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Laurent Younes

Publications and source records attributed to Laurent Younes.

At least 19 recordsLinked to original sources

Introduction to Machine Learning

This book introduces the mathematical foundations and techniques that lead to the development and analysis of many of the algorithms that are used in machine learning. It starts with an introductory chapter that describes notation used throughout the book and serve at a reminder of basic concepts in calculus, linear algebra and probability and also introduces some measure theoretic terminology, which can be used as a reading guide for the sections that use these tools. The introductory chapters also provide background material on matrix analysis and optimization. The latter chapter provides theoretical support to many algorithms that are used in the book, including stochastic gradient descent, proximal methods, etc. After discussing basic concepts for statistical prediction, the book includes an introduction to reproducing kernel theory and Hilbert space techniques, which are used in many places, before addressing the description of various algorithms for supervised statistical learning, including linear methods, support vector machines, decision trees, boosting, or neural networks. The subject then switches to generative methods, starting with a chapter that presents sampling methods and an introduction to the theory of Markov chains. The following chapter describe the theory of graphical models, an introduction to variational methods for models with latent variables, and to deep-learning based generative models. The next chapters focus on unsupervised learning methods, for clustering, factor analysis and manifold learning. The final chapter of the book is theory-oriented and discusses concentration inequalities and generalization bounds.

stat.ML

Shape Alignment via Allen-Cahn Nonlinear-Convection

This paper demonstrates the impact of a phase field method on shape registration to align shapes of possibly different topology. It yields new insights into the building of discrepancy measures between shapes regardless of topology, which would have applications in fields of image data analysis such as computational anatomy. A soft end-point optimal control problem is introduced whose minimum measures the minimal control norm required to align an initial shape to a final shape, up to a small error term. The initial data is spatially integrable, the paths in control spaces are integrable and the evolution equation is a generalized convective Allen-Cahn. Binary images are used to represent shapes for the initial data. Inspired by level-set methods and large diffeomorphic deformation metric mapping, the controls spaces are integrable scalar functions to serve as a normal velocity and smooth reproducing kernel Hilbert spaces to serve as velocity vector fields. The existence of mild solutions to the evolution equation is proved, the minimums of the time discretized optimal control problem are characterized, and numerical simulations of minimums to the fully discretized optimal control problem are displayed. The numerical implementation enforces the maximum-bounded principle, although it is not proved for these mild solutions. This research offers a novel discrepancy measure that provides valuable ways to analyze diverse image data sets. Future work involves proving the existence of minimums, existence and uniqueness of strong solutions and the maximum bounded principle.

math.OC

A continuous scale space of diffeomorphisms

In this paper, we define and study a nested family of reproducing kernel Hilbert spaces of vector fields that is indexed by a range of scales, from which we construct a reproducing kernel Hilbert space of scale-dependent vector fields. We provide a characterization of the reproducing kernel of that space, with numerical approximations ensuring quick evaluations when this kernel does not have a closed form. We then introduce a multiscale version of the large deformation diffeomorphic metric mapping (LDDMM) problem and prove the existence of solutions. Finally, we provide numerical experiments performing landmark matching using multiscale LDDMM.

math.NA

Preserving Derivative Information while Transforming Neuronal Curves

The international neuroscience community is building the first comprehensive atlases of brain cell types to understand how the brain functions from a higher resolution, and more integrated perspective than ever before. In order to build these atlases, subsets of neurons (e.g. serotonergic neurons, prefrontal cortical neurons etc.) are traced in individual brain samples by placing points along dendrites and axons. Then, the traces are mapped to common coordinate systems by transforming the positions of their points, which neglects how the transformation bends the line segments in between. In this work, we apply the theory of jets to describe how to preserve derivatives of neuron traces up to any order. We provide a framework to compute possible error introduced by standard mapping methods, which involves the Jacobian of the mapping transformation. We show how our first order method improves mapping accuracy in both simulated and real neuron traces under random diffeomorphisms. Our method is freely available in our open-source Python package brainlit.

q-bio.NC

FineMorphs: Affine-diffeomorphic sequences for regression

A multivariate regression model of affine and diffeomorphic transformation sequences - FineMorphs - is presented. Leveraging concepts from shape analysis, model states are optimally "reshaped" by diffeomorphisms generated by smooth vector fields during learning. Affine transformations and vector fields are optimized within an optimal control setting, and the model can naturally reduce (or increase) dimensionality and adapt to large datasets via suboptimal vector fields. An existence proof of solution and necessary conditions for optimality for the model are derived. Experimental results on real datasets from the UCI repository are presented, with favorable results in comparison with state-of-the-art in the literature and densely-connected neural networks in TensorFlow.

stat.ML

Image Varifolds on Meshes for Mapping Spatial Transcriptomics

Advances in the development of largely automated microscopy methods such as MERFISH for imaging cellular structures in mouse brains are providing spatial detection of micron resolution gene expression. While there has been tremendous progress made in the field Computational Anatomy (CA) to perform diffeomorphic mapping technologies at the tissue scales for advanced neuroinformatic studies in common coordinates, integration of molecular- and cellular-scale populations through statistical averaging via common coordinates remains yet unattained. This paper describes the first set of algorithms for calculating geodesics in the space of diffeomorphisms, what we term Image-Varifold LDDMM,extending the family of large deformation diffeomorphic metric mapping (LDDMM) algorithms to accommodate the "copy and paste" varifold action of particles which extends consistently to the tissue scales. We represent the brain data as geometric measures, termed as {\em image varifolds} supported by a large number of unstructured points, % (i.e., not aligned on a 2D or 3D grid), each point representing a small volume in space % (which may be incompletely described) and carrying a list of densities of {\em features} elements of a high-dimensional feature space. The shape of image varifold brain spaces is measured by transforming them by diffeomorphisms. The metric between image varifolds is obtained after embedding these objects in a linear space equipped with the norm, yielding a so-called "chordal metric."

math.NA

Shape spaces: From geometry to biological plausibility

This paper reviews several Riemannian metrics and evolution equations in the context of diffeomorphic shape analysis. After a short review of of various approaches at building Riemannian spaces of shapes, with a special focus on the foundations of the large deformation diffeomorphic metric mapping algorithm, the attention is turned to elastic metrics, and to growth models that can be derived from it. In the latter context, a new class of metrics, involving the optimization of a growth tensor, is introduced and some of its properties are studied.

math.DG

A generative neural network model for random dot product graphs

We present GraphMoE, a novel neural network-based approach to learning generative models for random graphs. The neural network is trained to match the distribution of a class of random graphs by way of a moment estimator. The features used for training are graphlets, subgraph counts of small order. The neural network accepts random noise as input and outputs vector representations for nodes in the graph. Random graphs are then realized by applying a kernel to the representations. Graphs produced this way are demonstrated to be able to imitate data from chemistry, medicine, and social networks. The produced graphs are similar enough to the target data to be able to fool discriminator neural networks otherwise capable of separating classes of random graphs.

stat.ML

Diffeomorphic shape evolution coupled with a reaction-diffusion PDE on a growth potential

This paper studies a longitudinal shape transformation model in which shapes are deformed in response to an internal growth potential that evolves according to an advection reaction diffusion process. This model extends prior works that considered a static growth potential, i.e., the initial growth potential is only advected by diffeomorphisms. We focus on the mathematical study of the corresponding system of coupled PDEs describing the joint dynamics of the diffeomorphic transformation together with the growth potential on the moving domain. Specifically, we prove the uniqueness and long time existence of solutions to this system with reasonable initial and boundary conditions as well as regularization on deformation fields. In addition, we provide a few simple simulations of this model in the case of isotropic elastic materials in 2D.

math.AP

Mechanistic Modeling of Longitudinal Shape Changes: equations of motion and inverse problems

This paper examines a longitudinal shape evolution model in which a 3D volume progresses through a family of elastic equilibria in response to the time-derivative of an internal force, or yank, with an additional regularization to ensure diffeomorphic transformations. We consider two different models of yank and address the long time existence and uniqueness of solutions for the equations of motion in both models. In addition, we derive sufficient conditions for the existence of an optimal yank that best describes the change from an observed initial volume to an observed volume at a later time. The main motivation for this work is the understanding of processes such as growth and atrophy in anatomical structures, where the yank could be roughly interpreted as a metabolic event triggering morphological changes. We provide preliminary results on simple examples to illustrate, under this model, the retrievability of some attributes of such events.

math.OC

Normal and Equivolumetric Coordinate Systems for Cortical Areas

We describe coordinate systems adapted for the space between two surfaces, such as those delineating the highly folded cortex in mammalian brains. These systems are estimated in order to satisfy geometric priors, including streamline normality or equivolumetric conditions on layers. We give a precise mathematical formulation of these problems, and present numerical simulations based on diffeomorphic registration methods, comparing them with recent approaches.

math.OC

Diffeomorphic Learning

We introduce in this paper a learning paradigm in which the training data is transformed by a diffeomorphic transformation before prediction. The learning algorithm minimizes a cost function evaluating the prediction error on the training set penalized by the distance between the diffeomorphism and the identity. The approach borrows ideas from shape analysis where diffeomorphisms are estimated for shape and image alignment, and brings them in a previously unexplored setting, estimating, in particular diffeomorphisms in much larger dimensions. After introducing the concept and describing a learning algorithm, we present diverse applications, mostly with synthetic examples, demonstrating the potential of the approach, as well as some insight on how it can be improved.

stat.ML

3D Normal Coordinate Systems for Cortical Areas

A surface-based diffeomorphic algorithm to generate 3D coordinate grids in the cortical ribbon is described. In the grid, normal coordinate lines are generated by the diffeomorphic evolution from the grey/white (inner) surface to the grey/csf (outer) surface. Specifically, the cortical ribbon is described by two triangulated surfaces with open boundaries. Conceptually, the inner surface sits on top of the white matter structure and the outer on top of the gray matter. It is assumed that the cortical ribbon consists of cortical columns which are orthogonal to the white matter surface. This might be viewed as a consequence of the development of the columns in the embryo. It is also assumed that the columns are orthogonal to the outer surface so that the resultant vector field is orthogonal to the evolving surface. Then the distance of the normal lines from the vector field such that the inner surface evolves diffeomorphically towards the outer one can be construed as a measure of thickness. Applications are described for the auditory cortices in human adults and cats with normal hearing or hearing loss. The approach offers great potential for cortical morphometry.

cs.CV

Diffeomorphic Medial Modeling

Deformable shape modeling approaches that describe objects in terms of their medial axis geometry (e.g., m-reps [Pizer et al., 2003]) yield rich geometrical features that can be useful for analyzing the shape of sheet-like biological structures, such as the myocardium. We present a novel shape analysis approach that combines the benefits of medial shape modeling and diffeomorphometry. Our algorithm is formulated as a problem of matching shapes using diffeomorphic flows under constraints that approximately preserve medial axis geometry during deformation. As the result, correspondence between the medial axes of similar shapes is maintained. The approach is evaluated in the context of modeling the shape of the left ventricular wall from 3D echocardiography images.

cs.GR

A Model for Elastic Evolution on Foliated Shapes

We study a shape evolution framework in which the deformation of shapes from time t to t + dt is governed by a regularized anisotropic elasticity model. More precisely, we assume that at each time shapes are infinitesimally deformed from a stress-free state to an elastic equilibrium as a result of the application of a small force. The configuration of equilibrium then becomes the new resting state for subsequent evolution. The primary motivation of this work is the modeling of slow changes in biological shapes like atrophy, where a body force applied to the volume represents the location and impact of the disease. Our model uses an optimal control viewpoint with the time derivative of force interpreted as a control, deforming a shape gradually from its observed initial state to an observed final state. Furthermore, inspired by the layered organization of cortical volumes, we consider a special case of our model in which shapes can be decomposed into a family of layers (forming a "foliation"). Preliminary experiments on synthetic layered shapes in two and three dimensions are presented to demonstrate the effect of elasticity.

math.OC

Metric Registration of Curves and Surfaces using Optimal Control

This paper presents an overview of recent developments in the analysis of shapes such as curves and surfaces through Riemannian metrics. We show that several constructions of metrics on spaces of submanifolds can be unified through the prism of Riemannian submersions, with shape space metrics being induced from metrics defined on the top spaces. Computing the resulting Riemannian distances involves solving geodesic matching problems with boundary conditions. To deal efficiently with such variational problems, one can rely on an auxiliary family of "chordal" distances to simplify the treatment of boundary conditions, which we use to come up with a relaxed inexact formulation of the matching problem. This also allows to turn shape matching into optimal control problems and give a common framework to address them in practice. We then specify our analysis to the cases of intrinsic shape metrics defined using invariant Sobolev metrics on parametrized immersions, outer shape metrics induced from metrics on diffeomorphism groups of the ambient space and finally a recent hybrid model that combines those two approaches.

math.DG

Elastic distance between curves under the metamorphosis viewpoint

We provide a new angle and obtain new results on a class of metrics on length-normalized curves in $d$ dimensions, represented by their unit tangents expressed as a function of arc-length, which are functions from the unit interval to the $(d-1)$-dimensional unit sphere. These metrics are derived from the combined action of diffeomorphisms (change of parameters) and arc-length-dependent rotation acting on the tangent. Minimizing a Riemannian metric balancing a right-invariant metric on diffeomorphisms and an $L^2$ norm on the motion of tangents leads to a special case of "metamorphosis", which provides a general framework adapted to similar situations when Lie groups acts on Riemannian manifolds. Within this framework and using a Sobolev norm with order 1 on the diffeomorphism group, we generalize previous results from the literature that provide explicit geodesic distances on parametrized curves.

math.DG

Hybrid Riemannian Metrics for Diffeomorphic Shape Registration

We consider the results of combining two approaches developed for the design of Riemannian metrics on curves and surfaces, namely parametrization-invariant metrics of the Sobolev type on spaces of immersions, and metrics derived through Riemannian submersions from right-invariant Sobolev metrics on groups of diffeomorphisms (the latter leading to the "large deformation diffeomorphic metric mapping" framework). We show that this quite simple approach inherits the advantages of both methods, both on the theoretical and experimental levels, and provide additional flexibility and modeling power, especially when dealing with complex configurations of shapes. Experimental results illustrating the method are provided for curve and surface registration.

math.DG