Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues

DOI10.1016/j.mbs.2013.10.003zbMath1308.92032OpenAlexW2087535060WikidataQ38157363 ScholiaQ38157363MaRDI QIDQ2437738

Florence d'Alché-Buc, George Michailidis

Publication date: 13 March 2014

Published in: Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.mbs.2013.10.003

zbMATH Keywords

stabilitycausalityautoregressive modelsdynamic Bayesian networkssparsitygene regulatory network inference

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Biochemistry, molecular biology (92C40)

Related Items (17)

Strong selection consistency of Bayesian vector autoregressive models based on a pseudo-likelihood approach ⋮ Sparse network identifiability via compressed sensing ⋮ High dimensional regression for regenerative time-series: an application to road traffic modeling ⋮ A posterior probability approach for gene regulatory network inference in genetic perturbation data ⋮ Inference of genetic regulatory networks with regulatory hubs using vector autoregressions and automatic relevance determination with model selections ⋮ Regularized Estimation in High-Dimensional Vector Auto-Regressive Models Using Spatio-Temporal Information ⋮ Rate-optimal robust estimation of high-dimensional vector autoregressive models ⋮ Multiple Change Point Detection in Reduced Rank High Dimensional Vector Autoregressive Models ⋮ Granger causality-based synaptic weights estimation for analyzing neuronal networks ⋮ Inference of biochemical S-systems via mixed-variable multiobjective evolutionary optimization ⋮ Roles of clustering coefficient for the network reconstruction ⋮ Identifying dynamical time series model parameters from equilibrium samples, with application to gene regulatory networks ⋮ Operator-valued kernel-based vector autoregressive models for network inference ⋮ Regularized joint estimation of related vector autoregressive models ⋮ Inference of gene regulatory networks using Bayesian nonparametric regression and topology information ⋮ Regularized estimation in sparse high-dimensional time series models ⋮ Testing for high-dimensional network parameters in auto-regressive models

Uses Software

• SimpleMKL
• ARACNE
• TRANSFAC
• SIRENE
• TIGRESS
• OKVAR-Boost

Cites Work

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• Statistics for high-dimensional data. Methods, theory and applications.
• Recent developments in parameter estimation and structure identification of biochemical and genomic systems
• Structure Learning in Nested Effects Models
• Emergence of Scaling in Random Networks
• Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression
• Stability Selection
• Investigating Causal Relations by Econometric Models and Cross-spectral Methods
• Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge
• Learning Bayesian Networks Does Not Have to Be NP-Hard

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