Related papers: Complexity of limit-cycle problems in Boolean netw…
We consider the multiplicity of limit cycles that appear when a hyperbolic polycycle is perturbed. We prove, in particular, that if such unfolding happens in generic finite-parameter families, the multiplicity of every new limit cycle does…
We consider a model for gene regulatory networks that is a modification of Kauffmann's (1969) random Boolean networks. There are three parameters: $n =$ the number of nodes, $r =$ the number of inputs to each node, and $p =$ the expected…
Improving information flow in deep networks helps to ease the training difficulties and utilize parameters more efficiently. Here we propose a new convolutional neural network architecture with alternately updated clique (CliqueNet). In…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
We study the target control of asynchronous Boolean networks, to identify efficacious interventions that can drive the dynamics of a given Boolean network from any initial state to the desired target attractor. Based on the application…
Inclusion dependencies form one of the most widely used dependency classes. We extend existing results on the axiomatization and computational complexity of their implication problem to two extended variants. We present an alternative…
Recently, different approaches have been proposed for studying basic properties of time series from a complex network perspective. In this work, the corresponding potentials and limitations of networks based on recurrences in phase space…
Boolean satisfiability problem has applications in various fields. An efficient algorithm to solve satisfiability problem can be used to solve many other problems efficiently. The input of satisfiability problem is a finite set of clauses.…
In the load balancing problem, each node in a network is assigned a load, and the goal is to equally distribute the loads among the nodes, by preforming local load exchanges. While load balancing was extensively studied in static networks,…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
The problem of controlling complex networks is of interest to disciplines ranging from biology to swarm robotics. However, controllability can be too strict a condition, failing to capture a range of desirable behaviors. Herdability, which…
In this report, we present a formal approach that addresses the problem of emergence of phase transitions in stochastic and attractive nonlinear threshold Boolean automata networks. Nonlinear networks considered are informally defined on…
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of…
The purpose of this paper is to provide efficient algorithms that decide membership for classes of several Boolean hierarchies for which efficiency (or even decidability) were previously not known. We develop new forbidden-chain…
The standard reasoning problem, concept satisfiability, in the basic description logic ALC is PSPACE-complete, and it is EXPTIME-complete in the presence of unrestricted axioms. Several fragments of ALC, notably logics in the FL, EL, and…
The control of complex systems is an ongoing challenge of complexity research. Recent advances using concepts of structural control deduce a wide range of control related properties from the network representation of complex systems. Here,…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
We consider the general problem of blocking all solutions of some given combinatorial problem with only few elements. For example, the problem of destroying all maximum cliques of a given graph by forbidding only few vertices. Problems of…
Discrete dynamical systems in which model components take on categorical values have been successfully applied to biological networks to study their global dynamic behavior. Boolean models in particular have been used extensively. However,…