Longest Common Sequence optimization problem

Question

I am trying to solve a problem which finds Longest Common Sequence between two strings. I used dynamic programming (DP) and I tried to optimize it. But I still get a timeout on HackerRank and I do not know why. I use the iterative version of Hunt–Szymanski algorithm.

Instead of using one matrix, I used only two rows and I interchange them. I also eliminated all common characters at the beginning and the end of the strings. I also used the iterative version of the algorithm. How else could I optimize this?

This is my code:

def commonChild(s1, s2):
    nr = 0
    while s1[0]==s2[0]:
        nr+=1
        s1=s1[1::]
        s2=s2[1::]
    while s1[-1]==s2[-1]:
        nr+=1
        s1=s1[0:-1]
        s2=s2[0:-1]

    row1 = [0]*(len(s1)+1)
    row2 = [0]*(len(s1)+1)


    for i in range(1,len(s1)+1):
        for j in range(1,len(s2)+1):


            if s1[j-1]==s2[i-1]:
                row2[j]=row1[j-1]+1


            else:

                row2[j]=max(row2[j-1], row1[j])


        row1=row2
        row2=[0]*(len(s1)+1)


    return row1[-1]+nr

Thank you.

Could you expand your question to be a [mcve]? Also, what is "DP"? — Alex, Apr 17 '20 at 13:19
@Alex DP is dynamic programming. Sure, firstly i eliminate all first and last elements that are the same, retaining the number of these elements in nr. After that, i use the iterative version of https://en.wikipedia.org/wiki/Hunt%E2%80%93Szymanski_algorithm this algorithm, and instead of using a matrix, i only use two rows which i interchange (row1 and row2). I retain the number of same elements end at the end i add nr which i calculated and the beginning — FallonPy, Apr 17 '20 at 16:38
You should update your question with these details. Add comments to the code and provide example input and corresponding output. That is a [mcve]. — Alex, Apr 17 '20 at 16:52
Are you sure the problem is a time out? I have noticed several bugs in your implementation. — mcskinner, Apr 17 '20 at 19:14

Siong Thye Goh · Accepted Answer · 2020-04-18T06:28:45.087

Good attempt.

Notice that you use index i to loop through s1 in the outer loop and index j to loop through s2 in the inner loop.

You should let s1 and s2 to have the length of s2 plus 1, the inner loop length plus 1.

Also, you mistakenly use j to access s1 and i to access s2 in your implementation.

Lastly, to overcome the timeout issue, rather than the regular Python, use PyPy instead.

def commonChild(s1, s2):
    nr = 0
    while s1[0]==s2[0]:
        nr+=1
        s1=s1[1::]
        s2=s2[1::]
    while s1[-1]==s2[-1]:
        nr+=1
        s1=s1[0:-1]
        s2=s2[0:-1]
    #row1 = [0]*(len(s1)+1)
    #row2 = [0]*(len(s1)+1)
    row1 = [0]*(len(s2)+1)
    row2 = [0]*(len(s2)+1)
    for i in range(1,len(s1)+1):
        for j in range(1,len(s2)+1):
            #if s1[j-1]==s2[i-1]:
            if s1[i-1] == s2[j-1]:
                row2[j]=row1[j-1]+1
            else:
                row2[j]=max(row2[j-1], row1[j])
        row1=row2
        #row2=[0]*(len(s1)+1)
        row2 = [0]*(len(s2)+1)
    return row1[-1]+nr

Thank you so much, i was able to solve this by changing from Py3 to PyPy3 and it worked fine both with my first implementation and with the changes you brought. Thanks again! — FallonPy, Apr 19 '20 at 15:12

Longest Common Sequence optimization problem

1 Answers1