Tag: algorithms


Graphs for Bioinformatics, Part 1: de Bruijn Graphs, Hamiltonian Paths, and Eulerian Paths

Posted in Computational Biology

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The Context: Rosalind.info

To provide a bit of context for a discussion of Euler paths and Euler cycles: starting around December, a group of us in the Lab for Data Intensive Biology (DIB Lab) started working through the textbook Bioinformatics Algorithms: An Active Learning Approach and the associated website, Rosalind.info.

Rosalind.info is a site that is similar in style …



Tags:    go    golang    rosalind    computational biology    bioinformatics    euler    recursion    backtracking    graphs    algorithms    hamiltonian    eulerian   


The Josephus Problem: Part 3: Solving the Double Step Case

Posted in Computer Science

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Tags:    graphs    puzzles    algorithms    josephus    latex   


The Josephus Problem: Part 2: Two Examples

Posted in Computer Science

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Tags:    graphs    puzzles    algorithms    josephus    latex   


The Josephus Problem: Part 1: The Problem

Posted in Computer Science

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Tags:    graphs    puzzles    algorithms    josephus    latex   


Five Letter Words: Part 5: The Try Trie Tree

Posted in Computer Science

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Tags:    python    computer science    graphs    algorithms    art of computer programming    knuth    five letter words    tries    trees   


Five Letter Words: Part 4: Revisiting Diff by One

Posted in Computer Science

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About the Five-Letter Words

In Volume 4, Facsimile 0 of Donald Knuth's Art of Computer Programming, in which Knuth covers graph theory, he introduces a list of five-letter words as part of a data set useful in exploring graph theory and graph algorithms.

The list of words is part of the Stanford Graph Base, a set of data sets that are useful for studying graph theory and networks.

See Five Letter Words on the charlesreid1.com wiki for details.

Different by 1, Revisited

This post …




Let's Generate Permutations!

Posted in Computer Science

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Generating Permutations

In today's post we're going to discuss the generation of permutations.

Often, in combinatorics problems, we are interested in how many different instances or configurations of a particular thing we can have (what we'll call "enumeration" or "counting"). However, that is different from wanting to actually see all of those configurations. Indeed, if we are counting something with an astronomical number of configurations, we don't want to try to list all of them.

However, as usual, Donald Knuth, who covers the topic of permutation generation in Volume 4A of his classic work, The Art of Computer Programming, uncovers …




Five Letter Words: Part 3: Letter Coverage and Dynamic Programming

Posted in Computer Science

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NOTE: The code covered in this post uses Python 3. The scripts can be converted to Python 2 with minimal effort, but the author would encourage any user of Python 2 to "put on your big kid pants" and make the switch to Python 3. Let's all make this painful, drawn-out switch from Python 2 to Python 3 a thing of the past, shall we?

Table of Contents

Introduction

The letter/word coverage problem, as presented by Donald Knuth in Volume 4, Facicle 0 of his masterpiece Art of …




Five Letter Words: Part 2: More Five-Word Algorithms

Posted in Computer Science

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NOTE: The code covered in this post uses Python 3. The scripts can be converted to Python 2 with minimal effort, but the author would encourage any user of Python 2 to "put on your big kid pants" and make the switch to Python 3. Let's all make this painful, drawn-out switch from Python 2 to Python 3 a thing of the past, shall we?

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Five Letter Words: Part 1: Getting Familiar With The List

Posted in Computer Science

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NOTE: The code covered in this post uses Python 3. The scripts can be converted to Python 2 with minimal effort, but the author would encourage any user of Python 2 to "put on your big kid pants" and make the switch to Python 3. Let's all make this painful, drawn-out switch from Python 2 to Python 3 a thing of the past, shall we?

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About the Five-Letter …




CSE 143 Final Project: Classy

Posted in Computer Science

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Problem Description

Comedian John Cleese, in his memoir So Anyway..., described the social classes of his mother and father as "upper-uper-lower-middle class" and "middle-middle-middle-lower-middle class", respectively. Write a program that will sort individuals based on a labeling of their social standing by class.

The three main classes are upper, middle, and lower. Classes progress hierarchically from right to left. For example, lower-upper would come before lower-lower. There is also ordering within a class, so upper-upper is a higher class than middle-upper.

Once you have reached …




Teaching Recursion with the N Queens Problem

Posted in Computer Science

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Table of Contents:

A Gentle Introduction to Recursion

Recursion, particularly recursive backtracking, is far and away the most challenging topic I cover when I teach the CSE 143 (Java Programming II) course at South Seattle College. Teaching the concept of recursion, on its own, is challenging: the concept is a hard one to encounter in everyday life, making it unfamiliar, and that creates a lot of friction when students try to understand how to apply recursion.

The …



Tags:    java    algorithms    recursion    n-queens   


Python vs. Perl: N Queens Problem

Posted in Computer Science

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Background

Revisiting the N queens problem, this time implementing the solution in Python.

Verb-oriented solution, functional, and based on Perl solution

More fair comparison - both are interpreted languages, not compiled languages

Compare Python and Perl, ease of implementation, speed, flexibility

N Queens Problem

As a recap from the …



Tags:    python    perl    java    algorithms    recursion    n-queens   


Perl vs. Java: N Queens Problem

Posted in Computer Science

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Summary

In this post, we describe an implementation of the N Queens Problem, which is a puzzle related to optimization, combinatorics, and recursive backtracking. The puzzle asks: how many configurations are there for placing 8 queens on a chessboard such that no queen can attack any othr queen?

This problem was implemented in Perl …



Tags:    java    perl    algorithms    recursion    n-queens