Longest Common Subsequence

 Problem: Given 2 sequences, X = x1,...,xm and

Y = y1,...,yn, find a common subsequence whose
length is maximum.

springtime ncaa tournament basketball

printing north carolina krzyzewski

Subsequence need not be consecutive, but must be in order.

dynprog - 1
Comp 122, Lin / Devi
 Other sequence questions
 Edit distance: Given 2 sequences, X = x1,...,xm
and Y = y1,...,yn, what is the minimum number of
deletions, insertions, and changes that you must do
to change one to another?
 Protein sequence alignment: Given a score matrix
on amino acid pairs, s(a,b) for a,b{}A,
and 2 amino acid sequences, X = x1,...,xmAm
and Y = y1,...,ynAn, find the alignment with
lowest score…

dynprog - 2
Comp 122, Lin / Devi
 More problems
Optimal BST: Given sequence K = k1 < k2 <··· < kn
of n sorted keys, with a search probability pi for
each key ki, build a binary search tree (BST) with
minimum expected search cost.
Matrix chain multiplication: Given a sequence of
matrices A1 A2 … An, with Ai of dimension mini,
insert parenthesis to minimize the total number of
scalar multiplications.
Minimum convex decomposition of a polygon,
Hydrogen placement in protein structures, …
dynprog - 3
Comp 122, Lin / Devi
 Dynamic Programming
 Dynamic Programming is an algorithm design technique for
optimization problems: often minimizing or maximizing.
 Like divide and conquer, DP solves problems by combining
solutions to subproblems.
 Unlike divide and conquer, subproblems are not independent.
 Subproblems may share subsubproblems,
 However, solution to one subproblem may not affect the solutions to other
subproblems of the same problem. (More on this later.)
 DP reduces computation by
 Solving subproblems in a bottom-up fashion.
 Storing solution to a subproblem the first time it is solved.
 Looking up the solution when subproblem is encountered again.
 Key: determine structure of optimal solutions

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Comp 122, Lin / Devi
 Steps in Dynamic Programming
1. Characterize structure of an optimal solution.
2. Define value of optimal solution recursively.
3. Compute optimal solution values either top-
down with caching or bottom-up in a table.
4. Construct an optimal solution from computed
values.
We’ll study these with the help of examples.

dynprog - 5
Comp 122, Lin / Devi
 Longest Common Subsequence
 Problem: Given 2 sequences, X = x1,...,xm and
Y = y1,...,yn, find a common subsequence whose
length is maximum.

springtime ncaa tournament basketball

printing north carolina snoeyink

Subsequence need not be consecutive, but must be in order.

dynprog - 6
Comp 122, Lin / Devi
 Naïve Algorithm
 For every subsequence of X, check whether it’s a
subsequence of Y .
 Time: Θ(n2m).
2m subsequences of X to check.
Each subsequence takes Θ(n) time to check:
scan Y for first letter, for second, and so on.

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Comp 122, Lin / Devi
 Optimal Substructure
Theorem
Let Z = z1, . . . , zk be any LCS of X and Y .
1. If xm = yn, then zk = xm = yn and Zk-1 is an LCS of Xm-1 and Yn-1.
2. If xm  yn, then either zk  xm and Z is an LCS of Xm-1 and Y .
3. or zk  yn and Z is an LCS of X and Yn-1.

Notation:
prefix Xi = x1,...,xi is the first i letters of X.
This says what any longest common subsequence must look like;
do you believe it?

dynprog - 8
Comp 122, Lin / Devi
 Optimal Substructure
Theorem
Let Z = z1, . . . , zk be any LCS of X and Y .
1. If xm = yn, then zk = xm = yn and Zk-1 is an LCS of Xm-1 and Yn-1.
2. If xm  yn, then either zk  xm and Z is an LCS of Xm-1 and Y .
3. or zk  yn and Z is an LCS of X and Yn-1.

Proof: (case 1: xm = yn)

Any sequence Z’ that does not end in xm = yn can be made longer by adding xm = yn
to the end. Therefore,
(1) longest common subsequence (LCS) Z must end in xm = yn.
(2) Zk-1 is a common subsequence of Xm-1 and Yn-1, and
(3) there is no longer CS of Xm-1 and Yn-1, or Z would not be an LCS.

dynprog - 9
Comp 122, Lin / Devi
 Optimal Substructure
Theorem
Let Z = z1, . . . , zk be any LCS of X and Y .
1. If xm = yn, then zk = xm = yn and Zk-1 is an LCS of Xm-1 and Yn-1.
2. If xm  yn, then either zk  xm and Z is an LCS of Xm-1 and Y .
3. or zk  yn and Z is an LCS of X and Yn-1.

Proof: (case 2: xm  yn, and zk  xm)

Since Z does not end in xm,
(1) Z is a common subsequence of Xm-1 and Y, and
(2) there is no longer CS of Xm-1 and Y, or Z would not be an LCS.

dynprog - 10
Comp 122, Lin / Devi
 Recursive Solution
 Define c[i, j] = length of LCS of Xi and Yj .
 We want c[m,n].


0 
if
i0 
or
j0,

c
[
i
,j
]
c
[
i
1,
j
1
]1 if
i
,j
0and
xiy
,
j
 [
i
max(
c 1
,
j],
c
[
i
,j
1])
if
i
,j
0and
x y
.
 i j

This gives a recursive algorithm and solves the problem.

But does it solve it well?

dynprog - 11
Comp 122, Lin / Devi
 Recursive Solution
 

  
0 if
emp
or
em,

  

 
c
[,]c[
prefix
,
prefix
]1 if
end(
)end
),
 

max(
c[
prefix
,],
c[,
prefix
])
if
end(
)end
).

c[springtime, printing]

c[springtim, printing] c[springtime, printin]

[springti, printing] [springtim, printin] [springtim, printin] [springtime, printi]

[springt, printing] [springti, printin] [springtim, printi] [springtime, print]

dynprog - 12
Comp 122, Lin / Devi
 Recursive Solution
 

  
0 if
emp
or
em,

  

 
c
[,]c[
prefix
,
prefix
]1 if
end(
)end
),
 

max(
c[
prefix
,],
c[,
prefix
])
if
end(
)end
).

p r i n t i n g
•Keep track of c[] in a
table of nm entries: s
p
•top/down
r
•bottom/up i
n
g
t
i
m
dynprog - 13
Compe 122, Lin / Devi
 Computing the length of an LCS
LCS-LENGTH (X, Y)
1. m ← length[X]
2. n ← length[Y]
3. for i ← 1 to m
4. do c[i, 0] ← 0
5. for j ← 0 to n
6. do c[0, j ] ← 0 b[i, j ] points to table entry
7. for i ← 1 to m
whose subproblem we used
8. do for j ← 1 to n
9. do if xi = yj in solving LCS of Xi
10. then c[i, j ] ← c[i1, j1] + 1 and Yj.
11. b[i, j ] ← “ ”
12. else if c[i1, j ] ≥ c[i, j1]
13. then c[i, j ] ← c[i 1, j ]
c[m,n] contains the length
14. b[i, j ] ← “↑” of an LCS of X and Y.
15. else c[i, j ] ← c[i, j1]
 b[i, j ] ← “←” Time: O(mn)
1. return c and b

dynprog - 14
Comp 122, Lin / Devi
 Constructing an LCS
PRINT-LCS (b, X, i, j)
1. if i = 0 or j = 0
2. then return
3. if b[i, j ] = “ ”
4. then PRINT-LCS(b, X, i1, j1)
5. print xi
6. elseif b[i, j ] = “↑”
7. then PRINT-LCS(b, X, i1, j)
8. else PRINT-LCS(b, X, i, j1)

•Initial call is PRINT-LCS (b, X,m, n).

•When b[i, j ] = , we have extended LCS by one character. So
LCS = entries with in them.
•Time: O(m+n)
dynprog - 15
Comp 122, Lin / Devi
 Steps in Dynamic Programming
1. Characterize structure of an optimal solution.
2. Define value of optimal solution recursively.
3. Compute optimal solution values either top-
down with caching or bottom-up in a table.
4. Construct an optimal solution from computed
values.
We’ll study these with the help of examples.

dynprog - 16
Comp 122, Lin / Devi
 Optimal Binary Search Trees
 Problem
Given sequence K = k1 < k2 <··· < kn of n sorted keys,
with a search probability pi for each key ki.
Want to build a binary search tree (BST)
with minimum expected search cost.
Actual cost = # of items examined.
For key ki, cost = depthT(ki)+1, where depthT(ki) = depth of ki in
BST T .

dynprog - 17
Comp 122, Lin / Devi
 Expected Search Cost
E[search
costinT]
n
(depth
T (ki ) 1) pi
i1
n n
depth
T (ki ) pi pi
i1 i1
n Sum of probabilities is 1.
1depth
T (ki ) pi (15.16)
i1

dynprog - 18
Comp 122, Lin / Devi
 Example
 Consider 5 keys with these search probabilities:
p1 = 0.25, p2 = 0.2, p3 = 0.05, p4 = 0.2, p5 = 0.3.
k2 i depthT(ki) depthT(ki)·pi
1 1 0.25
2 0 0
k1 k4 3 2 0.1
4 1 0.2
5 2 0.6
1.15
k3 k5
Therefore, E[search cost] = 2.15.

dynprog - 19
Comp 122, Lin / Devi
 Example
 p1 = 0.25, p2 = 0.2, p3 = 0.05, p4 = 0.2, p5 = 0.3.

k2 i depthT(ki) depthT(ki)·pi
1 1 0.25
2 0 0
k1 k5 3 3 0.15
4 2 0.4
5 1 0.3
1.10
k4
Therefore, E[search cost] = 2.10.

k3 This tree turns out to be optimal for this set of keys.

dynprog - 20
Comp 122, Lin / Devi
 Example
 Observations:
Optimal BST may not have smallest height.
Optimal BST may not have highest-probability key at
root.
 Build by exhaustive checking?
Construct each n-node BST.
For each,
assign keys and compute expected search cost.
But there are (4n/n3/2) different BSTs with n nodes.

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Comp 122, Lin / Devi
 Optimal Substructure
 Any subtree of a BST contains keys in a contiguous range
ki, ..., kj for some 1 ≤ i ≤ j ≤ n.

T

 If T is an optimal BST and

T contains subtree T with keys ki, ... ,kj ,
then T must be an optimal BST for keys ki, ..., kj.
 Proof: Cut and paste.

dynprog - 22
Comp 122, Lin / Devi
 Optimal Substructure
 One of the keys in ki, …,kj, say kr, where i ≤ r ≤ j,
must be the root of an optimal subtree for these keys.
 Left subtree of kr contains ki,...,kr1.
kr
 Right subtree of kr contains kr+1, ...,kj.

ki kr-1 kr+1 kj
 To find an optimal BST:
Examine all candidate roots kr , for i ≤ r ≤ j
Determine all optimal BSTs containing ki,...,kr1 and
containing kr+1,...,kj

dynprog - 23
Comp 122, Lin / Devi
 Recursive Solution
 Find optimal BST for ki,...,kj, where i ≥ 1, j ≤ n, j ≥ i1.
When j = i1, the tree is empty.
 Define e[i, j ] = expected search cost of optimal BST for ki,...,kj.

 If j = i1, then e[i, j ] = 0.

 If j ≥ i,
Select a root kr, for some i ≤ r ≤ j .
Recursively make an optimal BSTs
for ki,..,kr1 as the left subtree, and
for kr+1,..,kj as the right subtree.

dynprog - 24
Comp 122, Lin / Devi
 Recursive Solution
 When the OPT subtree becomes a subtree of a node:
Depth of every node in OPT subtree goes up by 1.
Expected search cost increases by
j
(i,j)
w p
l from (15.16)
l
i

 If kr is the root of an optimal BST for ki,..,kj :

e[i, j ] = pr + (e[i, r1] + w(i, r1))+(e[r+1, j] + w(r+1, j))
= e[i, r1] + e[r+1, j] + w(i, j). (because w(i, j)=w(i,r1) + pr + w(r + 1, j))
 But, we don’t know kr. Hence,

0 
if
ji
1
e
[
i
,
j
]
min
{e
[i
,
r
1
]e
[
r
1
,
j
]w(
i
,j
)} 
if
ij

i
rj

dynprog - 25
Comp 122, Lin / Devi
 Computing an Optimal Solution
For each subproblem (i,j), store:
 expected search cost in a table e[1 ..n+1 , 0 ..n]
Will use only entries e[i, j ], where j ≥ i1.
 root[i, j ] = root of subtree with keys ki,..,kj, for 1 ≤ i ≤ j ≤ n.
 w[1..n+1, 0..n] = sum of probabilities
w[i, i1] = 0 for 1 ≤ i ≤ n.
w[i, j ] = w[i, j-1] + pj for 1 ≤ i ≤ j ≤ n.

dynprog - 26
Comp 122, Lin / Devi
 Pseudo-code
OPTIMAL-BST(p, q, n)
1. for i ← 1 to n + 1
2. do e[i, i 1] ← 0
Consider all trees with l keys.
3. w[i, i 1] ← 0
4. for l ← 1 to n Fix the first key.
5. do for i ← 1 to nl + 1 Fix the last key
6. do j ←i + l1
7. e[i, j ]←∞
8. w[i, j ] ← w[i, j1] + pj
9. for r ←i to j
10. do t ← e[i, r1] + e[r + 1, j ] + w[i, j ] Determine the root
11. if t < e[i, j ] of the optimal
12. then e[i, j ] ← t (sub)tree
13. root[i, j ] ←r
14. return e and root

Time: O(n3)
dynprog - 27
Comp 122, Lin / Devi
 Elements of Dynamic Programming
 Optimal substructure
 Overlapping subproblems

dynprog - 28
Comp 122, Lin / Devi
 Optimal Substructure
 Show that a solution to a problem consists of making a
choice, which leaves one or more subproblems to solve.
 Suppose that you are given this last choice that leads to an
optimal solution.
 Given this choice, determine which subproblems arise and
how to characterize the resulting space of subproblems.
 Show that the solutions to the subproblems used within
the optimal solution must themselves be optimal. Usually
use cut-and-paste.
 Need to ensure that a wide enough range of choices and
subproblems are considered.
dynprog - 29
Comp 122, Lin / Devi
 Optimal Substructure
 Optimal substructure varies across problem domains:
1. How many subproblems are used in an optimal solution.
2. How many choices in determining which subproblem(s) to
use.
 Informally, running time depends on (# of subproblems
overall)  (# of choices).
 How many subproblems and choices do the examples
considered contain?
 Dynamic programming uses optimal substructure bottom
up.
First find optimal solutions to subproblems.
Then choose which to use in optimal solution to the problem.
dynprog - 30
Comp 122, Lin / Devi
 Optimal Substucture
 Does optimal substructure apply to all optimization
problems? No.
 Applies to determining the shortest path but NOT the
longest simple path of an unweighted directed graph.
 Why?
Shortest path has independent subproblems.
Solution to one subproblem does not affect solution to another
subproblem of the same problem.
Subproblems are not independent in longest simple path.
Solution to one subproblem affects the solutions to other subproblems.
Example:

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Comp 122, Lin / Devi
 Overlapping Subproblems
 The space of subproblems must be “small”.
 The total number of distinct subproblems is a polynomial
in the input size.
A recursive algorithm is exponential because it solves the same
problems repeatedly.
If divide-and-conquer is applicable, then each problem solved
will be brand new.

dynprog - 32
Comp 122, Lin / Devi