Adaptive Binary Search Trees
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1 Suffix Trees
This material takes about 1.5 hours. 1 Suffix Trees Gusfield: Algorithms on Strings, Trees, and Sequences. Weiner 73 “Linear Pattern-matching algorithms” IEEE conference on automata and switching theory McCreight 76 “A space-economical suffix tree construction algorithm” JACM 23(2) 1976 Chen and Seifras 85 “Efficient and Elegegant Suffix tree construction” in Apos- tolico/Galil Combninatorial Algorithms on Words Another “search” structure, dedicated to strings. Basic problem: match a “pattern” (of length m) to “text” (of length n) • goal: decide if a given string (“pattern”) is a substring of the text • possibly created by concatenating short ones, eg newspaper • application in IR, also computational bio (DNA seqs) • if pattern avilable first, can build DFA, run in time linear in text • if text available first, can build suffix tree, run in time linear in pattern. • applications in computational bio. First idea: binary tree on strings. Inefficient because run over pattern many times. • fractional cascading? • realize only need one character at each node! Tries: • used to store dictionary of strings • trees with children indexed by “alphabet” • time to search equal length of query string • insertion ditto. • optimal, since even hashing requires this time to hash. • but better, because no “hash function” computed. • space an issue: – using array increases stroage cost by |Σ| – using binary tree on alphabet increases search time by log |Σ| 1 – ok for “const alphabet” – if really fussy, could use hash-table at each node. • size in worst case: sum of word lengths (so pretty much solves “dictionary” problem. But what about substrings? • Relevance to DNA searches • idea: trie of all n2 substrings • equivalent to trie of all n suffixes. -
Managing Unbounded-Length Keys in Comparison-Driven Data
Managing Unbounded-Length Keys in Comparison-Driven Data Structures with Applications to On-Line Indexing∗ Amihood Amir Gianni Franceschini Department of Computer Science Dipartimento di Informatica Bar-Ilan University, Israel Universita` di Pisa, Italy and Department of Computer Science John Hopkins University, Baltimore MD Roberto Grossi Tsvi Kopelowitz Dipartimento di Informatica Department of Computer Science Universita` di Pisa, Italy Bar-Ilan University, Israel Moshe Lewenstein Noa Lewenstein Department of Computer Science Department of Computer Science Bar-Ilan University, Israel Netanya College, Israel arXiv:1306.0406v1 [cs.DS] 3 Jun 2013 ∗Parts of this paper appeared as extended abstracts in [3, 20]. 1 Abstract This paper presents a general technique for optimally transforming any dynamic data struc- ture that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose comparison cost is not a constant. Exam- ples of these keys are strings, multi-dimensional points, multiple-precision numbers, multi-key data (e.g. records), XML paths, URL addresses, etc. The technique is more general than what has been done in previous work as no particular exploitation of the underlying structure of is required. The only requirement is that the insertion of a key must identify its predecessor or its successor. Using the proposed technique, online suffix tree construction can be done in worst case time O(log n) per input symbol (as opposed to amortized O(log n) time per symbol, achieved by previously known algorithms). To our knowledge, our algorithm is the first that achieves O(log n) worst case time per input symbol. -
Trans-Dichotomous Algorithms for Minimum Spanning Trees and Shortest Paths
JOURNAL or COMPUTER AND SYSTEM SCIENCES 48, 533-551 (1994) Trans-dichotomous Algorithms for Minimum Spanning Trees and Shortest Paths MICHAEL L. FREDMAN* University of California at San Diego, La Jolla, California 92093, and Rutgers University, New Brunswick, New Jersey 08903 AND DAN E. WILLARDt SUNY at Albany, Albany, New York 12203 Received February 5, 1991; revised October 20, 1992 Two algorithms are presented: a linear time algorithm for the minimum spanning tree problem and an O(m + n log n/log log n) implementation of Dijkstra's shortest-path algorithm for a graph with n vertices and m edges. The second algorithm surpasses information theoretic limitations applicable to comparison-based algorithms. Both algorithms utilize new data structures that extend the fusion tree method. © 1994 Academic Press, Inc. 1. INTRODUCTION We extend the fusion tree method [7J to develop a linear-time algorithm for the minimum spanning tree problem and an O(m + n log n/log log n) implementation of Dijkstra's shortest-path algorithm for a graph with n vertices and m edges. The implementation of Dijkstra's algorithm surpasses information theoretic limitations applicable to comparison-based algorithms. Our extension of the fusion tree method involves the development of a new data structure, the atomic heap. The atomic heap accommodates heap (priority queue) operations in constant amortized time under suitable polylog restrictions on the heap size. Our linear-time minimum spanning tree algorithm results from a direct application of the atomic heap. To obtain the shortest-path algorithm, we first use the atomic heat as a building block to construct a new data structure, the AF-heap, which has no explicit size restric- tion and surpasses information theoretic limitations applicable to comparison-based algorithms. -
Augmentation: Range Trees (PDF)
Lecture 9 Augmentation 6.046J Spring 2015 Lecture 9: Augmentation This lecture covers augmentation of data structures, including • easy tree augmentation • order-statistics trees • finger search trees, and • range trees The main idea is to modify “off-the-shelf” common data structures to store (and update) additional information. Easy Tree Augmentation The goal here is to store x.f at each node x, which is a function of the node, namely f(subtree rooted at x). Suppose x.f can be computed (updated) in O(1) time from x, children and children.f. Then, modification a set S of nodes costs O(# of ancestors of S)toupdate x.f, because we need to walk up the tree to the root. Two examples of O(lg n) updates are • AVL trees: after rotating two nodes, first update the new bottom node and then update the new top node • 2-3 trees: after splitting a node, update the two new nodes. • In both cases, then update up the tree. Order-Statistics Trees (from 6.006) The goal of order-statistics trees is to design an Abstract Data Type (ADT) interface that supports the following operations • insert(x), delete(x), successor(x), • rank(x): find x’s index in the sorted order, i.e., # of elements <x, • select(i): find the element with rank i. 1 Lecture 9 Augmentation 6.046J Spring 2015 We can implement the above ADT using easy tree augmentation on AVL trees (or 2-3 trees) to store subtree size: f(subtree) = # of nodes in it. Then we also have x.size =1+ c.size for c in x.children. -
Search Trees
Lecture III Page 1 “Trees are the earth’s endless effort to speak to the listening heaven.” – Rabindranath Tagore, Fireflies, 1928 Alice was walking beside the White Knight in Looking Glass Land. ”You are sad.” the Knight said in an anxious tone: ”let me sing you a song to comfort you.” ”Is it very long?” Alice asked, for she had heard a good deal of poetry that day. ”It’s long.” said the Knight, ”but it’s very, very beautiful. Everybody that hears me sing it - either it brings tears to their eyes, or else -” ”Or else what?” said Alice, for the Knight had made a sudden pause. ”Or else it doesn’t, you know. The name of the song is called ’Haddocks’ Eyes.’” ”Oh, that’s the name of the song, is it?” Alice said, trying to feel interested. ”No, you don’t understand,” the Knight said, looking a little vexed. ”That’s what the name is called. The name really is ’The Aged, Aged Man.’” ”Then I ought to have said ’That’s what the song is called’?” Alice corrected herself. ”No you oughtn’t: that’s another thing. The song is called ’Ways and Means’ but that’s only what it’s called, you know!” ”Well, what is the song then?” said Alice, who was by this time completely bewildered. ”I was coming to that,” the Knight said. ”The song really is ’A-sitting On a Gate’: and the tune’s my own invention.” So saying, he stopped his horse and let the reins fall on its neck: then slowly beating time with one hand, and with a faint smile lighting up his gentle, foolish face, he began.. -
Lock-Free Search Data Structures: Throughput Modeling with Poisson Processes
Lock-Free Search Data Structures: Throughput Modeling with Poisson Processes Aras Atalar Chalmers University of Technology, S-41296 Göteborg, Sweden [email protected] Paul Renaud-Goud Informatics Research Institute of Toulouse, F-31062 Toulouse, France [email protected] Philippas Tsigas Chalmers University of Technology, S-41296 Göteborg, Sweden [email protected] Abstract This paper considers the modeling and the analysis of the performance of lock-free concurrent search data structures. Our analysis considers such lock-free data structures that are utilized through a sequence of operations which are generated with a memoryless and stationary access pattern. Our main contribution is a new way of analyzing lock-free concurrent search data structures: our execution model matches with the behavior that we observe in practice and achieves good throughput predictions. Search data structures are formed of basic blocks, usually referred to as nodes, which can be accessed by two kinds of events, characterized by their latencies; (i) CAS events originated as a result of modifications of the search data structure (ii) Read events that occur during traversals. An operation triggers a set of events, and the running time of an operation is computed as the sum of the latencies of these events. We identify the factors that impact the latency of such events on a multi-core shared memory system. The main challenge (though not the only one) is that the latency of each event mainly depends on the state of the caches at the time when it is triggered, and the state of caches is changing due to events that are triggered by the operations of any thread in the system. -
Persistent Predecessor Search and Orthogonal Point Location on the Word
Persistent Predecessor Search and Orthogonal Point Location on the Word RAM∗ Timothy M. Chan† August 17, 2012 Abstract We answer a basic data structuring question (for example, raised by Dietz and Raman [1991]): can van Emde Boas trees be made persistent, without changing their asymptotic query/update time? We present a (partially) persistent data structure that supports predecessor search in a set of integers in 1,...,U under an arbitrary sequence of n insertions and deletions, with O(log log U) { } expected query time and expected amortized update time, and O(n) space. The query bound is optimal in U for linear-space structures and improves previous near-O((log log U)2) methods. The same method solves a fundamental problem from computational geometry: point location in orthogonal planar subdivisions (where edges are vertical or horizontal). We obtain the first static data structure achieving O(log log U) worst-case query time and linear space. This result is again optimal in U for linear-space structures and improves the previous O((log log U)2) method by de Berg, Snoeyink, and van Kreveld [1995]. The same result also holds for higher-dimensional subdivisions that are orthogonal binary space partitions, and for certain nonorthogonal planar subdivisions such as triangulations without small angles. Many geometric applications follow, including improved query times for orthogonal range reporting for dimensions 3 on the RAM. ≥ Our key technique is an interesting new van-Emde-Boas–style recursion that alternates be- tween two strategies, both quite simple. 1 Introduction Van Emde Boas trees [60, 61, 62] are fundamental data structures that support predecessor searches in O(log log U) time on the word RAM with O(n) space, when the n elements of the given set S come from a bounded integer universe 1,...,U (U n). -
Optimal Finger Search Trees in the Pointer Machine
Alcom-FT Technical Report Series ALCOMFT-TR-02-77 Optimal Finger Search Trees in the Pointer Machine Gerth Stølting Brodal∗ George Lagogiannis† Christos Makris† Athanasios Tsakalidis† Kostas Tsichlas† Abstract We develop a new finger search tree with worst-case constant update time in the Pointer Machine (PM) model of computation. This was a major problem in the field of Data Structures and was tantalizingly open for over twenty years while many attempts by researchers were made to solve it. The result comes as a consequence of the innovative mechanism that guides the rebalancing operations combined with incremental multiple splitting and fusion techniques over nodes. Keywords balanced trees, update operations, finger search trees, data structures, complexity 1 Introduction The balanced search tree is one of the most common data structures used in algorithms. Assuming that the update position is known, balanced search trees with O(1) amortized update time have been presented long ago ([6, 14]). It has also been known ([6, 16]) that updates can be performed in O(1) structural changes, but the nodes to be changed have to be searched in Ω(log n) time. Levcopoulos and Overmars ([13]) presented an algorithm achieving O(1) worst case update time by using a global splitting lemma that is based on a pebble game combined with the bucketing technique of Overmars ([14]). Instead of storing single keys in the leaves of the search tree, each leaf can store a list of several keys. Unfortunately, the buckets in [13] have size O(log2 n), so they need a two level hierarchy of lists in order to guarantee O(log n) query time within the buckets. -
Bulk Updates and Cache Sensitivity in Search Trees
BULK UPDATES AND CACHE SENSITIVITY INSEARCHTREES TKK Research Reports in Computer Science and Engineering A Espoo 2009 TKK-CSE-A2/09 BULK UPDATES AND CACHE SENSITIVITY INSEARCHTREES Doctoral Dissertation Riku Saikkonen Dissertation for the degree of Doctor of Science in Technology to be presented with due permission of the Faculty of Information and Natural Sciences, Helsinki University of Technology for public examination and debate in Auditorium T2 at Helsinki University of Technology (Espoo, Finland) on the 4th of September, 2009, at 12 noon. Helsinki University of Technology Faculty of Information and Natural Sciences Department of Computer Science and Engineering Teknillinen korkeakoulu Informaatio- ja luonnontieteiden tiedekunta Tietotekniikan laitos Distribution: Helsinki University of Technology Faculty of Information and Natural Sciences Department of Computer Science and Engineering P.O. Box 5400 FI-02015 TKK FINLAND URL: http://www.cse.tkk.fi/ Tel. +358 9 451 3228 Fax. +358 9 451 3293 E-mail: [email protected].fi °c 2009 Riku Saikkonen Layout: Riku Saikkonen (except cover) Cover image: Riku Saikkonen Set in the Computer Modern typeface family designed by Donald E. Knuth. ISBN 978-952-248-037-8 ISBN 978-952-248-038-5 (PDF) ISSN 1797-6928 ISSN 1797-6936 (PDF) URL: http://lib.tkk.fi/Diss/2009/isbn9789522480385/ Multiprint Oy Espoo 2009 AB ABSTRACT OF DOCTORAL DISSERTATION HELSINKI UNIVERSITY OF TECHNOLOGY P.O. Box 1000, FI-02015 TKK http://www.tkk.fi/ Author Riku Saikkonen Name of the dissertation Bulk Updates and Cache Sensitivity in Search Trees Manuscript submitted 09.04.2009 Manuscript revised 15.08.2009 Date of the defence 04.09.2009 £ Monograph ¤ Article dissertation (summary + original articles) Faculty Faculty of Information and Natural Sciences Department Department of Computer Science and Engineering Field of research Software Systems Opponent(s) Prof. -
Space-Efficient Data Structures, Streams, and Algorithms
Andrej Brodnik Alejandro López-Ortiz Venkatesh Raman Alfredo Viola (Eds.) Festschrift Space-Efficient Data Structures, Streams, LNCS 8066 and Algorithms Papers in Honor of J. Ian Munro on the Occasion of His 66th Birthday 123 Lecture Notes in Computer Science 8066 Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen Editorial Board David Hutchison Lancaster University, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Alfred Kobsa University of California, Irvine, CA, USA Friedemann Mattern ETH Zurich, Switzerland John C. Mitchell Stanford University, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel Oscar Nierstrasz University of Bern, Switzerland C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen TU Dortmund University, Germany Madhu Sudan Microsoft Research, Cambridge, MA, USA Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max Planck Institute for Informatics, Saarbruecken, Germany Andrej Brodnik Alejandro López-Ortiz Venkatesh Raman Alfredo Viola (Eds.) Space-Efficient Data Structures, Streams, and Algorithms Papers in Honor of J. Ian Munro on the Occasion of His 66th Birthday 13 Volume Editors Andrej Brodnik University of Ljubljana, Faculty of Computer and Information Science Ljubljana, Slovenia and University of Primorska, -
Indexing Tree-Based Indexing
Indexing Chapter 8, 10, 11 Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 1 Tree-Based Indexing The data entries are arranged in sorted order by search key value. A hierarchical search data structure (tree) is maintained that directs searches to the correct page of data entries. Tree-structured indexing techniques support both range searches and equality searches. Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 2 Trees Tree A structure with a unique starting node (the root), in which each node is capable of having child nodes and a unique path exists from the root to every other node Root The top node of a tree structure; a node with no parent Leaf Node A tree node that has no children Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 3 Trees Level Distance of a node from the root Height The maximum level Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 4 Time Complexity of Tree Operations Time complexity of Searching: . O(height of the tree) Time complexity of Inserting: . O(height of the tree) Time complexity of Deleting: . O(height of the tree) Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 5 Multi-way Tree If we relax the restriction that each node can have only one key, we can reduce the height of the tree. A multi-way search tree is a tree in which the nodes hold between 1 to m-1 distinct keys Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 6 Range Searches ``Find all students with gpa > 3.0’’ . -
Lecture III BALANCED SEARCH TREES
§1. Keyed Search Structures Lecture III Page 1 Lecture III BALANCED SEARCH TREES Anthropologists inform that there is an unusually large number of Eskimo words for snow. The Computer Science equivalent of snow is the tree word: we have (a,b)-tree, AVL tree, B-tree, binary search tree, BSP tree, conjugation tree, dynamic weighted tree, finger tree, half-balanced tree, heaps, interval tree, kd-tree, quadtree, octtree, optimal binary search tree, priority search tree, R-trees, randomized search tree, range tree, red-black tree, segment tree, splay tree, suffix tree, treaps, tries, weight-balanced tree, etc. The above list is restricted to trees used as search data structures. If we include trees arising in specific applications (e.g., Huffman tree, DFS/BFS tree, Eskimo:snow::CS:tree alpha-beta tree), we obtain an even more diverse list. The list can be enlarged to include variants + of these trees: thus there are subspecies of B-trees called B - and B∗-trees, etc. The simplest search tree is the binary search tree. It is usually the first non-trivial data structure that students encounter, after linear structures such as arrays, lists, stacks and queues. Trees are useful for implementing a variety of abstract data types. We shall see that all the common operations for search structures are easily implemented using binary search trees. Algorithms on binary search trees have a worst-case behaviour that is proportional to the height of the tree. The height of a binary tree on n nodes is at least lg n . We say that a family of binary trees is balanced if every tree in the family on n nodes has⌊ height⌋ O(log n).