88 research outputs found
Local Similarity Between Quotiented Ordered Trees
International audienceIn this paper we propose a dynamic programming algorithm to evaluate local similarity between ordered quotiented trees using a constrained edit scoring scheme. A quotiented tree is a tree defined with an additional equivalent relation on vertices and such that the quotient graph is also a tree. The core of the method relies on two adaptations of an algorithm proposed by Zhang et al. [K. Zhang, D. Shasha, Simple fast algorithms for the editing distance between trees and related problems (1989) 1245-1262] for comparing ordered rooted trees. After some preliminary definitions and the description of this tree edit algorithm, we propose extensions to globally and locally compare two quotiented trees. This last method allows to find the region in each tree with the highest similarity. Algorithms are currently being used in genomic analysis to evaluate variability between RNA secondary structures
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets
A multiple layer model to compare RNA secondary structures
International audienceWe formally introduce a new data structure, called MiGaL for ``Multiple Graph Layers'', that is composed of various graphs linked together by relations of abstraction/refinement. The new structure is useful for representing information that can be described at different levels of abstraction, each level corresponding to a graph. We then propose an algorithm for comparing two MiGaLs. The algorithm performs a step-by-step comparison starting with the most ``abstract'' level. The result of the comparison at a given step is communicated to the next step using a special colouring scheme. MiGaLs represent a very natural model for comparing RNA secondary structures that may be seen at different levels of detail, going from the sequence of nucleotides, single or paired with another to participate in a helix, to the network of multiple loops that is believed to represent the most conserved part of RNAs having similar function. We therefore show how to use MiGaLs to very efficiently compare two RNAs of any size at different levels of detail
Ackermann Encoding, Bisimulations, and OBDDs
We propose an alternative way to represent graphs via OBDDs based on the
observation that a partition of the graph nodes allows sharing among the
employed OBDDs. In the second part of the paper we present a method to compute
at the same time the quotient w.r.t. the maximum bisimulation and the OBDD
representation of a given graph. The proposed computation is based on an
OBDD-rewriting of the notion of Ackermann encoding of hereditarily finite sets
into natural numbers.Comment: To appear on 'Theory and Practice of Logic Programming
A constrained edit distance algorithm between semi-ordered trees
AbstractIn this paper, we propose a formal definition of a new class of trees called semi-ordered trees and a polynomial dynamic programming algorithm to compute a constrained edit distance between such trees. The core of the method relies on a similar approach to compare unordered [Kaizhong Zhang, A constrained edit distance between unordered labeled trees, Algorithmica 15 (1996) 205â222] and ordered trees [Kaizhong Zhang, Algorithms for the constrained editing distance between ordered labeled trees and related problems, Pattern Recognition 28 (3) (1995) 463â474]. The method is currently applied to evaluate the similarity between architectures of apple trees [Vincent Segura, Aida Ouangraoua, Pascal Ferraro, Evelyne Costes, Comparison of tree architecture using tree edit distances: Application to two-year-old apple tree, Euphytica 161 (2007) 155â164]
Quantifying the degree of self-nestedness of trees. Application to the structural analysis of plants
17 pagesInternational audienceIn this paper we are interested in the problem of approximating trees by trees with a particular self-nested structure. Self-nested trees are such that all their subtrees of a given height are isomorphic. We show that these trees present remarkable compression properties, with high compression rates. In order to measure how far a tree is from being a self-nested tree, we then study how to quantify the degree of self-nestedness of any tree. For this, we deïŹne a measure of the self-nestedness of a tree by constructing a self-nested tree that minimizes the distance of the original tree to the set of self-nested trees that embed the initial tree. We show that this measure can be computed in polynomial time and depict the corresponding algorithm. The distance to this nearest embedding self-nested tree (NEST) is then used to deïŹne compression coefïŹcients that reïŹect the compressibility of a tree. To illustrate this approach, we then apply these notions to the analysis of plant branching structures. Based on a database of simulated theoretical plants in which different levels of noise have been introduced, we evaluate the method and show that the NESTs of such branching structures restore partly or completely the original, noiseless, branching structures. The whole approach is then applied to the analysis of a real plant (a rice panicle) whose topological structure was completely measured. We show that the NEST of this plant may be interpreted in biological terms and may be used to reveal important aspects of the plant growth
Polynomial functors and combinatorial Dyson-Schwinger equations
We present a general abstract framework for combinatorial Dyson-Schwinger
equations, in which combinatorial identities are lifted to explicit bijections
of sets, and more generally equivalences of groupoids. Key features of
combinatorial Dyson-Schwinger equations are revealed to follow from general
categorical constructions and universal properties. Rather than beginning with
an equation inside a given Hopf algebra and referring to given Hochschild
-cocycles, our starting point is an abstract fixpoint equation in groupoids,
shown canonically to generate all the algebraic structure. Precisely, for any
finitary polynomial endofunctor defined over groupoids, the system of
combinatorial Dyson-Schwinger equations has a universal solution,
namely the groupoid of -trees. The isoclasses of -trees generate
naturally a Connes-Kreimer-like bialgebra, in which the abstract
Dyson-Schwinger equation can be internalised in terms of canonical
-operators. The solution to this equation is a series (the Green function)
which always enjoys a Fa\`a di Bruno formula, and hence generates a
sub-bialgebra isomorphic to the Fa\`a di Bruno bialgebra. Varying yields
different bialgebras, and cartesian natural transformations between various
yield bialgebra homomorphisms and sub-bialgebras, corresponding for example to
truncation of Dyson-Schwinger equations. Finally, all constructions can be
pushed inside the classical Connes-Kreimer Hopf algebra of trees by the
operation of taking core of -trees. A byproduct of the theory is an
interpretation of combinatorial Green functions as inductive data types in the
sense of Martin-L\"of Type Theory (expounded elsewhere).Comment: v4: minor adjustments, 49pp, final version to appear in J. Math. Phy
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