Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development

Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x), derived from interactions in the gene regulatory network (GRN) of a cell, quantifies the relative stability of network states, which determine the effort required for state transitions in a multi-stable dynamical system. However, quasi-potential landscapes, originally developed for continuous systems, are not suitable for discrete-valued networks which are important tools to study complex systems. In this paper, we provide a framework to quantify the landscape for discrete Boolean networks (BNs). We apply our framework to study pancreas cell differentiation where an ensemble of BN models is considered based on the structure of a minimal GRN for pancreas development. We impose biologically motivated structural constraints (corresponding to specific type of Boolean functions) and dynamical constraints (corresponding to stable attractor states) to limit the space of BN models for pancreas development. In addition, we enforce a novel functional constraint corresponding to the relative ordering of attractor states in BN models to restrict the space of BN models to the biological relevant class. We find that BNs with canalyzing/sign-compatible Boolean functions best capture the dynamics of pancreas cell differentiation. This framework can also determine the genes' influence on cell state transitions, and thus can facilitate the rational design of cell reprogramming protocols.Comment: 24 pages, 6 figures, 1 tabl

Algebras for Agent Norm-Regulation

An abstract architecture for idealized multi-agent systems whose behaviour is regulated by normative systems is developed and discussed. Agent choices are determined partially by the preference ordering of possible states and partially by normative considerations: The agent chooses that act which leads to the best outcome of all permissible actions. If an action is non-permissible depends on if the result of performing that action leads to a state satisfying a condition which is forbidden, according to the norms regulating the multi-agent system. This idea is formalized by defining set-theoretic predicates characterizing multi-agent systems. The definition of the predicate uses decision theory, the Kanger-Lindahl theory of normative positions, and an algebraic representation of normative systems.Comment: 25 page

Generalizations of Swierczkowski's lemma and the arity gap of finite functions

Swierczkowski's Lemma - as it is usually formulated - asserts that if f is an at least quaternary operation on a finite set A and every operation obtained from f by identifying a pair of variables is a projection, then f is a semiprojection. We generalize this lemma in various ways. First, it is extended to B-valued functions on A instead of operations on A and to essentially at most unary functions instead of projections. Then we characterize the arity gap of functions of small arities in terms of quasi-arity, which in turn provides a further generalization of Swierczkowski's Lemma. Moreover, we explicitly classify all pseudo-Boolean functions according to their arity gap. Finally, we present a general characterization of the arity gaps of B-valued functions on arbitrary finite sets A.Comment: 11 pages, proofs simplified, contents reorganize

On the Error Resilience of Ordered Binary Decision Diagrams

Ordered Binary Decision Diagrams (OBDDs) are a data structure that is used in an increasing number of fields of Computer Science (e.g., logic synthesis, program verification, data mining, bioinformatics, and data protection) for representing and manipulating discrete structures and Boolean functions. The purpose of this paper is to study the error resilience of OBDDs and to design a resilient version of this data structure, i.e., a self-repairing OBDD. In particular, we describe some strategies that make reduced ordered OBDDs resilient to errors in the indexes, that are associated to the input variables, or in the pointers (i.e., OBDD edges) of the nodes. These strategies exploit the inherent redundancy of the data structure, as well as the redundancy introduced by its efficient implementations. The solutions we propose allow the exact restoring of the original OBDD and are suitable to be applied to classical software packages for the manipulation of OBDDs currently in use. Another result of the paper is the definition of a new canonical OBDD model, called {\em Index-resilient Reduced OBDD}, which guarantees that a node with a faulty index has a reconstruction cost $O(k)$, where $k$ is the number of nodes with corrupted index

Observation of implicit complexity by non confluence

We propose to consider non confluence with respect to implicit complexity. We come back to some well known classes of first-order functional program, for which we have a characterization of their intentional properties, namely the class of cons-free programs, the class of programs with an interpretation, and the class of programs with a quasi-interpretation together with a termination proof by the product path ordering. They all correspond to PTIME. We prove that adding non confluence to the rules leads to respectively PTIME, NPTIME and PSPACE. Our thesis is that the separation of the classes is actually a witness of the intentional properties of the initial classes of programs

Join-irreducible Boolean functions

This paper is a contribution to the study of a quasi-order on the set $\Omega$ of Boolean functions, the \emph{simple minor} quasi-order. We look at the join-irreducible members of the resulting poset $\tilde{\Omega}$. Using a two-way correspondence between Boolean functions and hypergraphs, join-irreducibility translates into a combinatorial property of hypergraphs. We observe that among Steiner systems, those which yield join-irreducible members of $\tilde{\Omega}$ are the -2-monomorphic Steiner systems. We also describe the graphs which correspond to join-irreducible members of $\tilde{\Omega}$.Comment: The current manuscript constitutes an extension to the paper "Irreducible Boolean Functions" (arXiv:0801.2939v1