A hierarchical structure for surface approximation

Hierarchical triangulation is a method for point selection and surface representation where the surface is approximated at successively finer levels of detail by triangular patches whose projections in the horizontal plane are nested. A tree data structure for this representation can be constructed in O(n²) worst case and O(n log n) average case time, where n is the number of data points considered. Efficient algorithms for approximation of the elevation of an arbitrary point, contour extraction, and conversion of the hierarchical structure into an ordinary triangulated irregular network, are demonstrated. The convergence and the optimality of the approximation and the relationship of the hierarchical triangulation to a structured graph representation are examined.     

Using spine decompositions to efficiently solve the length-constrained heaviest path problem for trees

The length-constrained heaviest path (LCHP) in a weighted tree T, where each edge is assigned a weight and a length, is the path P in T with maximum total path weight and total path length bounded by a given value B. This paper presents an O(nlogn) time LCHP algorithm which utilizes a data structure constructed from the spine decomposition of the input tree. This is an improvement over the existing algorithm by Wu et al. (1999), which runs in O(nlog²n) time. Our method also improves on a previous O(nlogn) time algorithm by Kim (2005) for the special case of finding a longest nonnegative path in a constant degree tree in that we can handle trees of arbitrary degree within the same time bounds.     

Improved Bounds for Finger Search on a RAM

We present a new finger search tree with O(loglogd) expected search time in the Random Access Machine (RAM) model of computation for a large class of input distributions. The parameter d represents the number of elements (distance) between the search element and an element pointed to by a finger, in a finger search tree that stores n elements. Our data structure improves upon a previous result by Andersson and Mattsson that exhibits expected O(loglogn) search time by incorporating the distance d into the search time complexity, and thus removing the dependence on n. We are also able to show that the search time is O(loglogd+?(n)) with high probability, where ?(n) is any slowly growing function of n. For the need of the analysis we model the updates by a “balls and bins” combinatorial game that is interesting in its own right as it involves insertions and deletions of balls according to an unknown distribution.     

Uniform Generation of Binary Trees in Parallel

An unbiased random generator for binary trees is developed for a CREW-PRAM. The generator is capable of generating a binary tree on n nodes in time O(log n), space O(n), with O(n) processors; it is also capable of generating various related combinatorial objects.     

Reconstructing a Binary Tree from Its Traversals in Doubly Logarithmic CREW Time

We consider the following problem. For a binary tree T = (V, E) where V = {1, 2, ..., n}, given its inorder traversal and either its preorder or its postorder traversal, reconstruct the binary tree. We present a new parallel algorithm for this problem. Our algorithm requires O(n) space. The main idea of our algorithm is to reduce the reconstruction process to merging two sorted sequences. With the best parallel merging algorithms, our algorithm can be implemented in O(log log n) time using O(n/log log n) processors on the CREW PRAM (or in O(log n) time using O(n/log n) processors on the EREW PRAM). Our result provides one more example of a fundamental problem which can be solved by optimal parallel algorithms in O(log log n)time on the CREW PRAM.     

Faster index for property matching

In this paper, we revisit the Property Matching problem studied by Amir et al. [Property Matching and Weighted Matching, CPM 2006] and present a better indexing scheme for the problem. In particular, the data structure by Amir et al., namely PST, requires O(nlog|Σ|+nloglogn) construction time and O(mlog|Σ|+K) query time, where n and m are the length of, respectively, the text and the pattern, Σ is the alphabet and K is the output size. On the other hand, the construction time of our data structure, namely IDS_PIP, is dominated by the suffix tree construction time and hence is O(n) time for alphabets that are natural numbers from 1 to a polynomial in n and O(nlogσ) time otherwise, where σ=min(n,|Σ|). The query time is same as that of PST. Also, IDS_PIP has the advantage that it can be built on either a suffix tree or a suffix array and additionally, it retains the capability of answering normal pattern matching queries.     

An optimal algorithm for the maximum-density path in a tree

We studied the problem of finding the maximum-density path in a tree. By spine decomposition and a linear-time algorithm for the maximum density segment problem, we developed an O(nlogn) time algorithm, which improves the previously best result of O(nlog²n) by using centroid decomposition. We also show the time complexity is optimal in the algebraic computation tree model.     

Efficient Parallel Algorithms for Permutation Graphs

In this paper, we present optimal O(log n) time, O(n/log n) processor EREW PRAM parallel algorithms for finding the connected components, cut vertices, and bridges of a permutation graph. We also present an O(log n) time, O(n) processor, CREW PRAM model parallel algorithm for finding a Breadth First Search (BFS) spanning tree of a permutation graph rooted at vertex 1 and use the same to derive an efficient parallel algorithm for the All Pairs Shortest Path problem on permutation graphs.     

Algorithms for updating minimal spanning trees

The problem of finding the minimal spanning tree on an undirected weighted graph has been investigated by many people and O(n²) algorithms are well known. P. M. Spira and A. Pan (Siam J. Computing4 (1975), 375–380) present an O(n) algorithm for updating the minimal spanning tree if a new vertex is inserted into the graph. In this paper, we present another O(n) algorithm simpler than that presented by Spira and Pan for the insertion of a vertex. Spira and Pan further show that the deletion of a vertex requires O(n²) steps. If all the vertices are considered, O(n³) steps may be used. The algorithm which we present here takes only O(n²) steps and labels the vertices of the graph in such a way that any vertex may be deleted from the graph and the minimal spanning tree can be updated in constant time. Similar results are obtained for the insertion and the deletion of an edge.     

A fast algorithm for point-location in a finite element mesh

An algorithm for the point-location problem in 2D finite element meshes as a special case of plane straight-line graphs (PSLG) is presented. The element containing a given point P is determined combining a quadtree data structure to generate a quaternary search tree and a local search wave using adjacency information. The preprocessing construction of the search tree has a complexity ofO(n·log(n)) and requires only pointer swap operations. The query time to locate a start element for local search isO(log(n)) and the final point search by ‘point-in-polygon’ tests is independent of the total number of elements in the mesh and thus determined in constant time. Although the theoretical efficiency estimates are only given for quasi-uniform meshes, it is shown in numerical examples, that the algorithm performs equally well for meshes with extreme local refenement.     

Fast heuristic algorithms for rectilinear steiner trees

A fundamental problem in circuit design is how to connectn points in the plane, to make them electrically common using the least amount of wire. The tree formed, a Steiner tree, is usually constructed with respect to the rectilinear metric. The problem is known to be NP-complete; an extensive review of proposed heuristics is given. An early algorithm by Hanan is shown to have anO(n logn) time implementation using computational geometry techniques. The algorithm can be modified to do sequential searching inO(n ²) total time. However, it is shown that the latter approach runs inO(n ^3/2) expected time, forn points selected from anm×m grid. Empirical results are presented for problems up to 10,000 points.     

Efficient Techniques for Nested and Disjoint Barrier Synchronization

Current MIMD computers support the execution of data parallel programs by providing a tree network to perform fast barrier synchronizations. However, there are two major limitations to using tree networks: The first arises due to control nesting in programs, and the second arises when the MIMD computer needs to run several programs simultaneously. First, we present two hardware barrier synchronization schemes which can support deep levels of control nesting in data parallel programs. Hardware barriers are usually an order of magnitude faster than software implementations. Since large data parallel programs often have several levels of nested barriers, these schemes provide significant speedups in the execution of such programs on MIMD computers. The first scheme performs code transformations and uses two single-bit-trees to implement unlimited levels of nested barriers. However, this scheme increases the code size. The second scheme uses a more expensive integer-tree to support an exponential number of nesting levels without increasing the code size: we-show that up to n nested barriers can be supported by a network with bisection bandwidth O(log n) and a latency of O(log p log n) gate delays. Using tree network hardware already available on commercial MIMD computers, this scheme can support more than four billion levels of nesting. Second, we present a design for a barrier synchronization network that is free from the partitioning constraints imposed by barrier trees. When the MIMD computer is partitioned among several jobs, then, rather than barrier synchronizations, we desire multiple disjoint barrier synchronizations (MDBSs), where processors within each partition barrier synchronize among themselves without interfering with other partitions. Barrier trees can be adapted to handle MDBSs, but only if the partitions are constrained to be of very special sizes and shapes. These stringent constraints on partitioning often run contrary to other important considerations, such as the contiguity of the processors of each partition within the data network. Our MDBS network design allows for any number of partitions of any size and shape, as long as the processors comprising each partition are contiguous in the data network.     

Visibility of disjoint polygons

Consider a collection of disjoint polygons in the plane containing a total ofn edges. We show how to build, inO(n ²) time and space, a data structure from which inO(n) time we can compute the visibility polygon of a given point with respect to the polygon collection. As an application of this structure, the visibility graph of the given polygons can be constructed inO(n ²) time and space. This implies that the shortest path that connects two points in the plane and avoids the polygons in our collection can be computed inO(n ²) time, improving earlierO(n ² logn) results.     

Self-stabilizing leader election in optimal space under an arbitrary scheduler

A silent self-stabilizing asynchronous distributed algorithm, SSLE, is given for the leader election problem in a connected unoriented (bidirectional) network with unique IDs. SSLE also constructs a BFS tree on the network rooted at that leader. SSLE uses O(logn) space per process and stabilizes in O(n) rounds, against the unfair daemon, where n is the number of processes in the network.     

Towards optimal range medians

We consider the following problem: Given an unsorted array of n elements, and a sequence of intervals in the array, compute the median in each of the subarrays defined by the intervals. We describe a simple algorithm which needs O(nlogk+klogn) time to answer k such median queries. This improves previous algorithms by a logarithmic factor and matches a comparison lower bound for k=O(n). The space complexity of our simple algorithm is O(nlogn) in the pointer machine model, and O(n) in the RAM model. In the latter model, a more involved O(n) space data structure can be constructed in O(nlogn) time where the time per query is reduced to O(logn/loglogn). We also give efficient dynamic variants of both data structures, achieving O(log²n) query time using O(nlogn) space in the comparison model and O((logn/loglogn)²) query time using O(nlogn/loglogn) space in the RAM model, and show that in the cell-probe model, any data structure which supports updates in O(log^O(1)n) time must have Ω(logn/loglogn) query time.Our approach naturally generalizes to higher-dimensional range median problems, where element positions and query ranges are multidimensional—it reduces a range median query to a logarithmic number of range counting queries.     

Communication-efficient parallel algorithms for distributed random-access machines

This paper introduces a model for parallel computation, called thedistributed randomaccess machine (DRAM), in which the communication requirements of parallel algorithms can be evaluated. A DRAM is an abstraction of a parallel computer in which memory accesses are implemented by routing messages through a communication network. A DRAM explicitly models the congestion of messages across cuts of the network. We introduce the notion of aconservative algorithm as one whose communication requirements at each step can be bounded by the congestion of pointers of the input data structure across cuts of a DRAM. We give a simple lemma that shows how to “shortcut” pointers in a data structure so that remote processors can communicate without causing undue congestion. We giveO(lgn)-step, linear-processor, linear-space, conservative algorithms for a variety of problems onn-node trees, such as computing treewalk numberings, finding the separator of a tree, and evaluating all subexpressions in an expression tree. We giveO(lg² n)-step, linear-processor, linear-space, conservative algorithms for problems on graphs of sizen, including finding a minimum-cost spanning forest, computing biconnected components, and constructing an Eulerian cycle. Most of these algorithms use as a subroutine a generalization of the prefix computation to trees. We show that any suchtreefix computation can be performed inO(lgn) steps using a conservative variant of Miller and Reif's tree-contraction technique.     

Compressed Directed Acyclic Word Graph with Application in Local Alignment

Suffix tree, suffix array, and directed acyclic word graph (DAWG) are data-structures for indexing a text. Although they enable efficient pattern matching, their data-structures require O(nlogn) bits, which make them impractical to index long text like human genome. Recently, the development of compressed data-structures allow us to simulate suffix tree and suffix array using O(n) bits. However, there is still no O(n)-bit data-structure for DAWG with full functionality. This work introduces an $n(H_{k}(\overline{S})+ 2 H_{0}^{*}(\mathcal {T}_{\overline{S}}))+o(n)$ -bit compressed data-structure for simulating DAWG (where $H_{k}(\overline{S})$ and $H_{0}^{*}(\mathcal{T}_{\overline{S}})$ are the empirical entropies of the reversed sequence and the reversed suffix tree topology, respectively.) Besides, we also propose an application of DAWG to improve the time complexity for the local alignment problem. In this application, the previously proposed solutions using BWT (a version of compressed suffix array) run in O(n ² m) worst case time and O(n ^0.628 m) average case time where n and m are the lengths of the database and the query, respectively. Using compressed DAWG proposed in this paper, the problem can be solved in O(nm) worst case time and the same average case time.     

Fast Arc-Annotated Subsequence Matching in Linear Space

An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings P and Q the arc-preserving subsequence problem is to determine if P can be obtained from Q by deleting bases from Q. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are “nested” are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. (ACM Trans. Algorithms 2(1): 44–65, 2006) gave an algorithm for this problem using O(nm) time and space, where m and n are the lengths of P and Q, respectively. In this paper we present a new algorithm using O(nm) time and O(n+m) space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc-annotated strings.     

Dominance made simple

In this note we show that it is extremely easy to answer dominance queries in three dimensions using only range minima routine (and a binary tree). The algorithm after preprocessing takes O(logn+S) time, where S is the size of output (after O(nlogn) time for pre-processing).The algorithm can also be used to answer 5-sided range queries, in same time bounds.     

Parallel construction of a suffix tree with applications

Many string manipulations can be performed efficiently on suffix trees. In this paper a CRCW parallel RAM algorithm is presented that constructs the suffix tree associated with a string ofn symbols inO(logn) time withn processors. The algorithm requires Θ(n ²) space. However, the space needed can be reduced toO(n ^1+?) for any 0< ? ≤1, with a corresponding slow-down proportional to 1/?. Efficient parallel procedures are also given for some string problems that can be solved with suffix trees.