Construction of probabilistic Boolean networks from a prescribed transition probability matrix: a maximum entropy rate approach.

DOI10.4208/EAJAM.080310.200910AzbMATH Open1287.65045OpenAlexW2060535971MaRDI QIDQ5406887FDOQ5406887

Authors: Xi Chen, Wai-Ki Ching, Xiao Shan Chen, Yang Cong, Nam-Kiu Tsing 

Publication date: 4 April 2014

Published in: East Asian Journal on Applied Mathematics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.4208/eajam.080310.200910a

Recommendations

• Generating probabilistic Boolean networks from a prescribed stationary distribution
• On generating optimal sparse probabilistic Boolean networks with maximum entropy from a positive stationary distribution.
• On construction of sparse probabilistic Boolean networks.
• A matrix perturbation method for computing the steady-state probability distributions of probabilistic Boolean networks with gene perturbations
• A modified orthogonal matching pursuit for construction of sparse probabilistic Boolean networks

zbMATH Keywords

convergenceinverse problemMarkov chainsgenetic regulatory networksnumerical exampleconjugate gradient methodNewton's methodBoolean networksprobabilistic Boolean networkstransition-probability matrixgenetic regulatory interactions

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Numerical analysis or methods applied to Markov chains (65C40) Numerical mathematical programming methods (65K05) Systems biology, networks (92C42) Minimax problems in mathematical programming (90C47) Iterative numerical methods for linear systems (65F10) Numerical computation of solutions to systems of equations (65H10)

Cites Work

• Immunological bioinformatics.
• Title not available (Why is that?)
• Trust Region Methods
• Markov chains: models, algorithms and applications
• Genomic signal processing
• Steady-state probabilities for attractors in probabilistic Boolean networks
• Bioinformatics

Cited In (13)

• Bayesian selection probability estimation for probabilistic Boolean networks
• Construction of a Boolean model of gene and protein regulatory network with memory
• Generating probabilistic Boolean networks from a prescribed stationary distribution
• On construction of sparse probabilistic Boolean networks.
• A matrix perturbation method for computing the steady-state probability distributions of probabilistic Boolean networks with gene perturbations
• A modified orthogonal matching pursuit for construction of sparse probabilistic Boolean networks
• On generating optimal sparse probabilistic Boolean networks with maximum entropy from a positive stationary distribution.
• A geometric proximal gradient method for sparse least squares regression with probabilistic simplex constraint
• Sparse solution of nonnegative least squares problems with applications in the construction of probabilistic Boolean networks.
• An efficient Hessian based algorithm for singly linearly and box constrained least squares regression
• Optimal reconstruction of noisy dynamics and selection probabilities in Boolean networks
• Mappings between probabilistic Boolean networks
• Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

This page was built for publication: Construction of probabilistic Boolean networks from a prescribed transition probability matrix: a maximum entropy rate approach.

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5406887)