Ernst C. Wit

Igor Artico, Ernst Wit

Relational events are a type of social interactions, that sometimes are referred to as dynamic networks. Its dynamics typically depends on emerging patterns, so-called endogenous variables, or external forces, referred to as exogenous variables. Comprehensive information on the actors in the network, especially for huge networks, is rare, however. A latent space approach in network analysis has been a popular way to account for unmeasured covariates that are driving network configurations. Bayesian and EM-type algorithms have been proposed for inferring the latent space, but both the sheer size many social network applications as well as the dynamic nature of the process, and therefore the latent space, make computations prohibitively expensive. In this work we propose a likelihood-based algorithm that can deal with huge relational event networks. We propose a hierarchical strategy for inferring network community dynamics embedded into an interpretable latent space. Node dynamics are described by smooth spline processes. To make the framework feasible for large networks we borrow from machine learning optimization methodology. Model-based clustering is carried out via a convex clustering penalization, encouraging shared trajectories for ease of interpretation. We propose a model-based approach for separating macro-microstructures and perform a hierarchical analysis within successive hierarchies. The method can fit millions of nodes on a public Colab GPU in a few minutes. The code and a tutorial are available in a Github repository.

Edoardo Filippi-Mazzola, Ernst C. Wit

Dynamic networks offer an insight of how relational systems evolve. However, modeling these networks efficiently remains a challenge, primarily due to computational constraints, especially as the number of observed events grows. This paper addresses this issue by introducing the Deep Relational Event Additive Model (DREAM) as a solution to the computational challenges presented by modeling non-linear effects in Relational Event Models (REMs). DREAM relies on Neural Additive Models to model non-linear effects, allowing each effect to be captured by an independent neural network. By strategically trading computational complexity for improved memory management and leveraging the computational capabilities of Graphic Processor Units (GPUs), DREAM efficiently captures complex non-linear relationships within data. This approach demonstrates the capability of DREAM in modeling dynamic networks and scaling to larger networks. Comparisons with traditional REM approaches showcase DREAM superior computational efficiency. The model potential is further demonstrated by an examination of the patent citation network, which contains nearly 8 million nodes and 100 million events.

Reza Mohammadi, Ernst C. Wit

Graphical models provide powerful tools to uncover complicated patterns in multivariate data and are commonly used in Bayesian statistics and machine learning. In this paper, we introduce the R package BDgraph which performs Bayesian structure learning for general undirected graphical models (decomposable and non-decomposable) with continuous, discrete, and mixed variables. The package efficiently implements recent improvements in the Bayesian literature, including that of Mohammadi and Wit (2015) and Dobra and Mohammadi (2018). To speed up computations, the computationally intensive tasks have been implemented in C++ and interfaced with R, and the package has parallel computing capabilities. In addition, the package contains several functions for simulation and visualization, as well as several multivariate datasets taken from the literature and used to describe the package capabilities. The paper includes a brief overview of the statistical methods which have been implemented in the package. The main part of the paper explains how to use the package. Furthermore, we illustrate the package's functionality in both real and artificial examples.

Javier González, Ivan Vujačić, Ernst Wit

Non-linear systems of differential equations have attracted the interest in fields like system biology, ecology or biochemistry, due to their flexibility and their ability to describe dynamical systems. Despite the importance of such models in many branches of science they have not been the focus of systematic statistical analysis until recently. In this work we propose a general approach to estimate the parameters of systems of differential equations measured with noise. Our methodology is based on the maximization of the penalized likelihood where the system of differential equations is used as a penalty. To do so, we use a Reproducing Kernel Hilbert Space approach that allows to formulate the estimation problem as an unconstrained numeric maximization problem easy to solve. The proposed method is tested with synthetically simulated data and it is used to estimate the unobserved transcription factor CdaR in Steptomyes coelicolor using gene expression data of the genes it regulates.

Anani Lotsi, Ernst Wit

This paper considers the problem of networks reconstruction from heterogeneous data using a Gaussian Graphical Mixture Model (GGMM). It is well known that parameter estimation in this context is challenging due to large numbers of variables coupled with the degeneracy of the likelihood. We propose as a solution a penalized maximum likelihood technique by imposing an $l_{1}$ penalty on the precision matrix. Our approach shrinks the parameters thereby resulting in better identifiability and variable selection. We use the Expectation Maximization (EM) algorithm which involves the graphical LASSO to estimate the mixing coefficients and the precision matrices. We show that under certain regularity conditions the Penalized Maximum Likelihood (PML) estimates are consistent. We demonstrate the performance of the PML estimator through simulations and we show the utility of our method for high dimensional data analysis in a genomic application.