Variational inference for sparse network reconstruction from count data

In multivariate statistics, the question of finding direct interactions can be formulated as a problem of network inference - or network reconstruction - for which the Gaussian graphical model (GGM) provides a canonical framework. Unfortunately, the Gaussian assumption does not apply to count data which are encountered in domains such as genomics, social sciences or ecology. To circumvent this limitation, state-of-the-art approaches use two-step strategies that first transform counts to pseudo Gaussian observations and then apply a (partial) correlation-based approach from the abundant literature of GGM inference. We adopt a different stance by relying on a latent model where we directly model counts by means of Poisson distributions that are conditional to latent (hidden) Gaussian correlated variables. In this multivariate Poisson lognormal-model, the dependency structure is completely captured by the latent layer. This parametric model enables to account for the effects of covariates on the counts. To perform network inference, we add a sparsity inducing constraint on the inverse covariance matrix of the latent Gaussian vector. Unlike the usual Gaussian setting, the penalized likelihood is generally not tractable, and we resort instead to a variational approach for approximate likelihood maximization. The corresponding optimization problem is solved by alternating a gradient ascent on the variational parameters and a graphical-Lasso step on the covariance matrix. We show that our approach is highly competitive with the existing methods on simulation inspired from microbiological data. We then illustrate on three various data sets how accounting for sampling efforts via offsets and integrating external covariates (which is mostly never done in the existing literature) drastically changes the topology of the inferred network

Expectation Propagation for Poisson Data

The Poisson distribution arises naturally when dealing with data involving counts, and it has found many applications in inverse problems and imaging. In this work, we develop an approximate Bayesian inference technique based on expectation propagation for approximating the posterior distribution formed from the Poisson likelihood function and a Laplace type prior distribution, e.g., the anisotropic total variation prior. The approach iteratively yields a Gaussian approximation, and at each iteration, it updates the Gaussian approximation to one factor of the posterior distribution by moment matching. We derive explicit update formulas in terms of one-dimensional integrals, and also discuss stable and efficient quadrature rules for evaluating these integrals. The method is showcased on two-dimensional PET images.Comment: 25 pages, to be published at Inverse Problem

DeepVoxels: Learning Persistent 3D Feature Embeddings

In this work, we address the lack of 3D understanding of generative neural networks by introducing a persistent 3D feature embedding for view synthesis. To this end, we propose DeepVoxels, a learned representation that encodes the view-dependent appearance of a 3D scene without having to explicitly model its geometry. At its core, our approach is based on a Cartesian 3D grid of persistent embedded features that learn to make use of the underlying 3D scene structure. Our approach combines insights from 3D geometric computer vision with recent advances in learning image-to-image mappings based on adversarial loss functions. DeepVoxels is supervised, without requiring a 3D reconstruction of the scene, using a 2D re-rendering loss and enforces perspective and multi-view geometry in a principled manner. We apply our persistent 3D scene representation to the problem of novel view synthesis demonstrating high-quality results for a variety of challenging scenes.Comment: Video: https://www.youtube.com/watch?v=HM_WsZhoGXw Supplemental material: https://drive.google.com/file/d/1BnZRyNcVUty6-LxAstN83H79ktUq8Cjp/view?usp=sharing Code: https://github.com/vsitzmann/deepvoxels Project page: https://vsitzmann.github.io/deepvoxels

Distributed Reconstruction of Nonlinear Networks: An ADMM Approach

In this paper, we present a distributed algorithm for the reconstruction of large-scale nonlinear networks. In particular, we focus on the identification from time-series data of the nonlinear functional forms and associated parameters of large-scale nonlinear networks. Recently, a nonlinear network reconstruction problem was formulated as a nonconvex optimisation problem based on the combination of a marginal likelihood maximisation procedure with sparsity inducing priors. Using a convex-concave procedure (CCCP), an iterative reweighted lasso algorithm was derived to solve the initial nonconvex optimisation problem. By exploiting the structure of the objective function of this reweighted lasso algorithm, a distributed algorithm can be designed. To this end, we apply the alternating direction method of multipliers (ADMM) to decompose the original problem into several subproblems. To illustrate the effectiveness of the proposed methods, we use our approach to identify a network of interconnected Kuramoto oscillators with different network sizes (500~100,000 nodes).Comment: To appear in the Preprints of 19th IFAC World Congress 201