The rotation graph of binary trees is Hamiltonian

In this paper we study the rotation transformation on binary trees and consider the properties of binary trees under this operation. The rotation is the universal primitive used to rebalance dynamic binary search trees. New binary search tree algorithms have recently been introduced by Sleator and Tarjan. It has been conjectured that these algorithms are as efficient as any algorithm that dynamically restructures the tree using rotations. We hope that by studying rotations in binary trees we shall gain a better understanding of the nature of binary search trees, which in turn will lead to a proof of this “dynamic optimality conjecture”. We define a graph, RG(n), whose vertex set consists of all binary trees containing n nodes, and which has an edge between two trees if they differ by only one rotation. We shall introduce a new characterization of the structure of RG(n) and use it to demonstrate the existence of a Hamiltonian cycle in the graph. The proof is constructive and can be used to enumerate all binary trees with n nodes in constant time per tree.     

On Rotations and the Generation of Binary Trees

The rotation graph, G_n, has vertex set consisting of all binary trees with n nodes. Two vertices are connected by an edge if a single rotation will transform one tree into the other. We provide a simpler proof of a result of Lucas that G_n, contains a Hamilton path. Our proof deals directly with the pointer representation of the binary tree. This proof provides the basis of an algorithm for generating all binary trees that can be implemented to run on a pointer machine and to use only constant time between the output of successive trees. Ranking and unranking algorithms are developed for the ordering of binary trees implied by the generation algorithm. These algorithms have time complexity O(n²) (arithmetic operations). We also show strong relationships amongst various representations of binary trees and amongst binary tree generation algorithms that have recently appeared in the literature.     

A note on the cubical dimension of new classes of binary trees

The cubical dimension of a graph G is the smallest dimension of a hypercube into which G is embeddable as a subgraph. The conjecture of Havel (1984) claims that the cubical dimension of every balanced binary tree with 2 ⁿ vertices, n ? 1, is n. The 2-rooted complete binary tree of depth n is obtained from two copies of the complete binary tree of depth n by adding an edge linking their respective roots. In this paper, we determine the cubical dimension of trees obtained by subdividing twice a 2-rooted complete binary tree and prove that every such balanced tree satisfies the conjecture of Havel.     

Evolutionary trees and the Ising model on the Bethe lattice: a proof of Steel��s conjecture

A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct the leaf-labelled tree. It is well known that in order to reconstruct a tree on n leaves, sample sequences of length ??(log n) are needed. It was conjectured by Steel that for the CFN/Ising evolutionary model, if the mutation probability on all edges of the tree is less than ${p^{\ast} = (\sqrt{2}-1)/2^{3/2}}$ , then the tree can be recovered from sequences of length O(log n). The value p* is given by the transition point for the extremality of the free Gibbs measure for the Ising model on the binary tree. Steel??s conjecture was proven by the second author in the special case where the tree is ??balanced.?? The second author also proved that if all edges have mutation probability larger than p* then the length needed is n ^??(1). Here we show that Steel??s conjecture holds true for general trees by giving a reconstruction algorithm that recovers the tree from O(log n)-length sequences when the mutation probabilities are discretized and less than p*. Our proof and results demonstrate that extremality of the free Gibbs measure on the infinite binary tree, which has been studied before in probability, statistical physics and computer science, determines how distinguishable are Gibbs measures on finite binary trees.     

Twist–Rotation Transformations of Binary Trees and Arithmetic Expressions

The paper studies the computational complexity and efficient algorithms for the twist–rotation transformations of binary trees, which is equivalent to the transformation of arithmetic expressions over an associative and commutative binary operation. The main results are (1) a full binary tree with n labeled leaves can be transformed into any other in at most 3n log n + 2n twist and rotation operations, (2) deciding the twist–rotation distance between two binary trees is NP-complete, and (3) the twist–rotation transformation can be approximated with ratio 6 log n + 4 in polynomial time for full binary trees with n uniquely labeled leaves.     

Patterns in random binary search trees

In a randomly grown binary search tree (BST) of size n, any fixed pattern occurs with a frequency that is on average proportional to n. Deviations from the average case are highly unlikely and well quantified by a Gaussian law. Trees with forbidden patterns occur with an exponentially small probability that is characterized in terms of Bessel functions. The results obtained extend to BSTs a type of property otherwise known for strings and combinatorial tree models. They apply to paged trees or to quicksort with halting on short subfiles. As a consequence, various pointer saving strategies for maintaining trees obeying the random BST model can be precisely quantified. The methods used are based on analytic models, especially bivariate generating function subjected to singularity perturbation asymptotics. © 1997 John Wiley & Sons, Inc. Random Struct. Alg., 11 : 223–244, 1997     

On the distribution of distances between specified nodes in increasing trees

We study the quantity distance between nodejand nodenin a random tree of sizen chosen from a family of increasing trees. For those subclass of increasing tree families, which can be constructed via a tree evolution process, we give closed formulæ for the probability distribution, the expectation and the variance. Furthermore we derive a distributional decomposition of the random variable considered and we show a central limit theorem of this quantity, for arbitrary labels 1≤j<n and n→∞.Such tree models are of particular interest in applications, e.g., the widely used models of recursive trees, plane-oriented recursive trees and binary increasing trees are special instances and are thus covered by our results.     

Limiting Distributions for the Number of Inversions in Labelled Tree Families

We consider the so-called simple families of labelled trees, which contain, e.g., ordered, unordered, binary, and cyclic labelled trees as special instances, and study the global and local behaviour of the number of inversions. In particular, we obtain limiting distribution results for the total number of inversions as well as the number of inversions induced by the node labelled j in a random tree of size n.     

Boxicity of Leaf Powers

The boxicity of a graph G, denoted as boxi(G), is defined as the minimum integer t such that G is an intersection graph of axis-parallel t-dimensional boxes. A graph G is a k-leaf power if there exists a tree T such that the leaves of the tree correspond to the vertices of G and two vertices in G are adjacent if and only if their corresponding leaves in T are at a distance of at most k. Leaf powers are used in the construction of phylogenetic trees in evolutionary biology and have been studied in many recent papers. We show that for a k-leaf power G, boxi(G)??? k?1. We also show the tightness of this bound by constructing a k-leaf power with boxicity equal to k?1. This result implies that there exist strongly chordal graphs with arbitrarily high boxicity which is somewhat counterintuitive.     

On the degree distribution of the nodes in increasing trees

Simple families of increasing trees can be constructed from simply generated tree families, if one considers for every tree of size n all its increasing labellings, i.e., labellings of the nodes by distinct integers of the set {1,…,n} in such a way that each sequence of labels along any branch starting at the root is increasing. Three such tree families are of particular interest: recursive trees, plane-oriented recursive trees and binary increasing trees. We study the quantity degree of node j in a random tree of size n and give closed formulae for the probability distribution and all factorial moments for those subclass of tree families, which can be constructed via a tree evolution process. Furthermore limiting distribution results of this parameter are given, which completely characterize the phase change behavior depending on the growth of j compared to n.     

Invariant subsets of scattered trees and the tree alternative property of Bonato and Tardif

A tree is scattered if it does not contain a subdivision of the complete binary tree as a subtree. We show that every scattered tree contains a vertex, an edge, or a set of at most two ends preserved by every embedding of T. This extends results of Halin, Polat and Sabidussi. Calling two trees equimorphic if each embeds in the other, we then prove that either every tree that is equimorphic to a scattered tree T is isomorphic to T, or there are infinitely many pairwise non-isomorphic trees which are equimorphic to T. This proves the tree alternative conjecture of Bonato and Tardif for scattered trees, and a conjecture of Tyomkyn for locally finite scattered trees.     

A forbidden induced subgraph characterization of distance-hereditary 5-leaf powers

A graph G is a k-leaf power if there is a tree T such that the vertices of G are the leaves of T and two vertices are adjacent in G if and only if their distance in T is at most k. In this situation T is called a k-leaf root of G. Motivated by the search for underlying phylogenetic trees, the notion of a k-leaf power was introduced and studied by Nishimura, Ragde and Thilikos and subsequently in various other papers. While the structure of 3- and 4-leaf powers is well understood, for k≥5 the characterization of k-leaf powers remains a challenging open problem.In the present paper, we give a forbidden induced subgraph characterization of distance-hereditary 5-leaf powers. Our result generalizes known characterization results on 3-leaf powers since these are distance-hereditary 5-leaf powers.     

Slim sets of binary trees

A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree T that contains all information of a given collection P of phylogenetic trees. If the answer is “yes” we say that P is compatible and T displays P. This decision problem is NP-complete even if all input trees are quartets, that is binary trees with exactly four leaves. In this paper, we prove a sufficient condition for a set of binary phylogenetic trees to be compatible. That result is used to give a short and self-contained proof of the known characterization of quartet sets of minimal cardinality which are displayed by a unique phylogenetic tree.     

On multiple pattern avoiding set partitions

We study classes of set partitions determined by the avoidance of multiple patterns, applying a natural notion of partition containment that has been introduced by Sagan. We say that two sets S and T of patterns are equivalent if for each n the number of partitions of size n avoiding all the members of S is the same as the number of those that avoid all the members of T.     

Analysis of three graph parameters for random trees

We consider three basic graph parameters, the node‐independence number, the path node‐covering number, and the size of the kernel, and study their distributional behavior for an important class of random tree models, namely the class of simply generated trees, which contains, e.g., binary trees, rooted labeled trees, and planted plane trees, as special instances. We can show for simply generated tree families that the mean and the variance of each of the three parameters under consideration behave for a randomly chosen tree of size n asymptotically ～μn and ～νn, where the constants μ and ν depend on the tree family and the parameter studied. Furthermore we show for all parameters, suitably normalized, convergence in distribution to a Gaussian distributed random variable. © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2009     

A new constrained edit distance between quotiented ordered trees

In this paper we propose a dynamic programming algorithm to compare two quotiented ordered trees using a constrained edit distance. An ordered tree is a tree in which the left-to-right order among siblings is significant. A quotiented ordered tree is an ordered tree T with an equivalence relation on vertices and such that, when the equivalence classes are collapsed to super-nodes, the graph so obtained is an ordered tree as well. Based on an algorithm proposed by Zhang and Shasha [K. Zhang, D. Shasha, Simple fast algorithms for the editing distance between trees and related problems, SIAM Journal on Computing 18 (6) (1989) 1245–1262] and introducing new notations, we describe a tree edit distance between quotiented ordered trees preserving equivalence relations on vertices during computation which works in polynomial time. Its application to RNA secondary structures comparison is finally presented.     

Rooted directed path graphs are leaf powers

Leaf powers are a graph class which has been introduced to model the problem of reconstructing phylogenetic trees. A graph G=(V,E) is called k-leaf power if it admits a k-leaf root, i.e., a tree T with leaves V such that uv is an edge in G if and only if the distance between u and v in T is at most k. Moroever, a graph is simply called leaf power if it is a k-leaf power for some k∈N. This paper characterizes leaf powers in terms of their relation to several other known graph classes. It also addresses the problem of deciding whether a given graph is a k-leaf power.We show that the class of leaf powers coincides with fixed tolerance NeST graphs, a well-known graph class with absolutely different motivations. After this, we provide the largest currently known proper subclass of leaf powers, i.e, the class of rooted directed path graphs.Subsequently, we study the leaf rank problem, the algorithmic challenge of determining the minimum k for which a given graph is a k-leaf power. Firstly, we give a lower bound on the leaf rank of a graph in terms of the complexity of its separators. Secondly, we use this measure to show that the leaf rank is unbounded on both the class of ptolemaic and the class of unit interval graphs. Finally, we provide efficient algorithms to compute 2|V|-leaf roots for given ptolemaic or (unit) interval graphs G=(V,E).     

Tree-edges deletion problems with bounded diameter obstruction sets

We study the following problem: given a tree G and a finite set of trees H, find a subset O of the edges of G such that G-O does not contain a subtree isomorphic to a tree from H, and O has minimum cardinality. We give sharp boundaries on the tractability of this problem: the problem is polynomial when all the trees in H have diameter at most 5, while it is NP-hard when all the trees in H have diameter at most 6. We also show that the problem is polynomial when every tree in H has at most one vertex with degree more than 2, while it is NP-hard when the trees in H can have two such vertices.The polynomial-time algorithms use a variation of a known technique for solving graph problems. While the standard technique is based on defining an equivalence relation on graphs, we define a quasiorder. This new variation might be useful for giving more efficient algorithm for other graph problems.     

Some remarks about leaf roots

Nishimura et al. [On graph powers for leaf-labeled trees, J. Algorithms 42 (2002) 69-108] define a k-leaf root of a graph G=(V_G,E_G) as a tree T=(V_T,E_T) such that the vertices of G are exactly the leaves of T and two vertices in V_G are adjacent in G if and only if their distance in T is at most k. Solving a problem posed by Niedermeier [Personal communication, May 2004] we give a structural characterization of the graphs that have a 4-leaf root. Furthermore, we show that the graphs that have a 3-leaf root are essentially the trees, which simplifies a characterization due to Dom et al. [Error compensation in leaf power problems, Algorithmica 44 (2006) 363-381. (A preliminary version appeared under the title “Error compensation in leaf root problems”, in: Proceedings of the 15th Annual International Symposium on Algorithms and Computation (ISAAC 2004), Lecture Notes in Computer Science, vol. 3341, pp. 389-401)] and also a related recognition algorithm due to Nishimura et al. [On graph powers for leaf-labeled trees, J. Algorithms 42 (2002) 69-108].