Binary Heaps
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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. -
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. -
Data Structures and Algorithms Binary Heaps (S&W 2.4)
Data structures and algorithms DAT038/TDA417, LP2 2019 Lecture 12, 2019-12-02 Binary heaps (S&W 2.4) Some slides by Sedgewick & Wayne Collections A collection is a data type that stores groups of items. stack Push, Pop linked list, resizing array queue Enqueue, Dequeue linked list, resizing array symbol table Put, Get, Delete BST, hash table, trie, TST set Add, ontains, Delete BST, hash table, trie, TST A priority queue is another kind of collection. “ Show me your code and conceal your data structures, and I shall continue to be mystified. Show me your data structures, and I won't usually need your code; it'll be obvious.” — Fred Brooks 2 Priority queues Collections. Can add and remove items. Stack. Add item; remove the item most recently added. Queue. Add item; remove the item least recently added. Min priority queue. Add item; remove the smallest item. Max priority queue. Add item; remove the largest item. return contents contents operation argument value size (unordered) (ordered) insert P 1 P P insert Q 2 P Q P Q insert E 3 P Q E E P Q remove max Q 2 P E E P insert X 3 P E X E P X insert A 4 P E X A A E P X insert M 5 P E X A M A E M P X remove max X 4 P E M A A E M P insert P 5 P E M A P A E M P P insert L 6 P E M A P L A E L M P P insert E 7 P E M A P L E A E E L M P P remove max P 6 E M A P L E A E E L M P A sequence of operations on a priority queue 3 Priority queue API Requirement. -
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() { . -
Priority Queues and Binary Heaps Chapter 6.5
Priority Queues and Binary Heaps Chapter 6.5 1 Some animals are more equal than others • A queue is a FIFO data structure • the first element in is the first element out • which of course means the last one in is the last one out • But sometimes we want to sort of have a queue but we want to order items according to some characteristic the item has. 107 - Trees 2 Priorities • We call the ordering characteristic the priority. • When we pull something from this “queue” we always get the element with the best priority (sometimes best means lowest). • It is really common in Operating Systems to use priority to schedule when something happens. e.g. • the most important process should run before a process which isn’t so important • data off disk should be retrieved for more important processes first 107 - Trees 3 Priority Queue • A priority queue always produces the element with the best priority when queried. • You can do this in many ways • keep the list sorted • or search the list for the minimum value (if like the textbook - and Unix actually - you take the smallest value to be the best) • You should be able to estimate the Big O values for implementations like this. e.g. O(n) for choosing the minimum value of an unsorted list. • There is a clever data structure which allows all operations on a priority queue to be done in O(log n). 107 - Trees 4 Binary Heap Actually binary min heap • Shape property - a complete binary tree - all levels except the last full. -
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. -
CS210-Data Structures-Module-29-Binary-Heap-II
Data Structures and Algorithms (CS210A) Lecture 29: • Building a Binary heap on 풏 elements in O(풏) time. • Applications of Binary heap : sorting • Binary trees: beyond searching and sorting 1 Recap from the last lecture 2 A complete binary tree How many leaves are there in a Complete Binary tree of size 풏 ? 풏/ퟐ 3 Building a Binary heap Problem: Given 풏 elements {푥0, …, 푥푛−1}, build a binary heap H storing them. Trivial solution: (Building the Binary heap incrementally) CreateHeap(H); For( 풊 = 0 to 풏 − ퟏ ) What is the time Insert(푥,H); complexity of this algorithm? 4 Building a Binary heap incrementally What useful inference can you draw from Top-down this Theorem ? approach The time complexity for inserting a leaf node = ?O (log 풏 ) # leaf nodes = 풏/ퟐ , Theorem: Time complexity of building a binary heap incrementally is O(풏 log 풏). 5 Building a Binary heap incrementally What useful inference can you draw from Top-down this Theorem ? approach The O(풏) time algorithm must take O(1) time for each of the 풏/ퟐ leaves. 6 Building a Binary heap incrementally Top-down approach 7 Think of alternate approach for building a binary heap In any complete 98 binaryDoes treeit suggest, how a manynew nodes approach satisfy to heapbuild propertybinary heap ? ? 14 33 all leaf 37 11 52 32 nodes 41 21 76 85 17 25 88 29 Bottom-up approach 47 75 9 57 23 heap property: “Every ? node stores value smaller than its children” We just need to ensure this property at each node. -
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 -
CS 270 Algorithms
CS 270 Algorithms Week 10 Oliver Kullmann Binary heaps Sorting Heapification Building a heap 1 Binary heaps HEAP- SORT Priority 2 Heapification queues QUICK- 3 Building a heap SORT Analysing 4 QUICK- HEAP-SORT SORT 5 Priority queues Tutorial 6 QUICK-SORT 7 Analysing QUICK-SORT 8 Tutorial CS 270 General remarks Algorithms Oliver Kullmann Binary heaps Heapification Building a heap We return to sorting, considering HEAP-SORT and HEAP- QUICK-SORT. SORT Priority queues CLRS Reading from for week 7 QUICK- SORT 1 Chapter 6, Sections 6.1 - 6.5. Analysing 2 QUICK- Chapter 7, Sections 7.1, 7.2. SORT Tutorial CS 270 Discover the properties of binary heaps Algorithms Oliver Running example Kullmann Binary heaps Heapification Building a heap HEAP- SORT Priority queues QUICK- SORT Analysing QUICK- SORT Tutorial CS 270 First property: level-completeness Algorithms Oliver Kullmann Binary heaps In week 7 we have seen binary trees: Heapification Building a 1 We said they should be as “balanced” as possible. heap 2 Perfect are the perfect binary trees. HEAP- SORT 3 Now close to perfect come the level-complete binary Priority trees: queues QUICK- 1 We can partition the nodes of a (binary) tree T into levels, SORT according to their distance from the root. Analysing 2 We have levels 0, 1,..., ht(T ). QUICK- k SORT 3 Level k has from 1 to 2 nodes. Tutorial 4 If all levels k except possibly of level ht(T ) are full (have precisely 2k nodes in them), then we call the tree level-complete. CS 270 Examples Algorithms Oliver The binary tree Kullmann 1 ❚ Binary heaps ❥❥❥❥ ❚❚❚❚ ❥❥❥❥ ❚❚❚❚ ❥❥❥❥ ❚❚❚❚ Heapification 2 ❥ 3 ❖ ❄❄ ❖❖ Building a ⑧⑧ ❄ ⑧⑧ ❖❖ heap ⑧⑧ ❄ ⑧⑧ ❖❖❖ 4 5 6 ❄ 7 ❄ HEAP- ⑧ ❄ ⑧ ❄ SORT ⑧⑧ ❄ ⑧⑧ ❄ Priority 10 13 14 15 queues QUICK- is level-complete (level-sizes are 1, 2, 4, 4), while SORT ❥ 1 ❚❚ Analysing ❥❥❥❥ ❚❚❚❚ QUICK- ❥❥❥ ❚❚❚ SORT ❥❥❥ ❚❚❚❚ 2 ❥❥ 3 ♦♦♦ ❄❄ ⑧ Tutorial ♦♦ ❄❄ ⑧⑧ ♦♦♦ ⑧ 4 ❄ 5 ❄ 6 ❄ ⑧⑧ ❄❄ ⑧ ❄ ⑧ ❄ ⑧⑧ ❄ ⑧⑧ ❄ ⑧⑧ ❄ 8 9 10 11 12 13 is not (level-sizes are 1, 2, 3, 6). -
Kd Trees What's the Goal for This Course? Data St
Today’s Outline - kd trees CSE 326: Data Structures Too much light often blinds gentlemen of this sort, Seeing the forest for the trees They cannot see the forest for the trees. - Christoph Martin Wieland Hannah Tang and Brian Tjaden Summer Quarter 2002 What’s the goal for this course? Data Structures - what’s in a name? Shakespeare It is not possible for one to teach others, until one can first teach herself - Confucious • Stacks and Queues • Asymptotic analysis • Priority Queues • Sorting – Binary heap, Leftist heap, Skew heap, d - heap – Comparison based sorting, lower- • Trees bound on sorting, radix sorting – Binary search tree, AVL tree, Splay tree, B tree • World Wide Web • Hash Tables – Open and closed hashing, extendible, perfect, • Implement if you had to and universal hashing • Understand trade-offs between • Disjoint Sets various data structures/algorithms • Graphs • Know when to use and when not to – Topological sort, shortest path algorithms, Dijkstra’s algorithm, minimum spanning trees use (Prim’s algorithm and Kruskal’s algorithm) • Real world applications Range Query Range Query Example Y A range query is a search in a dictionary in which the exact key may not be entirely specified. Bellingham Seattle Spokane Range queries are the primary interface Tacoma Olympia with multi-D data structures. Pullman Yakima Walla Walla Remember Assignment #2? Give an algorithm that takes a binary search tree as input along with 2 keys, x and y, with xÃÃy, and ÃÃ ÃÃ prints all keys z in the tree such that x z y. X 1 Range Querying in 1-D -
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 .