Related papers: On Minimizers of Minimum Density
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 initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on the walks of a graph. We establish that…
The size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to…
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…
A popular approach to sentence compression is to formulate the task as a constrained optimization problem and solve it with integer linear programming (ILP) tools. Unfortunately, dependence on ILP may make the compressor prohibitively slow,…
We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers $w_{\min}$ and $w_{\max}$ and a sequence $S$ of $n$ number pairs $(a_i,w_i)$ with $w_i>0$. Let {\em segment} $S(i,j)$ of $S$…
Consistent sampling is a technique for specifying, in small space, a subset $S$ of a potentially large universe $U$ such that the elements in $S$ satisfy a suitably chosen sampling condition. Given a subset $\mathcal{I}\subseteq U$ it…
The problem of k-minimisation for a DFA M is the computation of a smallest DFA N (where the size |M| of a DFA M is the size of the domain of the transition function) such that their recognized languages differ only on words of length less…
A string $w$ is called a minimal absent word (MAW) for another string $T$ if $w$ does not occur (as a substring) in $T$ and any proper substring of $w$ occurs in $T$. State-of-the-art data structures for reporting the set $\mathsf{MAW}(T)$…
Minimal perfect hashing is the problem of mapping a static set of $n$ distinct keys into the address space $\{1,\ldots,n\}$ bijectively. It is well-known that $n\log_2(e)$ bits are necessary to specify a minimal perfect hash function (MPHF)…
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…
This paper presents an algorithm to solve the Soft k-Means problem globally. Unlike Fuzzy c-Means, Soft k-Means (SkM) has a matrix factorization-type objective and has been shown to have a close relation with the popular probability…
Given a graph $G$, the sparsest-cut problem asks to find the set of vertices $S$ which has the least expansion defined as $$\phi_G(S) := \frac{w(E(S,\bar{S}))}{\min \set{w(S), w(\bar{S})}}, $$ where $w$ is the total edge weight of a subset.…
We consider the unconstrained $L_2$-$L_p$ minimization: find a minimizer of $\|Ax-b\|^2_2+\lambda \|x\|^p_p$ for given $A \in R^{m\times n}$, $b\in R^m$ and parameters $\lambda>0$, $p\in [0,1)$. This problem has been studied extensively in…
Estimating the abundances of all $k$-mers in a set of biological sequences is a fundamental and challenging problem with many applications in biological analysis. While several methods have been designed for the exact or approximate…
Sequential minimum optimization is a machine-learning global search training algorithm. It is applicable when the functional dependence of the cost function on a tunable parameter given the other parameters can be cheaply determined. This…
The efficiency of exact subset sum problem algorithms which compute individual subset sums is defined as $e=min(T/z, 1)$, where $z$ is the number of subset sums computed. $e$ is related to these algorithms' computational complexity. This…
We solve explicitly a certain minimization problem for probability measures in one dimension involving an interaction energy that arises in the modelling of aggregation phenomena. We show that in a certain regime minimizers are absolutely…
In this paper we consider two problems concerning string factorisation. Specifically given a string $w$ and an integer $k$ find a factorisation of $w$ where each factor has length bounded by $k$ and has the minimum (the FmD problem) or the…
Identifying the most frequent induced subgraph of size $k$ in a target graph is a fundamental graph mining problem with direct implications for Web-related data mining and social network analysis. Despite its importance, finding the most…