Data Structures for Strings
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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. -
Pattern Matching Using Similarity Measures
Pattern matching using similarity measures Patroonvergelijking met behulp van gelijkenismaten (met een samenvatting in het Nederlands) PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van Rector Magnificus, Prof. Dr. H. O. Voorma, ingevolge het besluit van het College voor Promoties in het openbaar te verdedigen op maandag 18 september 2000 des morgens te 10:30 uur door Michiel Hagedoorn geboren op 13 juli 1972, te Renkum promotor: Prof. Dr. M. H. Overmars Faculteit Wiskunde & Informatica co-promotor: Dr. R. C. Veltkamp Faculteit Wiskunde & Informatica ISBN 90-393-2460-3 PHILIPS '$ The&&% research% described in this thesis has been made possible by financial support from Philips Research Laboratories. The work in this thesis has been carried out in the graduate school ASCI. Contents 1 Introduction 1 1.1Patternmatching.......................... 1 1.2Applications............................. 4 1.3Obtaininggeometricpatterns................... 7 1.4 Paradigms in geometric pattern matching . 8 1.5Similaritymeasurebasedpatternmatching........... 11 1.6Overviewofthisthesis....................... 16 2 A theory of similarity measures 21 2.1Pseudometricspaces........................ 22 2.2Pseudometricpatternspaces................... 30 2.3Embeddingpatternsinafunctionspace............. 40 2.4TheHausdorffmetric........................ 46 2.5Thevolumeofsymmetricdifference............... 54 2.6 Reflection visibility based distances . 60 2.7Summary.............................. 71 2.8Experimentalresults....................... -
Pattern Matching Using Fuzzy Methods David Bell and Lynn Palmer, State of California: Genetic Disease Branch
Pattern Matching Using Fuzzy Methods David Bell and Lynn Palmer, State of California: Genetic Disease Branch ABSTRACT The formula is : Two major methods of detecting similarities Euclidean Distance and 2 a "fuzzy Hamming distance" presented in a paper entitled "F %%y Dij : ; ( <3/i - yj 4 Hamming Distance: A New Dissimilarity Measure" by Bookstein, Klein, and Raita, will be compared using entropy calculations to Euclidean distance is especially useful for comparing determine their abilities to detect patterns in data and match data matching whole word object elements of 2 vectors. The records. .e find that both means of measuring distance are useful code in Java is: depending on the context. .hile fuzzy Hamming distance outperforms in supervised learning situations such as searches, the Listing 1: Euclidean Distance Euclidean distance measure is more useful in unsupervised pattern matching and clustering of data. /** * EuclideanDistance.java INTRODUCTION * * Pattern matching is becoming more of a necessity given the needs for * Created: Fri Oct 07 08:46:40 2002 such methods for detecting similarities in records, epidemiological * * @author David Bell: DHS-GENETICS patterns, genetics and even in the emerging fields of criminal * @version 1.0 behavioral pattern analysis and disease outbreak analysis due to */ possible terrorist activity. 0nfortunately, traditional methods for /** Abstact Distance class linking or matching records, data fields, etc. rely on exact data * @param None matches rather than looking for close matches or patterns. 1f course * @return Distance Template proximity pattern matches are often necessary when dealing with **/ messy data, data that has inexact values and/or data with missing key abstract class distance{ values. -
C Programming: Data Structures and Algorithms
C Programming: Data Structures and Algorithms An introduction to elementary programming concepts in C Jack Straub, Instructor Version 2.07 DRAFT C Programming: Data Structures and Algorithms, Version 2.07 DRAFT C Programming: Data Structures and Algorithms Version 2.07 DRAFT Copyright © 1996 through 2006 by Jack Straub ii 08/12/08 C Programming: Data Structures and Algorithms, Version 2.07 DRAFT Table of Contents COURSE OVERVIEW ........................................................................................ IX 1. BASICS.................................................................................................... 13 1.1 Objectives ...................................................................................................................................... 13 1.2 Typedef .......................................................................................................................................... 13 1.2.1 Typedef and Portability ............................................................................................................. 13 1.2.2 Typedef and Structures .............................................................................................................. 14 1.2.3 Typedef and Functions .............................................................................................................. 14 1.3 Pointers and Arrays ..................................................................................................................... 16 1.4 Dynamic Memory Allocation ..................................................................................................... -
Abstract Data Types
Chapter 2 Abstract Data Types The second idea at the core of computer science, along with algorithms, is data. In a modern computer, data consists fundamentally of binary bits, but meaningful data is organized into primitive data types such as integer, real, and boolean and into more complex data structures such as arrays and binary trees. These data types and data structures always come along with associated operations that can be done on the data. For example, the 32-bit int data type is defined both by the fact that a value of type int consists of 32 binary bits but also by the fact that two int values can be added, subtracted, multiplied, compared, and so on. An array is defined both by the fact that it is a sequence of data items of the same basic type, but also by the fact that it is possible to directly access each of the positions in the list based on its numerical index. So the idea of a data type includes a specification of the possible values of that type together with the operations that can be performed on those values. An algorithm is an abstract idea, and a program is an implementation of an algorithm. Similarly, it is useful to be able to work with the abstract idea behind a data type or data structure, without getting bogged down in the implementation details. The abstraction in this case is called an \abstract data type." An abstract data type specifies the values of the type, but not how those values are represented as collections of bits, and it specifies operations on those values in terms of their inputs, outputs, and effects rather than as particular algorithms or program code. -
Data Structures, Buffers, and Interprocess Communication
Data Structures, Buffers, and Interprocess Communication We’ve looked at several examples of interprocess communication involving the transfer of data from one process to another process. We know of three mechanisms that can be used for this transfer: - Files - Shared Memory - Message Passing The act of transferring data involves one process writing or sending a buffer, and another reading or receiving a buffer. Most of you seem to be getting the basic idea of sending and receiving data for IPC… it’s a lot like reading and writing to a file or stdin and stdout. What seems to be a little confusing though is HOW that data gets copied to a buffer for transmission, and HOW data gets copied out of a buffer after transmission. First… let’s look at a piece of data. typedef struct { char ticker[TICKER_SIZE]; double price; } item; . item next; . The data we want to focus on is “next”. “next” is an object of type “item”. “next” occupies memory in the process. What we’d like to do is send “next” from processA to processB via some kind of IPC. IPC Using File Streams If we were going to use good old C++ filestreams as the IPC mechanism, our code would look something like this to write the file: // processA is the sender… ofstream out; out.open(“myipcfile”); item next; strcpy(next.ticker,”ABC”); next.price = 55; out << next.ticker << “ “ << next.price << endl; out.close(); Notice that we didn’t do this: out << next << endl; Why? Because the “<<” operator doesn’t know what to do with an object of type “item”. -
CSCI 2041: Pattern Matching Basics
CSCI 2041: Pattern Matching Basics Chris Kauffman Last Updated: Fri Sep 28 08:52:58 CDT 2018 1 Logistics Reading Assignment 2 I OCaml System Manual: Ch I Demo in lecture 1.4 - 1.5 I Post today/tomorrow I Practical OCaml: Ch 4 Next Week Goals I Mon: Review I Code patterns I Wed: Exam 1 I Pattern Matching I Fri: Lecture 2 Consider: Summing Adjacent Elements 1 (* match_basics.ml: basic demo of pattern matching *) 2 3 (* Create a list comprised of the sum of adjacent pairs of 4 elements in list. The last element in an odd-length list is 5 part of the return as is. *) 6 let rec sum_adj_ie list = 7 if list = [] then (* CASE of empty list *) 8 [] (* base case *) 9 else 10 let a = List.hd list in (* DESTRUCTURE list *) 11 let atail = List.tl list in (* bind names *) 12 if atail = [] then (* CASE of 1 elem left *) 13 [a] (* base case *) 14 else (* CASE of 2 or more elems left *) 15 let b = List.hd atail in (* destructure list *) 16 let tail = List.tl atail in (* bind names *) 17 (a+b) :: (sum_adj_ie tail) (* recursive case *) The above function follows a common paradigm: I Select between Cases during a computation I Cases are based on structure of data I Data is Destructured to bind names to parts of it 3 Pattern Matching in Programming Languages I Pattern Matching as a programming language feature checks that data matches a certain structure the executes if so I Can take many forms such as processing lines of input files that match a regular expression I Pattern Matching in OCaml/ML combines I Case analysis: does the data match a certain structure I Destructure Binding: bind names to parts of the data I Pattern Matching gives OCaml/ML a certain "cool" factor I Associated with the match/with syntax as follows match something with | pattern1 -> result1 (* pattern1 gives result1 *) | pattern2 -> (* pattern 2.. -
Subtyping Recursive Types
ACM Transactions on Programming Languages and Systems, 15(4), pp. 575-631, 1993. Subtyping Recursive Types Roberto M. Amadio1 Luca Cardelli CNRS-CRIN, Nancy DEC, Systems Research Center Abstract We investigate the interactions of subtyping and recursive types, in a simply typed λ-calculus. The two fundamental questions here are whether two (recursive) types are in the subtype relation, and whether a term has a type. To address the first question, we relate various definitions of type equivalence and subtyping that are induced by a model, an ordering on infinite trees, an algorithm, and a set of type rules. We show soundness and completeness between the rules, the algorithm, and the tree semantics. We also prove soundness and a restricted form of completeness for the model. To address the second question, we show that to every pair of types in the subtype relation we can associate a term whose denotation is the uniquely determined coercion map between the two types. Moreover, we derive an algorithm that, when given a term with implicit coercions, can infer its least type whenever possible. 1This author's work has been supported in part by Digital Equipment Corporation and in part by the Stanford-CNR Collaboration Project. Page 1 Contents 1. Introduction 1.1 Types 1.2 Subtypes 1.3 Equality of Recursive Types 1.4 Subtyping of Recursive Types 1.5 Algorithm outline 1.6 Formal development 2. A Simply Typed λ-calculus with Recursive Types 2.1 Types 2.2 Terms 2.3 Equations 3. Tree Ordering 3.1 Subtyping Non-recursive Types 3.2 Folding and Unfolding 3.3 Tree Expansion 3.4 Finite Approximations 4. -
4 Hash Tables and Associative Arrays
4 FREE Hash Tables and Associative Arrays If you want to get a book from the central library of the University of Karlsruhe, you have to order the book in advance. The library personnel fetch the book from the stacks and deliver it to a room with 100 shelves. You find your book on a shelf numbered with the last two digits of your library card. Why the last digits and not the leading digits? Probably because this distributes the books more evenly among the shelves. The library cards are numbered consecutively as students sign up, and the University of Karlsruhe was founded in 1825. Therefore, the students enrolled at the same time are likely to have the same leading digits in their card number, and only a few shelves would be in use if the leadingCOPY digits were used. The subject of this chapter is the robust and efficient implementation of the above “delivery shelf data structure”. In computer science, this data structure is known as a hash1 table. Hash tables are one implementation of associative arrays, or dictio- naries. The other implementation is the tree data structures which we shall study in Chap. 7. An associative array is an array with a potentially infinite or at least very large index set, out of which only a small number of indices are actually in use. For example, the potential indices may be all strings, and the indices in use may be all identifiers used in a particular C++ program.Or the potential indices may be all ways of placing chess pieces on a chess board, and the indices in use may be the place- ments required in the analysis of a particular game. -
Compiling Pattern Matching to Good Decision Trees
Submitted to ML’08 Compiling Pattern Matching to good Decision Trees Luc Maranget INRIA Luc.marangetinria.fr Abstract In this paper we study compilation to decision tree, whose We address the issue of compiling ML pattern matching to efficient primary advantage is never testing a given subterm of the subject decisions trees. Traditionally, compilation to decision trees is op- value more than once (and whose primary drawback is potential timized by (1) implementing decision trees as dags with maximal code size explosion). Our aim is to refine naive compilation to sharing; (2) guiding a simple compiler with heuristics. We first de- decision trees, and to compare the output of such an optimizing sign new heuristics that are inspired by necessity, a notion from compiler with optimized backtracking automata. lazy pattern matching that we rephrase in terms of decision tree se- Compilation to decision can be very sensitive to the testing mantics. Thereby, we simplify previous semantical frameworks and order of subject value subterms. The situation can be explained demonstrate a direct connection between necessity and decision by the example of an human programmer attempting to translate a ML program into a lower-level language without pattern matching. tree runtime efficiency. We complete our study by experiments, 1 showing that optimized compilation to decision trees is competi- Let f be the following function defined on triples of booleans : tive. We also suggest some heuristics precisely. l e t f x y z = match x,y,z with | _,F,T -> 1 Categories and Subject Descriptors D 3. 3 [Programming Lan- | F,T,_ -> 2 guages]: Language Constructs and Features—Patterns | _,_,F -> 3 | _,_,T -> 4 General Terms Design, Performance, Sequentiality. -
CSE 307: Principles of Programming Languages Classes and Inheritance
OOP Introduction Type & Subtype Inheritance Overloading and Overriding CSE 307: Principles of Programming Languages Classes and Inheritance R. Sekar 1 / 52 OOP Introduction Type & Subtype Inheritance Overloading and Overriding Topics 1. OOP Introduction 3. Inheritance 2. Type & Subtype 4. Overloading and Overriding 2 / 52 OOP Introduction Type & Subtype Inheritance Overloading and Overriding Section 1 OOP Introduction 3 / 52 OOP Introduction Type & Subtype Inheritance Overloading and Overriding OOP (Object Oriented Programming) So far the languages that we encountered treat data and computation separately. In OOP, the data and computation are combined into an “object”. 4 / 52 OOP Introduction Type & Subtype Inheritance Overloading and Overriding Benefits of OOP more convenient: collects related information together, rather than distributing it. Example: C++ iostream class collects all I/O related operations together into one central place. Contrast with C I/O library, which consists of many distinct functions such as getchar, printf, scanf, sscanf, etc. centralizes and regulates access to data. If there is an error that corrupts object data, we need to look for the error only within its class Contrast with C programs, where access/modification code is distributed throughout the program 5 / 52 OOP Introduction Type & Subtype Inheritance Overloading and Overriding Benefits of OOP (Continued) Promotes reuse. by separating interface from implementation. We can replace the implementation of an object without changing client code. Contrast with C, where the implementation of a data structure such as a linked list is integrated into the client code by permitting extension of new objects via inheritance. Inheritance allows a new class to reuse the features of an existing class. -
Combinatorial Pattern Matching
Combinatorial Pattern Matching 1 A Recurring Problem Finding patterns within sequences Variants on this idea Finding repeated motifs amoungst a set of strings What are the most frequent k-mers How many time does a specific k-mer appear Fundamental problem: Pattern Matching Find all positions of a particular substring in given sequence? 2 Pattern Matching Goal: Find all occurrences of a pattern in a text Input: Pattern p = p1, p2, … pn and text t = t1, t2, … tm Output: All positions 1 < i < (m – n + 1) such that the n-letter substring of t starting at i matches p def bruteForcePatternMatching(p, t): locations = [] for i in xrange(0, len(t)-len(p)+1): if t[i:i+len(p)] == p: locations.append(i) return locations print bruteForcePatternMatching("ssi", "imissmissmississippi") [11, 14] 3 Pattern Matching Performance Performance: m - length of the text t n - the length of the pattern p Search Loop - executed O(m) times Comparison - O(n) symbols compared Total cost - O(mn) per pattern In practice, most comparisons terminate early Worst-case: p = "AAAT" t = "AAAAAAAAAAAAAAAAAAAAAAAT" 4 We can do better! If we preprocess our pattern we can search more effciently (O(n)) Example: imissmissmississippi 1. s 2. s 3. s 4. SSi 5. s 6. SSi 7. s 8. SSI - match at 11 9. SSI - match at 14 10. s 11. s 12. s At steps 4 and 6 after finding the mismatch i ≠ m we can skip over all positions tested because we know that the suffix "sm" is not a prefix of our pattern "ssi" Even works for our worst-case example "AAAAT" in "AAAAAAAAAAAAAAT" by recognizing the shared prefixes ("AAA" in "AAAA").