On straight words and minimal permutators in finite transformation semigroups.

“The original publication is available at www.springerlink.com”. Copyright SpringerMotivated by issues arising in computer science, we investigate the loop-free paths from the identity transformation and corresponding straight words in the Cayley graph of a finite transformation semigroup with a fixed generator set. Of special interest are words that permute a given subset of the state set. Certain such words, called minimal permutators, are shown to comprise a code, and the straight ones comprise a finite code. Thus, words that permute a given subset are uniquely factorizable as products of the subset's minimal permutators, and these can be further reduced to straight minimal permutators. This leads to insight into structure of local pools of reversibility in transformation semigroups in terms of the set of words permuting a given subset. These findings can be exploited in practical calculations for hierarchical decompositions of finite automata. As an example we consider groups arising in biological systems

Hierarchical coordinate systems for understanding complexity and its evolution with applications to genetic regulatory networks

Original article can be found at : http://www.mitpressjournals.org/ Copyright MIT PressBeyond complexity measures, sometimes it is worth in addition investigating how complexity changes structurally, especially in artificial systems where we have complete knowledge about the evolutionary process. Hierarchical decomposition is a useful way of assessing structural complexity changes of organisms modeled as automata, and we show how recently developed computational tools can be used for this purpose, by computing holonomy decompositions and holonomy complexity. To gain insight into the evolution of complexity, we investigate the smoothness of the landscape structure of complexity under minimal transitions. As a proof of concept, we illustrate how the hierarchical complexity analysis reveals symmetries and irreversible structure in biological networks by applying the methods to the lac operon mechanism in the genetic regulatory network of Escherichia coli.Peer reviewe

Computational understanding and manipulation of symmetries

Attila Egri-Nagy, Chrystopher L Nehaniv, "Computational Understanding and Manipulation of Symmetries", in Chalup S. K., Blair A. D., Randall M. (Eds) Artificial Life and Computational Intelligence ACALCI, First Australasian Conference, Newcastle, NSW, Australia, February 5-7 2015, Proceedings, Lecture Notes in Computer Science, Vol. 8955, 2015 © Springer International Publishing Switzerland 2015 Final, published version of this paper is available online via doi: 10.1007/978-3-319-14803-8_2For natural and artificial systems with some symmetry structure, computational understanding and manipulation can be achieved without learning by exploiting the algebraic structure. This algebraic coordinatization is based on a hierarchical (de)composition method. Here we describe this method and apply it to permutation puzzles. Coordinatization yields a structural understanding, not just solutions for the puzzles. In the case of the Rubik’s Cubes, different solving strategies correspond to different decompositions

Symmetries of automata

For a given reachable automaton A, we prove that the (state-) endomorphism monoid End(A) divides its characteristic monoid M(A). Hence so does its (state-)automorphism group Aut(A), and, for finite A, Aut(A) is a homomorphic image of a subgroup of the characteristic monoid. It follows that in the presence of a (state-) automorphism group G of A, a finite automaton A (and its transformation monoid) always has a decomposition as a divisor of the wreath product of two transformation semigroups whose semigroups are divisors of M(A), namely the symmetry group G and the quotient of M(A) induced by the action of G. Moreover, this division is an embedding if M(A) is transitive on states of A. For more general automorphisms, which may be non-trivial on input letters, counterexamples show that they need not be induced by any corresponding characteristic monoid element

A path-deformation framework for determining weighted genome rearrangement distance

Measuring the distance between two bacterial genomes under the inversion process is usually done by assuming all inversions to occur with equal probability. Recently, an approach to calculating inversion distance using group theory was introduced, and is effective for the model in which only very short inversions occur. In this paper, we show how to use the group-theoretic framework to establish minimal distance for any weighting on the set of inversions, generalizing previous approaches. To do this we use the theory of rewriting systems for groups, and exploit the Knuth--Bendix algorithm, the first time this theory has been introduced into genome rearrangement problems. The central idea of the approach is to use existing group theoretic methods to find an initial path between two genomes in genome space (for instance using only short inversions), and then to deform this path to optimality using a confluent system of rewriting rules generated by the Knuth--Bendix algorithm

Sorting signed circular permutations by super short reversals

We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works.We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version rema9096272283FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2013/08293-72014/04718-6306730/2012-0; 477692/2012-5; 483370/2013-411th International Symposium on Bioinformatics Research and Application

Sorting Signed Circular Permutations by Super Short Reversals

International audienceWe consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works