Point-set manifold processing for computational mechanics: thin shells, reduced order modeling, cell motility and molecular conformations

In many applications, one would like to perform calculations on smooth manifolds of dimension d embedded in a high-dimensional space of dimension D. Often, a continuous description of such manifold is not known, and instead it is sampled by a set of scattered points in high dimensions. This poses a serious challenge. In this thesis, we approximate the point-set manifold as an overlapping set of smooth parametric descriptions, whose geometric structure is revealed by statistical learning methods, and then parametrized by meshfree methods. This approach avoids any global parameterization, and hence is applicable to manifolds of any genus and complex geometry. It combines four ingredients: (1) partitioning of the point set into subregions of trivial topology, (2) the automatic detection of the local geometric structure of the manifold by nonlinear dimensionality reduction techniques, (3) the local parameterization of the manifold using smooth meshfree (here local maximum-entropy) approximants, and (4) patching together the local representations by means of a partition of unity. In this thesis we show the generality, flexibility, and accuracy of the method in four different problems. First, we exercise it in the context of Kirchhoff-Love thin shells, (d=2, D=3). We test our methodology against classical linear and non linear benchmarks in thin-shell analysis, and highlight its ability to handle point-set surfaces of complex topology and geometry. We then tackle problems of much higher dimensionality. We perform reduced order modeling in the context of finite deformation elastodynamics, considering a nonlinear reduced configuration space, in contrast with classical linear approaches based on Principal Component Analysis (d=2, D=10000's). We further quantitatively unveil the geometric structure of the motility strategy of a family of micro-organisms called Euglenids from experimental videos (d=1, D~30000's). Finally, in the context of enhanced sampling in molecular dynamics, we automatically construct collective variables for the molecular conformational dynamics (d=1...6, D~30,1000's)

Numerical Methods in Shape Spaces and Optimal Branching Patterns

The contribution of this thesis is twofold. The main part deals with numerical methods in the context of shape space analysis, where the shape space at hand is considered as a Riemannian manifold. In detail, we apply and extend the time-discrete geodesic calculus (established by Rumpf and Wirth [WBRS11, RW15]) to the space of discrete shells, i.e. triangular meshes with fixed connectivity. The essential building block is a variational time-discretization of geodesic curves, which is based on a local approximation of the squared Riemannian distance on the manifold. On physical shape spaces this approximation can be derived e.g. from a dissimilarity measure. The dissimilarity measure between two shell surfaces can naturally be defined as an elastic deformation energy capturing both membrane and bending distortions. Combined with a non-conforming discretization of a physically sound thin shell model the time-discrete geodesic calculus applied to the space of discrete shells is shown to be suitable to solve important problems in computer graphics and animation. To extend the existing calculus, we introduce a generalized spline functional based on the covariant derivative along a curve in shape space whose minimizers can be considered as Riemannian splines. We establish a corresponding time-discrete functional that fits perfectly into the framework of Rumpf and Wirth, and prove this discretization to be consistent. Several numerical simulations reveal that the optimization of the spline functional—subject to appropriate constraints—can be used to solve the multiple interpolation problem in shape space, e.g. to realize keyframe animation. Based on the spline functional, we further develop a simple regression model which generalizes linear regression to nonlinear shape spaces. Numerical examples based on real data from anatomy and botany show the capability of the model. Finally, we apply the statistical analysis of elastic shape spaces presented by Rumpf and Wirth [RW09, RW11] to the space of discrete shells. To this end, we compute a Fréchet mean within a class of shapes bearing highly nonlinear variations and perform a principal component analysis with respect to the metric induced by the Hessian of an elastic shell energy. The last part of this thesis deals with the optimization of microstructures arising e.g. at austenite-martensite interfaces in shape memory alloys. For a corresponding scalar problem, Kohn and Müller [KM92, KM94] proved existence of a minimizer and provided a lower and an upper bound for the optimal energy. To establish the upper bound, they studied a particular branching pattern generated by mixing two different martensite phases. We perform a finite element simulation based on subdivision surfaces that suggests a topologically different class of branching patterns to represent an optimal microstructure. Based on these observations we derive a novel, low dimensional family of patterns and show—numerically and analytically—that our new branching pattern results in a significantly better upper energy bound

Symmetry in Graph Theory

This book contains the successful invited submissions to a Special Issue of Symmetry on the subject of ""Graph Theory"". Although symmetry has always played an important role in Graph Theory, in recent years, this role has increased significantly in several branches of this field, including but not limited to Gromov hyperbolic graphs, the metric dimension of graphs, domination theory, and topological indices. This Special Issue includes contributions addressing new results on these topics, both from a theoretical and an applied point of view

Proceedings of the First International Workshop on Mathematical Foundations of Computational Anatomy (MFCA'06) - Geometrical and Statistical Methods for Modelling Biological Shape Variability

International audienceNon-linear registration and shape analysis are well developed research topic in the medical image analysis community. There is nowadays a growing number of methods that can faithfully deal with the underlying biomechanical behaviour of intra-subject shape deformations. However, it is more difficult to relate the anatomical shape of different subjects. The goal of computational anatomy is to analyse and to statistically model this specific type of geometrical information. In the absence of any justified physical model, a natural attitude is to explore very general mathematical methods, for instance diffeomorphisms. However, working with such infinite dimensional space raises some deep computational and mathematical problems. In particular, one of the key problem is to do statistics. Likewise, modelling the variability of surfaces leads to rely on shape spaces that are much more complex than for curves. To cope with these, different methodological and computational frameworks have been proposed. The goal of the workshop was to foster interactions between researchers investigating the combination of geometry and statistics for modelling biological shape variability from image and surfaces. A special emphasis was put on theoretical developments, applications and results being welcomed as illustrations. Contributions were solicited in the following areas: * Riemannian and group theoretical methods on non-linear transformation spaces * Advanced statistics on deformations and shapes * Metrics for computational anatomy * Geometry and statistics of surfaces 26 submissions of very high quality were recieved and were reviewed by two members of the programm committee. 12 papers were finally selected for oral presentations and 8 for poster presentations. 16 of these papers are published in these proceedings, and 4 papers are published in the proceedings of MICCAI'06 (for copyright reasons, only extended abstracts are provided here)

Transformées basées graphes pour la compression de nouvelles modalités d’image

Due to the large availability of new camera types capturing extra geometrical information, as well as the emergence of new image modalities such as light fields and omni-directional images, a huge amount of high dimensional data has to be stored and delivered. The ever growing streaming and storage requirements of these new image modalities require novel image coding tools that exploit the complex structure of those data. This thesis aims at exploring novel graph based approaches for adapting traditional image transform coding techniques to the emerging data types where the sampled information are lying on irregular structures. In a first contribution, novel local graph based transforms are designed for light field compact representations. By leveraging a careful design of local transform supports and a local basis functions optimization procedure, significant improvements in terms of energy compaction can be obtained. Nevertheless, the locality of the supports did not permit to exploit long term dependencies of the signal. This led to a second contribution where different sampling strategies are investigated. Coupled with novel prediction methods, they led to very prominent results for quasi-lossless compression of light fields. The third part of the thesis focuses on the definition of rate-distortion optimized sub-graphs for the coding of omni-directional content. If we move further and give more degree of freedom to the graphs we wish to use, we can learn or define a model (set of weights on the edges) that might not be entirely reliable for transform design. The last part of the thesis is dedicated to theoretically analyze the effect of the uncertainty on the efficiency of the graph transforms.En raison de la grande disponibilité de nouveaux types de caméras capturant des informations géométriques supplémentaires, ainsi que de l'émergence de nouvelles modalités d'image telles que les champs de lumière et les images omnidirectionnelles, il est nécessaire de stocker et de diffuser une quantité énorme de hautes dimensions. Les exigences croissantes en matière de streaming et de stockage de ces nouvelles modalités d’image nécessitent de nouveaux outils de codage d’images exploitant la structure complexe de ces données. Cette thèse a pour but d'explorer de nouvelles approches basées sur les graphes pour adapter les techniques de codage de transformées d'image aux types de données émergents où les informations échantillonnées reposent sur des structures irrégulières. Dans une première contribution, de nouvelles transformées basées sur des graphes locaux sont conçues pour des représentations compactes des champs de lumière. En tirant parti d’une conception minutieuse des supports de transformées locaux et d’une procédure d’optimisation locale des fonctions de base , il est possible d’améliorer considérablement le compaction d'énergie. Néanmoins, la localisation des supports ne permettait pas d'exploiter les dépendances à long terme du signal. Cela a conduit à une deuxième contribution où différentes stratégies d'échantillonnage sont étudiées. Couplés à de nouvelles méthodes de prédiction, ils ont conduit à des résultats très importants en ce qui concerne la compression quasi sans perte de champs de lumière statiques. La troisième partie de la thèse porte sur la définition de sous-graphes optimisés en distorsion de débit pour le codage de contenu omnidirectionnel. Si nous allons plus loin et donnons plus de liberté aux graphes que nous souhaitons utiliser, nous pouvons apprendre ou définir un modèle (ensemble de poids sur les arêtes) qui pourrait ne pas être entièrement fiable pour la conception de transformées. La dernière partie de la thèse est consacrée à l'analyse théorique de l'effet de l'incertitude sur l'efficacité des transformées basées graphes

Analysis of 3D objects at multiple scales (application to shape matching)

Depuis quelques années, l évolution des techniques d acquisition a entraîné une généralisation de l utilisation d objets 3D très dense, représentés par des nuages de points de plusieurs millions de sommets. Au vu de la complexité de ces données, il est souvent nécessaire de les analyser pour en extraire les structures les plus pertinentes, potentiellement définies à plusieurs échelles. Parmi les nombreuses méthodes traditionnellement utilisées pour analyser des signaux numériques, l analyse dite scale-space est aujourd hui un standard pour l étude des courbes et des images. Cependant, son adaptation aux données 3D pose des problèmes d instabilité et nécessite une information de connectivité, qui n est pas directement définie dans les cas des nuages de points. Dans cette thèse, nous présentons une suite d outils mathématiques pour l analyse des objets 3D, sous le nom de Growing Least Squares (GLS). Nous proposons de représenter la géométrie décrite par un nuage de points via une primitive du second ordre ajustée par une minimisation aux moindres carrés, et cela à pour plusieurs échelles. Cette description est ensuite derivée analytiquement pour extraire de manière continue les structures les plus pertinentes à la fois en espace et en échelle. Nous montrons par plusieurs exemples et comparaisons que cette représentation et les outils associés définissent une solution efficace pour l analyse des nuages de points à plusieurs échelles. Un défi intéressant est l analyse d objets 3D acquis dans le cadre de l étude du patrimoine culturel. Dans cette thèse, nous nous étudions les données générées par l acquisition des fragments des statues entourant par le passé le Phare d Alexandrie, Septième Merveille du Monde. Plus précisément, nous nous intéressons au réassemblage d objets fracturés en peu de fragments (une dizaine), mais avec de nombreuses parties manquantes ou fortement dégradées par l action du temps. Nous proposons un formalisme pour la conception de systèmes d assemblage virtuel semi-automatiques, permettant de combiner à la fois les connaissances des archéologues et la précision des algorithmes d assemblage. Nous présentons deux systèmes basés sur cette conception, et nous montrons leur efficacité dans des cas concrets.Over the last decades, the evolution of acquisition techniques yields the generalization of detailed 3D objects, represented as huge point sets composed of millions of vertices. The complexity of the involved data often requires to analyze them for the extraction and characterization of pertinent structures, which are potentially defined at multiple scales. Amongthe wide variety of methods proposed to analyze digital signals, the scale-space analysis istoday a standard for the study of 2D curves and images. However, its adaptation to 3D dataleads to instabilities and requires connectivity information, which is not directly availablewhen dealing with point sets.In this thesis, we present a new multi-scale analysis framework that we call the GrowingLeast Squares (GLS). It consists of a robust local geometric descriptor that can be evaluatedon point sets at multiple scales using an efficient second-order fitting procedure. We proposeto analytically differentiate this descriptor to extract continuously the pertinent structuresin scale-space. We show that this representation and the associated toolbox define an effi-cient way to analyze 3D objects represented as point sets at multiple scales. To this end, we demonstrate its relevance in various application scenarios.A challenging application is the analysis of acquired 3D objects coming from the CulturalHeritage field. In this thesis, we study a real-world dataset composed of the fragments ofthe statues that were surrounding the legendary Alexandria Lighthouse. In particular, wefocus on the problem of fractured object reassembly, consisting of few fragments (up to aboutten), but with missing parts due to erosion or deterioration. We propose a semi-automaticformalism to combine both the archaeologist s knowledge and the accuracy of geometricmatching algorithms during the reassembly process. We use it to design two systems, andwe show their efficiency in concrete cases.BORDEAUX1-Bib.electronique (335229901) / SudocSudocFranceF

Analysis of 3D objects at multiple scales (application to shape matching)

Depuis quelques années, l évolution des techniques d acquisition a entraîné une généralisation de l utilisation d objets 3D très dense, représentés par des nuages de points de plusieurs millions de sommets. Au vu de la complexité de ces données, il est souvent nécessaire de les analyser pour en extraire les structures les plus pertinentes, potentiellement définies à plusieurs échelles. Parmi les nombreuses méthodes traditionnellement utilisées pour analyser des signaux numériques, l analyse dite scale-space est aujourd hui un standard pour l étude des courbes et des images. Cependant, son adaptation aux données 3D pose des problèmes d instabilité et nécessite une information de connectivité, qui n est pas directement définie dans les cas des nuages de points. Dans cette thèse, nous présentons une suite d outils mathématiques pour l analyse des objets 3D, sous le nom de Growing Least Squares (GLS). Nous proposons de représenter la géométrie décrite par un nuage de points via une primitive du second ordre ajustée par une minimisation aux moindres carrés, et cela à pour plusieurs échelles. Cette description est ensuite derivée analytiquement pour extraire de manière continue les structures les plus pertinentes à la fois en espace et en échelle. Nous montrons par plusieurs exemples et comparaisons que cette représentation et les outils associés définissent une solution efficace pour l analyse des nuages de points à plusieurs échelles. Un défi intéressant est l analyse d objets 3D acquis dans le cadre de l étude du patrimoine culturel. Dans cette thèse, nous nous étudions les données générées par l acquisition des fragments des statues entourant par le passé le Phare d Alexandrie, Septième Merveille du Monde. Plus précisément, nous nous intéressons au réassemblage d objets fracturés en peu de fragments (une dizaine), mais avec de nombreuses parties manquantes ou fortement dégradées par l action du temps. Nous proposons un formalisme pour la conception de systèmes d assemblage virtuel semi-automatiques, permettant de combiner à la fois les connaissances des archéologues et la précision des algorithmes d assemblage. Nous présentons deux systèmes basés sur cette conception, et nous montrons leur efficacité dans des cas concrets.Over the last decades, the evolution of acquisition techniques yields the generalization of detailed 3D objects, represented as huge point sets composed of millions of vertices. The complexity of the involved data often requires to analyze them for the extraction and characterization of pertinent structures, which are potentially defined at multiple scales. Amongthe wide variety of methods proposed to analyze digital signals, the scale-space analysis istoday a standard for the study of 2D curves and images. However, its adaptation to 3D dataleads to instabilities and requires connectivity information, which is not directly availablewhen dealing with point sets.In this thesis, we present a new multi-scale analysis framework that we call the GrowingLeast Squares (GLS). It consists of a robust local geometric descriptor that can be evaluatedon point sets at multiple scales using an efficient second-order fitting procedure. We proposeto analytically differentiate this descriptor to extract continuously the pertinent structuresin scale-space. We show that this representation and the associated toolbox define an effi-cient way to analyze 3D objects represented as point sets at multiple scales. To this end, we demonstrate its relevance in various application scenarios.A challenging application is the analysis of acquired 3D objects coming from the CulturalHeritage field. In this thesis, we study a real-world dataset composed of the fragments ofthe statues that were surrounding the legendary Alexandria Lighthouse. In particular, wefocus on the problem of fractured object reassembly, consisting of few fragments (up to aboutten), but with missing parts due to erosion or deterioration. We propose a semi-automaticformalism to combine both the archaeologist s knowledge and the accuracy of geometricmatching algorithms during the reassembly process. We use it to design two systems, andwe show their efficiency in concrete cases.BORDEAUX1-Bib.electronique (335229901) / SudocSudocFranceF

Interactive Segmentation of 3D Medical Images with Implicit Surfaces

To cope with a variety of clinical applications, research in medical image processing has led to a large spectrum of segmentation techniques that extract anatomical structures from volumetric data acquired with 3D imaging modalities. Despite continuing advances in mathematical models for automatic segmentation, many medical practitioners still rely on 2D manual delineation, due to the lack of intuitive semi-automatic tools in 3D. In this thesis, we propose a methodology and associated numerical schemes enabling the development of 3D image segmentation tools that are reliable, fast and interactive. These properties are key factors for clinical acceptance. Our approach derives from the framework of variational methods: segmentation is obtained by solving an optimization problem that translates the expected properties of target objects in mathematical terms. Such variational methods involve three essential components that constitute our main research axes: an objective criterion, a shape representation and an optional set of constraints. As objective criterion, we propose a unified formulation that extends existing homogeneity measures in order to model the spatial variations of statistical properties that are frequently encountered in medical images, without compromising efficiency. Within this formulation, we explore several shape representations based on implicit surfaces with the objective to cover a broad range of typical anatomical structures. Firstly, to model tubular shapes in vascular imaging, we introduce convolution surfaces in the variational context of image segmentation. Secondly, compact shapes such as lesions are described with a new representation that generalizes Radial Basis Functions with non-Euclidean distances, which enables the design of basis functions that naturally align with salient image features. Finally, we estimate geometric non-rigid deformations of prior templates to recover structures that have a predictable shape such as whole organs. Interactivity is ensured by restricting admissible solutions with additional constraints. Translating user input into constraints on the sign of the implicit representation at prescribed points in the image leads us to consider inequality-constrained optimization

New Directions for Contact Integrators

Contact integrators are a family of geometric numerical schemes which guarantee the conservation of the contact structure. In this work we review the construction of both the variational and Hamiltonian versions of these methods. We illustrate some of the advantages of geometric integration in the dissipative setting by focusing on models inspired by recent studies in celestial mechanics and cosmology.Comment: To appear as Chapter 24 in GSI 2021, Springer LNCS 1282

Data analysis with merge trees

Today’s data are increasingly complex and classical statistical techniques need growingly more refined mathematical tools to be able to model and investigate them. Paradigmatic situations are represented by data which need to be considered up to some kind of trans- formation and all those circumstances in which the analyst finds himself in the need of defining a general concept of shape. Topological Data Analysis (TDA) is a field which is fundamentally contributing to such challenges by extracting topological information from data with a plethora of interpretable and computationally accessible pipelines. We con- tribute to this field by developing a series of novel tools, techniques and applications to work with a particular topological summary called merge tree. To analyze sets of merge trees we introduce a novel metric structure along with an algorithm to compute it, define a framework to compare different functions defined on merge trees and investigate the metric space obtained with the aforementioned metric. Different geometric and topolog- ical properties of the space of merge trees are established, with the aim of obtaining a deeper understanding of such trees. To showcase the effectiveness of the proposed metric, we develop an application in the field of Functional Data Analysis, working with functions up to homeomorphic reparametrization, and in the field of radiomics, where each patient is represented via a clustering dendrogram