Efficient In-Memory Indexing with Generalized Prefix Trees
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Application of TRIE Data Structure and Corresponding Associative Algorithms for Process Optimization in GRID Environment
Application of TRIE data structure and corresponding associative algorithms for process optimization in GRID environment V. V. Kashanskya, I. L. Kaftannikovb South Ural State University (National Research University), 76, Lenin prospekt, Chelyabinsk, 454080, Russia E-mail: a [email protected], b [email protected] Growing interest around different BOINC powered projects made volunteer GRID model widely used last years, arranging lots of computational resources in different environments. There are many revealed problems of Big Data and horizontally scalable multiuser systems. This paper provides an analysis of TRIE data structure and possibilities of its application in contemporary volunteer GRID networks, including routing (L3 OSI) and spe- cialized key-value storage engine (L7 OSI). The main goal is to show how TRIE mechanisms can influence de- livery process of the corresponding GRID environment resources and services at different layers of networking abstraction. The relevance of the optimization topic is ensured by the fact that with increasing data flow intensi- ty, the latency of the various linear algorithm based subsystems as well increases. This leads to the general ef- fects, such as unacceptably high transmission time and processing instability. Logically paper can be divided into three parts with summary. The first part provides definition of TRIE and asymptotic estimates of corresponding algorithms (searching, deletion, insertion). The second part is devoted to the problem of routing time reduction by applying TRIE data structure. In particular, we analyze Cisco IOS switching services based on Bitwise TRIE and 256 way TRIE data structures. The third part contains general BOINC architecture review and recommenda- tions for highly-loaded projects. -
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. -
Lecture 26 Fall 2019 Instructors: B&S Administrative Details
CSCI 136 Data Structures & Advanced Programming Lecture 26 Fall 2019 Instructors: B&S Administrative Details • Lab 9: Super Lexicon is online • Partners are permitted this week! • Please fill out the form by tonight at midnight • Lab 6 back 2 2 Today • Lab 9 • Efficient Binary search trees (Ch 14) • AVL Trees • Height is O(log n), so all operations are O(log n) • Red-Black Trees • Different height-balancing idea: height is O(log n) • All operations are O(log n) 3 2 Implementing the Lexicon as a trie There are several different data structures you could use to implement a lexicon— a sorted array, a linked list, a binary search tree, a hashtable, and many others. Each of these offers tradeoffs between the speed of word and prefix lookup, amount of memory required to store the data structure, the ease of writing and debugging the code, performance of add/remove, and so on. The implementation we will use is a special kind of tree called a trie (pronounced "try"), designed for just this purpose. A trie is a letter-tree that efficiently stores strings. A node in a trie represents a letter. A path through the trie traces out a sequence ofLab letters that9 represent : Lexicon a prefix or word in the lexicon. Instead of just two children as in a binary tree, each trie node has potentially 26 child pointers (one for each letter of the alphabet). Whereas searching a binary search tree eliminates half the words with a left or right turn, a search in a trie follows the child pointer for the next letter, which narrows the search• Goal: to just words Build starting a datawith that structure letter. -
HARD DRIVES How Is Data Read and Stored on a Hard Drive?
HARD DRIVES Alternatively referred to as a hard disk drive and abbreviated as HD or HDD, thehard drive is the computer's main storage media device that permanently stores all data on the computer. The hard drive was first introduced on September 13, 1956 and consists of one or more hard drive platters inside of air sealed casing. Most computer hard drives are in an internal drive bay at the front of the computer and connect to themotherboard using either ATA, SCSI, or a SATA cable and power cable. Below, is a picture of what the inside of a hard drive looks like for a desktop and laptop hard drive. As can be seen in the above picture, the desktop hard drive has six components: the head actuator, read/write actuator arm, read/write head, spindle, and platter. On the back of a hard drive is a circuit board called the disk controller. Tip: New users often confuse memory (RAM) with disk drive space. See our memory definition for a comparison between memory and storage. How is data read and stored on a hard drive? Data sent to and from the hard drive is interpreted by the disk controller, which tells the hard drive what to do and how to move the components within the drive. When the operating system needs to read or write information, it examines the hard drives File Allocation Table (FAT) to determine file location and available areas. Once this has been determined, the disk controller instructs the actuator to move the read/write arm and align the read/write head. -
Search Trees for Strings a Balanced Binary Search Tree Is a Powerful Data Structure That Stores a Set of Objects and Supports Many Operations Including
Search Trees for Strings A balanced binary search tree is a powerful data structure that stores a set of objects and supports many operations including: Insert and Delete. Lookup: Find if a given object is in the set, and if it is, possibly return some data associated with the object. Range query: Find all objects in a given range. The time complexity of the operations for a set of size n is O(log n) (plus the size of the result) assuming constant time comparisons. There are also alternative data structures, particularly if we do not need to support all operations: • A hash table supports operations in constant time but does not support range queries. • An ordered array is simpler, faster and more space efficient in practice, but does not support insertions and deletions. A data structure is called dynamic if it supports insertions and deletions and static if not. 107 When the objects are strings, operations slow down: • Comparison are slower. For example, the average case time complexity is O(log n logσ n) for operations in a binary search tree storing a random set of strings. • Computing a hash function is slower too. For a string set R, there are also new types of queries: Lcp query: What is the length of the longest prefix of the query string S that is also a prefix of some string in R. Prefix query: Find all strings in R that have S as a prefix. The prefix query is a special type of range query. 108 Trie A trie is a rooted tree with the following properties: • Edges are labelled with symbols from an alphabet Σ. -
X-Fast and Y-Fast Tries
x-Fast and y-Fast Tries Outline for Today ● Bitwise Tries ● A simple ordered dictionary for integers. ● x-Fast Tries ● Tries + Hashing ● y-Fast Tries ● Tries + Hashing + Subdivision + Balanced Trees + Amortization Recap from Last Time Ordered Dictionaries ● An ordered dictionary is a data structure that maintains a set S of elements drawn from an ordered universe � and supports these operations: ● insert(x), which adds x to S. ● is-empty(), which returns whether S = Ø. ● lookup(x), which returns whether x ∈ S. ● delete(x), which removes x from S. ● max() / min(), which returns the maximum or minimum element of S. ● successor(x), which returns the smallest element of S greater than x, and ● predecessor(x), which returns the largest element of S smaller than x. Integer Ordered Dictionaries ● Suppose that � = [U] = {0, 1, …, U – 1}. ● A van Emde Boas tree is an ordered dictionary for [U] where ● min, max, and is-empty run in time O(1). ● All other operations run in time O(log log U). ● Space usage is Θ(U) if implemented deterministically, and O(n) if implemented using hash tables. ● Question: Is there a simpler data structure meeting these bounds? The Machine Model ● We assume a transdichotomous machine model: ● Memory is composed of words of w bits each. ● Basic arithmetic and bitwise operations on words take time O(1) each. ● w = Ω(log n). A Start: Bitwise Tries Tries Revisited ● Recall: A trie is a simple data 0 1 structure for storing strings. 0 1 0 1 ● Integers can be thought of as strings of bits. 1 0 1 1 0 ● Idea: Store integers in a bitwise trie. -
Tries and String Matching
Tries and String Matching Where We've Been ● Fundamental Data Structures ● Red/black trees, B-trees, RMQ, etc. ● Isometries ● Red/black trees ≡ 2-3-4 trees, binomial heaps ≡ binary numbers, etc. ● Amortized Analysis ● Aggregate, banker's, and potential methods. Where We're Going ● String Data Structures ● Data structures for storing and manipulating text. ● Randomized Data Structures ● Using randomness as a building block. ● Integer Data Structures ● Breaking the Ω(n log n) sorting barrier. ● Dynamic Connectivity ● Maintaining connectivity in an changing world. String Data Structures Text Processing ● String processing shows up everywhere: ● Computational biology: Manipulating DNA sequences. ● NLP: Storing and organizing huge text databases. ● Computer security: Building antivirus databases. ● Many problems have polynomial-time solutions. ● Goal: Design theoretically and practically efficient algorithms that outperform brute-force approaches. Outline for Today ● Tries ● A fundamental building block in string processing algorithms. ● Aho-Corasick String Matching ● A fast and elegant algorithm for searching large texts for known substrings. Tries Ordered Dictionaries ● Suppose we want to store a set of elements supporting the following operations: ● Insertion of new elements. ● Deletion of old elements. ● Membership queries. ● Successor queries. ● Predecessor queries. ● Min/max queries. ● Can use a standard red/black tree or splay tree to get (worst-case or expected) O(log n) implementations of each. A Catch ● Suppose we want to store a set of strings. ● Comparing two strings of lengths r and s takes time O(min{r, s}). ● Operations on a balanced BST or splay tree now take time O(M log n), where M is the length of the longest string in the tree. -
String Algorithm
Trie: A data-structure for a set of words All words over the alphabet Σ={a,b,..z}. In the slides, let say that the alphabet is only {a,b,c,d} S – set of words = {a,aba, a, aca, addd} Need to support the operations Tries and suffixes trees • insert(w) – add a new word w into S. • delete(w) – delete the word w from S. • find(w) is w in S ? Alon Efrat • Future operation: Computer Science Department • Given text (many words) where is w in the text. University of Arizona • The time for each operation should be O(k), where k is the number of letters in w • Usually each word is associated with addition info – not discussed here. 2 Trie (Tree+Retrive) for S A trie - example p->ar[‘b’-’a’] Note: The label of an edge is the label of n A tree where each node is a struct consist the cell from which this edge exits n Struct node { p a b c d n char[4] *ar; 0 a n char flag ; /* 1 if a word ends at this node. b d Otherwise 0 */ a b c d a b c d Corresponding to w=“d” } a b c d a b c d flag 1 1 0 ar 1 b Corr. To w=“db” (not in S, flag=0) S={a,b,dbb} a b c d 0 a b c d flag ar 1 b Rule: a b c d Corr. to w= dbb Each node corresponds to a word w 1 “ ” (w which is in S iff the flag is 1) 3 In S, so flag=1 4 1 Finding if word w is in the tree Inserting a word w p=root; i =0 Recall – we need to modify the tree so find(w) would return While(1){ TRUE. -
Fast Binary and Multiway Prefix Searches for Packet Forwarding
Computer Networks 51 (2007) 588–605 www.elsevier.com/locate/comnet Fast binary and multiway prefix searches for packet forwarding Yeim-Kuan Chang * Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, ROC Received 24 June 2005; received in revised form 24 January 2006; accepted 12 May 2006 Available online 21 June 2006 Responsible Editor: J.C. de Oliveira Abstract Backbone routers with tens-of-gigabits-per-second links are indispensable communication devices to deploy on the Inter- net. The IP lookup operation is the most critical task that must be improved in routers. In this paper, we first present a systematic method to compare prefixes of different lengths. The list of prefixes can then be sorted and stored in a sequential array, which is contrary to the linked lists used in most of trie-based structures. Next, fast binary and multiway prefix searches assisted by auxiliary prefixes are proposed. We also developed a 32-bit representation to encode the prefixes of different lengths. For the large routing tables currently available on the Internet, the proposed multiway prefix search can achieve the worst-case number of memory accesses of three and four if the sizes of the CPU cache lines are 64 bytes and 32 bytes, respectively. The IPv4 simulation results show that the proposed prefix searches outperform the existing IP lookup schemes in terms of lookup times and memory consumption. The simulations using IPv6 routing tables also show the performance advantages of the proposed binary prefix searches. We also analyze the performance of the existing lookup schemes by con- currently considering the lookup speed, the update speed, and the memory consumption. -
B-Tries for Disk-Based String Management
The VLDB Journal (2009) 18:157–179 DOI 10.1007/s00778-008-0094-1 REGULAR PAPER B-tries for disk-based string management Nikolas Askitis · Justin Zobel Received: 11 June 2006 / Revised: 14 December 2007 / Accepted: 9 January 2008 / Published online: 11 March 2008 © Springer-Verlag 2008 Abstract A wide range of applications require that large tries that are efficient in memory cannot be directly mapped quantities of data be maintained in sort order on disk. The to disk without incurring high costs [52]. B-tree, and its variants, are an efficient general-purpose disk- The best-known structure for this task is the B-tree, pro- based data structure that is almost universally used for this posed by Bayer and McCreight [9], and its variants. In its task. The B-trie has the potential to be a competitive alter- most practical form, the B-tree is a multi-way balanced tree native for the storage of data where strings are used as keys, comprised of two types of nodes: internal and leaf. Internal but has not previously been thoroughly described or tested. nodes are used as an index or a road-map to leaf nodes, which We propose new algorithms for the insertion, deletion, and contain the data. The B-tree is considered to be the most effi- equality search of variable-length strings in a disk-resident cient data structure for maintaining sorted data on disk [3,43, B-trie, as well as novel splitting strategies which are a criti- 83]. A key characteristic is the use of a balanced tree struc- ( ) cal element of a practical implementation. -
Algorithm for Character Recognition Based on the Trie Structure
University of Montana ScholarWorks at University of Montana Graduate Student Theses, Dissertations, & Professional Papers Graduate School 1987 Algorithm for character recognition based on the trie structure Mohammad N. Paryavi The University of Montana Follow this and additional works at: https://scholarworks.umt.edu/etd Let us know how access to this document benefits ou.y Recommended Citation Paryavi, Mohammad N., "Algorithm for character recognition based on the trie structure" (1987). Graduate Student Theses, Dissertations, & Professional Papers. 5091. https://scholarworks.umt.edu/etd/5091 This Thesis is brought to you for free and open access by the Graduate School at ScholarWorks at University of Montana. It has been accepted for inclusion in Graduate Student Theses, Dissertations, & Professional Papers by an authorized administrator of ScholarWorks at University of Montana. For more information, please contact [email protected]. COPYRIGHT ACT OF 1 9 7 6 Th is is an unpublished manuscript in which copyright sub s i s t s , Any further r e p r in t in g of its contents must be approved BY THE AUTHOR, Ma n sfield L ibrary U n iv e r s it y of Montana Date : 1 987__ AN ALGORITHM FOR CHARACTER RECOGNITION BASED ON THE TRIE STRUCTURE By Mohammad N. Paryavi B. A., University of Washington, 1983 Presented in partial fulfillment of the requirements for the degree of Master of Science University of Montana 1987 Approved by lairman, Board of Examiners iean, Graduate School UMI Number: EP40555 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. -
Complexity Analysis of Tries and Spanning Tree Problems Bernd
◦ ◦ ◦ ◦ ECHNISCHE NIVERSITÄT ÜNCHEN ◦ ◦ ◦ ◦ T U M ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ FAKULTÄT FÜR INFORMATIK ◦ ◦ ◦ Lehrstuhl für Effiziente Algorithmen Complexity Analysis of Tries and Spanning Tree Problems Bernd Stefan Eckhardt Vollständiger Abdruck der von der Fakultät für Informatik der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. J. Schlichter Prüfer der Dissertation: 1. Univ.-Prof. Dr. E. W. Mayr 2. Univ.-Prof. A. Kemper, Ph. D. Die Dissertation wurde am 13.12.2007 bei der Technischen Universität München eingereicht und durch die Fakultät für Informatik am 23.11.2009 angenommen. ii Abstract Much of the research progress that is achieved nowadays in various scientific fields has its origin in the increasing computational power and the elaborated mathematical theory which are available for processing data. For example, efficient algorithms and data structures play an important role in modern biology: the research field that has only recently grown out of biology and informatics is called bioinformatics. String and prefix matching operations on DNA or protein sequences are among the most important kinds of operations in contemporary bioinformatics applications. The importance of those operations is based on the assumption that the function of a gene or protein and its sequence encoding are strongly related. Clearly, not all kinds of data that appear in bioinformatics can be modeled as textual data, but in many situations data are more appropriately modeled by networks, e.g., metabolic networks or phylogenetic networks. For such kinds of data algorithmic network analysis, i.e., applying graph algorithms to compute the relationship between the networks elements, is an indis- pensable tool in bioinformatics.