課程信息
4.5
529 個評分
102 個審閱

第 4 門課程(共 6 門)

100% 在線

立即開始,按照自己的計劃學習。

可靈活調整截止日期

根據您的日程表重置截止日期。

中級

完成時間大約為17 小時

建議:4 weeks of study, 4-8 hours/week...

英語(English)

字幕:英語(English)

您將獲得的技能

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

第 4 門課程(共 6 門)

100% 在線

立即開始,按照自己的計劃學習。

可靈活調整截止日期

根據您的日程表重置截止日期。

中級

完成時間大約為17 小時

建議:4 weeks of study, 4-8 hours/week...

英語(English)

字幕:英語(English)

教學大綱 - 您將從這門課程中學到什麼

1
完成時間為 4 小時

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 個視頻 (總計 27 分鐘), 5 個閱讀材料, 1 個測驗
5 個視頻
Brute Force Approach to Pattern Matching2分鐘
Herding Patterns into Trie5分鐘
Herding Text into Suffix Trie6分鐘
Suffix Trees4分鐘
5 個閱讀材料
Trie Construction - Pseudocode10分鐘
FAQ10分鐘
Slides and External References10分鐘
Available Programming Languages10分鐘
FAQ on Programming Assignments10分鐘
2
完成時間為 4 小時

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 個視頻 (總計 30 分鐘), 4 個閱讀材料, 1 個測驗
5 個視頻
Inverting Burrows-Wheeler Transform7分鐘
Using BWT for Pattern Matching6分鐘
Suffix Arrays5分鐘
Approximate Pattern Matching6分鐘
4 個閱讀材料
Using BWT for Pattern Matching10分鐘
Pattern Matching with Suffix Array10分鐘
FAQ10分鐘
Slides and External References10分鐘
3
完成時間為 3 小時

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 個視頻 (總計 35 分鐘), 2 個閱讀材料, 1 個測驗
5 個視頻
Safe Shift3分鐘
Prefix Function7分鐘
Computing Prefix Function9分鐘
Knuth-Morris-Pratt Algorithm5分鐘
2 個閱讀材料
Programming Assignment 3 lasts for two weeks
Slides and External References10分鐘
1 個練習
Exact Pattern Matching30分鐘
4
完成時間為 5 小時

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 個視頻 (總計 76 分鐘), 5 個閱讀材料, 2 個測驗
11 個視頻
General Strategy6分鐘
Initialization9分鐘
Sort Doubled Cyclic Shifts8分鐘
SortDouble Implementation6分鐘
Updating Classes8分鐘
Full Algorithm3分鐘
Suffix Array and Suffix Tree8分鐘
LCP Array5分鐘
Computing the LCP Array6分鐘
Construct Suffix Tree from Suffix Array and LCP Array6分鐘
5 個閱讀材料
Counting Sort10分鐘
Slides and External References2分鐘
Computing the LCP Array - Additional Slides10分鐘
Suffix Tree Construction - Pseudocode10分鐘
Slides and External References2分鐘
1 個練習
Suffix Array Construction12分鐘
4.5
102 個審閱Chevron Right

50%

完成這些課程後已開始新的職業生涯

42%

通過此課程獲得實實在在的工作福利

熱門審閱

創建者 HCMay 7th 2018

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

創建者 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

關於 加州大学圣地亚哥分校

UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory....

關於 国立高等经济大学

National Research University - Higher School of Economics (HSE) is one of the top research universities in Russia. Established in 1992 to promote new research and teaching in economics and related disciplines, it now offers programs at all levels of university education across an extraordinary range of fields of study including business, sociology, cultural studies, philosophy, political science, international relations, law, Asian studies, media and communicamathematics, engineering, and more. Learn more on www.hse.ru...

關於 数据结构与算法 專項課程

This specialization is a mix of theory and practice: you will learn algorithmic techniques for solving various computational problems and will implement about 100 algorithmic coding problems in a programming language of your choice. No other online course in Algorithms even comes close to offering you a wealth of programming challenges that you may face at your next job interview. To prepare you, we invested over 3000 hours into designing our challenges as an alternative to multiple choice questions that you usually find in MOOCs. Sorry, we do not believe in multiple choice questions when it comes to learning algorithms...or anything else in computer science! For each algorithm you develop and implement, we designed multiple tests to check its correctness and running time — you will have to debug your programs without even knowing what these tests are! It may sound difficult, but we believe it is the only way to truly understand how the algorithms work and to master the art of programming. The specialization contains two real-world projects: Big Networks and Genome Assembly. You will analyze both road networks and social networks and will learn how to compute the shortest route between New York and San Francisco (1000 times faster than the standard shortest path algorithms!) Afterwards, you will learn how to assemble genomes from millions of short fragments of DNA and how assembly algorithms fuel recent developments in personalized medicine....
数据结构与算法

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