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Influence Of Noise On The Inference Of Dynamic Bayesian Networks From Short Time Series

Frank Emmert Streib, Matthias Dehmer, Gökhan H. Bakır, Max Mühlhauser
2007 Zenodo  
In this paper we investigate the influence of external noise on the inference of network structures.  ...  Here external noise means, that the dynamics of the system under investigation, e.g., temporal changes of mRNA concentration, is affected by measurement errors.  ...  Influence of external noise on the overall performance The results for the Boolean network are shown in Fig. 4 and for the stochastic Boolean network in Fig. 5 .  ... 
doi:10.5281/zenodo.1332677 fatcat:hvmr6pu2cbd6vgjyizaz7yxnmy

Characteristics of Dynamical Phase Transitions for Noise Intensities

Muyoung Heo, Jong-Kil Park, Kyungsik Kim
2014 Procedia Computer Science  
The nature of the phase transition are found numerically and analytically in two connections of probability density function and one random network.  ...  We simulate and analyze dynamical phase transitions in a Boolean neural network with initial random connections.  ...  The influence of noise on the dynamics of Boolean networks has been analyzed in several published papers [26, 27] as well.  ... 
doi:10.1016/j.procs.2014.05.235 fatcat:uqj5x3dc2jdt3kfehsgr27m4we

2P274 Adaptive random Boolean network model based on local information transfer(24. Mathematical biology,Poster)

Taichi Haruna, Sayaka Tanaka
2013 Seibutsu Butsuri  
random Boolean network model based on local information transfer Taichi Haruna, Sayaka Tanaka (Graduate School of Science, Kobe University) It has been suggested that gene regulation networks of living  ...  We discuss the relevance of our findings to single molecule observations of membrane lipids and to theoretical findings on the influence of fluid dynamics on molecular transport in a 2-d fluid. 2P277  ... 
doi:10.2142/biophys.53.s204_3 fatcat:ka53d7ofrfcyzlz36g5xxpjjhy

Measures for information propagation in Boolean networks

Pauli Rämö, Stuart Kauffman, Juha Kesseli, Olli Yli-Harja
2007 Physica D : Non-linear phenomena  
In this paper, we study what kinds of Boolean networks best propagate and process signals, i.e. information, in the presence of stochasticity and noise.  ...  We propose a new measure for information propagation based on perturbation avalanches in Boolean networks and find that the measure is maximized in dynamically critical networks and in subcritical networks  ...  The average influence I is defined as the probability that a perturbation of an input to f (x) has an influence on its output value in the stationary state characterized by b * : I = E f ∈F   1 K K i  ... 
doi:10.1016/j.physd.2006.12.005 fatcat:owfqcy3kxfdtppw3rkvjdebeba

Stability of Boolean and Continuous Dynamics

Fakhteh Ghanbarnejad, Konstantin Klemm
2011 Physical Review Letters  
In particular, random networks of nodes with large sensitivity yield stable dynamics under small perturbations.  ...  Binary discretization of state space and time leads to Boolean dynamics. In the latter, the dynamics has been called unstable if flip perturbations lead to damage spreading.  ...  Acknowledgements This work has been funded by VolkswagenStiftung under the initiative on Complex Networks as Phenomena across Disciplines.  ... 
doi:10.1103/physrevlett.107.188701 pmid:22107682 fatcat:uo27ckppj5edtij4p43zoknay4

Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts

Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni de Matteis
2013 Electronic Proceedings in Theoretical Computer Science  
The model combines a morphological model, based on the Cellular Potts Model (CPM), and a gene regulatory network model, based on Noisy Random Boolean Networks (NRBNs).  ...  The preliminary analyses on a multiscale model of intestinal crypt dynamics are here presented.  ...  Cellular differentiation is modeled as a stochastic process whose dynamics emerge from a Noisy Random Boolean Network representation of a Gene Regulatory Network, along the lines of [5] .  ... 
doi:10.4204/eptcs.130.12 fatcat:mmu4glejgvac5feo35jxm52bpa

2P273 Gain Noise Relation in Adaptation Networks(24. Mathematical biology,Poster)

Prabhat Shankar, Masatoshi Nishikawa, Tatsuo Shibata
2013 Seibutsu Butsuri  
random Boolean network model based on local information transfer Taichi Haruna, Sayaka Tanaka (Graduate School of Science, Kobe University) It has been suggested that gene regulation networks of living  ...  We discuss the relevance of our findings to single molecule observations of membrane lipids and to theoretical findings on the influence of fluid dynamics on molecular transport in a 2-d fluid. 2P277  ... 
doi:10.2142/biophys.53.s204_2 fatcat:64zqi6n7qvbmbb6lvylsbsqvbm

The influence of the basin structure of Boolean networks on their long range correlated dynamics

Peng Xu, Xianghong Wang, Wenbin Liu
2012 2012 IEEE 6th International Conference on Systems Biology (ISB)  
An important question is what kind of networks can generate such dynamics? In this paper, we investigate this issue based on the attractor structure of Boolean networks.  ...  Recently we studied the long-range correlated dynamics of Boolean networks, and found that some networks could present the 1 / f dynamics while others couldn't.  ...  random Boolean networks could only present white noise dynamics [4] .  ... 
doi:10.1109/isb.2012.6314106 dblp:conf/isb/XuWL12 fatcat:jfs5ksw6mracbblyavdwfy4r3i

Eukaryotic cells are dynamically ordered or critical but not chaotic

I. Shmulevich, S. A. Kauffman, M. Aldana
2005 Proceedings of the National Academy of Sciences of the United States of America  
differential equations, and the Boolean approach, based on difference equations and discrete logical rules.  ...  Using the Boolean approach, here we show what we believe to be the first direct evidence that the underlying genetic network of HeLa cells appears to operate either in the ordered regime or at the border  ...  This work was partially supported by National Institutes of Health Grant R21 GM070600-01 and National Science Foundation Grant INT-0336343.  ... 
doi:10.1073/pnas.0506771102 pmid:16155121 pmcid:PMC1224670 fatcat:atfgow7x4fetzjqqbrmdgzaw6q

Noise analysis of time series data in gene regulatory networks

Haixin Wang, James E. Glover
2011 2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)  
In this paper, the quantitative analysis of noisy time-series gene expression data on inference of gene regulatory networks is performed. We propose a two-step algorithm to solve the problem.  ...  One of the most important properties in gene expression is the stochasticity. Gene expression process is noisy and fluctuant.  ...  The influence of external noise on the system dynamics is by flipping the value of a gene X i at each time step with a probability P ǫ .  ... 
doi:10.1109/bmei.2011.6098729 dblp:conf/bmei/WangG11 fatcat:ggyexqovdzeqrbboqutxmnbn7m

2P276 Diffusion in the plasma membrane with immobile molecules : significance of fluid dynamical interactions(24. Mathematical biology,Poster)

Ziya Kalay, Takahiro K. Fujiwara, Akihiro Kusumi
2013 Seibutsu Butsuri  
random Boolean network model based on local information transfer Taichi Haruna, Sayaka Tanaka (Graduate School of Science, Kobe University) It has been suggested that gene regulation networks of living  ...  We discuss the relevance of our findings to single molecule observations of membrane lipids and to theoretical findings on the influence of fluid dynamics on molecular transport in a 2-d fluid. 2P277  ... 
doi:10.2142/biophys.53.s204_5 fatcat:lykhurorlbadvi27vwcxwhz5iq

Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks

Pablo Villegas, José Ruiz-Franco, Jorge Hidalgo, Miguel A. Muñoz
2016 Scientific Reports  
Here, we study the effect of noise within the context of Boolean networks trained to learn complex tasks under supervision.  ...  On the other hand, when additional sources of intrinsic noise in the network states and/or in its wiring pattern are introduced, the optimally performing networks become clearly subcritical.  ...  Acknowledgements We acknowledge the Spanish-MINECO grant FIS2013-43201-P (FEDER funds) for financial support. We thank P. Moretti for very useful comments.  ... 
doi:10.1038/srep34743 pmid:27713479 pmcid:PMC5054426 fatcat:wajjacvro5effnn7b7pyn7r4ne

2P272 Evolutionary, population, and reaction dynamics of experimental ecosystems(23. Ecology & Environment,Poster)
2P272 実験生態系の進化、個体群、反応ダイナミクス(23.生態/環境,ポスター,日本生物物理学会年会第51回(2013年度))

Kazufumi Hosoda, Makoto Sueyoshi, Itsuka Kumano, Masumi Habuchi, Kayo Yamamoto, Risa Takami, Yuhki Azuma, Isao Kubo, Shingo Suzuki, Tetsuya Yomo
2013 Seibutsu Butsuri  
random Boolean network model based on local information transfer Taichi Haruna, Sayaka Tanaka (Graduate School of Science, Kobe University) It has been suggested that gene regulation networks of living  ...  We discuss the relevance of our findings to single molecule observations of membrane lipids and to theoretical findings on the influence of fluid dynamics on molecular transport in a 2-d fluid. 2P277  ... 
doi:10.2142/biophys.53.s204_1 fatcat:ojl4vgbqtbfahd5btzyxcg2s5m

2P277 Competitive reaction between enzymes with normal and anomalous diffusivity(24. Mathematical biology,Poster)

Kenta Yashima, Jun Nakabayashi, Akira Sasaki
2013 Seibutsu Butsuri  
We discuss the relevance of our findings to single molecule observations of membrane lipids and to theoretical findings on the influence of fluid dynamics on molecular transport in a 2-d fluid. 2P277  ...  Adaptive random Boolean network model based on local information transfer Taichi Haruna, Sayaka Tanaka (Graduate School of Science, Kobe University) It has been suggested that gene regulation networks  ... 
doi:10.2142/biophys.53.s204_6 fatcat:3dikiu47ezdp7c7pfccvyei4ca

2P275 Benefits of Acquiring Phototrophy by Hosting Algal Endosymbionts(24. Mathematical biology,Poster)
2P275 光合成生物との共生による利益とはーミドリゾウリムシの増殖解析(24.数理生物学,ポスター,日本生物物理学会年会第51回(2013年度))

Sosuke Iwai
2013 Seibutsu Butsuri  
random Boolean network model based on local information transfer Taichi Haruna, Sayaka Tanaka (Graduate School of Science, Kobe University) It has been suggested that gene regulation networks of living  ...  We discuss the relevance of our findings to single molecule observations of membrane lipids and to theoretical findings on the influence of fluid dynamics on molecular transport in a 2-d fluid. 2P277  ... 
doi:10.2142/biophys.53.s204_4 fatcat:mo4pblidxjckhegdammqoqyu4u
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