课程信息
4.5
480 个评分
97 个审阅
专项课程
100% 在线

100% 在线

立即开始,按照自己的计划学习。
可灵活调整截止日期

可灵活调整截止日期

根据您的日程表重置截止日期。
中级

中级

完成时间(小时)

完成时间大约为18 小时

建议:4 weeks of study, 4-8 hours/week...
可选语言

英语(English)

字幕:英语(English)

您将获得的技能

Suffix TreeSuffix ArrayKnuth–Morris–Pratt (KMP) AlgorithmAlgorithms On Strings
专项课程
100% 在线

100% 在线

立即开始,按照自己的计划学习。
可灵活调整截止日期

可灵活调整截止日期

根据您的日程表重置截止日期。
中级

中级

完成时间(小时)

完成时间大约为18 小时

建议:4 weeks of study, 4-8 hours/week...
可选语言

英语(English)

字幕:英语(English)

教学大纲 - 您将从这门课程中学到什么

1
完成时间(小时)
完成时间为 4 小时

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....
Reading
5 个视频 (总计 27 分钟), 5 个阅读材料, 1 个测验
Video5 个视频
Brute Force Approach to Pattern Matching2分钟
Herding Patterns into Trie5分钟
Herding Text into Suffix Trie6分钟
Suffix Trees4分钟
Reading5 个阅读材料
Trie Construction - Pseudocode10分钟
FAQ10分钟
Slides and External References10分钟
Available Programming Languages10分钟
FAQ on Programming Assignments10分钟
2
完成时间(小时)
完成时间为 4 小时

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....
Reading
5 个视频 (总计 30 分钟), 4 个阅读材料, 1 个测验
Video5 个视频
Inverting Burrows-Wheeler Transform7分钟
Using BWT for Pattern Matching6分钟
Suffix Arrays5分钟
Approximate Pattern Matching6分钟
Reading4 个阅读材料
Using BWT for Pattern Matching10分钟
Pattern Matching with Suffix Array10分钟
FAQ10分钟
Slides and External References10分钟
3
完成时间(小时)
完成时间为 3 小时

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....
Reading
5 个视频 (总计 35 分钟), 2 个阅读材料, 1 个测验
Video5 个视频
Safe Shift3分钟
Prefix Function7分钟
Computing Prefix Function9分钟
Knuth-Morris-Pratt Algorithm5分钟
Reading2 个阅读材料
Programming Assignment 3 lasts for two weeks分钟
Slides and External References10分钟
Quiz1 个练习
Exact Pattern Matching30分钟
4
完成时间(小时)
完成时间为 5 小时

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....
Reading
11 个视频 (总计 76 分钟), 5 个阅读材料, 2 个测验
Video11 个视频
General Strategy6分钟
Initialization9分钟
Sort Doubled Cyclic Shifts8分钟
SortDouble Implementation6分钟
Updating Classes8分钟
Full Algorithm3分钟
Suffix Array and Suffix Tree8分钟
LCP Array5分钟
Computing the LCP Array6分钟
Construct Suffix Tree from Suffix Array and LCP Array6分钟
Reading5 个阅读材料
Counting Sort10分钟
Slides and External References2分钟
Computing the LCP Array - Additional Slides10分钟
Suffix Tree Construction - Pseudocode10分钟
Slides and External References2分钟
Quiz1 个练习
Suffix Array Construction12分钟
4.5
97 个审阅Chevron Right
职业方向

75%

完成这些课程后已开始新的职业生涯
工作福利

83%

通过此课程获得实实在在的工作福利

热门审阅

创建者 HCMay 7th 2018

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

创建者 PGNov 19th 2017

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

讲师

Avatar

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

关于 University of California San Diego

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....

关于 National Research University Higher School of Economics

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 communications, IT, mathematics, engineering, and more. Learn more on www.hse.ru...

关于 Data Structures and Algorithms 专项课程

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....
Data Structures and Algorithms

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