21,439 research outputs found
Structural characterization of decomposition in rate-insensitive stochastic Petri nets
This paper focuses on stochastic Petri nets that have an equilibrium distribution that is a product form over the number of tokens at the places. We formulate a decomposition result for the class of nets that have a product form solution irrespective of the values of the transition rates. These nets where algebraically characterized by Haddad et al.~as nets. By providing an intuitive interpretation of this algebraical characterization, and associating state machines to sets of -invariants, we obtain a one-to-one correspondence between the marking of the original places and the places of the added state machines. This enables us to show that the subclass of stochastic Petri nets under study can be decomposed into subnets that are identified by sets of its -invariants
On functional module detection in metabolic networks
Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models
Invariant Generation for Multi-Path Loops with Polynomial Assignments
Program analysis requires the generation of program properties expressing
conditions to hold at intermediate program locations. When it comes to programs
with loops, these properties are typically expressed as loop invariants. In
this paper we study a class of multi-path program loops with numeric variables,
in particular nested loops with conditionals, where assignments to program
variables are polynomial expressions over program variables. We call this class
of loops extended P-solvable and introduce an algorithm for generating all
polynomial invariants of such loops. By an iterative procedure employing
Gr\"obner basis computation, our approach computes the polynomial ideal of the
polynomial invariants of each program path and combines these ideals
sequentially until a fixed point is reached. This fixed point represents the
polynomial ideal of all polynomial invariants of the given extended P-solvable
loop. We prove termination of our method and show that the maximal number of
iterations for reaching the fixed point depends linearly on the number of
program variables and the number of inner loops. In particular, for a loop with
m program variables and r conditional branches we prove an upper bound of m*r
iterations. We implemented our approach in the Aligator software package.
Furthermore, we evaluated it on 18 programs with polynomial arithmetic and
compared it to existing methods in invariant generation. The results show the
efficiency of our approach
Rational invariants of even ternary forms under the orthogonal group
In this article we determine a generating set of rational invariants of
minimal cardinality for the action of the orthogonal group on
the space of ternary forms of even degree . The
construction relies on two key ingredients: On one hand, the Slice Lemma allows
us to reduce the problem to dermining the invariants for the action on a
subspace of the finite subgroup of signed permutations. On the
other hand, our construction relies in a fundamental way on specific bases of
harmonic polynomials. These bases provide maps with prescribed
-equivariance properties. Our explicit construction of these
bases should be relevant well beyond the scope of this paper. The expression of
the -invariants can then be given in a compact form as the
composition of two equivariant maps. Instead of providing (cumbersome) explicit
expressions for the -invariants, we provide efficient algorithms
for their evaluation and rewriting. We also use the constructed
-invariants to determine the -orbit locus and
provide an algorithm for the inverse problem of finding an element in
with prescribed values for its invariants. These are
the computational issues relevant in brain imaging.Comment: v3 Changes: Reworked presentation of Neuroimaging application,
refinement of Definition 3.1. To appear in "Foundations of Computational
Mathematics
Higher dimensional Automorphic Lie Algebras
The paper presents the complete classification of Automorphic Lie Algebras
based on , where the symmetry group is finite
and the orbit is any of the exceptional -orbits in .
A key feature of the classification is the study of the algebras in the context
of classical invariant theory. This provides on one hand a powerful tool from
the computational point of view, on the other it opens new questions from an
algebraic perspective, which suggest further applications of these algebras,
beyond the context of integrable systems. In particular, the research shows
that Automorphic Lie Algebras associated to the
groups (tetrahedral, octahedral and
icosahedral groups) depend on the group through the automorphic functions only,
thus they are group independent as Lie algebras. This can be established by
defining a Chevalley normal form for these algebras, generalising this
classical notion to the case of Lie algebras over a polynomial ring.Comment: 43 pages, standard LaTeX2
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