COMP3010 - 7.0

COMP3010: Algorithm Theory and Design

Daniel Sutantyo, Department of Computing, Macquarie University

7.0 - Longest Common Subsequence

Prelude

7.0 - Longest Common Subsequence

In the first half of the semester, we concentrated on three topics:
- brute force $\rightarrow$ dynamic programming $\rightarrow$ greedy algorithm
- plus complexity and correctness
Longest common subsequence
- we have done this topic earlier when discussing overlapping subproblems in Week 4
- plus, you have also covered this topic in COMP225/2010
- so at this point, I really expect you to already understand LCSS

Definition

7.0 - Longest Common Subsequence

Given two sequences
$X = \{x_1,x_2,\dots\,x_m\}$ and $Y= \{y_1,y_2,\dots,y_n\}$ ,
find the longest common subsequence of $X$ and $Y$
- e.g. $X = \{ k,i,t,t,e,n \}$
  $Y = \{ s,i,t,t,i,n,g \}$
  the sequence $\{ i,t,t,n \}$ is a solution
What is the brute-force solution?

Brute Force

7.0 - Longest Common Subsequence

Brute force solution:
- Let $X$ be a sequence of length $m$ and $Y$ be a sequence of length $n$
- Generate all subsequences of $X \rightarrow 2^m$
- Generate all subsequences of $Y \rightarrow 2^n$
- For each subsequence of $X$ , compare it with a subsequence of $Y$
  - cost is $2^m * 2^n = 2^{mn}$
- Hence complexity is $O(2^{m+n})$

How to Approach It

7.0 - Longest Common Subsequence

Example:
- $X = \{ k,i,t,t,e,n \}$
- $Y = \{ s,i,t,t,i,n,g \}$
Can you improve the brute force approach?
- do you need to compare all these?
  - $\{k,i,t,t\}$ with $\{s,i,t,t\}$
  - $\{k,i,t,t\}$ with $\{s,i,t,t,i\}$
  - $\{k,i,t,t\}$ with $\{s,i,t,t,i,n\}$
  - $\{k,i,t,t\}$ with $\{s,i,t,t,i,n,g\}$

How to Approach It

7.0 - Longest Common Subsequence

Example:
- $X = \{ k,i,t,t,e,n \}$
- $Y = \{ s,i,t,t,i,n,g \}$
Let's get some intuition:
- $\{k,i,t,t\}$ with $\{s,i,t,t\}$
- $\{k,i,t,t\}$ with $\{s,i,t,t,i\}$
- $\{k,i,t,t\}$ with $\{s,i,t,t,i,n\}$
- $\{k,i,t,t\}$ with $\{s,i,t,t,i,n,g\}$
Why do we keep comparing $k$ ? Can we drop it?

How to Approach It

7.0 - Longest Common Subsequence

Example:
- $X = \{ k,i,t,t,e,n \}$
- $Y = \{ s,i,t,t,i,n,g \}$
Let's get some intuition:
- $\{i,t,t\}$ with $\{s,i,t,t\}$
- $\{i,t,t\}$ with $\{s,i,t,t,i\}$
- $\{i,t,t\}$ with $\{s,i,t,t,i,n\}$
- $\{i,t,t\}$ with $\{s,i,t,t,i,n,g\}$
Why do we keep comparing $s$ ? Can we drop it?

How to Approach It

7.0 - Longest Common Subsequence

Example:
- $X = \{ k,i,t,t,e,n \}$
- $Y = \{ s,i,t,t,i,n,g \}$
Let's get some intuition:
- $\{i,t,t\}$ with $\{i,t,t\}$
- $\{i,t,t\}$ with $\{i,t,t,i\}$
- $\{i,t,t\}$ with $\{i,t,t,i,n\}$
- $\{i,t,t\}$ with $\{i,t,t,i,n,g\}$
Why do we keep comparing $i$ ? Can we drop it?

How to Approach It

7.0 - Longest Common Subsequence

If the first characters of both string matches, then we should take the first character off from both strings (i.e. don't compare them again)
If they do not match, then
- should we keep both?
  - then we'll never progress
- should we take both first characters off?
  - no, why?
- should we take one off from one
  - yes, because clearly it's not helping, but we have to do it to both strings

How to Approach It

7.0 - Longest Common Subsequence

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7.0 - Longest Common Subsequence

Recursive Relation

$x_1\ x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_1 = y_1$

$x_1 \ne y_1$

7.0 - Longest Common Subsequence

Recursive Relation

$x_1\ x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_1 = y_1$

$x_1 \ne y_1$

$\text{LCSS}(X,Y) = \begin{cases} 0 & \text{if $X$ or $Y$ is empty}\\1 + \text{LCSS}(X_2,Y_2) & \text{if $x_1 = y_1$}\\\max\left(\text{LCSS}(X_2,Y_1),\text{LCSS}(X_1,Y_2)\right) & \text{if $x_1 \ne y_1$}\end{cases}$

7.0 - Longest Common Subsequence

Overlapping Subproblems

$x_1\ x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$\dots$

7.0 - Longest Common Subsequence

Overlapping Subproblems

$x_1\ x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$\dots$

7.0 - Longest Common Subsequence

Overlapping Subproblems

$x_1\ x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_3\dots y_n$

$x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$\dots$

7.0 - Longest Common Subsequence

Overlapping Subproblems

kitten

sitting

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sitting

kitten

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sitting

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kitten

tting

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tting

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tting

Optimal Substructure

7.0 - Longest Common Subsequence

Example:
- $X = \{ k,i,t,t,e,n \}$
- $Y = \{ s,i,t,t,i,n,g \}$
Does it have overlapping subproblems?
Does the longest common subsequence problem have an optimal substructure?

Optimal Substructure

7.0 - Longest Common Subsequence

$X = \{ x_1, x_2, x_3, \dots, x_m \}$
$Y = \{ y_1, y_2, y_3, \dots, y_n \}$
Let $Z = \{ z_1, z_2, z_3, \dots, z_k \}$ be the LCSS of $X$ and $Y$

If $x_1 = y_1$ , then $Z$ should contain $x_1 = y_1$ , i.e. $z_1 = x_1 = y_1$ , and $Z_2 = \{z_2,z_3,\dots,z_k\}$ is the LCSS of $X_2$ and $Y_2$

Case A:

Case B:

If $x_1 \ne y_1$ , then $Z$ is either
- the LCSS of $X_2 =\{x_2,x_3,\dots,x_m\}$ , and $Y=\{y_1,y_2,\dots,y_n\}$ , or
- the LCSS of $X = \{x_1,x_2,\dots,x_m\}$ and $Y_2 =\{y_2,y_3,\dots,y_n\}$

Optimal Substructure

7.0 - Longest Common Subsequence

kitten

If $x_1 \ne y_1$ , then $Z$ is either
- the LCSS of $X_2 =\{x_2,x_3,\dots,x_m\}$ , and $Y=\{y_1,y_2,\dots,y_n\}$ , or
- the LCSS of $X = \{x_1,x_2,\dots,x_m\}$ and $Y_2 =\{y_2,y_3,\dots,y_n\}$

Case A:

sitting

itten

sitting

kitten

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Optimal Substructure

7.0 - Longest Common Subsequence

Proof (by contradiction):

Let $Z$ be the LCSS of $X$ and $Y$
- if $Z$ is NOT the LCSS of $X_2$ and $Y$ , that means they have a longer common subsequence than $Z$ , say $Z^*$ .
Therefore $Z^*$ is the LCSS of $X$ and $Y$ , a contradiction!
Proof is symmetrical for the case $X$ and $Y_2$

If $x_1 \ne y_1$ , then $Z$ is either
- the LCSS of $X_2 =\{x_2,x_3,\dots,x_m\}$ , and $Y=\{y_1,y_2,\dots,y_n\}$ , or
- the LCSS of $X = \{x_1,x_2,\dots,x_m\}$ and $Y_2 =\{y_2,y_3,\dots,y_n\}$

Case A:

Optimal Substructure

7.0 - Longest Common Subsequence

Case B:

If $x_1 = y_1$ , then $Z$ should contain $x_1 = y_1$ , i.e. $z_1 = x_1 = y_1$ , and $Z_2 = \{z_2,z_3,\dots,z_k\}$ is the LCSS of $X_2$ and $Y_2$

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tting

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tting

Optimal Substructure

7.0 - Longest Common Subsequence

Proof (by contradiction):

if $Z$ does not contain $x_1$ , then we can always append $x_1$ to it, making a longer common subsequence, so $Z$ MUST contain $x_1$
if $Z_2$ is not the LCSS of $X_2$ and $Y_2$ , then there is another common subsequence $Z^*$ that is longer. If we append $x_1$ to $Z^*$ , $Z^*$ would be longer than $Z$ , a contradiction!

Case B:

If $x_1 = y_1$ , then $Z$ should contain $x_1 = y_1$ , i.e. $z_1 = x_1 = y_1$ , and $Z_2 = \{z_2,z_3,\dots,z_k\}$ is the LCSS of $X_2$ and $Y_2$

Recursive Relation

$x_1\ x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_1\ y_2\ y_3\dots y_n$

$x_1\ x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_2\ x_3 \dots x_m$

$y_2\ y_3\dots y_n$

$x_1 = y_1$

$x_1 \ne y_1$

Bottom Up Solution

7.0 - Longest Common Subsequence

kitten

sitting

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sitting

kitten

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sitting

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kitten

tting

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Bottom Up Solution

7.0 - Longest Common Subsequence

kitten

sitting

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Bottom Up Solution

7.0 - Longest Common Subsequence

for (int i = 0; i < n+1; i++) lcss[m][i] = 0;
for (int i = 0; i < m+1; i++) lcss[i][n] = 0;
		
for (int i = m-1; i > -1; i--){
  for (int j = n-1; j > -1; j--){
    // if character matches, then go diagonally 
    if(a.charAt(i) == b.charAt(j))
      lcss[i][j] = 1 + lcss[i+1][j+1];
    // else, compare the cell to your right and to your bottom, 
    // and pick the larger one
    else
      lcss[i][j] = Integer.max(lcss[i][j+1], lcss[i+1][j]);
  }
}

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten								0
itten								0
tten								0
ten								0
en								0
n								0
	0	0	0	0	0	0	0	0

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten							0	0
itten							0	0
tten							0	0
ten							0	0
en							0	0
n	1	1	1	1	1	1	0	0
	0	0	0	0	0	0	0	0

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten						1	0	0
itten						1	0	0
tten						1	0	0
ten						1	0	0
en	1	1	1	1	1	1	0	0
n	1	1	1	1	1	1	0	0
	0	0	0	0	0	0	0	0

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten					2	1	0	0
itten					2	1	0	0
tten					1	1	0	0
ten					1	1	0	0
en	1	1	1	1	1	1	0	0
n	1	1	1	1	1	1	0	0
	0	0	0	0	0	0	0	0

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten					2	1	0	0
itten					2	1	0	0
tten					1	1	0	0
ten	2	2	2	2	1	1	0	0
en	1	1	1	1	1	1	0	0
n	1	1	1	1	1	1	0	0
	0	0	0	0	0	0	0	0

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten			3	2	2	1	0	0
itten			3	2	2	1	0	0
tten	3	3	3	2	1	1	0	0
ten	2	2	2	2	1	1	0	0
en	1	1	1	1	1	1	0	0
n	1	1	1	1	1	1	0	0
	0	0	0	0	0	0	0	0

Bottom Up Solution

7.0 - Longest Common Subsequence

	sitting	itting	tting	ting	ing	ng	g
kitten	4	4	3	2	2	1	0	0
itten	4	4	3	2	2	1	0	0
tten	3	3	3	2	1	1	0	0
ten	2	2	2	2	1	1	0	0
en	1	1	1	1	1	1	0	0
n	1	1	1	1	1	1	0	0
	0	0	0	0	0	0	0	0

COMP3010: Algorithm Theory and Design

7.0 - Longest Common Subsequence

Prelude

Definition

Brute Force

How to Approach It

How to Approach It

How to Approach It

How to Approach It

How to Approach It

How to Approach It

Recursive Relation

Recursive Relation

Overlapping Subproblems

Overlapping Subproblems

Overlapping Subproblems

Overlapping Subproblems

Optimal Substructure

Optimal Substructure

Optimal Substructure

Optimal Substructure

Optimal Substructure

Optimal Substructure

Top Down Solution

Recursive Relation

Top Down Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution

Bottom Up Solution