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Subset Sum is a classical optimization problem taught to undergraduates as an example of an NP-hard problem, which is amenable to dynamic programming, yielding polynomial running time if the input numbers are relatively small. Formally,…
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…
Covers are a kind of quasiperiodicity in strings. A string $C$ is a cover of another string $T$ if any position of $T$ is inside some occurrence of $C$ in $T$. The shortest and longest cover arrays of $T$ have the lengths of the shortest…
Longest Increasing Subsequence (LIS) is a fundamental problem in combinatorics and computer science. Previously, there have been numerous works on both upper bounds and lower bounds of the time complexity of computing and approximating LIS,…
We consider the problem of preprocessing two strings $S$ and $T$, of lengths $m$ and $n$, respectively, in order to be able to efficiently answer the following queries: Given positions $i,j$ in $S$ and positions $a,b$ in $T$, return the…
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
We consider a small cell network (SCN) consisting of N cells, with the small cell base stations (SCBSs) equipped with Nt \geq 1 antennas each, serving K single antenna user terminals (UTs) per cell. Under this set up, we address the…
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…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
In this paper, we propose a data structure, a quadruple neighbor list (QN-list, for short), to support real time queries of all longest increasing subsequence (LIS) and LIS with constraints over sequential data streams. The QN-List built by…
The longest common substring with $k$-mismatches problem is to find, given two strings $S_1$ and $S_2$, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance between $A_1$ and $A_2$ is $\le k$. We introduce a…
We study the classic set cover problem from the perspective of sub-linear algorithms. Given access to a collection of $m$ sets over $n$ elements in the query model, we show that sub-linear algorithms derived from existing techniques have…
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…
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…
A fundamental concept related to strings is that of repetitions. It has been extensively studied in many versions, from both purely combinatorial and algorithmic angles. One of the most basic questions is how many distinct squares, i.e.,…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
Given an integer array $A[1..n]$, the Range Minimum Query problem (RMQ) asks to preprocess $A$ into a data structure, supporting RMQ queries: given $a,b\in [1,n]$, return the index $i\in[a,b]$ that minimizes $A[i]$, i.e.,…
We consider the canonical generalization of the well-studied Longest Increasing Subsequence problem to multiple sequences, called $k$-LCIS: Given $k$ integer sequences $X_1,\dots,X_k$ of length at most $n$, the task is to determine the…
Given a graph and an integer $k$, Densest $k$-Subgraph is the algorithmic task of finding the subgraph on $k$ vertices with the maximum number of edges. This is a fundamental problem that has been subject to intense study for decades, with…