:PariSanté Campus, 10 Rue d'Oradour-sur-Glane. Métro Balard or Porte de Versailles. Seminar room of the HeKA team (3rd floor, South corridor).
DESCRIPTION:Louis Pujol and others (Université Paris-Cité)  - Open discussion on multiscale methods - We will have an open chat on multiscale implementations of shape analysis methods, from both practical and theoretical perspectives. You may prepare up to 5 slides to present a method or implementation that you would like to discuss.
END:VEVENT

BEGIN:VEVENT
UID:20230915T120000@shape-analysis
SUMMARY:Shape Sem. - Anna Song
DTSTART;TZID=Europe/Paris:20230915T120000
DTEND;TZID=Europe/Paris:20230915T140000
LOCATION:Jussieu, room 15-16.309 (i.e. in the corridor that links column 15 to column 16, on the third floor).  This is the seminar room of the Laboratoire Jacques-Louis Lions.
DESCRIPTION:Anna Song (Imperial College London and The Francis Crick Institute)  - The geometry and topology of shape patterns, with applications to leukaemia - Anna will present the results of 4 years of work on 3D shape textures. This includes a new generative model based on curvature minimization, contributions to topological data analysis in 3D and a study of the microscopic structure of bone marrow vessels.
END:VEVENT

BEGIN:VEVENT
UID:20230626T123000@shape-analysis
SUMMARY:Shape Sem. - François-Xavier Vialard
DTSTART;TZID=Europe/Paris:20230626T123000
DTEND;TZID=Europe/Paris:20230626T130000
LOCATION:Inria Paris centre, 2 rue Simone Iff, A building, ground floor, Emmy Noether room (Startup Studio entrance).
DESCRIPTION:François-Xavier Vialard (Université Gustave Eiffel)  - Some open mathematical problems - François-Xavier will present a collection of open mathematical questions related to diffeomorphic registration and residual networks.
END:VEVENT

BEGIN:VEVENT
UID:20230626T130000@shape-analysis
SUMMARY:Shape Sem. - Vincent Mallet
DTSTART;TZID=Europe/Paris:20230626T130000
DTEND;TZID=Europe/Paris:20230626T133000
LOCATION:
DESCRIPTION:Vincent Mallet (École Polytechnique, CNRS)  - Modeling structural biology with geometric deep learning - Vincent will present his work on the representation of RNA strands as 2.5D graphs, proteins as surfaces and antibody detection on Cryo-EM images.
END:VEVENT

BEGIN:VEVENT
UID:20230626T133000@shape-analysis
SUMMARY:Shape Sem. - Guillaume Sérieys
DTSTART;TZID=Europe/Paris:20230626T133000
DTEND;TZID=Europe/Paris:20230626T140000
LOCATION:
DESCRIPTION:Guillaume Sérieys (Université Paris-Cité, MAP5)  - Metamorphoses of manifold-valued images - Guillaume will present his work on the generalization of continuous metamorphoses to images with values in spaces of probability distributions or diffusion tensors.
END:VEVENT

BEGIN:VEVENT
UID:20230626T140000@shape-analysis
SUMMARY:Shape Sem. - Thomas Pierron
DTSTART;TZID=Europe/Paris:20230626T140000
DTEND;TZID=Europe/Paris:20230626T143000
LOCATION:
DESCRIPTION:Thomas Pierron (ENS, Centre Borelli)  - An extended orbit model - Thomas will present his work on a hierarchical, multi-scale model for diffeomorphic shape registration.
END:VEVENT

BEGIN:VEVENT
UID:20230602T123000@shape-analysis
SUMMARY:Shape Sem. - Louis Pujol
DTSTART;TZID=Europe/Paris:20230602T123000
DTEND;TZID=Europe/Paris:20230602T143000
LOCATION:the seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - [detailed path](https://map5.mi.parisdescartes.fr/accueil/acces-contact/).
DESCRIPTION:Louis Pujol (Université Paris-Cité)  - Two Python libraries for 3D visualization - Louis will present two modern libraries for visualizing and interacting with 3D shapes, [Pyvista](https://docs.pyvista.org/version/stable/) and [Vedo](https://vedo.embl.es/). The talk will be followed by an informal lab session - feel free to bring your laptop!
END:VEVENT


END:VCALENDAR