Lecture 7: Randomized Search Trees 1 Treaps
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
KP-Trie Algorithm for Update and Search Operations
The International Arab Journal of Information Technology, Vol. 13, No. 6, November 2016 722 KP-Trie Algorithm for Update and Search Operations Feras Hanandeh1, Izzat Alsmadi2, Mohammed Akour3, and Essam Al Daoud4 1Department of Computer Information Systems, Hashemite University, Jordan 2, 3Department of Computer Information Systems, Yarmouk University, Jordan 4Computer Science Department, Zarqa University, Jordan Abstract: Radix-Tree is a space optimized data structure that performs data compression by means of cluster nodes that share the same branch. Each node with only one child is merged with its child and is considered as space optimized. Nevertheless, it can’t be considered as speed optimized because the root is associated with the empty string. Moreover, values are not normally associated with every node; they are associated only with leaves and some inner nodes that correspond to keys of interest. Therefore, it takes time in moving bit by bit to reach the desired word. In this paper we propose the KP-Trie which is consider as speed and space optimized data structure that is resulted from both horizontal and vertical compression. Keywords: Trie, radix tree, data structure, branch factor, indexing, tree structure, information retrieval. Received January 14, 2015; accepted March 23, 2015; Published online December 23, 2015 1. Introduction the exception of leaf nodes, nodes in the trie work merely as pointers to words. Data structures are a specialized format for efficient A trie, also called digital tree, is an ordered multi- organizing, retrieving, saving and storing data. It’s way tree data structure that is useful to store an efficient with large amount of data such as: Large data associative array where the keys are usually strings, bases. -
Balanced Trees Part One
Balanced Trees Part One Balanced Trees ● Balanced search trees are among the most useful and versatile data structures. ● Many programming languages ship with a balanced tree library. ● C++: std::map / std::set ● Java: TreeMap / TreeSet ● Many advanced data structures are layered on top of balanced trees. ● We’ll see several later in the quarter! Where We're Going ● B-Trees (Today) ● A simple type of balanced tree developed for block storage. ● Red/Black Trees (Today/Thursday) ● The canonical balanced binary search tree. ● Augmented Search Trees (Thursday) ● Adding extra information to balanced trees to supercharge the data structure. Outline for Today ● BST Review ● Refresher on basic BST concepts and runtimes. ● Overview of Red/Black Trees ● What we're building toward. ● B-Trees and 2-3-4 Trees ● Simple balanced trees, in depth. ● Intuiting Red/Black Trees ● A much better feel for red/black trees. A Quick BST Review Binary Search Trees ● A binary search tree is a binary tree with 9 the following properties: 5 13 ● Each node in the BST stores a key, and 1 6 10 14 optionally, some auxiliary information. 3 7 11 15 ● The key of every node in a BST is strictly greater than all keys 2 4 8 12 to its left and strictly smaller than all keys to its right. Binary Search Trees ● The height of a binary search tree is the 9 length of the longest path from the root to a 5 13 leaf, measured in the number of edges. 1 6 10 14 ● A tree with one node has height 0. -
Lecture 04 Linear Structures Sort
Algorithmics (6EAP) MTAT.03.238 Linear structures, sorting, searching, etc Jaak Vilo 2018 Fall Jaak Vilo 1 Big-Oh notation classes Class Informal Intuition Analogy f(n) ∈ ο ( g(n) ) f is dominated by g Strictly below < f(n) ∈ O( g(n) ) Bounded from above Upper bound ≤ f(n) ∈ Θ( g(n) ) Bounded from “equal to” = above and below f(n) ∈ Ω( g(n) ) Bounded from below Lower bound ≥ f(n) ∈ ω( g(n) ) f dominates g Strictly above > Conclusions • Algorithm complexity deals with the behavior in the long-term – worst case -- typical – average case -- quite hard – best case -- bogus, cheating • In practice, long-term sometimes not necessary – E.g. for sorting 20 elements, you dont need fancy algorithms… Linear, sequential, ordered, list … Memory, disk, tape etc – is an ordered sequentially addressed media. Physical ordered list ~ array • Memory /address/ – Garbage collection • Files (character/byte list/lines in text file,…) • Disk – Disk fragmentation Linear data structures: Arrays • Array • Hashed array tree • Bidirectional map • Heightmap • Bit array • Lookup table • Bit field • Matrix • Bitboard • Parallel array • Bitmap • Sorted array • Circular buffer • Sparse array • Control table • Sparse matrix • Image • Iliffe vector • Dynamic array • Variable-length array • Gap buffer Linear data structures: Lists • Doubly linked list • Array list • Xor linked list • Linked list • Zipper • Self-organizing list • Doubly connected edge • Skip list list • Unrolled linked list • Difference list • VList Lists: Array 0 1 size MAX_SIZE-1 3 6 7 5 2 L = int[MAX_SIZE] -
Heaps a Heap Is a Complete Binary Tree. a Max-Heap Is A
Heaps Heaps 1 A heap is a complete binary tree. A max-heap is a complete binary tree in which the value in each internal node is greater than or equal to the values in the children of that node. A min-heap is defined similarly. 97 Mapping the elements of 93 84 a heap into an array is trivial: if a node is stored at 90 79 83 81 index k, then its left child is stored at index 42 55 73 21 83 2k+1 and its right child at index 2k+2 01234567891011 97 93 84 90 79 83 81 42 55 73 21 83 CS@VT Data Structures & Algorithms ©2000-2009 McQuain Building a Heap Heaps 2 The fact that a heap is a complete binary tree allows it to be efficiently represented using a simple array. Given an array of N values, a heap containing those values can be built, in situ, by simply “sifting” each internal node down to its proper location: - start with the last 73 73 internal node * - swap the current 74 81 74 * 93 internal node with its larger child, if 79 90 93 79 90 81 necessary - then follow the swapped node down 73 * 93 - continue until all * internal nodes are 90 93 90 73 done 79 74 81 79 74 81 CS@VT Data Structures & Algorithms ©2000-2009 McQuain Heap Class Interface Heaps 3 We will consider a somewhat minimal maxheap class: public class BinaryHeap<T extends Comparable<? super T>> { private static final int DEFCAP = 10; // default array size private int size; // # elems in array private T [] elems; // array of elems public BinaryHeap() { . -
CSCI 333 Data Structures Binary Trees Binary Tree Example Full And
Notes with the dark blue background CSCI 333 were prepared by the textbook author Data Structures Clifford A. Shaffer Chapter 5 Department of Computer Science 18, 20, 23, and 25 September 2002 Virginia Tech Copyright © 2000, 2001 Binary Trees Binary Tree Example A binary tree is made up of a finite set of Notation: Node, nodes that is either empty or consists of a children, edge, node called the root together with two parent, ancestor, binary trees, called the left and right descendant, path, subtrees, which are disjoint from each depth, height, level, other and from the root. leaf node, internal node, subtree. Full and Complete Binary Trees Full Binary Tree Theorem (1) Full binary tree: Each node is either a leaf or Theorem: The number of leaves in a non-empty internal node with exactly two non-empty children. full binary tree is one more than the number of internal nodes. Complete binary tree: If the height of the tree is d, then all leaves except possibly level d are Proof (by Mathematical Induction): completely full. The bottom level has all nodes to the left side. Base case: A full binary tree with 1 internal node must have two leaf nodes. Induction Hypothesis: Assume any full binary tree T containing n-1 internal nodes has n leaves. 1 Full Binary Tree Theorem (2) Full Binary Tree Corollary Induction Step: Given tree T with n internal Theorem: The number of null pointers in a nodes, pick internal node I with two leaf children. non-empty tree is one more than the Remove I’s children, call resulting tree T’. -
Tree Structures
Tree Structures Definitions: o A tree is a connected acyclic graph. o A disconnected acyclic graph is called a forest o A tree is a connected digraph with these properties: . There is exactly one node (Root) with in-degree=0 . All other nodes have in-degree=1 . A leaf is a node with out-degree=0 . There is exactly one path from the root to any leaf o The degree of a tree is the maximum out-degree of the nodes in the tree. o If (X,Y) is a path: X is an ancestor of Y, and Y is a descendant of X. Root X Y CSci 1112 – Algorithms and Data Structures, A. Bellaachia Page 1 Level of a node: Level 0 or 1 1 or 2 2 or 3 3 or 4 Height or depth: o The depth of a node is the number of edges from the root to the node. o The root node has depth zero o The height of a node is the number of edges from the node to the deepest leaf. o The height of a tree is a height of the root. o The height of the root is the height of the tree o Leaf nodes have height zero o A tree with only a single node (hence both a root and leaf) has depth and height zero. o An empty tree (tree with no nodes) has depth and height −1. o It is the maximum level of any node in the tree. CSci 1112 – Algorithms and Data Structures, A. -
Binary Search Tree
ADT Binary Search Tree! Ellen Walker! CPSC 201 Data Structures! Hiram College! Binary Search Tree! •" Value-based storage of information! –" Data is stored in order! –" Data can be retrieved by value efficiently! •" Is a binary tree! –" Everything in left subtree is < root! –" Everything in right subtree is >root! –" Both left and right subtrees are also BST#s! Operations on BST! •" Some can be inherited from binary tree! –" Constructor (for empty tree)! –" Inorder, Preorder, and Postorder traversal! •" Some must be defined ! –" Insert item! –" Delete item! –" Retrieve item! The Node<E> Class! •" Just as for a linked list, a node consists of a data part and links to successor nodes! •" The data part is a reference to type E! •" A binary tree node must have links to both its left and right subtrees! The BinaryTree<E> Class! The BinaryTree<E> Class (continued)! Overview of a Binary Search Tree! •" Binary search tree definition! –" A set of nodes T is a binary search tree if either of the following is true! •" T is empty! •" Its root has two subtrees such that each is a binary search tree and the value in the root is greater than all values of the left subtree but less than all values in the right subtree! Overview of a Binary Search Tree (continued)! Searching a Binary Tree! Class TreeSet and Interface Search Tree! BinarySearchTree Class! BST Algorithms! •" Search! •" Insert! •" Delete! •" Print values in order! –" We already know this, it#s inorder traversal! –" That#s why it#s called “in order”! Searching the Binary Tree! •" If the tree is -
Position Heaps for Cartesian-Tree Matching on Strings and Tries
Position Heaps for Cartesian-tree Matching on Strings and Tries Akio Nishimoto1, Noriki Fujisato1, Yuto Nakashima1, and Shunsuke Inenaga1;2 1Department of Informatics, Kyushu University, Japan fnishimoto.akio, noriki.fujisato, yuto.nakashima, [email protected] 2PRESTO, Japan Science and Technology Agency, Japan Abstract The Cartesian-tree pattern matching is a recently introduced scheme of pattern matching that detects fragments in a sequential data stream which have a similar structure as a query pattern. Formally, Cartesian-tree pattern matching seeks all substrings S0 of the text string S such that the Cartesian tree of S0 and that of a query pattern P coincide. In this paper, we present a new indexing structure for this problem, called the Cartesian-tree Position Heap (CPH ). Let n be the length of the input text string S, m the length of a query pattern P , and σ the alphabet size. We show that the CPH of S, denoted CPH(S), supports pattern matching queries in O(m(σ + log(minfh; mg)) + occ) time with O(n) space, where h is the height of the CPH and occ is the number of pattern occurrences. We show how to build CPH(S) in O(n log σ) time with O(n) working space. Further, we extend the problem to the case where the text is a labeled tree (i.e. a trie). Given a trie T with N nodes, we show that the CPH of T , denoted CPH(T ), supports pattern matching queries on the trie in O(m(σ2 +log(minfh; mg))+occ) time with O(Nσ) space. -
Assignment of Master's Thesis
CZECH TECHNICAL UNIVERSITY IN PRAGUE FACULTY OF INFORMATION TECHNOLOGY ASSIGNMENT OF MASTER’S THESIS Title: Approximate Pattern Matching In Sparse Multidimensional Arrays Using Machine Learning Based Methods Student: Bc. Anna Kučerová Supervisor: Ing. Luboš Krčál Study Programme: Informatics Study Branch: Knowledge Engineering Department: Department of Theoretical Computer Science Validity: Until the end of winter semester 2018/19 Instructions Sparse multidimensional arrays are a common data structure for effective storage, analysis, and visualization of scientific datasets. Approximate pattern matching and processing is essential in many scientific domains. Previous algorithms focused on deterministic filtering and aggregate matching using synopsis style indexing. However, little work has been done on application of heuristic based machine learning methods for these approximate array pattern matching tasks. Research current methods for multidimensional array pattern matching, discovery, and processing. Propose a method for array pattern matching and processing tasks utilizing machine learning methods, such as kernels, clustering, or PSO in conjunction with inverted indexing. Implement the proposed method and demonstrate its efficiency on both artificial and real world datasets. Compare the algorithm with deterministic solutions in terms of time and memory complexities and pattern occurrence miss rates. References Will be provided by the supervisor. doc. Ing. Jan Janoušek, Ph.D. prof. Ing. Pavel Tvrdík, CSc. Head of Department Dean Prague February 28, 2017 Czech Technical University in Prague Faculty of Information Technology Department of Knowledge Engineering Master’s thesis Approximate Pattern Matching In Sparse Multidimensional Arrays Using Machine Learning Based Methods Bc. Anna Kuˇcerov´a Supervisor: Ing. LuboˇsKrˇc´al 9th May 2017 Acknowledgements Main credit goes to my supervisor Ing. -
Balanced Binary Search Trees 1 Introduction 2 BST Analysis
csce750 — Analysis of Algorithms Fall 2020 — Lecture Notes: Balanced Binary Search Trees This document contains slides from the lecture, formatted to be suitable for printing or individ- ual reading, and with some supplemental explanations added. It is intended as a supplement to, rather than a replacement for, the lectures themselves — you should not expect the notes to be self-contained or complete on their own. 1 Introduction CLRS 12, 13 A binary search tree is a data structure that supports these operations: • INSERT(k) • SEARCH(k) • DELETE(k) Basic idea: Store one key at each node. • All keys in the left subtree of n are less than the key stored at n. • All keys in the right subtree of n are greater than the key stored at n. Search and insert are trivial. Delete is slightly trickier, but not too bad. You may notice that these operations are very similar to the opera- tions available for hash tables. However, data structures like BSTs remain important because they can be extended to efficiently sup- port other useful operations like iterating over the elements in order, and finding the largest and smallest elements. These things cannot be done efficiently in hash tables. 2 BST Analysis Each operation can be done in time O(h) on a BST of height h. Worst case: Θ(n) Aside: Does randomization help? • Answer: Sort of. If we know all of the keys at the start, and insert them in a random order, in which each of the n! permutations is equally likely, then the expected tree height is O(lg n). -
Suffix Trees and Suffix Arrays in Primary and Secondary Storage Pang Ko Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2007 Suffix trees and suffix arrays in primary and secondary storage Pang Ko Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Bioinformatics Commons, and the Computer Sciences Commons Recommended Citation Ko, Pang, "Suffix trees and suffix arrays in primary and secondary storage" (2007). Retrospective Theses and Dissertations. 15942. https://lib.dr.iastate.edu/rtd/15942 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Suffix trees and suffix arrays in primary and secondary storage by Pang Ko A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Computer Engineering Program of Study Committee: Srinivas Aluru, Major Professor David Fern´andez-Baca Suraj Kothari Patrick Schnable Srikanta Tirthapura Iowa State University Ames, Iowa 2007 UMI Number: 3274885 UMI Microform 3274885 Copyright 2007 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, MI 48106-1346 ii DEDICATION To my parents iii TABLE OF CONTENTS LISTOFTABLES ................................... v LISTOFFIGURES .................................. vi ACKNOWLEDGEMENTS. .. .. .. .. .. .. .. .. .. ... .. .. .. .. vii ABSTRACT....................................... viii CHAPTER1. INTRODUCTION . 1 1.1 SuffixArrayinMainMemory .