I'm trying to code this problem here:
but I'd like to find an algorithm that breaks down the steps for solving the problem. I can't seem to find anything too useful online so I've come here to ask if anyone knows of a resource which I can use to refer to an algorithm that solves this problem.
This is called the shortest common supersequence problem. The idea is that in order for the supersequence to be the shortest, we want to find as many shared bits of a and b as possible. We can solve the problem in two steps:
Find the longest common subsequence of a and b.
Insert the remaining bits of a and b while preserving the order of these bits.
We can solve the longest common subsequence problem using dynamic programming.
I agree with Terry Li: it is only NP-complete to find the SCS of multiple sequences. For 2 sequences (say s is of length n and t is of length m), my solution (doesn't use LCS but uses something similar) is done in O(nm) time:
1) Run a global alignment, in which you disallow mismatches, don't penalize indels, and give a positive score to matches (I did +1 for matches, -10 for mismatches, and 0 for indels, but these can be adjusted). (This is O(nm))
2) Iterate over the global alignment for both output strings v and w. If v[i] isn't a gap, output it. Otherwise, output w[i]. (This is O(n+m)).
Related
General problem
I have a set of short strings, each of different length with minimum X > 0 and maximum Y. What is an algorithm which will optimally fit together these short strings to make long strings of length M, where M >> Y? Optimal would be defined as the greatest number of long strings with lengths closest to M as possible.
Details
I am writing a tweet creator to practice javascript. I have a list of greetings and a list of account names. I want my program to create tweets such that each tweet has one greeting and the rest of the characters are used for account names. Each tweet has a limit of 140 characters.
Hello! #person1 #acc2 #mygoodfriend3 ...
Of course, each account has a different number of characters. I want each tweet to use up as many of the 140 characters as possible by optimally selecting combinations of account names.
I am pretty certain there is a class of problems / algorithm that is known to solve this problem but I can't remember it.
This kind of problem is called a knapsack problem, and an exact (or exactly optimal) solution is famous for being intractable.
However, there are reasonable approximate solvers, as well as a "pseudo-polynomial time" dynamic-programming algorithm.
I think it is related to the knapsack problem; it is a particular case of "multiple linear bin packing problem". Both are NP-hard problems. Here you can find a greedy algorithm for the linear bin packing problem, but the multiple case is much harder. A constraint programming language/library would help to solve these kind of problems.
A group of amusing students write essays exclusively by plagiarising portions of the complete works of WIlliam Shakespere. At one end of the scale, an essay might exclusively consist a verbatim copy of a soliloquy... at the other, one might see work so novel that - while using a common alphabet - no two adjacent characters in the essay were used adjacently by Will.
Essays need to be graded. A score of 1 is assigned to any essay which can be found (character-by-character identical) in the plain-text of the complete works. A score of 2 is assigned to any work that can be successfully constructed from no fewer than two distinct (character-by-character identical) passages in the complete works, and so on... up to the limit - for an essay with N characters - which scores N if, and only if, no two adjacent characters in the essay were also placed adjacently in the complete works.
The challenge is to implement a program which can efficiently (and accurately) score essays. While any (practicable) data-structure to represent the complete works is acceptable - the essays are presented as ASCII strings.
Having considered this teasing question for a while, I came to the conclusion that it is much harder than it sounds. The naive solution, for an essay of length N, involves 2**(N-1) traversals of the complete works - which is far too inefficient to be practical.
While, obviously, I'm interested in suggested solutions - I'd also appreciate pointers to any literature that deals with this, or any similar, problem.
CLARIFICATIONS
Perhaps some examples (ranging over much shorter strings) will help clarify the 'score' for 'essays'?
Assume Shakespere's complete works are abridged to:
"The quick brown fox jumps over the lazy dog."
Essays scoring 1 include "own fox jump" and "The quick brow". The essay "jogging" scores 6 (despite being short) because it can't be represented in fewer than 6 segments of the complete works... It can be segmented into six strings that are all substrings of the complete works as follows: "[j][og][g][i][n][g]". N.B. Establishing scores for this short example is trivial compared to the original problem - because, in this example "complete works" - there is very little repetition.
Hopefully, this example segmentation helps clarify the 2*(N-1) substring searches in the complete works. If we consider the segmentation, the (N-1) gaps between the N characters in the essay may either be a gap between segments, or not... resulting in ~ 2*(N-1) substring searches of the complete works to test each segmentation hypothesis.
An (N)DFA would be a wonderful solution - if it were practical. I can see how to construct something that solved 'substring matching' in this way - but not scoring. The state space for scoring, on the surface, at least, seems wildly too large (for any substantial complete works of Shakespere.) I'd welcome any explanation that undermines my assumptions that the (N)DFA would be too large to be practical to compute/store.
A general approach for plagiarism detection is to append the student's text to the source text separated by a character not occurring in either and then to build either a suffix tree or suffix array. This will allow you to find in linear time large substrings of the student's text which also appear in the source text.
I find it difficult to be more specific because I do not understand your explanation of the score - the method above would be good for finding the longest stretch in the students work which is an exact quote, but I don't understand your N - is it the number of distinct sections of source text needed to construct the student's text?
If so, there may be a dynamic programming approach. At step k, we work out the least number of distinct sections of source text needed to construct first k characters of the student's text. Using a suffix array built just from the source text or otherwise, we find the longest match between the source text and characters x..k of the student's text, where x is of course as small as possible. Then the least number of sections of source text needed to construct the first k characters of student text is the least needed to construct 1..x-1 (which we have already worked out) plus 1. By running this process for k=1..the length of the student text we find the least number of sections of source text needed to reconstruct the whole of it.
(Or you could just search StackOverflow for the student's text, on the grounds that students never do anything these days except post their question on StackOverflow :-)).
I claim that repeatedly moving along the target string from left to right, using a suffix array or tree to find the longest match at any time, will find the smallest number of different strings from the source text that produces the target string. I originally found this by looking for a dynamic programming recursion but, as pointed out by Evgeny Kluev, this is actually a greedy algorithm, so let's try and prove this with a typical greedy algorithm proof.
Suppose not. Then there is a solution better than the one you get by going for the longest match every time you run off the end of the current match. Compare the two proposed solutions from left to right and look for the first time when the non-greedy solution differs from the greedy solution. If there are multiple non-greedy solutions that do better than the greedy solution I am going to demand that we consider the one that differs from the greedy solution at the last possible instant.
If the non-greedy solution is going to do better than the greedy solution, and there isn't a non-greedy solution that does better and differs later, then the non-greedy solution must find that, in return for breaking off its first match earlier than the greedy solution, it can carry on its next match for longer than the greedy solution. If it can't, it might somehow do better than the greedy solution, but not in this section, which means there is a better non-greedy solution which sticks with the greedy solution until the end of our non-greedy solution's second matching section, which is against our requirement that we want the non-greedy better solution that sticks with the greedy one as long as possible. So we have to assume that, in return for breaking off the first match early, the non-greedy solution gets to carry on its second match longer. But this doesn't work, because, when the greedy solution finally has to finish using its first match, it can jump on to the same section of matching text that the non-greedy solution is using, just entering that section later than the non-greedy solution did, but carrying on for at least as long as the non-greedy solution. So there is no non-greedy solution that does better than the greedy solution and the greedy solution is optimal.
Have you considered using N-Grams to solve this problem?
http://en.wikipedia.org/wiki/N-gram
First read the complete works of Shakespeare and build a trie. Then process the string left to right. We can greedily take the longest substring that matches one in the data because we want the minimum number of strings, so there is no factor of 2^N. The second part is dirt cheap O(N).
The depth of the trie is limited by the available space. With a gigabyte of ram you could reasonably expect to exhaustively cover Shakespearean English string of length at least 5 or 6. I would require that the leaf nodes are unique (which also gives a rule for constructing the trie) and keep a pointer to their place in the actual works, so you have access to the continuation.
This feels like a problem of partial matching a very large regular expression.
If so it can be solved by a very large non deterministic finite state automata or maybe more broadly put as a graph representing for every character in the works of Shakespeare, all the possible next characters.
If necessary for efficiency reasons the NDFA is guaranteed to be convertible to a DFA. But then this construction can give rise to 2^n states, maybe this is what you were alluding to?
This aspect of the complexity does not really worry me. The NDFA will have M + C states; one state for each character and C states where C = 26*2 + #punctuation to connect to each of the M states to allow the algorithm to (re)start when there are 0 matched characters. The question is would the corresponding DFA have O(2^M) states and if so is it necessary to make that DFA, theoretically it's not necessary. However, consider that in the construction, each state will have one and only one transition to exactly one other state (the next state corresponding to the next character in that work). We would expect that each one of the start states will be connected to on average M/C states, but in the worst case M meaning the NDFA will have to track at most M simultaneous states. That's a large number but not an impossibly large number for computers these days.
The score would be derived by initializing to 1 and then it would incremented every time a non-accepting state is reached.
It's true that one of the approaches to string searching is building a DFA. In fact, for the majority of the string search algorithms, it looks like a small modification on failure to match (increment counter) and success (keep going) can serve as a general strategy.
I don't want a direct solution to the problem that's the source of this question but it's this one link:
So I take in the strings and add them to a suffix array which is implemented as a sorted set internally, what I obtain then is a lexicographically sorted list of the two given strings.
S1 = "banana"
S2 = "panama"
SuffixArray.add S1, S2
To make searching for the k-th smallest substring efficient I preprocess this sorted set to add in information about the longest common prefix between a suffix and it's predecessor as well as keeping tabs on a cumulative substrings count. So I know that for a given k greater than the cumulative substrings count of the last item, it's an invalid query.
This works really well for small inputs as well as random large inputs of the constraints given in the problem definition, which is at most 50 strings of length 2000. I am able to pass the 4 out of 7 cases and was pretty surprised I didn't get them all.
So I went searching for the bottleneck and it hit me. Given large number of inputs like these
anananananananana.....ananana
bkbkbkbkbkbkbkbkb.....bkbkbkb
The queries for k-th smallest substrings are still fast as expected but not the way I preprocess the sorted set... The way I calculate the longest common prefix between the elements of the set is not efficient and linear O(m), like this, I did the most naïve thing expecting it to be good enough:
m = anananan
n = anananana
Start at 0 and find the point where `m[i] != n[i]`
It is like this because a suffix and his predecessor might no be related (i.e. coming from different input strings) and so I thought I couldn't help but using brute force.
Here is the question then and where I ended up reducing the problem as. Given a list of lexicographically sorted suffix like in the manner I described above (made up of multiple strings):
What is an efficient way of computing the longest common prefix array?.
The subquestion would then be, am I completely off the mark in my approach? Please propose further avenues of investigation if that's the case.
Foot note, I do not want to be shown implemented algorithm and I don't mind to be told to go read so and so book or resource on the subject as that is what I do anyway while attempting these challenges.
Accepted answer will be something that guides me on the right path or in the case that that fails; something that teaches me how to solve these types of problem in a broader sense, a book or something
READING
I would recommend this tutorial pdf from Stanford.
This tutorial explains a simple O(nlog^2n) algorithm with O(nlogn) space to compute suffix array and a matrix of intermediate results. The matrix of intermediate results can be used to compute the longest common prefix between two suffixes in O(logn).
HINTS
If you wish to try to develop the algorithm yourself, the key is to sort the strings based on their 2^k long prefixes.
From the tutorial:
Let's denote by A(i,k) be the subsequence of A of length 2^k starting at position i.
The position of A(i,k) in the sorted array of A(j,k) subsequences (j=1,n) is kept in P(k,i).
and
Using matrix P, one can iterate descending from the biggest k down to 0 and check whether A(i,k) = A(j,k). If the two prefixes are equal, a common prefix of length 2^k had been found. We only have left to update i and j, increasing them both by 2^k and check again if there are any more common prefixes.
Given a string S, consisting of the lowercase Latin letters. I want to find for each position S[i] max length L[i] for which there exists a position i' < i that s[i'..i'+L[i]-1] = s[i..i+L[i]-1]. For example: s = ababaab, L= {0,0,3,2,1,2,1}. I want to do it for time < O(|S|^2). I guess the problem is solved with the suffix array but how?
You should look at the ZBlock Algorithm, although this algorithm solve a slightly different problem (where i' is always equal to 0), it runs in O(|S|). You should be able to modify it at your convenience.
Dynamic programming would solve this in O(|S|^2) using a modified version of substring matching but I guess you are not looking for such solution.
What you are looking for is called "longest previous factor" and there is indeed a paper by Crochemore and Ilie with two suffix array algorithms to compute this. The good news is that it is that both are linear time. The second algorithm uses the Lcp table and looks to me to be a bit easier.
This is a problem appeared in today's Pacific NW Region Programming Contest during which no one solved it. It is problem B and the complete problem set is here: http://www.acmicpc-pacnw.org/icpc-statements-2011.zip. There is a well-known O(n^2) algorithm for LCS of two strings using Dynamic Programming. But when these strings are extended to rings I have no idea...
P.S. note that it is subsequence rather than substring, so the elements do not need to be adjacent to each other
P.S. It might not be O(n^2) but O(n^2lgn) or something that can give the result in 5 seconds on a common computer.
Searching the web, this appears to be covered by section 4.3 of the paper "Incremental String Comparison", by Landau, Myers, and Schmidt at cost O(ne) < O(n^2), where I think e is the edit distance. This paper also references a previous paper by Maes giving cost O(mn log m) with more general edit costs - "On a cyclic string to string correcting problem". Expecting a contestant to reproduce either of these papers seems pretty demanding to me - but as far as I can see the question does ask for the longest common subsequence on cyclic strings.
You can double the first and second string and then use the ordinary method, and later wrap the positions around.
It is a good idea to "double" the strings and apply the standard dynamic programing algorithm. The problem with it is that to get the optimal cyclic LCS one then has to "start the algorithm from multiple initial conditions". Just one initial condition (e.g. setting all Lij variables to 0 at the boundaries) will not do in general. In practice it turns out that the number of initial states that are needed are O(N) in number (they span a diagonal), so one gets back to an O(N^3) algorithm.
However, the approach does has some virtue as it can be used to design efficient O(N^2) heuristics (not exact but near exact) for CLCS.
I do not know if a true O(N^2) exist, and would be very interested if someone knows one.
The CLCS problem has quite interesting properties of "periodicity": the length of a CLCS of
p-times reapeated strings is p times the CLCS of the strings. This can be proved by adopting a geometric view off the problem.
Also, there are some additional benefits of the problem: it can be shown that if Lc(N) denotes the averaged value of the CLCS length of two random strings of length N, then
|Lc(N)-CN| is O(\sqrt{N}) where C is Chvatal-Sankoff's constant. For the averaged length L(N) of the standard LCS, the only rate result of which I know says that |L(N)-CN| is O(sqrt(Nlog N)). There could be a nice way to compare Lc(N) with L(N) but I don't know it.
Another question: it is clear that the CLCS length is not superadditive contrary to the LCS length. By this I mean it is not true that CLCS(X1X2,Y1Y2) is always greater than CLCS(X1,Y1)+CLCS(X2,Y2) (it is very easy to find counter examples with a computer).
But it seems possible that the averaged length Lc(N) is superadditive (Lc(N1+N2) greater than Lc(N1)+Lc(N2)) - though if there is a proof I don't know it.
One modest interest in this question is that the values Lc(N)/N for the first few values of N would then provide good bounds to the Chvatal-Sankoff constant (much better than L(N)/N).
As a followup to mcdowella's answer, I'd like to point out that the O(n^2 lg n) solution presented in Maes' paper is the intended solution to the contest problem (check http://www.acmicpc-pacnw.org/ProblemSet/2011/solutions.zip). The O(ne) solution in Landau et al's paper does NOT apply to this problem, as that paper is targeted at edit distance, not LCS. In particular, the solution to cyclic edit distance only applies if the edit operations (add, delete, replace) all have unit (1, 1, 1) cost. LCS, on the other hand, is equivalent to edit distances with (add, delete, replace) costs (1, 1, 2). These are not equivalent to each other; for example, consider the input strings "ABC" and "CXY" (for the acyclic case; you can construct cyclic counterexamples similarly). The LCS of the two strings is "C", but the minimum unit-cost edit is to replace each character in turn.
At 110 lines but no complex data structures, Maes' solution falls towards the upper end of what is reasonable to implement in a contest setting. Even if Landau et al's solution could be adapted to handle cyclic LCS, the complexity of the data structure makes it infeasible in a contest setting.
Last but not least, I'd like to point out that an O(n^2) solution DOES exist for CLCS, described here: http://arxiv.org/abs/1208.0396 At 60 lines, no complex data structures, and only 2 arrays, this solution is quite reasonable to implement in a contest setting. Arriving at the solution might be a different matter, though.