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

DOI10.4208/EAJAM.080310.200910AMaRDI QIDQ5406887zbMATH OpenOpenAlexFDO

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

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)

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Cites work

• scientific article; zbMATH DE number 47363 (Why is no real title available?)
• Bioinformatics
• Genomic signal processing
• Immunological bioinformatics.
• Markov chains: models, algorithms and applications
• Steady-state probabilities for attractors in probabilistic Boolean networks
• Trust Region Methods

Cited in

(13)

• Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks
• 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

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