Geometric Aspects of Multiagent Systems

Recent advances in Multiagent Systems (MAS) and Epistemic Logic within Distributed Systems Theory, have used various combinatorial structures that model both the geometry of the systems and the Kripke model structure of models for the logic. Examining one of the simpler versions of these models, interpreted systems, and the related Kripke semantics of the logic $S5_n$ (an epistemic logic with $n$-agents), the similarities with the geometric / homotopy theoretic structure of groupoid atlases is striking. These latter objects arise in problems within algebraic K-theory, an area of algebra linked to the study of decomposition and normal form theorems in linear algebra. They have a natural well structured notion of path and constructions of path objects, etc., that yield a rich homotopy theory.Comment: 14 pages, 1 eps figure, prepared for GETCO200

Logspace computations in graph products

We consider three important and well-studied algorithmic problems in group theory: the word, geodesic, and conjugacy problem. We show transfer results from individual groups to graph products. We concentrate on logspace complexity because the challenge is actually in small complexity classes, only. The most difficult transfer result is for the conjugacy problem. We have a general result for graph products, but even in the special case of a graph group the result is new. Graph groups are closely linked to the theory of Mazurkiewicz traces which form an algebraic model for concurrent processes. Our proofs are combinatorial and based on well-known concepts in trace theory. We also use rewriting techniques over traces. For the group-theoretical part we apply Bass-Serre theory. But as we need explicit formulae and as we design concrete algorithms all our group-theoretical calculations are completely explicit and accessible to non-specialists

Identification of control targets in Boolean molecular network models via computational algebra

Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. Experimentally, node manipulation requires technology to completely repress or fully activate a particular gene product while edge manipulations only require a drug that inactivates the interaction between two gene products. Results: This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network.Comment: 12 pages, 4 figures, 2 table

Computation with Polynomial Equations and Inequalities arising in Combinatorial Optimization

The purpose of this note is to survey a methodology to solve systems of polynomial equations and inequalities. The techniques we discuss use the algebra of multivariate polynomials with coefficients over a field to create large-scale linear algebra or semidefinite programming relaxations of many kinds of feasibility or optimization questions. We are particularly interested in problems arising in combinatorial optimization.Comment: 28 pages, survey pape

Toric algebra of hypergraphs

The edges of any hypergraph parametrize a monomial algebra called the edge subring of the hypergraph. We study presentation ideals of these edge subrings, and describe their generators in terms of balanced walks on hypergraphs. Our results generalize those for the defining ideals of edge subrings of graphs, which are well-known in the commutative algebra community, and popular in the algebraic statistics community. One of the motivations for studying toric ideals of hypergraphs comes from algebraic statistics, where generators of the toric ideal give a basis for random walks on fibers of the statistical model specified by the hypergraph. Further, understanding the structure of the generators gives insight into the model geometry.Comment: Section 3 is new: it explains connections to log-linear models in algebraic statistics and to combinatorial discrepancy. Section 6 (open problems) has been moderately revise