Об этом курсе
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Промежуточный уровень

Английский

Субтитры: Английский

Приобретаемые навыки

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

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Промежуточный уровень

Английский

Субтитры: Английский

Программа курса: что вы изучите

Неделя
1
4 ч. на завершение

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.

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5 видео ((всего 27 мин.)), 5 материалов для самостоятельного изучения, 1 тест
5 видео
Herding Text into Suffix Trie6мин
Suffix Trees4мин
5 материала для самостоятельного изучения
Trie Construction - Pseudocode10мин
FAQ10мин
Slides and External References10мин
Available Programming Languages10мин
FAQ on Programming Assignments10мин
Неделя
2
4 ч. на завершение

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.

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5 видео ((всего 30 мин.)), 4 материалов для самостоятельного изучения, 1 тест
5 видео
Suffix Arrays5мин
Approximate Pattern Matching6мин
4 материала для самостоятельного изучения
Using BWT for Pattern Matching10мин
Pattern Matching with Suffix Array10мин
FAQ10мин
Slides and External References10мин
Неделя
3
3 ч. на завершение

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.

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5 видео ((всего 35 мин.)), 2 материалов для самостоятельного изучения, 1 тест
5 видео
Safe Shift3мин
Computing Prefix Function9мин
Knuth-Morris-Pratt Algorithm5мин
2 материала для самостоятельного изучения
Programming Assignment 3 lasts for two weeks
Slides and External References10мин
1 практическое упражнение
Exact Pattern Matching30мин
Неделя
4
5 ч. на завершение

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.

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11 видео ((всего 76 мин.)), 5 материалов для самостоятельного изучения, 2 тестов
11 видео
Sort Doubled Cyclic Shifts8мин
SortDouble Implementation6мин
Updating Classes8мин
Full Algorithm3мин
Suffix Array and Suffix Tree8мин
LCP Array5мин
Computing the LCP Array6мин
Construct Suffix Tree from Suffix Array and LCP Array6мин
5 материала для самостоятельного изучения
Counting Sort10мин
Slides and External References2мин
Computing the LCP Array - Additional Slides10мин
Suffix Tree Construction - Pseudocode10мин
Slides and External References2мин
1 практическое упражнение
Suffix Array Construction12мин
4.5
Рецензии: 106Chevron Right

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Лучшие отзывы о курсе Строковые алгоритмы

автор: HCMay 7th 2018

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

автор: PGNov 19th 2017

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

Преподаватели

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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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Структуры и алгоритмы данных

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