Related papers: Finding Diverse Strings and Longest Common Subsequ…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…
Let G be a simple connected graph with vertex set V(G) and edge set E(G. Each vertex of V(G) is colored by a color from the set of colors {c_1, c_2,\dots, c_{\alpha}}. We take a subset S of V(G), such that for every vertex v in V(G)\S, at…
Analyzing patterns in data streams generated by network traffic, sensor networks, or satellite feeds is a challenge for systems in which the available storage is limited. In addition, real data is noisy, which makes designing data stream…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
We introduce and study four optimization problems that generalize the well-known subset sum problem. Given a node-weighted digraph, select a subset of vertices whose total weight does not exceed a given budget. Some additional constraints…
We are interested in the statistics of the length of the longest increasing subsequence of 2-rowed lexicographically sorted arrays chosen according to distinct families of distributions D = (D_n)_n, and when n goes to infinity. This…
Given a labeled graph, the frequent-subgraph mining (FSM) problem asks to find all the $k$-vertex subgraphs that appear with frequency greater than a given threshold. FSM has numerous applications ranging from biology to network science, as…
Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the…
We investigate the question whether Subset Sum can be solved by a polynomial-time algorithm with access to a certificate of length poly(k) where k is the maximal number of bits in an input number. In other words, can it be solved using only…
Given a sequence of n numbers, the Maximum Consecutive Subsums Problem (MCSP) asks for the maximum consecutive sum of lengths l for each l = 1,...,n. No algorithm is known for this problem which is significantly better than the naive…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
We give a sublinear quantum algorithm for the longest common substring (LCS) problem on the run-length encoded (RLE) inputs, under the assumption that the prefix-sums of the runs are given. Our algorithm costs $\tilde{O}(n^{5/6})\cdot…
In this work, we present a plethora of results for the range longest increasing subsequence problem (Range-LIS) and its variants. The input to RLIS is a sequence $S$ of $n$ real numbers and a collection $Q$ of $m$ query ranges, and for each…
Approximating the length of the longest increasing sequence (LIS) of an array is a well-studied problem. We study this problem in the data stream model, where the algorithm is allowed to make a single left-to-right pass through the array…
In this paper we consider the $p$-Norm Hamming Centroid problem which asks to determine whether some given binary strings have a centroid with a bound on the $p$-norm of its Hamming distances to the strings. Specifically, given a set of…