Related papers: Minimizers in Semi-Dynamic Strings
An initializable array is an array that supports the read and write operations for any element and the initialization of the entire array. This paper proposes a simple in-place algorithm to implement an initializable array of length $N$…
Space efficient algorithms play a central role in dealing with large amount of data. In such settings, one would like to analyse the large data using small amount of "working space". One of the key steps in many algorithms for analysing…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
A sliding window algorithm receives a stream of symbols and has to output at each time instant a certain value which only depends on the last $n$ symbols. If the algorithm is randomized, then at each time instant it produces an incorrect…
The construction of shortest feedback shift registers for a finite sequence S_1,...,S_N is considered over the finite ring Z_{p^r}. A novel algorithm is presented that yields a parametrization of all shortest feedback shift registers for…
We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem…
We consider the {\it indexable dictionary} problem, which consists of storing a set $S \subseteq \{0,...,m-1\}$ for some integer $m$, while supporting the operations of $\Rank(x)$, which returns the number of elements in $S$ that are less…
In this paper, we explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
In order to generate prime implicants for a given cube (minterm), most of minimization methods increase the dimension of this cube by removing one literal from it at a time. But there are two problems of exponential complexity. One of them…
Given a video with $T$ frames, frame sampling is a task to select $N \ll T$ frames, so as to maximize the performance of a fixed video classifier. Not just brute-force search, but most existing methods suffer from its vast search space of…
String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we…
Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
We present a method for non-smooth convex minimization which is based on subgradient directions and string-averaging techniques. In this approach, the set of available data is split into sequences (strings) and a given iterate is processed…
We consider the problem of finding a minimum cut of a weighted graph presented as a single-pass stream. While graph sparsification in streams has been intensively studied, the specific application of finding minimum cuts in streams is less…
In this paper, we develop the first one-pass streaming algorithm for submodular maximization that does not evaluate the entire stream even once. By carefully subsampling each element of data stream, our algorithm enjoys the tightest…
In many applications including integer-forcing linear multiple-input and multiple-output (MIMO) receiver design, one needs to solve a successive minima problem (SMP) on an $n$-dimensional lattice to get an optimal integer coefficient matrix…