Questions tagged [subsequences]

Questions about algorithms related to subsequences, or about properties of subsequences.

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24 views

Sequential subsequence removal with arbitrary predicate

I want to extract sub-sequences from a sequence of float values. The "scale" and range of these values is arbitrary (as I can manipulate it at will) but the "shape" is consistent. For a visual ...
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1answer
24 views

Minimize sequence storage by overlapping prefixes

I bumped into this problem today, and after a bit of pondering, I think I have a solution in $O(n^3)$, which is better than no solution or an $O(n!)$ solution, but my answer still isn't great. Can ...
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1answer
47 views

Time complexity of finding subsequences of a string segmented into parts

Let $S$ be a string of length $N$, consisting of digits 0 to 9. For convenience, we assume $N$ to be a multiple of 3. Then, we split $S$ into $N/3$ equal parts, each of length 3. For each equal part,...
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1answer
51 views

ILP representation of the number of maximal 1 sequences in a row

I am currently using an ILP to model events which occur on some input sequence from $1...n$. These events modify the input sequence in order to obtain a desired sequence. Each event can happen on some ...
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0answers
180 views

Interleave two arrays such that collisions are minimised (dynamic programming) [closed]

This is a fascinating bioinformatics dynamic programming that I am solving. I am not looking for an answer to the problem, but rather any algorithms, research papers, or other pointers that could be ...
3
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1answer
368 views

Use dynamic programming to merge two arrays such that the number of repetitions of the same element is minimised

Let's say we have two arrays m and n containing the characters from the set a, b, c , d, e. ...
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1answer
153 views

Maximum product of contiguous subsequence over $\mathbb{R}$

For the problem of a subsequence of maximum product with negative, zero and positive integers, I have the following working solution (inspiration from here). Let us first show how to solve the ...
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2answers
46 views

How can I efficiently find the largest positive interval in an unsorted array? [duplicate]

Given a set of values like [4, 8, 1, 5, 2, 6, 9, 2, 3, 5, 11, 9], how can I find the largest positive interval between any two of them? For example in the one I just listed, index 0 to index 1 has an ...
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0answers
214 views

Shortest Uncommon Subsequence

Here is another GeeksforGeeks problem that asks how to find the shortest Uncommon Subsequence of 2 strings? For example, Input : S = “babab” T = “babba” Output : 3The subsequence “aab” of ...
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0answers
185 views

Maximize interleaving subsequences two digit arrays/strings

Suppose I have two digit arrays, A and B as follows A = [3,4,5,6] B = [9,8,3] Now, I have ...
2
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0answers
18 views

How can I optimise a 8b10b encoding for maximum alignment?

Imagine you encode an 8 bit symbol as a 10 bit symbol that is sent sequentially over a wire. The goal at the receiver is to detect the byte boundary. Since there are 4 times more encoded symbols than ...
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1answer
57 views

Number of contiguous subsequences summing to a given target

I could not figure out an efficient way (better than $O(n^2)$) to count the number of contiguous subsequences of an array of both positive and negative integers summing up to a given number $k$. For ...
2
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1answer
189 views

How is the Longest Common Sub-sequence of two sequences is a special case of the Sequence Alignment problem?

Could anyone briefly show me how the Longest Common Sub-sequence of two sequences is a special case of the Sequence Alignment problem? I cannot wrap my head around this. Thank you.
2
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1answer
45 views

longest sub-sequence in both directions

Given a character array A of size n, compute the length of a longest sub-sequence S of A such that, S read backward is also a sub-sequence of A. Example: A = cabca the sub-sequence S = abc is the ...
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0answers
79 views

Matching relative order in subsequence of fixed length

I encountered this problem from game development which I will formulate in a more formal way: Given a sequence $A = a_1, a_2, \dots, a_m$ and a permutation of $\{1, \dots, n\}$, $B = b_1, b_2, \...
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1answer
45 views

How can I efficiently generate the shortest list of arguments for the range() function that will generate a given list of integers?

I ran into an interesting problem at work when trying to generate the inputs for an API given the expected output. I've tried to formalize and anonymize the problem below. I've been trying to design a ...
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2answers
434 views

Counting number of perfect squares in an subarrays

A sequence is good if the bitwise AND of all its elements is a perfect square. So counting number of "good" sequences, in a subarray . For example : in [1, 2, 3] There are 6 sub-sequences: So ...
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1answer
152 views

DFA for strings with number of 0's odd only in substring longer than 1

I'm trying to design and DFA that accept string with an odd number of 0`s, but counting only the ones within sub-strings with two or more 0. So, for example, 011000, will be accepted since it has 4 0`...
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1answer
399 views

Complexity of Longest Palindromic Subsequence Algorithm

I'm trying to find the longest palindromic subsequence for any string and I've tried two approaches: Recursive Algoritm Dynamic Programming Dynamic programming should be the better option in this ...
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0answers
27 views

How many optimal alignments can be there for a string of length m with a string of length n?

So I was practicing optimal alignment algorithm and I was stuck with this question of finding optimal alignment for a string of length m with a string length n ? Also is it possible to run it in theta(...
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1answer
64 views

How to check if $m$ numbers in a sequence satisfy a condition, such that all these numbers are spaced apart by at least $k$?

Suppose we have a sequence $s$ with $n$ elements from $s[1..n]$. I want to check if there exists $m \leq n$ elements in this sequence that each satisfy some simple condition (that can be tested in $O(...
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0answers
55 views

Activity planning problem

Given a sequence of N activity durations, the time P of pause between activities, and D, the length of a day (there are no breaks between days, only between activities in a day), what is the minimum ...
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1answer
416 views

Number of possible sequence partitioning

Given a sequence of 1 and 0 elements, what is the number of possible partitioning of the sequence in sub-sequences (not necessarily consecutive elements, and any number of sub-sequences are allowed) ...
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2answers
451 views

Count the unique subsequences

I'm trying to count the number of subsequences of a long string. e.g. BANANA -> B, A, N, BA, BN, AA, NN, NA, BAN, BAA, BNA, BNN, ANA, AAA, NAN, NNA, etc There's the horribly inefficient way, which ...
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1answer
69 views

Finding a (Small-Big-Medium) subsequence

Given a list of $n$ non repeating integer numbers $L:=(x_1,\dots,x_n)$ develop an algorithm that decides if there are $x_{i_1},x_{i_2},x_{i_3}\in L$ such that $i_1<i_2<i_3$ and $x_{i_1}<x_{...
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1answer
95 views

Find the longest contigous subsequence where each pair's difference is at most p

Given input sequence $x_1,...,x_n$, find the longest contigous subsequence $x_i,... x_l$ where each pair $(x_j,x_k)$ satisfies that $|x_j - x_k| \le p$. I have come up with simple $\mathcal{O}(n^2)$ ...
3
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1answer
145 views

Shortest Non-Subsequence String With Constant-Size Alphabet

Let $S[1..n] \in \Sigma^*$ be a string of $n$ symbols over the alphabet $\Sigma$ where $|\Sigma| \in \mathcal{O}(1)$. Determine a shortest string which cannot be obtained from $S$ by deleting some (...
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1answer
54 views

Implementing SUM(i,j) and CHANGE(i,j) in O(log(n)) using a datastructure with O(n) space complexity

I have two operations: $Sum(i,j)$ : Calculate $A[i]+A[i+1]+....+A[j]$ $Change(i,x)$: Set $A[i]=x$ I need to implement these operations in an appropriate data structure using $O(n)$ space ($n$ is ...
3
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2answers
737 views

Find longest subsequence in array with given condition

I am given an array $A$ having $n$ elements and an integer $k$. I need to find the longest subsequence which always includes the first element and the subsequence follows the given condition: for ...
4
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1answer
228 views

Why does Banded Needleman-Wunsch give alignments with no more than d base pairs of indels?

A common modification to the Needleman-Wunsch to reduce running time is to only fill in the cells along a diagonal band of the matrix (slides 27/28). Let 2d + 1 represent the width of the band. Then ...
2
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1answer
878 views

How to count all contiguous subsequences with positive sum?

I have array $t$ with size $n \leq 10^6$. It has only two kinds of elements inside: $1$ or $-1$. I need to count how many contiguous subsequences have positive sum. This pseudocode demonstrates ...
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1answer
202 views

Longest increasing subsequence on pairs

Given a sequence of pairs $(a_1, b_1), (a_2, b_2), ..., (a_n, b_n)$ such that $a_1 \le a_2 \le ... \le a_n$ (i.e, sorted in ascending order by $a$'s), we solve the longest increasing subsequence ...
7
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1answer
104 views

Subsequence of one string but not of others

Let $\Sigma$ be an alphabet, and let $x^+,x^-_1,\dots,x^-_n \in \Sigma^*$ be strings over that alphabet. Call a string $s \in \Sigma^*$ good if $s$ is a subsequence of $x^+$ but not a subsequence of ...
7
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2answers
893 views

Count of distinct substrings in string inside range

Having string $S$ of length $n$, finding the count of distinct substrings can be done in linear time using LCP array. Instead of asking for unique substrings count in whole string $S$, query $q$ ...
2
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1answer
657 views

ZigZag sequence without dynamic programming

I just came across the maximum zigzag sequence problem, defined as follows: A zigzag sequence is defined as a sequence of numbers such that the difference between two consecutive numbers alternates ...
2
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1answer
316 views

Longest common subsequence of a set of sequences

There is as input a set of $m$ sequences of length $n$. I thought it was pretty straightforward at first that the time complexity of the algorithm provided below is $O(m^2n^4)$ but then it occurred ...
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1answer
52 views

Finding a subarray of time series data in which all values are less than X for specified time Y?

The idea is to find an anomalous value (i.e. it's less than X) in time series data (sorted by time), and check if this behavior continues during specified time (Y=2 hours). If all values in sub-array ...
2
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1answer
877 views

Algorithm to identify if a string of numbers is a lottery sequence

Suppose that a valid lottery ticket consists of a sequence of 7 numbers drawn from the set $\{1,2,\ldots,59\}$. Given a string like "$12345678$", I want to efficiently print all the lottery sequences ...
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0answers
120 views

Sequence Alignment with Skips

In my thesis I am working on a problem connected with sequence alignment, in particular, I deal with the Dynamic Time Warping (DTW) algorithm (see this for more), which is used to evaluate the ...
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0answers
83 views

proving that local sequence alignment can be done in linear space

according to the Smith-Waterman setup, I have 2 string sequences S and T, and I want to identify their respective subsequences $\alpha$ and $\beta$ whose global alignment have maximum score over all ...
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2answers
147 views

How to efficiently code Dynamic Time Warping algorithm with a locality constrain?

For given two lists $[s_1, s_2, ... s_n]$ and $[t_1, t_2, ..., t_m]$ I need to implement DTW algorithm with one extra constraint: If $s_i$ is matched with $t_j$ then the next element $s_{i+1}$ has ...
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0answers
225 views

Find equal length subsequences with maximum difference of sums, for given maximum subsequence length

The problem is the following. Suppose we have a sequence of n non-negative numbers, each element with index i having its own ...
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0answers
294 views

Proof that the length of the largest ascending subsequence is the number of decreasing subsequences

Given a sequence of numbers, I have to prove that the number of decreasing subsequences (non-strictly), so that every number is included in one subsequence and the number of subsequences is minimum is ...
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2answers
459 views

Find long connected similar subsequences in two given sequences

I'm looking for pointers to algorithms which will find long connected similar subsequences which two given sequences have in common. For example, in case of two strings: ...
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1answer
596 views

How is n-gram different from k-mer?

How is n-gram different from k-mer? Both seem to be (n or k) length substrings of a larger string. Are these just terms common with different practitioners? viz. Computer Scientists and ...
3
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1answer
440 views

Remove contiguous subsequence so the remaining numbers will created a sorted sequence

You are given $N$ numbers. Remove contiguous subsequence of those numbers, so the remaining numbers will create a sorted sequence. For example, if the sequence is $5$, $7$, $8$, $2$, $1$, $9$ then we ...
3
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1answer
427 views

Counting the number of permutations of string with given repeated interwoven subsequence

Given string $S$ of length $n$, count the number of distinct permutations $P_n$ of a string of length $2n$ such that each of them contains $S$ twice as an interwoven subsequence. Example. $S=abc$. ...
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1answer
3k views

Finding the longest repeating subsequence

Given a string $s$, I would like to find the longest repeating (at least twice) subsequence. That is, I would like to find a string $w$ which is a subsequence (doesn't have to be a contiguous) of $s$ ...
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1answer
262 views

Check if a string can be split into two subsequences

Given a string S of length N, a string A of length M, a string B of length O such that N >= M + O. Check if the string S can be split into two subsequences X and Y such that A = X and B = Y. Example: ...
6
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1answer
2k views

Computing the mode of XOR subsequences

I was confronted with this problem in an online programming challenge and it has been bugging me since: In the problem, you are given a list of 16-bit numbers, say $a_0, a_1, ..., a_n$. An "XOR ...