I have given n strings . I have to find a string S so that, given n strings are sub-sequence of S.
For example, I have given the following 5 strings:
AATT
CGTT
CAGT
ACGT
ATGC
Then the string is "ACAGTGCT" . . Because, ACAGTGCT contains all given strings as super-sequence.
To solve this problem I have to know the algorithm . But I have no idea how to solve this . Guys, can you help me by telling technique to solve this problem ?
This is a NP-complete problem called multiple sequence alignment.
The wiki page describes solution methods such as dynamic programming which will work for small n, but becomes prohibitively expensive for larger n.
The basic idea is to construct an array f[a,b,c,...] representing the length of the shortest string S that generates "a" characters of the first string, "b" characters of the second, and "c" characters of the third.
My Approach: using Trie
Building a Trie from the given words.
create empty string (S)
create empty string (prev)
for each layer in the trie
create empty string (curr)
for each character used in the current layer
if the character not used in the previous layer (not in prev)
add the character to S
add the character to curr
prev = curr
Hope this helps :)
1 Definitions
A sequence of length n is a concatenation of n symbols taken from an alphabet .
If S is a sequence of length n and T is a sequence of length m and n m then S is a subsequence of T if S can be obtained by deleting m-n symbols from T. The symbols need not be contiguous.
A sequence T of length m is a supersequence of S of length n if T can be obtained by inserting m-n symbols. That is, T is a supersequence of S if and only if S is a subsequence of T.
A sequence T is a common supersequence of the sequences S1 and S2 of T is a supersequence of both S1 and S2.
2 The problem
The problem is to find a shortest common supersequence (SCS), which is a common supersequence of minimal length. There could be more than one SCS for a given problem.
2.1 Example
S= {a, b, c}
S1 = bcb
S2 = baab
S3 = babc
One shortest common supersequence is babcab (babacb, baabcb, bcaabc, bacabc, baacbc).
3 Techniques
Dynamic programming Requires too much memory unless the number of input-sequences are very small.
Branch and bound Requires too much time unless the alphabet is very small.
Majority merge The best known heuristic when the number of sequences is large compared to the alphabet size. [1]
Greedy (take two sequences and replace them by their optimal shortest common supersequence until a single string is left) Worse than majority merge. [1]
Genetic algorithms Indications that it might be better than majority merge. [1]
4 Implemented heuristics
4.1 The trivial solution
The trivial solution is at most || times the optimal solution length and is obtained by concatenating the concatenation of all characters in sigma as many times as the longest sequence. That is, if = {a, b, c} and the longest input sequence is of length 4 we get abcabcabcabc.
4.2 Majority merge heuristic
The Majority merge heuristic builds up a supersequence from the empty sequence (S) in the following way:
WHILE there are non-empty input sequences
s <- The most frequent symbol at the start of non-empty input-sequences.
Add s to the end of S.
Remove s from the beginning of each input sequence that starts with s.
END WHILE
Majority merge performs very well when the number of sequences is large compared to the alphabet size.
5 My approach - Local search
My approach was to apply a local search heuristic to the SCS problem and compare it to the Majority merge heuristic to see if it might do better in the case when the alphabet size is larger than the number of sequences.
Since the length of a valid supersequence may vary and any change to the supersequence may give an invalid string a direct representation of a supersequence as a feasible solution is not an option.
I chose to view a feasible solution (S) as a sequence of mappings x1...xSl where Sl is the sum of the lengths of all sequences and xi is a mapping to a sequencenumber and an index.
That means, if L={{s1,1...s1,m1}, {s2,1...s2,m2} ...{sn,1...s3,mn}} is the set of input sequences and L(i) is the ith sequence the mappings are represented like this:
xi {k, l}, where k L and l L(k)
To be sure that any solution is valid we need to introduce the following constraints:
Every symbol in every sequence may only have one xi mapped to it.
If xi ss,k and xj ss,l and k < l then i < j.
If xi ss,k and xj ss,l and k > l then i > j.
The second constraint enforces that the order of each sequence is preserved but not its position in S. If we have two mappings xi and xj then we may only exchange mappings between them if they map to different sequences.
5.1 The initial solution
There are many ways to choose an initial solution. As long as the order of the sequences are preserved it is valid. I chose not to in some way randomize a solution but try two very different solution-types and compare them.
The first one is to create an initial solution by simply concatenating all the sequences.
The second one is to interleave the sequences one symbol at a time. That is to start with the first symbol of every sequence then, in the same order, take the second symbol of every sequence and so on.
5.2 Local change and the neighbourhood
A local change is done by exchanging two mappings in the solution.
One way of doing the iteration is to go from i to Sl and do the best exchange for each mapping.
Another way is to try to exchange the mappings in the order they are defined by the sequences. That is, first exchange s1,1, then s2,1. That is what we do.
There are two variants I have tried.
In the first one, if a single mapping exchange does not yield a better value I return otherwise I go on.
In the second one, I seperately for each sequence do as many exchanges as there are sequences so a symbol in each sequence will have a possibility of moving. The exchange that gives the best value I keep and if that value is worse than the value of the last step in the algorithm I return otherwise I go on.
A symbol may move any number of position to the left or to the right as long as the exchange does not change the order of the original sequences.
The neighbourhood in the first variant is the number of valid exchanges that can be made for the symbol. In the second variant it is the sum of valid exchanges of each symbol after the previous symbol has been exchanged.
5.3 Evaluation
Since the length of the solution is always constant it has to be compressed before the real length of the solution may be obtained.
The solution S, which consists of mappings is converted to a string by using the symbols each mapping points to. A new, initialy empty, solution T is created. Then this algorithm is performed:
T = {}
FOR i = 0 TO Sl
found = FALSE
FOR j = 0 TO |L|
IF first symbol in L(j) = the symbol xi maps to THEN
Remove first symbol from L(j)
found = TRUE
END IF
END FOR
IF found = TRUE THEN
Add the symbol xi maps to to the end of T
END IF
END FOR
Sl is as before the sum of the lengths of all sequences. L is the set of all sequences and L(j) is sequence number j.
The value of the solution S is obtained as |T|.
With Many Many Thanks to : Andreas Westling
Related
I have a collection S, typically containing 10-50 long strings. For illustrative purposes, suppose the length of each string ranges between 1000 and 10000 characters.
I would like to find strings of specified length k (typically in the range of 5 to 20) that are substrings of every string in S. This can obviously be done using a naive approach - enumerating every k-length substring in S[0] and checking if they exist in every other element of S.
Are there more efficient ways of approaching the problem? As far as I can tell, there are some similarities between this and the longest common subsequence problem, but my understanding of LCS is limited and I'm not sure how it could be adapted to the situation where we bound the desired common substring length to k, or if subsequence techniques can be applied to finding substrings.
Here's one fairly simple algorithm, which should be reasonably fast.
Using a rolling hash as in the Rabin-Karp string search algorithm, construct a hash table H0 of all the |S0|-k+1 length k substrings of S0. That's roughly O(|S0|) since each hash is computed in O(1) from the previous hash, but it will take longer if there are collisions or duplicate substrings. Using a better hash will help you with collisions but if there are a lot of k-length duplicate substrings in S0 then you could end up using O(k|S0|).
Now use the same rolling hash on S1. This time, look each substring up in H0 and if you find it, remove it from H0 and insert it into a new table H1. Again, this should be around O(|S1|) unless you have some pathological case, like both S0 and S1 are just long repetitions of the same character. (It's also going to be suboptimal if S0 and S0 are the same string, or have lots of overlapping pieces.)
Repeat step 2 for each Si, each time creating a new hash table. (At the end of each iteration of step 2, you can delete the hash table from the previous step.)
At the end, the last hash table will contain all the common k-length substrings.
The total run time should be about O(Σ|Si|) but in the worst case it could be O(kΣ|Si|). Even so, with the problem size as described, it should run in acceptable time.
Some thoughts (N is number of strings, M is average length, K is needed substring size):
Approach 1:
Walk through all strings, computing rolling hash for k-length strings and storing these hashes in the map (store tuple {key: hash; string_num; position})
time O(NxM), space O(NxM)
Extract groups with equal hash, check step-by-step:
1) that size of group >= number of strings
2) all strings are represented in this group 3
3) thorough checking of real substrings for equality (sometimes hashes of distinct substrings might coincide)
Approach 2:
Build suffix array for every string
time O(N x MlogM) space O(N x M)
Find intersection of suffix arrays for the first string pair, using merge-like approach (suffixes are sorted), considering only part of suffixes of length k, then continue with the next string and so on
I would treat each long string as a collection of overlapped short strings, so ABCDEFGHI becomes ABCDE, BCDEF, CDEFG, DEFGH, EFGHI. You can represent each short string as a pair of indexes, one specifying the long string and one the starting offset in that string (if this strikes you as naive, skip to the end).
I would then sort each collection into ascending order.
Now you can find the short strings common to the first two collection by merging the sorted lists of indexes, keeping only those from the first collection which are also present in the second collection. Check the survivors of this against the third collection, and so on and the survivors at the end correspond to those short strings which are present in all long strings.
(Alternatively you could maintain a set of pointers into each sorted list and repeatedly look to see if every pointer points at short strings with the same text, then advancing the pointer which points at the smallest short string).
Time is O(n log n) for the initial sort, which dominates. In the worst case - e.g. when every string is AAAAAAAA..AA - there is a factor of k on top of this, because all string compares check all characters and take time k. Hopefully, there is a clever way round this with https://en.wikipedia.org/wiki/Suffix_array which allows you to sort in time O(n) rather than O(nk log n) and the https://en.wikipedia.org/wiki/LCP_array, which should allow you to skip some characters when comparing substrings from different suffix arrays.
Thinking about this again, I think the usual suffix array trick of concatenating all of the strings in question, separated by a character not found in any of them, works here. If you look at the LCP of the resulting suffix array you can split it into sections, splitting at points where where the difference between suffixes occurs less than k characters in. Now each offset in any particular section starts with the same k characters. Now look at the offsets in each section and check to see if there is at least one offset from every possible starting string. If so, this k-character sequence occurs in all starting strings, but not otherwise. (There are suffix array constructions which work with arbitrarily large alphabets so you can always expand your alphabet to produce a character not in any string, if necessary).
I would try a simple method using HashSets:
Build a HashSet for each long string in S with all its k-strings.
Sort the sets by number of elements.
Scan the first set.
Lookup the term in the other sets.
The first step takes care of repetitions in each long string.
The second ensures the minimum number of comparisons.
let getHashSet k (lstr:string) =
let strs = System.Collections.Generic.HashSet<string>()
for i in 0..lstr.Length - k do
strs.Add lstr.[i..i + k - 1] |> ignore
strs
let getCommons k lstrs =
let strss = lstrs |> Seq.map (getHashSet k) |> Seq.sortBy (fun strs -> strs.Count)
match strss |> Seq.tryHead with
| None -> [||]
| Some h ->
let rest = Seq.tail strss |> Seq.toArray
[| for s in h do
if rest |> Array.forall (fun strs -> strs.Contains s) then yield s
|]
Test:
let random = System.Random System.DateTime.Now.Millisecond
let generateString n =
[| for i in 1..n do
yield random.Next 20 |> (+) 65 |> System.Convert.ToByte
|] |> System.Text.Encoding.ASCII.GetString
[ for i in 1..3 do yield generateString 10000 ]
|> getCommons 4
|> fun l -> printfn "found %d\n %A" l.Length l
result:
found 40
[|"PPTD"; "KLNN"; "FTSR"; "CNBM"; "SSHG"; "SHGO"; "LEHS"; "BBPD"; "LKQP"; "PFPH";
"AMMS"; "BEPC"; "HIPL"; "PGBJ"; "DDMJ"; "MQNO"; "SOBJ"; "GLAG"; "GBOC"; "NSDI";
"JDDL"; "OOJO"; "NETT"; "TAQN"; "DHME"; "AHDR"; "QHTS"; "TRQO"; "DHPM"; "HIMD";
"NHGH"; "EARK"; "ELNF"; "ADKE"; "DQCC"; "GKJA"; "ASME"; "KFGM"; "AMKE"; "JJLJ"|]
Here it is in fiddle: https://dotnetfiddle.net/ZK8DCT
Given a string A and a set of string S. Need to find an optimum method to find a prefix of A which is not a prefix of any of the strings in S.
Example
A={apple}
S={april,apprehend,apprehension}
Output should be "appl" and not "app" since "app" is prefix of both "apple" and "apprehension" but "appl" is not.
I know the trie approach; by making a trie of set S and then traversing in the trie for string A.
But what I want to ask is can we do it without trie?
Like can we compare every pair (A,Si), Si = ith string from set S and get the largest common prefix out of them.In this case that would be "app" , so now the required ans would be "appl".
This would take 2 loops(one for iterating through S and another for comparing Si and A).
Can we improve upon this??
Please suggest an optimum approach.
I'm not sure exactly what you had in mind, but here's one way to do it:
Keep a variable longest, initialised to 0.
Loop over all elements S[i] of S,
setting longest = max(longest, matchingPrefixLength(S[i], A)).
Return the prefix from A of length longest+1.
This uses O(1) space and takes O(length(S)*average length of S[i]) time.
This is optimal (at least for the worst case) since you can't get around needing to look at every character of every element in S.
Example:
A={apple}
S={april,apprehend,apprehension}
longest = 0
The longest prefix for S[0] and A is 2
So longest = max(0,2) = 2
The longest prefix for S[1] and A is 3
So longest = max(2,3) = 3
The longest prefix for S[2] and A is 3
So longest = max(3,3) = 3
Now we return the prefix of length longest+1 = 4, i.e. "appl"
Note that there are actually 2 trie-based approaches:
Store only A in the trie. Iterate through the trie for each element from S to eliminate prefixes.
This uses much less memory than the second approach (but still more than the approach above). At least assuming A isn't much, much longer than S[i], but you can optimise to stop at the longest element in S or construct the tree as we go to avoid this case.
Store all elements from S in the trie. Iterate through the trie with A to find the shortest non-matching prefix.
This approach is significantly faster if you have lots of A's that you want to query for a constant set S (since you only have to set up the trie once, and do a single lookup for each A, where-as you have to create a new trie and run through each S[i] for each A for the first approach).
What is your input size?
Let's model your input as being of N+1 strings whose lengths are about M characters. Your total input size is about M(N+1) character, plus some proportional amount of apparatus to encode that data in a usable format (data structure overhead).
Your algorithm ...
maxlen = 0
for i = 1 to N
for j = 1 to M
if A[j] = S[i][j] then
if j > maxlen then maxlen = j
break
print A[1...maxlen]
... performs up M x N iterations of the innermost loop, reading two characters each time, for a total of 2MN characters read.
Recall our input data size was about M(N+1) also. So our question now is whether we can solve this problem, in the worst case, looking at asymptotically less than the total input (you do a little less than looking at all the input twice, or linear in the input size). The answer is no. Consider this worst case:
length of A is M'
length of all strings in S is M'
A differs from N-1 strings in S by the last two characters
A differs from 1 string in S by only the last character
Any algorithm must look at M'-1 characters of N-1 strings, plus M' characters of 1 string, to correctly determine the answer of this problem instance is A.
(M'-1)(N'-1) + N = M'N - M' - N + 1 + N = M'N - M' + 1
For N >= 2, the dominant terms in both M'(N+1) and M'N' are both M'N, meaning that for N >= 2, both the input size and the amount of that input any correct algorithm must read is O(MN). Your algorithm is O(MN). Any other algorithm cannot be asymptotically better.
Suppose we are given two strings s1 and s2(both lowercase). We have two find the minimal lexographic string that can be formed by merging two strings.
At the beginning , it looks prettty simple as merge of the mergesort algorithm. But let us see what can go wrong.
s1: zyy
s2: zy
Now if we perform merge on these two we must decide which z to pick as they are equal, clearly if we pick z of s2 first then the string formed will be:
zyzyy
If we pick z of s1 first, the string formed will be:
zyyzy which is correct.
As we can see the merge of mergesort can lead to wrong answer.
Here's another example:
s1:zyy
s2:zyb
Now the correct answer will be zybzyy which will be got only if pick z of s2 first.
There are plenty of other cases in which the simple merge will fail. My question is Is there any standard algorithm out there used to perform merge for such output.
You could use dynamic programming. In f[x][y] store the minimal lexicographical string such that you've taken x charecters from the first string s1 and y characters from the second s2. You can calculate f in bottom-top manner using the update:
f[x][y] = min(f[x-1][y] + s1[x], f[x][y-1] + s2[y]) \\ the '+' here represents
\\ the concatenation of a
\\ string and a character
You start with f[0][0] = "" (empty string).
For efficiency you can store the strings in f as references. That is, you can store in f the objects
class StringRef {
StringRef prev;
char c;
}
To extract what string you have at certain f[x][y] you just follow the references. To udapate you point back to either f[x-1][y] or f[x][y-1] depending on what your update step says.
It seems that the solution can be almost the same as you described (the "mergesort"-like approach), except that with special handling of equality. So long as the first characters of both strings are equal, you look ahead at the second character, 3rd, etc. If the end is reached for some string, consider the first character of the other string as the next character in the string for which the end is reached, etc. for the 2nd character, etc. If the ends for both strings are reached, then it doesn't matter from which string to take the first character. Note that this algorithm is O(N) because after a look-ahead on equal prefixes you know the whole look-ahead sequence (i.e. string prefix) to include, not just one first character.
EDIT: you look ahead so long as the current i-th characters from both strings are equal and alphabetically not larger than the first character in the current prefix.
Given a source string s and n equal length strings, I need to find a quick algorithm to return those strings that have at most k characters that are different from the source string s at each corresponding position.
What is a fast algorithm to do so?
PS: I have to claim that this is a academic question. I want to find the most efficient algorithm if possible.
Also I missed one very important piece of information. The n equal length strings form a dictionary, against which many source strings s will be queried upon. There seems to be some sort of preprocessing step to make it more efficient.
My gut instinct is just to iterate over each String n, maintaining a counter of how many characters are different than s, but I'm not claiming it is the most efficient solution. However it would be O(n) so unless this is a known performance problem, or an academic question, I'd go with that.
Sedgewick in his book "Algorithms" writes that Ternary Search Tree allows "to locate all words within a given Hamming distance of a query word". Article in Dr. Dobb's
Given that the strings are fixed length, you can compute the Hamming distance between two strings to determine the similarity; this is O(n) on the length of the string. So, worst case is that your algorithm is O(nm) for comparing your string against m words.
As an alternative, a fast solution that's also a memory hog is to preprocess your dictionary into a map; keys are a tuple (p, c) where p is the position in the string and c is the character in the string at that position, values are the strings that have characters at that position (so "the" will be in the map at {(0, 't'), "the"}, {(1, 'h'), "the"}, {(2, 'e'), "the"}). To query the map, iterate through query string's characters and construct a result map with the retrieved strings; keys are strings, values are the number of times the strings have been retrieved from the primary map (so with the query string "the", the key "thx" will have a value of 2, and the key "tee" will have a value of 1). Finally, iterate through the result map and discard strings whose values are less than K.
You can save memory by discarding keys that can't possibly equal K when the result map has been completed. For example, if K is 5 and N is 8, then when you've reached the 4th-8th characters of the query string you can discard any retrieved strings that aren't already in the result map since they can't possibly have 5 matching characters. Or, when you've finished with the 6th character of the query string, you can iterate through the result map and remove all keys whose values are less than 3.
If need be you can offload the primary precomputed map to a NoSql key-value database or something along those lines in order to save on main memory (and also so that you don't have to precompute the dictionary every time the program restarts).
Rather than storing a tuple (p, c) as the key in the primary map, you can instead concatenate the position and character into a string (so (5, 't') becomes "5t", and (12, 'x') becomes "12x").
Without knowing where in each input string the match characters will be, for a particular string, you might need to check every character no matter what order you check them in. Therefore it makes sense to just iterate over each string character-by-character and keep a sum of the total number of mismatches. If i is the number of mismatches so far, return false when i == k and true when there are fewer than k-i unchecked characters remaining in the string.
Note that depending on how long the strings are and how many mismatches you'll allow, it might be faster to iterate over the whole string rather than performing these checks, or perhaps to perform them only after every couple characters. Play around with it to see how you get the fastest performance.
My method if we're thinking out loud :P I can't see a way to do this without going through each n string, but I'm happy to be corrected. On that it would begin with a pre-process to save a second set of your n strings so that the characters are in ascending order.
The first part of the comparison would then be to check each n string a character at a time say n' to each character in s say s'.
If s' is less than n' then not equal and move to the next s'. If n' is less than s' then go to next n'. Otherwise record a matching character. Repeat this until k miss matches are found or the alternate matches are found and mark n accordingly.
For further consideration, an added pre-processing could be done on each adjacent string in n to see the total number of characters that differ. This could then be used when comparing strings n to s and if sufficient difference exist between these and the adjacent n there may not be a need to compare it?
Given n strings S1, S2, ..., Sn, and an alphabet set A={a_1,a_2,....,a_m}. Assume that the alphabets in each string are all distinct. Now I want to create an inverted-index for each a_i (i=1,2...,m). My inverted-index has also something special: The alphabets in A are in some sequential order, if in the inverted-index a_i has included one string (say S_2), then a_j (j=i+1,i+2,...,m) don't need to include S_2 any more. In short, every string just appears in the inverted list only once. My question is how to build such list in a fast and efficient way? Any time complexity is bounded?
For example, A={a,b,e,g}, S1={abg}, S2={bg}, S3={gae}, S4={g}. Then my inverted-list should be:
a: S1,S3
b: S2 (since S1 has appeared previously, so we don't need to include it here)
e:
g: S4
If I understand your question correctly, a straightforward solution is:
for each string in n strings
find the "smallest" character in the string
put the string in the list for the character
The complexity is proportional to the total length of the strings, multiplying by a constant for the order testing.
If there is a simple way for testing, (e.g. the characters are in alphabetical order and all lower-case, a < will be enough), simply compare them; otherwise, I suggest using a hash table, each pair of which is a character and its order, later simply compare them.