56 research outputs found
Sorting by Prefix Block-Interchanges
We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation using as few such operations as possible. We give a 2-approximation algorithm for this problem, show how to obtain improved lower and upper bounds on the corresponding distance, and determine the largest possible value for that distance
Lower bounding edit distances between permutations
International audienceA number of fields, including the study of genome rearrangements and the design of interconnection networks, deal with the connected problems of sorting permutations in "as few moves as possible", using a given set of allowed operations, or computing the number of moves the sorting process requires, often referred to as the distance of the permutation. These operations often act on just one or two segments of the permutation, e.g. by reversing one segment or exchanging two segments. The cycle graph of the permutation to sort is a fundamental tool in the theory of genome rearrangements, and has proved useful in settling the complexity of many variants of the above problems. In this paper, we present an algebraic reinterpretation of the cycle graph of a permutation π as an even permutation π, and show how to reformulate our sorting problems in terms of particular factorisations of the latter permutation. Using our framework, we recover known results in a simple and unified way, and obtain a new lower bound on the prefix transposition distance (where a prefix transposition displaces the initial segment of a permutation), which is shown to outperform previous results. Moreover, we use our approach to improve the best known lower bound on the prefix transposition diameter from 2n/3 to ⌊3n/4⌋, and investigate a few relations between some statistics on π and π
Merging partially labelled trees: hardness and a declarative programming solution
International audienceIntraspecific studies often make use of haplotype networks instead of gene genealogies to represent the evolution of a set of genes. Cassens et al. proposed one such network reconstruction method, based on the global maximum parsimony principle, which was later recast by the first author of the present work as the problem of finding a minimum common supergraph of a set of t partially labelled trees. Although algorithms were proposed for solving the problem on two graphs, the complexity of the general problem remains unknown. In this paper, we show that the corresponding decision problem is NP-complete for t = 3. We then propose a declarative programming approach to solving the problem to optimality in practice, as well as a heuristic approach, both based on the IDP system, and assess the performance of both methods on randomly generated data
Decomposing Cubic Graphs into Connected Subgraphs of Size Three
Let be the set of connected graphs of size 3. We
study the problem of partitioning the edge set of a graph into graphs taken
from any non-empty . The problem is known to be NP-complete for
any possible choice of in general graphs. In this paper, we assume that
the input graph is cubic, and study the computational complexity of the problem
of partitioning its edge set for any choice of . We identify all polynomial
and NP-complete problems in that setting, and give graph-theoretic
characterisations of -decomposable cubic graphs in some cases.Comment: to appear in the proceedings of COCOON 201
The distribution of cycles in breakpoint graphs of signed permutations
Breakpoint graphs are ubiquitous structures in the field of genome
rearrangements. Their cycle decomposition has proved useful in computing and
bounding many measures of (dis)similarity between genomes, and studying the
distribution of those cycles is therefore critical to gaining insight on the
distributions of the genomic distances that rely on it. We extend here the work
initiated by Doignon and Labarre, who enumerated unsigned permutations whose
breakpoint graph contains cycles, to signed permutations, and prove
explicit formulas for computing the expected value and the variance of the
corresponding distributions, both in the unsigned case and in the signed case.
We also compare these distributions to those of several well-studied distances,
emphasising the cases where approximations obtained in this way stand out.
Finally, we show how our results can be used to derive simpler proofs of other
previously known results
Polynomial-time sortable stacks of burnt pancakes
Pancake flipping, a famous open problem in computer science, can be
formalised as the problem of sorting a permutation of positive integers using
as few prefix reversals as possible. In that context, a prefix reversal of
length k reverses the order of the first k elements of the permutation. The
burnt variant of pancake flipping involves permutations of signed integers, and
reversals in that case not only reverse the order of elements but also invert
their signs. Although three decades have now passed since the first works on
these problems, neither their computational complexity nor the maximal number
of prefix reversals needed to sort a permutation is yet known. In this work, we
prove a new lower bound for sorting burnt pancakes, and show that an important
class of permutations, known as "simple permutations", can be optimally sorted
in polynomial time.Comment: Accepted pending minor revisio
Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time
International audienceA phylogenetic network is a rooted acyclic digraph whose leaves are labeled with a set of taxa. The tree containment problem is a fundamental problem arising from model validation in the study of phylogenetic networks. It asks to determine whether or not a given network displays a given phylogenetic tree over the same leaf set. It is known to be NP-complete in general. Whether or not it remains NP-complete for stable networks is an open problem. We make progress towards answering that question by presenting a quadratic time algorithm to solve the tree containment problem for a new class of networks that we call genetically stable networks, which include tree-child networks and comprise a subclass of stable networks
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