1,160 research outputs found
Parameter estimation for Boolean models of biological networks
Boolean networks have long been used as models of molecular networks and play
an increasingly important role in systems biology. This paper describes a
software package, Polynome, offered as a web service, that helps users
construct Boolean network models based on experimental data and biological
input. The key feature is a discrete analog of parameter estimation for
continuous models. With only experimental data as input, the software can be
used as a tool for reverse-engineering of Boolean network models from
experimental time course data.Comment: Web interface of the software is available at
http://polymath.vbi.vt.edu/polynome
Data based identification and prediction of nonlinear and complex dynamical systems
We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin
Using synchronous Boolean networks to model several phenomena of collective behavior
In this paper, we propose an approach for modeling and analysis of a number
of phenomena of collective behavior. By collectives we mean multi-agent systems
that transition from one state to another at discrete moments of time. The
behavior of a member of a collective (agent) is called conforming if the
opinion of this agent at current time moment conforms to the opinion of some
other agents at the previous time moment. We presume that at each moment of
time every agent makes a decision by choosing from the set {0,1} (where
1-decision corresponds to action and 0-decision corresponds to inaction). In
our approach we model collective behavior with synchronous Boolean networks. We
presume that in a network there can be agents that act at every moment of time.
Such agents are called instigators. Also there can be agents that never act.
Such agents are called loyalists. Agents that are neither instigators nor
loyalists are called simple agents. We study two combinatorial problems. The
first problem is to find a disposition of instigators that in several time
moments transforms a network from a state where a majority of simple agents are
inactive to a state with a majority of active agents. The second problem is to
find a disposition of loyalists that returns the network to a state with a
majority of inactive agents. Similar problems are studied for networks in which
simple agents demonstrate the contrary to conforming behavior that we call
anticonforming. We obtained several theoretical results regarding the behavior
of collectives of agents with conforming or anticonforming behavior. In
computational experiments we solved the described problems for randomly
generated networks with several hundred vertices. We reduced corresponding
combinatorial problems to the Boolean satisfiability problem (SAT) and used
modern SAT solvers to solve the instances obtained
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