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中級レベル

英語

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Suffix TreeSuffix ArrayKnuth–Morris–Pratt (KMP) AlgorithmAlgorithms On Strings

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中級レベル

英語

字幕:英語

シラバス - 本コースの学習内容

1
4時間で修了

Suffix Trees

How would you search for a longest repeat in a string in LINEAR time? In 1973, Peter Weiner came up with a surprising solution that was based on suffix trees, the key data structure in pattern matching. Computer scientists were so impressed with his algorithm that they called it the Algorithm of the Year. In this lesson, we will explore some key ideas for pattern matching that will - through a series of trials and errors - bring us to suffix trees.

...
5件のビデオ (合計27分), 5 readings, 1 quiz
5件のビデオ
Brute Force Approach to Pattern Matching2 分
Herding Patterns into Trie5 分
Herding Text into Suffix Trie6 分
Suffix Trees4 分
5件の学習用教材
Trie Construction - Pseudocode10 分
FAQ10 分
Slides and External References10 分
Available Programming Languages10 分
FAQ on Programming Assignments10 分
2
4時間で修了

Burrows-Wheeler Transform and Suffix Arrays

Although EXACT pattern matching with suffix trees is fast, it is not clear how to use suffix trees for APPROXIMATE pattern matching. In 1994, Michael Burrows and David Wheeler invented an ingenious algorithm for text compression that is now known as Burrows-Wheeler Transform. They knew nothing about genomics, and they could not have imagined that 15 years later their algorithm will become the workhorse of biologists searching for genomic mutations. But what text compression has to do with pattern matching??? In this lesson you will learn that the fate of an algorithm is often hard to predict – its applications may appear in a field that has nothing to do with the original plan of its inventors.

...
5件のビデオ (合計30分), 4 readings, 1 quiz
5件のビデオ
Inverting Burrows-Wheeler Transform7 分
Using BWT for Pattern Matching6 分
Suffix Arrays5 分
Approximate Pattern Matching6 分
4件の学習用教材
Using BWT for Pattern Matching10 分
Pattern Matching with Suffix Array10 分
FAQ10 分
Slides and External References10 分
3
3時間で修了

Knuth–Morris–Pratt Algorithm

Congratulations, you have now learned the key pattern matching concepts: tries, suffix trees, suffix arrays and even the Burrows-Wheeler transform! However, some of the results Pavel mentioned remain mysterious: e.g., how can we perform exact pattern matching in O(|Text|) time rather than in O(|Text|*|Pattern|) time as in the naïve brute force algorithm? How can it be that matching a 1000-nucleotide pattern against the human genome is nearly as fast as matching a 3-nucleotide pattern??? Also, even though Pavel showed how to quickly construct the suffix array given the suffix tree, he has not revealed the magic behind the fast algorithms for the suffix tree construction!In this module, Miсhael will address some algorithmic challenges that Pavel tried to hide from you :) such as the Knuth-Morris-Pratt algorithm for exact pattern matching and more efficient algorithms for suffix tree and suffix array construction.

...
5件のビデオ (合計35分), 2 readings, 1 quiz
5件のビデオ
Safe Shift3 分
Prefix Function7 分
Computing Prefix Function9 分
Knuth-Morris-Pratt Algorithm5 分
2件の学習用教材
Programming Assignment 3 lasts for two weeks2 時間
Slides and External References10 分
1の練習問題
Exact Pattern Matching30 分
4
5時間で修了

Constructing Suffix Arrays and Suffix Trees

In this module we continue studying algorithmic challenges of the string algorithms. You will learn an O(n log n) algorithm for suffix array construction and a linear time algorithm for construction of suffix tree from a suffix array. You will also implement these algorithms and the Knuth-Morris-Pratt algorithm in the last Programming Assignment in this course.

...
11件のビデオ (合計76分), 5 readings, 2 quizzes
11件のビデオ
General Strategy6 分
Initialization9 分
Sort Doubled Cyclic Shifts8 分
SortDouble Implementation6 分
Updating Classes8 分
Full Algorithm3 分
Suffix Array and Suffix Tree8 分
LCP Array5 分
Computing the LCP Array6 分
Construct Suffix Tree from Suffix Array and LCP Array6 分
5件の学習用教材
Counting Sort10 分
Slides and External References2 分
Computing the LCP Array - Additional Slides10 分
Suffix Tree Construction - Pseudocode10 分
Slides and External References2 分
1の練習問題
Suffix Array Construction12 分
4.5
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文字列アルゴリズム からの人気レビュー

by HCMay 7th 2018

Excelentes algoritmos, nunca había pensado lo complicado que era hacer pattern matching eficientemente en términos de tiempo de procesamiento y memoria.

by PGNov 19th 2017

great course, interesting concepts and very well delivered content from lecture videos. challenging and rewarding programming assignments.

講師

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Alexander S. Kulikov

Visiting Professor
Department of Computer Science and Engineering
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Michael Levin

Lecturer
Computer Science
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Pavel Pevzner

Professor
Department of Computer Science and Engineering
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Neil Rhodes

Adjunct Faculty
Computer Science and Engineering

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