1. Dynamic Programming1

2. 2 Outline and Reading Matrix Chain-Product (§5.3.1) The General Technique (§5.3.2) 0-1 Knapsack Problem (§5.3.3)

3. Dynamic Programming3 Matrix Chain-Products Dynamic Programming is a general algorithm design paradigm. Rather than give the general structure, let us first give a motivating example: Matrix Chain-Products Review: Matrix Multiplication. C = A*B A is d × e and B is e × f O(d  e  f ) time AC B dd f e f e i j i,j

4. Dynamic Programming4 Matrix Chain-Products Matrix Chain-Product: Compute A=A 0 *A 1 *…*A n-1 A i is d i × d i+1 Problem: How to parenthesize? Example B is 3 × 100 C is 100 × 5 D is 5 × 5 (B*C)*D takes 1500 + 75 = 1575 ops B*(C*D) takes 1500 + 2500 = 4000 ops

5. Dynamic Programming5 Enumeration Approach Matrix Chain-Product Alg.: Try all possible ways to parenthesize A=A 0 *A 1 *…*A n-1 Calculate number of ops for each one Pick the one that is best Running time: The number of parenthesizations is equal to the number of binary trees with n nodes This is exponential! It is called the Catalan number, and it is almost 4 n. This is a terrible algorithm!

6. Dynamic Programming6 Greedy Approach Idea #1: repeatedly select the product that uses the fewest operations. Counter-example: A is 101 × 11 B is 11 × 9 C is 9 × 100 D is 100 × 99 Greedy idea #1 gives A*((B*C)*D)), which takes 109989+9900+108900=228789 ops (A*B)*(C*D) takes 9999+89991+89100=189090 ops The greedy approach is not giving us the optimal value.

7. Dynamic Programming7 “Recursive” Approach Define subproblems: Find the best parenthesization of A i *A i+1 *…*A j. Let N i,j denote the number of operations done by this subproblem. The optimal solution for the whole problem is N 0,n-1. Subproblem optimality: The optimal solution can be defined in terms of optimal subproblems There has to be a final multiplication (root of the expression tree) for the optimal solution. Say, the final multiplication is at index i: (A 0 *…*A i )*(A i+1 *…*A n-1 ). Then the optimal solution N 0,n-1 is the sum of two optimal subproblems, N 0,i and N i+1,n-1 plus the time for the last multiplication.

8. Dynamic Programming8 Characterizing Equation The global optimal has to be defined in terms of optimal subproblems, depending on where the final multiplication is at. Let us consider all possible places for that final multiplication: Recall that A i is a d i × d i+1 dimensional matrix. So, a characterizing equation for N i,j is the following: Note that subproblems are not independent–the subproblems overlap.

9. Dynamic Programming9 Subproblem Overlap Algorithm RecursiveMatrixChain(S, i, j): Input: sequence S of n matrices to be multiplied Output: number of operations in an optimal parenthesization of S if i=j then return 0 for k  i to j do N i, j  min{N i,j, RecursiveMatrixChain(S, i,k)+ RecursiveMatrixChain(S, k+1,j)+ d i d k+1 d j+1 } return N i,j

10. Dynamic Programming10 Subproblem Overlap 1..4 1..12..41..23..41..34..4 2..2 3..42..34..4 3..34..41..12..2 3..34..42..23..3...

11. Dynamic Programming11 Dynamic Programming Algorithm Since subproblems overlap, we don’t use recursion. Instead, we construct optimal subproblems “bottom-up.” N i,i ’s are easy, so start with them Then do problems of “length” 2,3,… subproblems, and so on. Running time: O(n 3 ) Algorithm matrixChain(S): Input: sequence S of n matrices to be multiplied Output: number of operations in an optimal parenthesization of S for i  1 to n  1 do N i,i  0 for b  1 to n  1 do { b  j  i is the length of the problem } for i  0 to n  b - 1 do j  i  b N i,j   for k  i to j  1 do N i,j  min{N i,j, N i,k + N k+1,j + d i d k+1 d j+1 } return N 0,n-1

12. Dynamic Programming12 answer N 01 0 1 2… n-1 … j i Dynamic Programming Algorithm Visualization The bottom-up construction fills in the N array by diagonals N i,j gets values from previous entries in i-th row and j-th column Filling in each entry in the N table takes O(n) time. Total run time: O(n 3 ) Getting actual parenthesization can be done by remembering “k” for each N entry i j

13. Dynamic Programming13 Dynamic Programming Algorithm Visualization A 0 : 30 X 35; A 1 : 35 X15; A 2 : 15X5; A 3 : 5X10; A 4 : 10X20; A 5 : 20 X 25

14. Dynamic Programming14 Dynamic Programming Algorithm Since subproblems overlap, we don’t use recursion. Instead, we construct optimal subproblems “bottom-up.” N i,i ’s are easy, so start with them Then do problems of “length” 2,3,… subproblems, and so on. Running time: O(n 3 ) Algorithm matrixChain(S): Input: sequence S of n matrices to be multiplied Output: number of operations in an optimal parenthesization of S for i  1 to n  1 do N i,i  0 ; T ii  i; for b  1 to n  1 do { b  j  i is the length of the problem } for i  0 to n  b - 1 do j  i  b N i,j   ; T ij  i; for k  i to j  1 do If (N i,j > N i,k + N k+1,j + d i d k+1 d j+1 ) T i,j  k N i,j  min{N i,j, N i,k + N k+1,j + d i d k+1 d j+1 } return N 0,n-1

15. Dynamic Programming15 Dynamic Programming Algorithm Visualization (A 0 *(A 1 *A 2 ))*((A 3 *A 4 )*A 5 )

16. Dynamic Programming16 The General Dynamic Programming Technique Applies to a problem that at first seems to require a lot of time (possibly exponential), provided we have: Subproblem optimality: the global optimum value can be defined in terms of optimal subproblems Subproblem overlap: the subproblems are not independent, but instead they overlap (hence, should be constructed bottom-up).

17. Dynamic Programming17 The 0/1 Knapsack Problem Given: A set S of n items, with each item i having w i - a positive weight b i - a positive benefit Goal: Choose items with maximum total benefit but with weight at most W. If we are not allowed to take fractional amounts, then this is the 0/1 knapsack problem. In this case, we let T denote the set of items we take Objective: maximize Constraint:

18. Dynamic Programming18 Given: A set S of n items, with each item i having b i - a positive “benefit” w i - a positive “weight” Goal: Choose items with maximum total benefit but with weight at most W. Example Weight: Benefit: 12345 4 in2 in 6 in2 in $20$3$6$25$80 Items: box of width 9 in Solution: item 5 ($80, 2 in) item 3 ($6, 2in) item 1 ($20, 4in) “knapsack”

19. Dynamic Programming19 A 0/1 Knapsack Algorithm, First Attempt S k : Set of items numbered 1 to k. Define B[k] = best selection from S k. Problem: does not have subproblem optimality: Consider set S={(3,2),(5,4),(8,5),(4,3),(10,9)} of (benefit, weight) pairs and total weight W = 20 Best for S 4 : Best for S 5 :

20. Dynamic Programming20 A 0/1 Knapsack Algorithm, Second Attempt S k : Set of items numbered 1 to k. Define B[k,w] to be the best selection from S k with weight at most w Good news: this does have subproblem optimality. I.e., the best subset of S k with weight at most w is either the best subset of S k-1 with weight at most w or the best subset of S k-1 with weight at most w  w k plus item k

21. Dynamic Programming21 0/1 Knapsack Algorithm Consider set S={(1,1),(2,2),(4,3),(2,2),(5,5)} of (benefit, weight) pairs and total weight W = 10

22. Dynamic Programming22 0/1 Knapsack Algorithm Trace back to find the items picked

23. Dynamic Programming23 0/1 Knapsack Algorithm Each diagonal arrow corresponds to adding one item into the bag Pick items 2,3,5 {(2,2),(4,3),(5,5)} are what you will take away

24. Dynamic Programming24 0/1 Knapsack Algorithm Recall the definition of B[k,w] Since B[k,w] is defined in terms of B[k  1,*], we can use two arrays of instead of a matrix Running time: O(nW). Not a polynomial-time algorithm since W may be large This is a pseudo-polynomial time algorithm Algorithm 01Knapsack(S, W): Input: set S of n items with benefit b i and weight w i ; maximum weight W Output: benefit of best subset of S with weight at most W let A and B be arrays of length W + 1 for w  0 to W do B[w]  0 for k  1 to n do copy array B into array A for w  w k to W do if A[w  w k ]  b k > A[w] then B[w]  A[w  w k ]  b k return B[W]

25. Dynamic Programming25 Longest Common Subsequence Given two strings, find a longest subsequence that they share substring vs. subsequence of a string Substring: the characters in a substring of S must occur contiguously in S Subsequence: the characters can be interspersed with gaps. Consider ababc and abdcb alignment 1 ababc. abd.cb the longest common subsequence is ab..c with length 3 alignment 2 aba.bc abdcb. the longest common subsequence is ab..b with length 3

26. Dynamic Programming26 Longest Common Subsequence Let’s give a score M an alignment in this way, M=sum s(x i,y i ), where x i is the i character in the first aligned sequence y i is the i character in the second aligned sequence s(x i,y i )= 1 if x i = y i s(x i,y i )= 0 if x i ≠y i or any of them is a gap The score for alignment: ababc. abd.cb M=s(a,a)+s(b,b)+s(a,d)+s(b,.)+s(c,c)+s(.,b)=3 To find the longest common subsequence between sequences S 1 and S 2 is to find the alignment that maximizes score M.

27. Dynamic Programming27 Longest Common Subsequence Subproblem optimality Consider two sequences Let the optimal alignment be x 1 x 2 x 3 …x n-1 x n y 1 y 2 y 3 …y n-1 y n There are three possible cases for the last pair (x n,y n ): S 1 : a 1 a 2 a 3 …a i S 2 : b 1 b 2 b 3 …b j

28. Dynamic Programming28 Longest Common Subsequence M i,j = MAX {M i-1, j-1 + S (a i, b j ) (match/mismatch) M i,j-1 + 0 (gap in sequence #1) M i-1,j + 0 (gap in sequence #2) } M i,j is the score for optimal alignment between strings a[1…i] (substring of a from index 1 to i) and b[1…j] S 1 : a 1 a 2 a 3 …a i S 2 : b 1 b 2 b 3 …b j There are three cases for (x n,y n ) pair: x 1 x 2 x 3 …x n-1 x n y 1 y 2 y 3 …y n-1 y n

29. Dynamic Programming29 Examples: G A A T T C A G T T A (sequence #1) G G A T C G A (sequence #2) s(a i,b j )= 1 if a i =b j s(a i,b j )= 0 if a i ≠b j or any of them is a gap M i,j = MAX { M i-1, j-1 + S(a i,b j ) M i,j-1 + 0 M i-1,j + 0 } Longest Common Subsequence

30. Dynamic Programming30 Longest Common Subsequence M 1,1 = MAX[M 0,0 + 1, M 1, 0 + 0, M 0,1 + 0] = MAX [1, 0, 0] = 1 Fill the score matrix M and trace back table B Score matrix M Trace back table B

31. Dynamic Programming31 Longest Common Subsequence Score matrix MTrace back table B M 7,11 =6 (lower right corner of Score matrix) This tells us that the best alignment has a score of 6 What is the best alignment?

32. Dynamic Programming32 Longest Common Subsequence We need to use trace back table to find out the best alignment, which has a score of 6 (1)Find the path from lower right corner to upper left corner

33. Dynamic Programming33 Longest Common Subsequence (2) At the same time, write down the alignment backward :Take one character from each sequence :Take one character from sequence S 1 (columns) :Take one character from sequence S 2 (rows) S1S1 S2S2

34. Dynamic Programming34 Longest Common Subsequence :Take one character from each sequence :Take one character from sequence S 1 (columns) :Take one character from sequence S 2 (rows)

35. Dynamic Programming35 Longest Common Subsequence Thus, the optimal alignment is The longest common subsequence is G.A.T.C.G..A There might be multiple longest common subsequences (LCSs) between two given sequences. These LCSs have the same number of characters (not include gaps )

36. Dynamic Programming36 Longest Common Subsequence Algorithm LCS (string A, string B) { Input strings A and B Output the longest common subsequence of A and B M: Score Matrix B: trace back table (use letter a, b, c for ) n=A.length() m=B.length() // fill in M and B for (i=0;i<m+1;i++) for (j=0;j<n+1;j++) if (i==0) || (j==0) then M(i,j)=0; else if (A[i]==B[j]) M(i,j)=max {M[i-1,j-1]+1, M[i-1,j], M[i,j-1]} {update the entry in trace table B} else M(i,j)=max {M[i-1,j-1], M[i-1,j], M[i,j-1]} {update the entry in trace table B} then use trace back table B to print out the optimal alignment …