Related papers: Algorithms for the Problems of Length-Constrained …
We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with…
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 $S$…
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 $Z$…
The Subset Sum problem asks whether a given set of $n$ positive integers contains a subset of elements that sum up to a given target $t$. It is an outstanding open question whether the $O^*(2^{n/2})$-time algorithm for Subset Sum by…
Partitioning a sequence of length $n$ into $k$ coherent segments (Seg) is one of the classic optimization problems. As long as the optimization criterion is additive, Seg can be solved exactly in $O(n^2k)$ time using a classic dynamic…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…
Sequence partition problems arise in many fields, such as sequential data analysis, information transmission, and parallel computing. In this paper, we study the following partition problem variant: given a sequence of $n$ items…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
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 study the densest subgraph problem and give algorithms via multiplicative weights update and area convexity that converge in $O\left(\frac{\log m}{\epsilon^{2}}\right)$ and $O\left(\frac{\log m}{\epsilon}\right)$ iterations,…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
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…
In this paper we suggest analytical methods and associated algorithms for determining the sum of the subsets $X_m$ of the set $X_n$ (subset sum problem). Our algorithm has time complexity $T=O(C_{n}^{k})$ ($k=[m/2]$, which significantly…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
Recently [Bhattacharya et al., STOC 2015] provide the first non-trivial algorithm for the densest subgraph problem in the streaming model with additions and deletions to its edges, i.e., for dynamic graph streams. They present a…
The subset sum problem (SSP) can be briefly stated as: given a target integer $E$ and a set $A$ containing $n$ positive integer $a_j$, find a subset of $A$ summing to $E$. The \textit{density} $d$ of an SSP instance is defined by the ratio…
In this work, we obtain the following new results. 1. Given a sequence $D=((h_1,s_1), (h_2,s_2) ..., (h_n,s_n))$ of number pairs, where $s_i>0$ for all $i$, and a number $L_h$, we propose an O(n)-time algorithm for finding an index interval…
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length…
A fundamental problem in shape matching and geometric similarity is computing the maximum area overlap between two polygons under translation. For general simple polygons, the best-known algorithm runs in $O((nm)^2 \log(nm))$ time [Mount,…