arXiv subjects

Michael A. Savageau

Publications and source records attributed to Michael A. Savageau.

5 recordsLinked to original sources

arXiv2008

Stabilizing and Destabilizing Effects of Embedding 3-node Subgraphs on State Space of Boolean Networks

We demonstrate the effects of embedding subgraphs using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical properties of network embedded seven different subgraphs including feedback and feedforward subgraphs, we found that complexity of the state space that increases with longer length of attractors and greater number of attractors is reduced for networks with more feedforward subgraphs. In addition, feedforward subgraphs can also provide higher mutual information with lower entropy in a temporal program of gene expression. Networks with other six subgraphs show opposite effects on dynamics of the networks, is roughly consistent with Thomas's conjecture. These results suggest that feedforward subgraphs are one of the favorable local structures in biological complex networks.

nlin.CG↗

arXiv2007

Effects of feedback and feedforward loops on dynamics of transcriptional regulatory model networks

We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and feedforward loops, we found that feedforward loops can provide higher temporal order (coherence) with lower entropy (randomness) in a temporal program of gene expression. In addition, complexity of the state space that increases with longer length of attractors and greater number of attractors is also reduced for networks with more feedforward loops. Feedback loops show opposite effects on dynamics of the networks. These results suggest that feedforward loops are one of the favorable local structures in biomolecular and neuronal networks.

nlin.CG↗

arXiv2006

Local cause of coherence in Boolean networks

We performed a numerical study on random Boolean networks with power-law rank outdegree distributions to find local structural cause for the emergence of high or low degree of coherence in binary state variables. The degree of randomness and coherence of the binary sequence are measured by entropy and mutual information, depending on local structure that consists of a node with a highly connected, called hub and its upstream nodes, and types of Boolean functions for the nodes. With a large number of output connections from a hub, the effects of Boolean function on the hub are more prominent. The local structures that give larger entropy tend to give rise to larger mutual information. Based on the numerical results and structural conditions we derived a time-independent transmission characteristic function of state variables for the local structures. We obtained good relationships between the numerical and analytical results, which indicate that dynamical properties from the whole networks can be inferred from the differences in the local structures.

nlin.CG↗

arXiv2005

Some properties of the Lerch family of discrete distributions

We extend the definition of the Lerch distribution to the set of nonnegative integers for greater applicability to modeling count data. We express its properties in terms of Lerch's transcendent, and study its unimodality, hazard function and variance-to-mean ratio.

math.PR↗

arXiv2001

Statistical inference and modeling with the S distribution

We consider the problem of statistical inference for the S distribution and introduce new minimum distance estimators for the four parameters of the S distribution using Kolmogorov-Smirnov, Cramer-von Mises and related distance metrics. Approximate goodness-of-fit and confidence intervals for parameters are calculated using bootstrap methods. We discuss further how the S distribution can be used to solve various problems of statistical modeling associated with parameter inference, including goodness-of-fit tests, Monte Carlo simulations and modeling trends in the distributions.

physics.data-an↗