Pattern Formation on Trees

Networks having the geometry and the connectivity of trees are considered as the spatial support of spatiotemporal dynamical processes. A tree is characterized by two parameters: its ramification and its depth. The local dynamics at the nodes of a tree is described by a nonlinear map, given rise to a coupled map lattice system. The coupling is expressed by a matrix whose eigenvectors constitute a basis on which spatial patterns on trees can be expressed by linear combination. The spectrum of eigenvalues of the coupling matrix exhibit a nonuniform distribution which manifest itself in the bifurcation structure of the spatially synchronized modes. These models may describe reaction-diffusion processes and several other phenomena occurring on heterogeneous media with hierarchical structure.Comment: Submitted to Phys. Rev. E, 15 pages, 9 fig

Non-Contiguous Pattern Avoidance in Binary Trees

In this paper we consider the enumeration of binary trees avoiding non-contiguous binary tree patterns. We begin by computing closed formulas for the number of trees avoiding a single binary tree pattern with 4 or fewer leaves and compare these results to analogous work for contiguous tree patterns. Next, we give an explicit generating function that counts binary trees avoiding a single non-contiguous tree pattern according to number of leaves. In addition, we enumerate binary trees that simultaneously avoid more than one tree pattern. Finally, we explore connections between pattern-avoiding trees and pattern-avoiding permutations.Comment: 21 pages, 2 figures, 1 tabl

Pattern avoidance in binary trees

This paper considers the enumeration of trees avoiding a contiguous pattern. We provide an algorithm for computing the generating function that counts n-leaf binary trees avoiding a given binary tree pattern t. Equipped with this counting mechanism, we study the analogue of Wilf equivalence in which two tree patterns are equivalent if the respective n-leaf trees that avoid them are equinumerous. We investigate the equivalence classes combinatorially. Toward establishing bijective proofs of tree pattern equivalence, we develop a general method of restructuring trees that conjecturally succeeds to produce an explicit bijection for each pair of equivalent tree patterns.Comment: 19 pages, many images; published versio

Pattern avoidance in labelled trees

We discuss a new notion of pattern avoidance motivated by the operad theory: pattern avoidance in planar labelled trees. It is a generalisation of various types of consecutive pattern avoidance studied before: consecutive patterns in words, permutations, coloured permutations etc. The notion of Wilf equivalence for patterns in permutations admits a straightforward generalisation for (sets of) tree patterns; we describe classes for trees with small numbers of leaves, and give several bijections between trees avoiding pattern sets from the same class. We also explain a few general results for tree pattern avoidance, both for the exact and the asymptotic enumeration.Comment: 27 pages, corrected various misprints, added an appendix explaining the operadic contex

Linear pattern matching on sparse suffix trees

Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse suffix tree} \cite{KU-96} with appropriately defined suffix links. Assuming, under the standard unit-cost RAM model, that a word can store up to $\log_{\sigma}n$ characters ($\sigma$ the alphabet size), our index takes $O(n/\log_{\sigma}n)$ space, i.e. the same space as the packed string itself. The resulting pattern matching algorithm runs in time $O(m+r^2+r\cdot occ)$, where $m$ is the length of the pattern, $r$ is the actual number of characters stored in a word and $occ$ is the number of pattern occurrences

On the sub-permutations of pattern avoiding permutations

There is a deep connection between permutations and trees. Certain sub-structures of permutations, called sub-permutations, bijectively map to sub-trees of binary increasing trees. This opens a powerful tool set to study enumerative and probabilistic properties of sub-permutations and to investigate the relationships between 'local' and 'global' features using the concept of pattern avoidance. First, given a pattern {\mu}, we study how the avoidance of {\mu} in a permutation {\pi} affects the presence of other patterns in the sub-permutations of {\pi}. More precisely, considering patterns of length 3, we solve instances of the following problem: given a class of permutations K and a pattern {\mu}, we ask for the number of permutations $\pi \in Av_n(\mu)$ whose sub-permutations in K satisfy certain additional constraints on their size. Second, we study the probability for a generic pattern to be contained in a random permutation {\pi} of size n without being present in the sub-permutations of {\pi} generated by the entry $1 \leq k \leq n$. These theoretical results can be useful to define efficient randomized pattern-search procedures based on classical algorithms of pattern-recognition, while the general problem of pattern-search is NP-complete

Order preserving pattern matching on trees and DAGs

The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem where a set of text strings is given as a tree or a DAG. We show that the OPPM problem for a single pattern $p$ of length $m$ and a text tree $T$ of size $N$ can be solved in $O(m+N)$ time if the characters of $p$ are drawn from an integer alphabet of polynomial size. The time complexity becomes $O(m \log m + N)$ if the pattern $p$ is over a general ordered alphabet. We then show that the OPPM problem for a single pattern and a text DAG is NP-complete

Pattern-based phylogenetic distance estimation and tree reconstruction

We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a dataset of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods on this dataset. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.Comment: 21 pages, 3 figures, 2 table

Generating trees and pattern avoidance in alternating permutations

We extend earlier work of the same author to enumerate alternating permutations avoiding the permutation pattern 2143. We use a generating tree approach to construct a recursive bijection between the set A_{2n}(2143) of alternating permutations of length 2n avoiding 2143 and standard Young tableaux of shape (n, n, n) and between the set A_{2n + 1}(2143) of alternating permutations of length 2n + 1 avoiding 2143 and shifted standard Young tableaux of shape (n + 2, n + 1, n). We also give a number of conjectures and open questions on pattern avoidance in alternating permutations and generalizations thereof.Comment: 21 pages. To be presented at FPSAC 2010. Comments welcome