On-line Construction of Suffix Tree Esko Ukkonen Algorithmica Vol. 14, No. 3, pp. 249-260, 1995.

Slides:

Advertisements

Similar presentations

1 Average Case Analysis of an Exact String Matching Algorithm Advisor: Professor R. C. T. Lee Speaker: S. C. Chen.

Advertisements

On-line Construction of Suffix Trees Chairman : Prof. R.C.T. Lee Speaker : C. S. Wu ( ) June 10, 2004 Dept. of CSIE National Chi Nan University.

Recognising Languages We will tackle the problem of defining languages by considering how we could recognise them. Problem: Is there a method of recognising.

Boosting Textual Compression in Optimal Linear Time.

Chapter 6 Languages: finite state machines

Cook’s Theorem The Foundation of NP-Completeness.

Suffix Trees Construction and Applications João Carreira 2008.

Suffix Tree. Suffix Tree Representation S=xabxac Represent every edge using its start and end text location.

Suffix Trees. 2 Outline Introduction Suffix Trees (ST) Building STs in linear time: Ukkonen’s algorithm Applications of ST.

Presented By Dr. Shazzad Hosain Asst. Prof. EECS, NSU Linear Time Construction of Suffix Tree.

Trie/Suffix Trie/Suffix Tree. Trie A trie (from retrieval), is a multi-way tree structure useful for storing strings over an alphabet. It has been used.

Data Compressor---Huffman Encoding and Decoding. Huffman Encoding Compression Typically, in files and messages, Each character requires 1 byte or 8 bits.

Two implementation issues Alphabet size Generalizing to multiple strings.

Suffix Trees Specialized form of keyword trees New ideas –preprocess text T, not pattern P O(m) preprocess time O(n+k) search time –k is number of occurrences.

What about the trees of the Mississippi? Suffix Trees explained in an algorithm for indexing large biological sequences Jacob Kleerekoper & Marjolijn Elsinga.

1 Suffix tree and suffix array techniques for pattern analysis in strings Esko Ukkonen Univ Helsinki Erice School 30 Oct 2005 Modified Alon Itai 2006.

1 Suffix Trees Charles Yan Suffix Trees: Motivations Substring problem: One is given a text T of length m. After O (m) preprocessing time, one.

Factor Oracle, Suffix Oracle 1 Factor Oracle Suffix Oracle.

SUFFIX TREES From exact to approximate string matching. 17 dicembre 2003 Luca Bortolussi.

Suffix Sorting & Related Algoritmics Martin Farach-Colton Rutgers University USA.

15-853Page : Algorithms in the Real World Suffix Trees.

296.3: Algorithms in the Real World

© 2004 Goodrich, Tamassia Tries1. © 2004 Goodrich, Tamassia Tries2 Preprocessing Strings Preprocessing the pattern speeds up pattern matching queries.

1 Prof. Dr. Th. Ottmann Theory I Algorithm Design and Analysis (12 - Text search: suffix trees)

1 Data structures for Pattern Matching Suffix trees and suffix arrays are a basic data structure in pattern matching Reported by: Olga Sergeeva, Saint.

CSE 746 – Introduction to Bioinformatics Research Project Two methods of DNA Sequencing – Comparing and Intertwining Suffix Trees and De Bruijn Graphs.

Combinatorial Pattern Matching CS 466 Saurabh Sinha.

Advanced Algorithm Design and Analysis (Lecture 4) SW5 fall 2004 Simonas Šaltenis E1-215b

Presented By Dr. Shazzad Hosain Asst. Prof. EECS, NSU Linear Time Construction of Suffix Tree.

Sequence Local Alignment using Directed Acyclic Word Graph Do Huy Hoang.

Suffix Trees String … any sequence of characters. Substring of string S … string composed of characters i through j, i ate is.

Windows Scheduling Problems for Broadcast System 1 Amotz Bar-Noy, and Richard E. Ladner Presented by Qiaosheng Shi.

1 Introduction to Computability Theory Lecture3: Regular Expressions Prof. Amos Israeli.

Introduction to Computability Theory

Advisor: Prof. R. C. T. Lee Reporter: Z. H. Pan

Transparency No. P2C4-1 Formal Language and Automata Theory Part II Chapter 4 Parse Trees and Parsing.

E.G.M. PetrakisTries1  Trees of order >= 2  Variable length keys  The decision on what path to follow is taken based on potion of the key  Static environment,

Faster Algorithm for String Matching with k Mismatches Amihood Amir, Moshe Lewenstin, Ely Porat Journal of Algorithms, Vol. 50, 2004, pp Date.

Building Suffix Trees in O(m) time Weiner had first linear time algorithm in 1973 McCreight developed a more space efficient algorithm in 1976 Ukkonen.

Survey: String Matching with k Mismatches Moshe Lewenstein Bar Ilan University.

On the Use of Regular Expressions for Searching Text Charles L.A. Clarke and Gordon V. Cormack Fast Text Searching.

Introduction to CS Theory Lecture 3 – Regular Languages Piotr Faliszewski

1. 2 Overview  Suffix tries  On-line construction of suffix tries in quadratic time  Suffix trees  On-line construction of suffix trees in linear.

Improved string matching with k mismatches (The Kangaroo Method) Galil, R. Giancarlo SIGACT News, Vol. 17, No. 4, 1986, pp. 52–54 Original: Moshe Lewenstein.

UNIVERSITY OF SOUTH CAROLINA College of Engineering & Information Technology Bioinformatics Algorithms and Data Structures Chapter 1: Exact String Matching.

Faster Algorithm for String Matching with k Mismatches (II) Amihood Amir, Moshe Lewenstin, Ely Porat Journal of Algorithms, Vol. 50, 2004, pp

B + -Trees Same structure as B-trees. Dictionary pairs are in leaves only. Leaves form a doubly-linked list. Remaining nodes have following structure:

1.7 Introduction to Solving Inequalities

Regular Grammars Chapter 7. Regular Grammars A regular grammar G is a quadruple (V, , R, S), where: ● V is the rule alphabet, which contains nonterminals.

Regular Grammars Chapter 7 1. Regular Grammars A regular grammar G is a quadruple (V, , R, S), where: ● V is the rule alphabet, which contains nonterminals.

Tries1. 2 Outline and Reading Standard tries (§9.2.1) Compressed tries (§9.2.2) Suffix tries (§9.2.3)

Ravello, /09C.E. On some researches... Chiara Epifanio.

CSCI 2670 Introduction to Theory of Computing September 13.

Algorithms for hard problems Automata and tree automata Juris Viksna, 2015.

Generalization of a Suffix Tree for RNA Structural Pattern Matching Tetsuo Shibuya Algorithmica (2004), vol. 39, pp Created by: Yung-Hsing Peng Date:

10/30/2012COMP 555 Bioalgorithms (Fall 2012)1 Lecture 16: Combinatorial Pattern Matching Study Chapter 9.1 – 9.5.

Dipankar Ranjan Baisya, Mir Md. Faysal & M. Sohel Rahman CSE, BUET Dhaka 1000 Degenerate String Reconstruction from Cover Arrays (Extended Abstract) 1.

Chapter 11. Chapter Summary  Introduction to trees (11.1)  Application of trees (11.2)  Tree traversal (11.3)  Spanning trees (11.4)

Nov String algorithms, Q Ukkonen’s suffix tree algorithm ● Recall McCreight’s approach: – For i = 1.. n+1, build compressed trie of {x[j..n]$

Generic Trees—Trie, Compressed Trie, Suffix Trie (with Analysi

Tries 4/16/2018 8:59 AM Presentation for use with the textbook Data Structures and Algorithms in Java, 6th edition, by M. T. Goodrich, R. Tamassia, and.

CSE202: Introduction to Formal Languages and Automata Theory

15-853:Algorithms in the Real World

Tries 07/28/16 11:04 Text Compression

1.7 Introduction to Solving Inequalities

Andrzej Ehrenfeucht, University of Colorado, Boulder

Ukkonen's suffix tree construction algorithm

Tries 9/14/ :13 AM Presentation for use with the textbook Data Structures and Algorithms in Java, 6th edition, by M. T. Goodrich, R. Tamassia, and.

Chapter 11 Data Compression

Tries 2/27/2019 5:37 PM Tries Tries.

Presentation transcript:

On-line Construction of Suffix Tree Esko Ukkonen Algorithmica Vol. 14, No. 3, pp , 1995

Abstract An on-line algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It has always the suffix tree for the scanned part of the string ready. The method is developed as a linear-time version of a very simple algorithm for (quadratic size) suffix tries.

Abstract Regardless of its quadratic worst-case this latter algorithm can be a good practical method when the string is not too long. Another variation of this method is shown to give in a natural way the well-known algorithms for constructing suffix automata (DAWGs).

Suffix Trie for (cacao) c c c Σ o o o a a a o a o

T = t 1 t 2 …t n is a string over an alphabet Σ. x, y are substrings of T. are states that corresponds to x, y. Transition function : for all such that y = xa. where. ex: Suffix function: if x=ay for some a. ex:

Construction of STrie(cacao) c a c a o a cao o o o Σ

Construction of STree(cacao) Σ c Σ ca Σ a cac Σ ac caca Σ aca ca Σ a cao o o o

States: Branching state (at least two transitions) Leaf (no transition) Implicit state (exactly one transition) Reference pair: r = (s, w) where s is some explicit state that is an ancestor of r and w is the string from s to r. w = (k, p) such that t k …t p = w ex:

Two Kinds of State to Add (i) Leaves get a transition Update (s, (k, i-1)) to (s, (k, i)). (s, (k, ∞ )) instead. (ii) New branches Active point : First state that is not a leaf. End point : First state that has a t i -transition.

Lemma Let (s, (k, i-1)) be a reference pair of the end point of STree(T i-1 ). Then (s, (k, i)) is a reference pair of the active point of STree(T i ).

Complexity Let r i be the active point of STree(T i ). The number of the visited states between r i-1 and r i are depth(r i-1 ) - depth(r i ) + 2. The total number of the visited states are = depth(r 0 ) - depth(r n ) +2n ≦ 2n