On subtrees of trees

On [formula omitted]-span and [formula omitted]-span of trees and full binary trees

This paper considers partitioning the vertices of an n-vertex tree into p disjoint sets C1, C2, . . . , Cp, called clusters so that the number of vertices in a cluster and the number of subtrees in a cluster are minimized. For this NP-hard problem we present greedy heuristics which differ in (i) how subtrees are identified (using either a best-fit, good-fit, or first-fit selection criteria), (ii) whether clusters are filled one at a time or simultaneously, and (iii) how much cluster sizes can differ from the ideal size of c vertices per cluster, n = cp. The last criteria is controlled by a constant α, 0 ≤ α < 1, such that cluster Ci satisfies (1− α2 )c ≤ |Ci| ≤ c(1 + α), 1 ≤ i ≤ p. For algorithms resulting from combinations of these criteria we develop worst-case bounds on the number of subtrees in a cluster in terms of c, α, and the maximum degree of a vertex. We present experimental results which give insight into how parameters c, α, and the maximum degree of a vertex impact the number of subtrees and the cluster sizes. Communicated by G. Liotta: submitted November 1999, revised August 2000. 1. Hambrusch’s research supported in part by the National Science Foundation under Grant 9988339-CCR. 2. Lim’s research supported in part by Korea Science and Engineering Foundation under Contract No. 98-0102-07-01-3. S. E. Hambrusch et al., Clustering in Trees, JGAA, 4(4) 1–26 (2000) 2

ABSTRACTThe number of subtrees in a graph is related to the reliability of a network with possible vertex failure and edge failure. It is known that networks with larger number of subtrees would be more reliable. Therefore, for given families of graphs, determining the graphs with maximum number of subtrees within the family becomes important. For a tree T of n vertices, let denote the number of all subtrees in T. Yan and Yeh gave a linear-time algorithm to count the number of subtrees in T and determined the tree of diameter d and order n with the maximum number of subtrees. In this paper, we present two recursive relations to count the number of subtrees of trees. We also characterize all trees of n vertices with.

Slim sets of binary trees

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the character which maximizes this difference. Here we show that computation of MP distance on two binary phylogenetic trees is NP-hard. This is a highly nontrivial extension of an earlier NP-hardness proof for two multifurcating phylogenetic trees, and it is particularly relevant given the prominence of binary trees in the phylogenetics literature. As a corollary to the main hardness result we show that computation of MP distance is also hard on binary trees if the number of states available is bounded. In fact, via a different reduction we show that it is hard even if only two states are available. Finally, as a first response to this hardness we give a simple Integer Linear Program (ILP) formulation which is capable of computing the MP distance exactly for small trees (and for larger trees when only a small number of character states are available) and which is used to computationally verify several auxiliary results required by the hardness proofs.

The greedy tree $\mathcal{G}(D)$ and the $\mathcal{M}$-tree $\mathcal{M}(D)$ are known to be extremal among trees with degree sequence $D$ with respect to various graph invariants. This paper provides a general theorem that covers a large family of invariants for which $\mathcal{G}(D)$ or $\mathcal{M}(D)$ is extremal. Many known results, for example on the Wiener index, the number of subtrees, the number of independent subsets and the number of matchings follow as corollaries, as do some new results on invariants such as the number of rooted spanning forests, the incidence energy and the solvability. We also extend our results on trees with fixed degree sequence $D$ to the set of trees whose degree sequence is majorised by a given sequence $D$, which also has a number of applications.

In this paper we present with algebraic trees a novel notion of (continuum) trees which generalizes countable graph-theoretic trees to (potentially) uncountable structures. For that purpose we focus on the tree structure given by the branch point map which assigns to each triple of points their branch point. We give an axiomatic definition of algebraic trees, define a natural topology, and equip them with a probability measure on the Borel-$\sigma$-field.Under an order-separability condition, algebraic (measure) trees can be considered as tree structure equivalence classes of metric (measure) trees (i.e.\ subtrees of R-trees). Using Gromov-weak convergence (i.e.\ sample distance convergence) of the particular representatives given by the metric arising from the distribution of branch points, we define a metrizable topology on the space of equivalence classes of algebraic measure trees. In many applications, binary trees are of particular interest. We introduce on that subspace with the sample shape and the sample subtree mass convergence two additional, natural topologies. Relying on the connection to triangulations of the circle, we show that all three topologies are actually the same, and the space of binary algebraic measure trees is compact. To this end, we provide a formal definition of triangulations of the circle, and show that the coding map which sends a triangulation to an algebraic measure tree is a continuous surjection onto the subspace of binary algebraic non-atomic measure trees.

In this paper we consider the class of binary trees and present the results of a comprehensive experimental study on the four most representative algorithms for drawing trees, one for each of the following treedrawing approaches: Separation-Based, Path-based, Level-based, and Ringed Circular Layout. We establish a simpler, more intuitive format for storing binary trees in files and create a large suite of randomlygenerated, unbalanced, complete, AVL, Fibonacci, and molecular combinatory binary trees of various sizes. Our study is therefore conducted on randomly-generated, unbalanced, and AVL binary trees with between 100 and 50, 000 nodes, on Fibonacci trees Tn for n = 1, 2, ..., 45, 46 (143 to 46, 367 nodes), on complete binary trees of size 2−1 for n = 7, 8, ..., 15, 16 (127 to 65, 535 nodes), and on molecular combinatory binary trees with between 133 and 50, 005 nodes. Our study yields 70 charts comparing the performance of the drawing algorithms with respect to ten quality measures, namely Area, Aspect Ratio, Size, Total Edge Length, Average Edge Length, Maximum Edge Length, Uniform Edge Length, Angular Resolution, Closest Leaf, and Farthest Leaf. None of the algorithms has been found to be the best in all categories. This observation leads us to create an adaptive system that determines the type of a binary tree and then selects an algorithm to draw the tree depending upon the specified quality measures. Currently, our adaptive tree drawing system recognizes all six types of binary trees and all ten measures included in our experimental study. Under our settings, our adaptive tree drawing system outperforms any system using a single binary tree drawing algorithm. Submitted: April 2007 Reviewed: June 2007 Revised: August 2007 Accepted: October 2007 Final: November 2007 Published: June 2008 Article type: Regular Paper Communicated by: S. Kobourov E-mail addresses: rusu@rowan.edu (Adrian Rusu) santia09@students.rowan.edu (Confesor Santiago) 132 Rusu & Santiago Grid Drawings of Binary Trees

Based on the observation that a single mutational event can delete or insert multiple residues, affine gap costs for sequence alignment charge a penalty for the existence of a gap, and a further length-dependent penalty. From structural or multiple alignments of distantly related proteins, it has been observed that conserved residues frequently fall into ungapped blocks separated by relatively nonconserved regions. To take advantage of this structure, a simple generalization of affine gap costs is proposed that allows nonconserved regions to be effectively ignored. The distribution of scores from local alignments using these generalized gap costs is shown empirically to follow an extreme value distribution. Examples are presented for which generalized affine gap costs yield superior alignments from the standpoints both of statistical significance and of alignment accuracy. Guidelines for selecting generalized affine gap costs are discussed, as is their possible application to multiple alignment. Proteins 32:88–96, 1998. Published 1998 Wiley-Liss, Inc.1 This article is a US government work and, as such, is in the public domain in the United States of America.

The authors propose a VLSI layout strategy for a full binary tree. This layout can support more border leaf processing elements (PEs) and thus can give a higher I-O bandwidth. It is superior to the H-tree layout in terms of the number of boundary leaves. The approach uses H-tree pattern for constructing subtree layouts and then combines a number of such subtrees following standard tree style to get a larger sized tree layout. Finally at the top level H-tree layout style is used to get the overall tree layout. Different I/O bandwidths can be obtained varying the subtree height. The authors derive expression for layout area, longest link and aspect ratio of the chip. It is observed that I/O bandwidth can be significantly increased without much area overhead using this approach. >

Multiple sequence alignment (MSA) is a problem in computational biology with the goal to discover similarities between DNA or protein sequences. One problem in larger instances is that the search exhausts main memory. This paper applies disk-based heuristic search to solve MSA benchmarks. We extend iterative-deepening dynamic programming, a hybrid of dynamic programming and IDA*, for which optimal alignments with respect to similarity metrics and affine gap cost are computed. We achieve considerable savings of main memory with an acceptable time overhead. By scaling buffer sizes, the space-time trade-off can be adapted to existing resources.KeywordsDynamic ProgrammingMultiple Sequence AlignmentMain MemoryTraversal SchemeMultiple Sequence Alignment ProblemThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

We consider random two‐colorings of random linear preferential attachment trees, which includes recursive trees, plane‐oriented recursive trees, binary search trees, and a class of d‐ary trees. The random coloring is defined by assigning the root the color red or blue with equal probability, and all other vertices are assigned the color of their parent with probability and the other color otherwise. These colorings have been previously studied in other contexts, including Ising models and broadcasting, and can be considered as generalizations of bond percolation. With the help of Pólya urns, we prove limiting distributions, after proper rescalings, for the number of vertices, monochromatic subtrees, and leaves of each color, as well as the number of fringe subtrees with two‐colorings. Using methods from analytic combinatorics, we also provide precise descriptions of the limiting distribution after proper rescaling of the size of the root cluster; the largest monochromatic subtree containing the root.

Multilevel Marketing (MLM) business visualizes a business network into a hierarchical tree consisting of relationships between nodes. In its application, a branch is generated from each node which when visualized becomes a tree with a height that continues to increase and will consume space which will have an impact in terms of less than optimal data access. In order for the tree structure to be formed from relationships between nodes with hierarchically ordered data, and to streamline time in the search and data access process, an MLM business process information system was built by applying the Binary Tree algorithm. The concept in the Binary tree itself is a hierarchical organization of several nodes, where each node has no more than 2. Nodes that are under a node are called children of the node. A node above a node is called the parent of that node. A binary search tree is a search in a binary tree by tracing nodes that are placed in the left branch if the information content sent is smaller than the information at the root, or tracing the right branch if the information content is stated to be greater than the root. The goal is to implement sorted data into the information system in accordance with the hierarchy of the MLM system and in this way data retrieval can be done quickly and easily.

In order to overcome the incontinuity and redundancy of data storage caused by the grids in representing the multi-resolution terrain, an adaptive hierarchical triangulation based on binary tree is used to represent the multi-resolution terrain model. It realizes the representation of the terrain data at different levels of detail and enables data compression by local omission of data values. The structure of binary tree is stored using a bit code of the underlying binary tree, while the height data are stored using an array, and relative pointers which allow a selective tree traversal. This method realizes the continuity and reduces the data volume in data storage of multi-resolution digital elevation model (DEM), and it is possible to work directly on the compressed data. We show that significant compression rates can be obtained already for small threshold values, and in a visualization application, it is possible to extracted and drawn triangulations at interactive rates.

Splay and randomized search trees (RSTs) are self‐balancing binary tree structures with little or no space overhead compared to a standard binary search tree (BST). Both trees are intended for use in applications where node accesses are skewed, for example in gathering the distinct words in a large text collection for index construction. We investigate the efficiency of these trees for such vocabulary accumulation. Surprisingly, unmodified splaying and RSTs are on average around 25% slower than using a standard binary tree. We investigate heuristics to limit splay tree reorganization costs and show their effectiveness in practice. In particular, a periodic rotation scheme improves the speed of splaying by 27%, while other proposed heuristics are less effective. We also report the performance of efficient bit‐wise hashing and red–blacktrees for comparison. Copyright © 2001 John Wiley &amp; Sons, Ltd.