Convergent Stochastic Expectation Maximization algorithm with efficient sampling in high dimension. Application to deformable template model estimation

Estimation in the deformable template model is a big challenge in image analysis. The issue is to estimate an atlas of a population. This atlas contains a template and the corresponding geometrical variability of the observed shapes. The goal is to propose an accurate algorithm with low computational cost and with theoretical guaranties of relevance. This becomes very demanding when dealing with high dimensional data which is particularly the case of medical images. We propose to use an optimized Monte Carlo Markov Chain method into a stochastic Expectation Maximization algorithm in order to estimate the model parameters by maximizing the likelihood. In this paper, we present a new Anisotropic Metropolis Adjusted Langevin Algorithm which we use as transition in the MCMC method. We first prove that this new sampler leads to a geometrically uniformly ergodic Markov chain. We prove also that under mild conditions, the estimated parameters converge almost surely and are asymptotically Gaussian distributed. The methodology developed is then tested on handwritten digits and some 2D and 3D medical images for the deformable model estimation. More widely, the proposed algorithm can be used for a large range of models in many fields of applications such as pharmacology or genetic

A stochastic algorithm for probabilistic independent component analysis

The decomposition of a sample of images on a relevant subspace is a recurrent problem in many different fields from Computer Vision to medical image analysis. We propose in this paper a new learning principle and implementation of the generative decomposition model generally known as noisy ICA (for independent component analysis) based on the SAEM algorithm, which is a versatile stochastic approximation of the standard EM algorithm. We demonstrate the applicability of the method on a large range of decomposition models and illustrate the developments with experimental results on various data sets.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS499 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Construction of Bayesian Deformable Models via Stochastic Approximation Algorithm: A Convergence Study

The problem of the definition and the estimation of generative models based on deformable templates from raw data is of particular importance for modelling non aligned data affected by various types of geometrical variability. This is especially true in shape modelling in the computer vision community or in probabilistic atlas building for Computational Anatomy (CA). A first coherent statistical framework modelling the geometrical variability as hidden variables has been given by Allassonni\`ere, Amit and Trouv\'e (JRSS 2006). Setting the problem in a Bayesian context they proved the consistency of the MAP estimator and provided a simple iterative deterministic algorithm with an EM flavour leading to some reasonable approximations of the MAP estimator under low noise conditions. In this paper we present a stochastic algorithm for approximating the MAP estimator in the spirit of the SAEM algorithm. We prove its convergence to a critical point of the observed likelihood with an illustration on images of handwritten digits

Learning distributions of shape trajectories from longitudinal datasets: a hierarchical model on a manifold of diffeomorphisms

We propose a method to learn a distribution of shape trajectories from longitudinal data, i.e. the collection of individual objects repeatedly observed at multiple time-points. The method allows to compute an average spatiotemporal trajectory of shape changes at the group level, and the individual variations of this trajectory both in terms of geometry and time dynamics. First, we formulate a non-linear mixed-effects statistical model as the combination of a generic statistical model for manifold-valued longitudinal data, a deformation model defining shape trajectories via the action of a finite-dimensional set of diffeomorphisms with a manifold structure, and an efficient numerical scheme to compute parallel transport on this manifold. Second, we introduce a MCMC-SAEM algorithm with a specific approach to shape sampling, an adaptive scheme for proposal variances, and a log-likelihood tempering strategy to estimate our model. Third, we validate our algorithm on 2D simulated data, and then estimate a scenario of alteration of the shape of the hippocampus 3D brain structure during the course of Alzheimer's disease. The method shows for instance that hippocampal atrophy progresses more quickly in female subjects, and occurs earlier in APOE4 mutation carriers. We finally illustrate the potential of our method for classifying pathological trajectories versus normal ageing

Efficient preconditioned stochastic gradient descent for estimation in latent variable models

Latent variable models are powerful tools for modeling complex phenomena involving in particular partially observed data, unobserved variables or underlying complex unknown structures. Inference is often difficult due to the latent structure of the model. To deal with parameter estimation in the presence of latent variables, well-known efficient methods exist, such as gradient-based and EM-type algorithms, but with practical and theoretical limitations. In this paper, we propose as an alternative for parameter estimation an efficient preconditioned stochastic gradient algorithm. Our method includes a preconditioning step based on a positive definite Fisher information matrix estimate. We prove convergence results for the proposed algorithm under mild assumptions for very general latent variables models. We illustrate through relevant simulations the performance of the proposed methodology in a nonlinear mixed effects model and in a stochastic block model

Learning distributions of shape trajectories from longitudinal datasets: a hierarchical model on a manifold of diffeomorphisms

International audienceWe propose a method to learn a distribution of shape tra-jectories from longitudinal data, i.e. the collection of individual objects repeatedly observed at multiple time-points. The method allows to compute an average spatiotemporal trajectory of shape changes at the group level, and the individual variations of this trajectory both in terms of geometry and time dynamics. First, we formulate a non-linear mixed-effects statistical model as the combination of a generic statistical model for manifold-valued longitudinal data, a deformation model defining shape trajectories via the action of a finite-dimensional set of diffeomorphisms with a man-ifold structure, and an efficient numerical scheme to compute parallel transport on this manifold. Second, we introduce a MCMC-SAEM algorithm with a specific approach to shape sampling, an adaptive scheme for proposal variances , and a log-likelihood tempering strategy to estimate our model. Third, we validate our algorithm on 2D simulated data, and then estimate a scenario of alteration of the shape of the hippocampus 3D brain structure during the course of Alzheimer's disease. The method shows for instance that hippocampal atrophy progresses more quickly in female subjects, and occurs earlier in APOE4 mutation carriers. We finally illustrate the potential of our method for classifying pathological trajectories versus normal ageing

Automatic Segmentation of Cells of Different Types in Fluorescence Microscopy Images

Recognition of different cell compartments, types of cells, and their interactions is a critical aspect of quantitative cell biology. This provides a valuable insight for understanding cellular and subcellular interactions and mechanisms of biological processes, such as cancer cell dissemination, organ development and wound healing. Quantitative analysis of cell images is also the mainstay of numerous clinical diagnostic and grading procedures, for example in cancer, immunological, infectious, heart and lung disease. Computer automation of cellular biological samples quantification requires segmenting different cellular and sub-cellular structures in microscopy images. However, automating this problem has proven to be non-trivial, and requires solving multi-class image segmentation tasks that are challenging owing to the high similarity of objects from different classes and irregularly shaped structures. This thesis focuses on the development and application of probabilistic graphical models to multi-class cell segmentation. Graphical models can improve the segmentation accuracy by their ability to exploit prior knowledge and model inter-class dependencies. Directed acyclic graphs, such as trees have been widely used to model top-down statistical dependencies as a prior for improved image segmentation. However, using trees, a few inter-class constraints can be captured. To overcome this limitation, polytree graphical models are proposed in this thesis that capture label proximity relations more naturally compared to tree-based approaches. Polytrees can effectively impose the prior knowledge on the inclusion of different classes by capturing both same-level and across-level dependencies. A novel recursive mechanism based on two-pass message passing is developed to efficiently calculate closed form posteriors of graph nodes on polytrees. Furthermore, since an accurate and sufficiently large ground truth is not always available for training segmentation algorithms, a weakly supervised framework is developed to employ polytrees for multi-class segmentation that reduces the need for training with the aid of modeling the prior knowledge during segmentation. Generating a hierarchical graph for the superpixels in the image, labels of nodes are inferred through a novel efficient message-passing algorithm and the model parameters are optimized with Expectation Maximization (EM). Results of evaluation on the segmentation of simulated data and multiple publicly available fluorescence microscopy datasets indicate the outperformance of the proposed method compared to state-of-the-art. The proposed method has also been assessed in predicting the possible segmentation error and has been shown to outperform trees. This can pave the way to calculate uncertainty measures on the resulting segmentation and guide subsequent segmentation refinement, which can be useful in the development of an interactive segmentation framework

Monocular 3d Object Recognition

Object recognition is one of the fundamental tasks of computer vision. Recent advances in the field enable reliable 2D detections from a single cluttered image. However, many challenges still remain. Object detection needs timely response for real world applications. Moreover, we are genuinely interested in estimating the 3D pose and shape of an object or human for the sake of robotic manipulation and human-robot interaction. In this thesis, a suite of solutions to these challenges is presented. First, Active Deformable Part Models (ADPM) is proposed for fast part-based object detection. ADPM dramatically accelerates the detection by dynamically scheduling the part evaluations and efficiently pruning the image locations. Second, we unleash the power of marrying discriminative 2D parts with an explicit 3D geometric representation. Several methods of such scheme are proposed for recovering rich 3D information of both rigid and non-rigid objects from monocular RGB images. (1) The accurate 3D pose of an object instance is recovered from cluttered images using only the CAD model. (2) A global optimal solution for simultaneous 2D part localization, 3D pose and shape estimation is obtained by optimizing a unified convex objective function. Both appearance and geometric compatibility are jointly maximized. (3) 3D human pose estimation from an image sequence is realized via an Expectation-Maximization algorithm. The 2D joint location uncertainties are marginalized out during inference and 3D pose smoothness is enforced across frames. By bridging the gap between 2D and 3D, our methods provide an end-to-end solution to 3D object recognition from images. We demonstrate a range of interesting applications using only a single image or a monocular video, including autonomous robotic grasping with a single image, 3D object image pop-up and a monocular human MoCap system. We also show empirical start-of-art results on a number of benchmarks on 2D detection and 3D pose and shape estimation

STANLEY: Stochastic Gradient Anisotropic Langevin Dynamics for Learning Energy-Based Models

We propose in this paper, STANLEY, a STochastic gradient ANisotropic LangEvin dYnamics, for sampling high dimensional data. With the growing efficacy and potential of Energy-Based modeling, also known as non-normalized probabilistic modeling, for modeling a generative process of different natures of high dimensional data observations, we present an end-to-end learning algorithm for Energy-Based models (EBM) with the purpose of improving the quality of the resulting sampled data points. While the unknown normalizing constant of EBMs makes the training procedure intractable, resorting to Markov Chain Monte Carlo (MCMC) is in general a viable option. Realizing what MCMC entails for the EBM training, we propose in this paper, a novel high dimensional sampling method, based on an anisotropic stepsize and a gradient-informed covariance matrix, embedded into a discretized Langevin diffusion. We motivate the necessity for an anisotropic update of the negative samples in the Markov Chain by the nonlinearity of the backbone of the EBM, here a Convolutional Neural Network. Our resulting method, namely STANLEY, is an optimization algorithm for training Energy-Based models via our newly introduced MCMC method. We provide a theoretical understanding of our sampling scheme by proving that the sampler leads to a geometrically uniformly ergodic Markov Chain. Several image generation experiments are provided in our paper to show the effectiveness of our method.Comment: arXiv admin note: text overlap with arXiv:1207.5938 by other author