Sparse graphical models have revolutionized multivariate inference. With the advent of high-dimensional multivariate data in many applied fields, these methods are able to detect a much ...lower-dimensional structure, often represented via a sparse conditional independence graph. There have been numerous extensions of such methods in the past decade. Many practical applications have additional covariates or suffer from missing or censored data. Despite the development of these extensions of sparse inference methods for graphical models, there have been so far no implementations for, e.g., conditional graphical models. Here we present the general-purpose package cglasso for estimating sparse conditional Gaussian graphical models with potentially missing or censored data. The method employs an efficient expectation-maximization estimation of an ℓ1 -penalized likelihood via a block-coordinate descent algorithm. The package has a user-friendly data manipulation interface. It estimates a solution path and includes various automatic selection algorithms for the two ℓ1 tuning parameters, associated with the sparse precision matrix and sparse regression coefficients, respectively. The package pays particular attention to the visualization of the results, both by means of marginal tables and figures, and of the inferred conditional independence graphs. This package provides a unique and computational efficient implementation of a conditional Gaussian graphical model that is able to deal with the additional complications of missing and censored data. As such it constitutes an important contribution for empirical scientists wishing to detect sparse structures in high-dimensional data.
In many applied fields, such as genomics, different types of data are collected on the same system, and it is not uncommon that some of these datasets are subject to censoring as a result of the ...measurement technologies used, such as data generated by polymerase chain reactions and flow cytometer. When the overall objective is that of network inference, at possibly different levels of a system, information coming from different sources and/or different steps of the analysis can be integrated into one model with the use of conditional graphical models. In this paper, we develop a doubly penalized inferential procedure for a conditional Gaussian graphical model when data can be subject to censoring. The computational challenges of handling censored data in high dimensionality are met with the development of an efficient expectation-maximization algorithm, based on approximate calculations of the moments of truncated Gaussian distributions and on a suitably derived two-step procedure alternating graphical lasso with a novel block-coordinate multivariate lasso approach. We evaluate the performance of this approach on an extensive simulation study and on gene expression data generated by RT-qPCR technologies, where we are able to integrate network inference, differential expression detection and data normalization into one model.
The authors of the paper “Bayesian Graphical Models for Modern Biological Applications” have put forward an important framework for making graphical models more useful in applied settings. In this ...discussion paper, we give a number of suggestions for making this framework even more suitable for practical scenarios. Firstly, we show that an alternative and simplified definition of covariate might make the framework more manageable in high-dimensional settings. Secondly, we point out that the inclusion of missing variables is important for practical data analysis. Finally, we comment on the effect that the Gaussianity assumption has in identifying the underlying conditional independence graph and how this can be circumvented. The Bayesian framework proposed by the authors is flexible enough to accommodate extensions that can deal with these aspects, which are often encountered in real data analyses such as the complex modern applications considered by the authors.
dglars is a publicly available R package that implements the method proposed in Augugliaro, Mineo, and Wit (2013), developed to study the sparse structure of a generalized linear model. This method, ...called dgLARS, is based on a differential geometrical extension of the least angle regression method proposed in Efron, Hastie, Johnstone, and Tibshirani (2004). The core of the dglars package consists of two algorithms implemented in Fortran 90 to efficiently compute the solution curve: a predictor-corrector algorithm, proposed in Augugliaro et al. (2013), and a cyclic coordinate descent algorithm, proposed in Augugliaro, Mineo, and Wit (2012). The latter algorithm, as shown here, is significantly faster than the predictor-corrector algorithm. For comparison purposes, we have implemented both algorithms.
Sparsity is an essential feature of many contemporary data problems. Remote sensing, various forms of automated screening and other high throughput measurement devices collect a large amount of ...information, typically about few independent statistical subjects or units. In certain cases it is reasonable to assume that the underlying process generating the data is itself sparse, in the sense that only a few of the measured variables are involved in the process. We propose an explicit method of monotonically decreasing sparsity for outcomes that can be modelled by an exponential family. In our approach we generalize the equiangular condition in a generalized linear model. Although the geometry involves the Fisher information in a way that is not obvious in the simple regression setting, the equiangular condition turns out to be equivalent with an intuitive condition imposed on the Rao score test statistics. In certain special cases the method can be tweaked to obtain L1-penalized generalized linear model solution paths, but the method itself defines sparsity more directly. Although the computation of the solution paths is not trivial, the method compares favourably with other path following algorithms.
Networks and society Vinciotti, Veronica; Augugliaro, Luigi; Wit, Ernst
Journal of the Royal Statistical Society. Series A, Statistics in society,
07/2023, Letnik:
186, Številka:
3
Journal Article
Graphical lasso is one of the most used estimators for inferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern ...measurement technologies make the use of this estimator theoretically unfounded, even when the assumption of a multivariate Gaussian distribution is satisfied. Typical examples are data generated by polymerase chain reactions and flow cytometer. The combination of censoring and high-dimensionality make inference of the underlying genetic networks from these data very challenging. In this article, we propose an $\ell_1$-penalized Gaussian graphical model for censored data and derive two EM-like algorithms for inference. We evaluate the computational efficiency of the proposed algorithms by an extensive simulation study and show that, when censored data are available, our proposal is superior to existing competitors both in terms of network recovery and parameter estimation. We apply the proposed method to gene expression data generated by microfluidic Reverse Transcription quantitative Polymerase Chain Reaction technology in order to make inference on the regulatory mechanisms of blood development. A software implementation of our method is available on github (https://github.com/LuigiAugugliaro/cglasso).
A large class of modeling and prediction problems involves outcomes that belong to an exponential family distribution. Generalized linear models (GLMs) are a standard way of dealing with such ...situations. Even in high-dimensional feature spaces GLMs can be extended to deal with such situations. Penalized inference approaches, such as the
ℓ
1
or SCAD, or extensions of least angle regression, such as dgLARS, have been proposed to deal with GLMs with high-dimensional feature spaces. Although the theory underlying these methods is in principle generic, the implementation has remained restricted to dispersion-free models, such as the Poisson and logistic regression models. The aim of this manuscript is to extend the differential geometric least angle regression method for high-dimensional GLMs to arbitrary exponential dispersion family distributions with arbitrary link functions. This entails, first, extending the predictor–corrector (PC) algorithm to arbitrary distributions and link functions, and second, proposing an efficient estimator of the dispersion parameter. Furthermore, improvements to the computational algorithm lead to an important speed-up of the PC algorithm. Simulations provide supportive evidence concerning the proposed efficient algorithms for estimating coefficients and dispersion parameter. The resulting method has been implemented in our R package (which will be merged with the original
dglars
package) and is shown to be an effective method for inference for arbitrary classes of GLMs.
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