Bounding restricted rotation distance

Restricted rotation distance between pairs of rooted binary trees quantifies differences in tree shape. Cleary exhibited a linear upper bound of 12n for the restricted rotation distance between two trees with n interior nodes, and a lower bound of (n−1)/3 if the two trees satisfy a reduction condition. We obtain a significantly improved sharp upper bound of 4n−8 for restricted rotation distance between two rooted binary trees with n interior nodes, and a significantly improved sharp lower bound of n−2, again with the requirement that the trees satisfy a reduction condition. These improvements use work of Fordham to compute the word metric in Thompson's group F.     

k-Restricted rotation distance between binary trees

The restricted rotation distancedR(S,T) between two binary trees S, T of n vertices is the minimum number of rotations to transform S into T, where rotations take place at the root of S, or at the right child of the root. A sharp upper bound dR(S,T)?4n−8 is known, based on group theory [S. Cleary, J. Taback, Bounding restricted rotation distance, Information Processing Letters 88 (5) (2003) 251-256]. We refine this bound to a sharp dR(S,T)?4n−8−ρS−ρT, where ρS and ρT are the numbers of vertices in the rightmost vertex chains of the two trees, using an elementary transformation algorithm. We then generalize the concept to k-restricted rotation, by allowing rotations to take place at all the vertices of the highest k levels of the tree, and study the new distance for k=2. The case k?3 is essentially open.     

A relation between edit distance for ordered trees and edit distance for Euler strings

We consider a relationship between the unit cost edit distance for two rooted ordered trees and the unit cost edit distance for the corresponding Euler strings. We show that the edit distance between trees is at least half of the edit distance between the Euler strings and is at most 2h+1 times the edit distance between the Euler strings, where h is the minimum height of two trees. The result can be extended for more general cost functions.     

Refinements to nearest-neighbor searching ink-dimensional trees

This note presents a simplification and generalization of an algorithm for searchingk-dimensional trees for nearest neighbors reported by Friedmanet al [3]. If the distance between records is measured usingL ₂ , the Euclidean norm, the data structure used by the algorithm to determine the bounds of the search space can be simplified to a single number. Moreover, because distance measurements inL ₂ are rotationally invariant, the algorithm can be generalized to allow a partition plane to have an arbitrary orientation, rather than insisting that it be perpendicular to a coordinate axis, as in the original algorithm. When ak-dimensional tree is built, this plane can be found from the principal eigenvector of the covariance matrix of the records to be partitioned. These techniques and others yield variants ofk-dimensional trees customized for specific applications. It is wrong to assume thatk-dimensional trees guarantee that a nearest-neighbor query completes in logarithmic expected time. For smallk, logarithmic behavior is observed on all but tiny trees. However, for largerk, logarithmic behavior is achievable only with extremely large numbers of records. Fork = 16, a search of ak-dimensional tree of 76,000 records examines almost every record.     

The Fermat star of binary trees

A Fermat point P is one that minimizes the sum δ of the distances between P and the points of a given set. The resulting arrangement, called here a Fermat star, is a particular Steiner tree with only one intermediate point. We extend these concepts to rooted binary trees under the known rotation distance that measures the difference in shape of such trees. Minimizing δ is hard, due to the intrinsic difficulty of computing the rotation distance. Then we limit our study to establishing significant upper bounds for δ. In particular, for m binary trees of n vertices, we show how to construct efficiently a Fermat star with δ?mn−3m, with a technique inherited from the studies on rotation distance.     

A constrained edit distance algorithm between semi-ordered trees

In 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) 205–222] and ordered trees [Kaizhong Zhang, Algorithms for the constrained editing distance between ordered labeled trees and related problems, Pattern Recognition 28 (3) (1995) 463–474]. 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) 155–164].     

Parallel construction of optimal independent spanning trees on hypercubes

The use of multiple independent spanning trees (ISTs) for data broadcasting in networks provides a number of advantages, including the increase of fault-tolerance and bandwidth. Thus, the designs of multiple ISTs on several classes of networks have been widely investigated. Tang et al. [S.-M. Tang, Y.-L. Wang, Y.-H. Leu, Optimal independent spanning trees on hypercubes, Journal of Information Science and Engineering 20 (2004) 143–155] studied the problem of constructing k ISTs on k-dimensional hypercube Q_k, and provided a recursive algorithm for their construction (i.e., for constructing k ISTs of Q_k, it needs to build k − 1 ISTs of Q_k−1 in advance). This kind of construction forbids the possibility that the algorithm could be parallelized. In this paper, based on a simple concept called Hamming distance Latin square, we design a new algorithm for generating k ISTs of Q_k. The newly proposed algorithm relies on a simple rule and is easy to be parallelized. As a result, we show that the ISTs we constructed are optimal in the sense that both the heights and the average path length of trees are minimized.     

A new algorithm for generation of different types of RNA

The structure of RNA is often the key to its function and there is a close relationship between structure and function in biology. In this paper, we present a new algorithm for generating the possible shapes of a single-stranded RNA molecule of length ?. We use a bijection between the secondary structure and specific ordered trees. Hence, generating different types of RNA becomes equivalent to the generation of these trees. The generated trees are encoded as integer sequences and are produced in A-order. The time complexity of the presented algorithm is O(??k) where ? is the number of bases and k, the number of pairings. Ranking and unranking algorithms with O(k??k ²) and O(?²+k ²) time complexity are also presented.     

A Uniform Paradigm to Succinctly Encode Various Families of Trees

We propose a uniform method to encode various types of trees succinctly. These families include ordered (ordinal), k-ary (cardinal), and unordered (free) trees. We will show the approach is intrinsically suitable for obtaining entropy-based encodings of trees (such as the degree-distribution entropy). Previously-existing succinct encodings of trees use ad hoc techniques to encode each particular family of trees. Additionally, the succinct encodings obtained using the uniform approach improve upon the existing succinct encodings of each family of trees; in the case of ordered trees, it simplifies the encoding while supporting the full set of navigational operations. It also simplifies the implementation of many supported operations. The approach applied to k-ary trees yields a succinct encoding that supports both cardinal-type operations (e.g. determining the child label i) as well as the full set of ordinal-type operations (e.g. reporting the number of siblings to the left of a node). Previous work on succinct encodings of k-ary trees does not support both types of operations simultaneously (Benoit et al. in Algorithmica 43(4):275–292, 2005; Raman et al. in ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 233–242, 2002). For unordered trees, the approach achieves the first succinct encoding. The approach is based on two recursive decompositions of trees into subtrees. Recursive decomposition of a structure into substructures is a common technique in succinct encodings and has even been used to encode (ordered) trees (Geary et al. in ACM Trans. Algorithms 2(4):510–534, 2006; He et al. in ICALP, pp. 509–520, 2007) and dynamic binary trees (Munro et al. in ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 529–536, 2001; Storm in Representing dynamic binary trees succinctly, Master’s thesis, 2000). The main distinction of the approach in this paper is that a tree is decomposed into subtrees in a manner that the subtrees are maximally isolated from each other. This intermediate decomposition result is interesting in its own right and has proved useful in other applications (Farzan et al. in ICALP (1), pp. 451–462, 2009; Farzan and Munro in ICALP (1), pp. 439–450, 2009; Farzan and Kamali in ICALP, 2011).     

Optical transpose k-ary n-cube networks

This paper derives a number of results related to the topological properties of OTIS k-ary n-cube interconnection networks. The basic topological metrics of size, degree, shortest distance, and diameter are obtained. Then results related to embedding in OTIS k-ary n-cubes of OTIS k-ary (n−1)-cubes, cycles, meshes, cubes, and spanning trees are derived. The OTIS k-ary n-cube is shown to be Hamiltonian. Minimal one-to-one routing and optimal broadcasting algorithms are proposed. The OTIS k-ary n-cube is shown to be maximally fault-tolerant. These results are derived based on known properties of k-ary n-cube networks and general properties of OTIS networks.     

A counterexample for the proof of implication conjecture on independent spanning trees

Khuller and Schieber (1992) in [1] developed a constructive algorithm to prove that the existence of k-vertex independent trees in a k-vertex connected graph implies the existence of k-edge independent trees in a k-edge connected graph. In this paper, we show a counterexample where their algorithm fails.     

Refinements to nearest-neighbor searching ink-dimensional trees

This note presents a simplification and generalization of an algorithm for searchingk-dimensional trees for nearest neighbors reported by Friedmanet al [3]. If the distance between records is measured usingL ₂ , the Euclidean norm, the data structure used by the algorithm to determine the bounds of the search space can be simplified to a single number. Moreover, because distance measurements inL ₂ are rotationally invariant, the algorithm can be generalized to allow a partition plane to have an arbitrary orientation, rather than insisting that it be perpendicular to a coordinate axis, as in the original algorithm. When ak-dimensional tree is built, this plane can be found from the principal eigenvector of the covariance matrix of the records to be partitioned. These techniques and others yield variants ofk-dimensional trees customized for specific applications.It is wrong to assume thatk-dimensional trees guarantee that a nearest-neighbor query completes in logarithmic expected time. For smallk, logarithmic behavior is observed on all but tiny trees. However, for largerk, logarithmic behavior is achievable only with extremely large numbers of records. Fork = 16, a search of ak-dimensional tree of 76,000 records examines almost every record.     

Two iteration theorems for the LL(k) languages

The structure of derivation trees over an LL(k) grammar is explored and a property of these trees obtained which is shown to characterize the LL(k) grammars. This characterization, called the LL(k) Left Part Theorem, makes it possible to establish a pair of iteration theorems for the LL(k) languages. These theorems provide a general and powerful method of showing that a language is not LL(k) when that is the case. They thus provide for the first time a flexible tool with which to explore the structure of the LL(k) languages and with which to discriminate between the LL(k) and LR(k) language classes.Examples are given of LR(k) languages which, for various reasons, fail to be LL(k). Easy and rigorous proofs to this effect are given using our LL(k) iteration theorems. In particular, it is proven that the dangling-ELSE construct allowed in PL/I and Pascal cannot be generated by any LL(k) grammar. We also give a new and straightforward proof based on the LL(k) Left Part Theorem that every LL(k) grammar is LR(k).     

Windowed pq-grams for approximate joins of data-centric XML

In data integration applications, a join matches elements that are common to two data sources. Since elements are represented slightly different in each source, an approximate join must be used to do the matching. For XML data, most existing approximate join strategies are based on some ordered tree matching technique, such as the tree edit distance. In data-centric XML, however, the sibling order is irrelevant, and two elements should match even if their subelement order varies. Thus, approximate joins for data-centric XML must leverage unordered tree matching techniques. This is computationally hard since the algorithms cannot rely on a predefined sibling order. In this paper, we give a solution for approximate joins based on unordered tree matching. The core of our solution are windowed pq-grams which are small subtrees of a specific shape. We develop an efficient technique to generate windowed pq-grams in a three-step process: sort the tree, extend the sorted tree with dummy nodes, and decompose the extended tree into windowed pq-grams. The windowed pq-grams distance between two trees is the number of pq-grams that are in one tree decomposition only. We show that our distance is a pseudo-metric and empirically demonstrate that it effectively approximates the unordered tree edit distance. The approximate join using windowed pq-grams can be efficiently implemented as an equality join on strings, which avoids the costly computation of the distance between every pair of input trees. Experiments with synthetic and real world data confirm the analytic results and show the effectiveness and efficiency of our technique.     

A Fan-type result on k-ordered graphs

For a positive integer k, a graph G is k-ordered hamiltonian if for every ordered sequence of k vertices there is a hamiltonian cycle that encounters the vertices of the sequence in the given order. In this paper, we show that if G is a ⌊3k/2⌋-connected graph of order n?100k, and d(u)+d(v)?n for any two vertices u and v with d(u,v)=2, then G is k-ordered hamiltonian. Our result implies the theorem of G. Chen et al. [Ars Combin. 70 (2004) 245-255] [1], which requires the degree sum condition for all pairs of non-adjacent vertices, not just those distance 2 apart.     

Approximation algorithms for the bandwidth minimization problem for a large class of trees

We present approximation algorithms for the bandwidth minimization problem (BMP) for a large class of trees. The BMP is NP-hard, even for trees of maximum node degree 3. The problem finds applications in many areas, including VLSI layout, multiprocessor scheduling, and matrix processing, and has been studied for both graphs and matrices. We study the problem on trees having the following property: given any tree nodev, the depth difference of any two nonempty subtrees rooted atv is bounded by a constantk. We call such treesh(k)trees orgeneralized height-balanced (GHB)trees. The above definition extends the class of balanced trees to trees with depthd=Θ(\N\). For any tree in the above defined class, anO (logd) times optimal algorithm is presented. Furthermore, we extend the application of the algorithm to trees that simulate theh(k) property, which we callh(k)-like trees, and also provide intuitive ideas for an approximation algorithm for general trees.     

One-sided k-height-balanced trees

The purpose of this paper is to generalize the recent results on one-sided height-balanced trees (OSHB trees) to the case of one-sidedk-height-balanced trees, fork≥2. Surprisingly, this generalization leads to 0 (log₂ n) insertion and deletion algorithms, which are simpler than those available for OSHB trees, and thus we claim this generalization is of independent interest.     

Approximating Tree Edit Distance through String Edit Distance

We present an algorithm to approximate edit distance between two ordered and rooted trees of bounded degree. In this algorithm, each input tree is transformed into a string by computing the Euler string, where labels of some edges in the input trees are modified so that structures of small subtrees are reflected to the labels. We show that the edit distance between trees is at least 1/6 and at most O(n ^3/4) of the edit distance between the transformed strings, where n is the maximum size of two input trees and we assume unit cost edit operations for both trees and strings. The algorithm works in O(n ²) time since computation of edit distance and reconstruction of tree mapping from string alignment takes O(n ²) time though transformation itself can be done in O(n) time.     

Spanners of bounded degree graphs

A k-spanner of a graph G is a spanning subgraph of G in which the distance between any pair of vertices is at most k times the distance in G. We prove that for fixed k,w, the problem of deciding if a given graph has a k-spanner of treewidth w is fixed-parameter tractable on graphs of bounded degree. In particular, this implies that finding a k-spanner that is a tree (a tree k-spanner) is fixed-parameter tractable on graphs of bounded degree. In contrast, we observe that if the graph has only one vertex of unbounded degree, then Treek-Spanner is NP-complete for k?4.     

An improved algorithm for the maximum agreement subtree problem

In this paper, we solve the maximum agreement subtree problem for a set T of k rooted leaf-labeled evolutionary trees on n leaves where T contains a binary tree. We show that the O(kn³)-time dynamic-programming algorithm proposed by Bryant [Building trees, hunting for trees, and comparing trees: theory and methods in phylogenetic analysis, Ph.D. thesis, Dept. Math., University of Canterbury, 1997, pp. 174-182] can be implemented in O(kn²+n²logk−2nloglogn) and O(kn3−1/(k−1)) time by using multidimensional range search related data structures proposed by Gabow et al. [Scaling and related techniques for geometry problems, in: Proc. 16th Annual ACM Symp. on Theory of Computing, 1984, pp. 135-143] and Bentley [Multidimensional binary search trees in database applications, IEEE Trans. Softw. Eng. SE-5 (4) (1979) 333-340], respectively. When k<2+(logn−logloglogn)/(loglogn), the first implementation will be significantly faster than Bryant's algorithm. For k=3, it yields the best known algorithm which runs in O(n²lognloglogn)-time.