Related papers: Efficient Seeds Computation Revisited
We study the optimization version of the set partition problem (where the difference between the partition sums are minimized), which has numerous applications in decision theory literature. While the set partitioning problem is NP-hard and…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
We study the task of selecting $k$ nodes, in a social network of size $n$, to seed a diffusion with maximum expected spread size, under the independent cascade model with cascade probability $p$. Most of the previous work on this problem…
A maximal repetition, or run, in a string, is a maximal periodic substring whose smallest period is at most half the length of the substring. In this paper, we consider runs that correspond to a path on a trie, or in other words, on a…
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 two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
We give an approximation algorithm for packing and covering linear programs (linear programs with non-negative coefficients). Given a constraint matrix with n non-zeros, r rows, and c columns, the algorithm computes feasible primal and dual…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
Given a collection $L$ of line segments, we consider its arrangement and study the problem of covering all cells with line segments of $L$. That is, we want to find a minimum-size set $L'$ of line segments such that every cell in the…
Many signal processing problems can be solved by maximizing the fitness of a segmented model over all possible partitions of the data interval. This letter describes a simple but powerful algorithm that searches the exponentially large…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…
We observe message-efficient distributed algorithms for the Set Cover problem. Given a ground set $U$ of $n$ elements and $m$ subsets of $U$, we aim to find the minimal number of these subsets that contain all elements. In the default…
We present an algorithm that computes a shortest non-contractible and a shortest non-separating cycle on an orientable combinatorial surface of bounded genus in O(n \log n) time, where n denotes the complexity of the surface. This solves a…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…