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10 Dynamic Programming I

This document discusses the algorithm design technique of dynamic programming. It begins by explaining dynamic programming as a technique that breaks problems down into subproblems and solves the smallest subproblems first, using their solutions to solve larger subproblems. It then provides examples of applying dynamic programming to problems like longest increasing subsequence (LIS) and edit distance. For LIS and edit distance, it defines the subproblems, outlines the recursive solutions, and explains how to construct DAGs to systematically solve all subproblems. Finally, it discusses applications of edit distance in computational genomics.

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64 views

10 Dynamic Programming I

This document discusses the algorithm design technique of dynamic programming. It begins by explaining dynamic programming as a technique that breaks problems down into subproblems and solves the smallest subproblems first, using their solutions to solve larger subproblems. It then provides examples of applying dynamic programming to problems like longest increasing subsequence (LIS) and edit distance. For LIS and edit distance, it defines the subproblems, outlines the recursive solutions, and explains how to construct DAGs to systematically solve all subproblems. Finally, it discusses applications of edit distance in computational genomics.

Uploaded by

harry_i3t
Copyright
© Attribution Non-Commercial (BY-NC)
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Download as PDF, TXT or read online on Scribd
You are on page 1/ 16

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Dynamic Programming
Atul Gupta

Problem Solving
Standard design principles/techniques looked so far
Divide and Conquer Graph Algorithms Greedy

Good aspect : Fast Algorithms Not so good aspect: specific and limited use

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Dynamic Programming
A sledgehammer of the algorithms craft Can be applied in many situations where the other techniques will fail However, a little more costly

DAG
There are two subclasses of graphs that have no negative cycles
Graph without negative edges Graph without cycles (DAG)

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

DAG
An important property
They can be linearized, i.e., In any path of a DAG, the vertices appear in increasing linearized order This allows to find shortest path in linear time

Shortest Paths in DAG

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Shortest Paths in DAG

Shortest Paths in DAG

The Algorithm

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Dynamic Programming
a problem is solved by identifying a collection of sub-problems and tackling them one by one,
smallest first, using the answers to small problems to help figure out larger ones, until the whole lot of them is solved

Dynamic Programming and DAG


A DAG is not given but implicit
Nodes are sub-problems Edges are dependencies between the subproblems An edge from A to B indicate, we require solution of A to solve for B, and hence, A have to be a smaller problem than B

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

DP Example 1: LIS
LIS Longest Increasing Subsequences
Input: A sequence of numbers Output: Find the increasing subsequence of greatest length

LIS
The DAG

The Goal: Find the longest path in the DAG

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

LIS
The Algorithm

The Complexity? n^2 The sequence itself?

Solving LIS by Recursion?

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Revisiting Fibonacci

Using Recursion
Why did recursion worked in Divide and Conquer (E.g. Binary Search, Merge sort, etc)
sub-problems were substantially smaller! the recursion tree had logarithmic depth and polynomial number of nodes !!!

Why recursion does not work here (i.e. say, in LIS)


sub-problems were not smaller! the recursion tree had polynomial depth and exponential number of nodes !!! Most of the sub-problems are REPEATS only

In Dynamic programming, the efficiency is achieve by


explicitly enumerating the distinct sub-problems, and solving them in the right order

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Another Problem: Edit Distance


How a spell checker search for a close match when encounters a misspelled word?
S S

N O W N N Cost: 3

Y Y

S U

N O W N Cost: 5

Y Y

Three edits for the first case: insert U, substitute O and delete W (Cost : 3)

N,

Terribly inefficient if we follow a nave approach!!!

A DP Solution for Edit Distance


1. What are the sub-problems? 2. There is an ordering on the sub-problems, and a relation that shows how to solve a subproblem, given the answers to smaller subproblems
(A DAG representing the problem graph)

CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Sub-Problems for Edit Distance


Given two strings of size x[1..m] and y[1..n], Find the minimum Edit Distance between them
Find Edit Distance between two prefix strings x[1..i] and y[1..j] Call this problem as E(i, j) The original problem is then E(m, n)

Solving A Sub-Problem
Solving E(i, j)
Three cases for the rightmost column

E(i 1, j),

E(i, j 1)

diff(i, j) + E(I 1, j1)}

E(i, j) = min{1 + E(i 1, j), 1 + E(i, j 1), diff(i, j) + E(I 1, j1)}, where diff(i, j) is defined to be 0 if x[i] = y[j] and 1 otherwise.

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CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Edit Distance: An Example

E(7, 5) =

Solving Sub-problems: Edit Distance

E(i, j) = min{1 + E(i 1, j), 1 + E(i, j 1), di(i, j) + E(I 1, j1)}

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CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Edit Distance: Smallest Sub-problems


The Base Cases
E(i, 0) = i E(j, 0) = j

Edit Distance
The Algorithm

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CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Edit Distance: The Example

Edit Distance: The Examples DAG

One Solution -

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CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Edit Distance
A category of efficient String matching algorithms A more general form of the problem may require considering different weights for insertions, deletions, and/or substitutions

Computational Genomics
Our bodies are extraordinary machines Capability is programmed as DNA sequence
3 billion characters long over the alphabet {A, C, G, T }

The DNA sequences of any two people differ by only about 0.1%
still leaves three million positions on which they vary

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CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

Computational Genomics
DNA is further broken down into smaller units called genes Computers have become a crucial tool in understanding the genes Computational Genomics
A new gene is discovered, and looked for places
A variation of Edit Distance and Dynamic Programming The database GenBank already has a total length of over 1010 and counting

Methods for sequencing DNA to construct it The EVOLUTION

More Problems on DP
DP solutions for some more problems are included in the next lecture slide

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CS 306 DAA, IIITDM Jabalpur, 2012

10/11/2012

References
Chapter 6, Algorithms by S. Dasgupta, C.H. Papadimitriou, and U.V. Vazirani

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