Dynamic

Dynamic Programming
Programming

Comp 122, Fall 2004

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 - 2

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,...,xmAm
and Y = y1,...,ynAn, find the alignment with
lowest score
dynprog - 3

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 mini,
insert parenthesis to minimize the total number of
scalar multiplications.
Minimum convex decomposition of a polygon,
Hydrogen placement in protein structures,
dynprog - 4

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

dynprog - 5

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 topdown with caching or bottom-up in a table.
4. Construct an optimal solution from computed
values.
Well study these with the help of examples.

dynprog - 6

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 - 7

Comp 122,

Lin / Devi

Nave Algorithm
For every subsequence of X, check whether its a
subsequence of Y .
Time: (n2m).
2m subsequences of X to check.
Each subsequence takes (n) time to check:
scan Y for first letter, for second, and so on.

dynprog - 8

Comp 122,

Lin / Devi

Optimal Substructure
Theorem
Theorem
Let
LetZZ==zz1,,......,,zzkbe
beany
anyLCS
LCSof
ofXXand
andYY..
1

1.1.IfIfxxm ==yyn,,then
z = x = y and Z isisan
and Y ..
anLCS
LCSof
ofXXm-1
m
n then zkk = xmm = ynn and Zk-1
k-1
m-1 and Yn-1
n-1
2.2.IfIfxxm yyn,,then
theneither
eitherzzk xxm and
andZZisisan
anLCS
LCSof
ofXXm-1 and
andYY..
m

3.3.

m-1

or
..
or zzkkyynnand
andZZisisan
anLCS
LCSof
ofXXand
andYYn-1
n-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 - 9

Comp 122,

Lin / Devi

Optimal Substructure
Theorem
Theorem
Let
LetZZ==zz1,,......,,zzkbe
beany
anyLCS
LCSof
ofXXand
andYY..
1

1.1.IfIfxxm ==yyn,,then
z = x = y and Z isisan
and Y ..
anLCS
LCSof
ofXXm-1
m
n then zkk = xmm = ynn and Zk-1
k-1
m-1 and Yn-1
n-1
2.2.IfIfxxm yyn,,then
theneither
eitherzzk xxm and
andZZisisan
anLCS
LCSof
ofXXm-1 and
andYY..
m

3.3.

m-1

or
..
or zzkkyynnand
andZZisisan
anLCS
LCSof
ofXXand
andYYn-1
n-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 - 10

Comp 122,

Lin / Devi

Optimal Substructure
Theorem
Theorem
Let
LetZZ==zz1,,......,,zzkbe
beany
anyLCS
LCSof
ofXXand
andYY..
1

1.1.IfIfxxm ==yyn,,then
z = x = y and Z isisan
and Y ..
anLCS
LCSof
ofXXm-1
m
n then zkk = xmm = ynn and Zk-1
k-1
m-1 and Yn-1
n-1
2.2.IfIfxxm yyn,,then
theneither
eitherzzk xxm and
andZZisisan
anLCS
LCSof
ofXXm-1 and
andYY..
m

3.3.

m-1

or
..
or zzkkyynnand
andZZisisan
anLCS
LCSof
ofXXand
andYYn-1
n-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 - 11

Comp 122,

Lin / Devi

Recursive Solution
Define c[i, j] = length of LCS of Xi and Yj .
We want c[m,n].
00

cc[[ii,, jj]] cc[[ii11,, jj11]]11

max(c[i 1, j ], c[i, j 1])
max(c[i 1, j ], c[i, j 1])

ifif ii 00or
or jj 00,,
ifif ii,, jj 00and
and xxi i yyj j,,
ifif ii,, jj 00and
and xxi i yyj j..

This gives a recursive algorithm and solves the problem.

But does it solve it well?

dynprog - 12

Comp 122,

Lin / Devi

Recursive Solution
00

cc[[,,]] cc[[prefix
prefix,,prefix
prefix]]11
max(c[ prefix , ], c[ , prefix ])
max(c[ prefix , ], c[ , prefix ])

ififempty
emptyor
or empty
empty,,
ifif end(
end())end(
end()),,
ifif end(
end())end(
end())..

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

c[springtime, printin]
[springtim, printin] [springtime, printi]

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

dynprog - 13

Comp 122,

Lin / Devi

Recursive Solution
ififempty
emptyor
or empty
empty,,
ifif end(
end())end(
end()),,
ifif end(
end())end(
end())..

00

cc[[,,]] cc[[prefix
prefix,,prefix
prefix]]11
max(c[ prefix , ], c[ , prefix ])
max(c[ prefix , ], c[ , prefix ])

Keep track of c[] in a

table of nm entries:

top/down

bottom/up

r
n
g
t
i
m

dynprog - 14

e 122,
Comp

Lin / Devi

Computing the length of an LCS

LCS-LENGTH
LCS-LENGTH(X,
(X,Y)
Y)
1.1. mm
length[X]
length[X]
2.2. nn
length[Y]
length[Y]
3.3. for
forii
11to
tomm
4.4.
do
doc[i,
c[i,0]
0]
00
5.5. for
forjj
00to
tonn
6.6.
do
doc[0,
c[0,jj]]
00
7.7. for
forii
11to
tomm
8.8.
do
dofor
forjj
11to
tonn
9.9.
do
doififxxi i==yyj j
10.
then
10.
thenc[i,
c[i,jj]]
c[i
c[i1,1,j
j1]
1]++11
11.
b[i,
11.
b[i,jj]]

12.
else
12.
elseififc[i
c[i1,1,jj]]c[i,
c[i,j
j1]
1]
13.
then
13.
thenc[i,
c[i,jj]]
c[i
c[i1,1,jj]]
14.
b[i,
14.
b[i,jj]]

15.
else
15.
elsec[i,
c[i,jj]]
c[i,
c[i,j
j1]
1]
16.
b[i,
16.
b[i,jj]]

17.
17.return
returnccand
andbb
dynprog - 15

Comp 122,

b[i, j ] points to table entry

whose subproblem we used
in solving LCS of Xi
and Yj.
c[m,n] contains the length
of an LCS of X and Y.
Time: O(mn)
Lin / Devi

Constructing an LCS
PRINT-LCS
PRINT-LCS(b,
(b,X,
X,i,i,j)j)
1.1. ififii==00or
orjj==00
2.2.
then
thenreturn
return
3.3. ififb[i,
b[i,jj]]==
4.4.
then
thenPRINT-LCS(b,
PRINT-LCS(b,X,
X,ii1,1,jj1)
1)
5.5.
print
printxxi i
6.6.
elseif
elseifb[i,
b[i,jj]]==

7.7.
then
thenPRINT-LCS(b,
PRINT-LCS(b,X,
X,ii1,
1,j)j)
8.8. else
elsePRINT-LCS(b,
PRINT-LCS(b,X,
X,i,i,jj1)
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 - 16

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 topdown with caching or bottom-up in a table.
4. Construct an optimal solution from computed
values.
Well study these with the help of examples.

dynprog - 17

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 - 18

Comp 122,

Lin / Devi

Expected Search Cost

E[search cost in T ]
n

(depth T (ki ) 1) pi
i 1
n

i 1

i 1

depth T (ki ) pi pi
n

1 depth T (ki ) pi (15.16)

Sum of probabilities is 1.

i 1

dynprog - 19

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
k1

k4
k3

k5

i depthT(ki) depthT(ki)pi
1
1
0.25
2
0
0
3
2
0.1
4
1
0.2
5
2
0.6
1.15

Therefore, E[search cost] = 2.15.

dynprog - 20

Comp 122,

Lin / Devi

Example
p1 = 0.25, p2 = 0.2, p3 = 0.05, p4 = 0.2, p5 = 0.3.
k2
k1

k5
k4

i depthT(ki) depthT(ki)pi
1
1
0.25
2
0
0
3
3
0.15
4
2
0.4
5
1
0.3
1.10

Therefore, E[search cost] = 2.10.

k3
dynprog - 21

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

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.

dynprog - 22

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
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 - 23

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,...,kr1.
k
Right subtree of kr contains kr+1, ...,kj.
r

ki

kr-1

To find an optimal BST:

Examine all candidate roots kr , for i r j

kr+1

kj

Determine all optimal BSTs containing ki,...,kr1 and

containing kr+1,...,kj
dynprog - 24

Comp 122,

Lin / Devi

Recursive Solution
Find optimal BST for ki,...,kj, where i 1, j n, j i1.
When j = i1, the tree is empty.
Define e[i, j ] = expected search cost of optimal BST for ki,...,kj.
If j = i1, then e[i, j ] = 0.
If j i,
Select a root kr, for some i r j .
Recursively make an optimal BSTs
for ki,..,kr1 as the left subtree, and
for kr+1,..,kj as the right subtree.
dynprog - 25

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
jj

ww((ii,, jj))
ppl l
l l i i

from (15.16)

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

e[i, j ] = pr + (e[i, r1] + w(i, r1))+(e[r+1, j] + w(r+1, j))
= e[i, r1] + e[r+1, j] + w(i, j). (because w(i, j)=w(i,r1) + p

+ w(r + 1, j))

But, we dont know kr. Hence,

00
ee[[ii, ,jj]]
{{ee[[ii, ,rr11]]ee[[rr11, ,jj]]ww((ii, ,jj)}
)}
min
i min
r

j
i

dynprog - 26

Comp 122,

ifif jjii11
ififii jj
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 i1.

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, i1] = 0 for 1 i n.
w[i, j ] = w[i, j-1] + pj for 1 i j n.

dynprog - 27

Comp 122,

Lin / Devi

Pseudo-code
OPTIMAL-BST(p,
OPTIMAL-BST(p,q,q,n)
n)
1.1. for
forii
11to
tonn++11
2.2.
do
Consider all trees with l keys.
doe[i,
e[i,ii1]
1]
00
3.3.
w[i,
w[i,ii1]
1]
00
Fix the first key.
4.4. for
l

1
to
n
for l 1 to n
Fix the last key
5.5.
do
dofor
forii
11to
tonnll++11
6.6.
do
dojji
i++ll11
7.7.
e[i,
e[i,jj]
]
8.8.
w[i,
w[i,jj]]
w[i,
w[i,jj1]
1]++ppj j
9.9.
for
forrri
ito
tojj
Determine the root
10.
do
10.
dott
e[i,
e[i,rr1]
1]++e[r
e[r++1,1,jj]]++w[i,
w[i,jj]]
of the optimal
11.
ififtt<<e[i,
11.
e[i,jj]]
(sub)tree
12.
then
12.
thene[i,
e[i,jj]]
tt
13.
root[i,
13.
root[i,jj]]r
r
14.
14. return
returneeand
androot
root

Time: O(n3)
dynprog - 28

Comp 122,

Lin / Devi

Elements of Dynamic Programming

Optimal substructure
Overlapping subproblems

dynprog - 29

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 - 30

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 - 31

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:
dynprog - 32

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 - 33

Comp 122,

Lin / Devi