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The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…
We introduce and study the problem of computing the similarity self-join in a streaming context (SSSJ), where the input is an unbounded stream of items arriving continuously. The goal is to find all pairs of items in the stream whose…
In the Equal-Subset-Sum problem, we are given a set $S$ of $n$ integers and the problem is to decide if there exist two disjoint nonempty subsets $A,B \subseteq S$, whose elements sum up to the same value. The problem is NP-complete. The…
In ill-posed dynamic inverse problems expected spatial features and temporal correlation between frames can be leveraged to improve the quality of the computed solution, in particular when the available data are limited and the…
A binary string transmitted via a memoryless i.i.d. deletion channel is received as a subsequence of the original input. From this, one obtains a posterior distribution on the channel input, corresponding to a set of candidate…
Submodularity is an important property of set functions and has been extensively studied in the literature. It models set functions that exhibit a diminishing returns property, where the marginal value of adding an element to a set…
Sorting networks are oblivious sorting algorithms with many practical applications and rich theoretical properties. Propositional encodings of sorting networks are a key tool for proving concrete bounds on the minimum number of comparators…
We study a broad class of algorithmic problems with an "additive flavor" such as computing sumsets, 3SUM, Subset Sum and geometric pattern matching. Our starting point is that these problems can often be solved efficiently for integers,…
We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. 2022, we consider the setting when the distance (i. e., the gap) between two consecutive symbols of…
Betweenness centrality ranks the importance of nodes by their participation in all shortest paths of the network. Therefore computing exact betweenness values is impractical in large networks. For static networks, approximation based on…
While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of {\em both} time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a…
We study the fundamental problem of sampling independent events, called subset sampling. Specifically, consider a set of $n$ events $S=\{x_1, \ldots, x_n\}$, where each event $x_i$ has an associated probability $p(x_i)$. The subset sampling…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
A novel integer sorting technique was proposed replacing bucket sort, distribution counting sort and address calculation sort family of algorithms which requires only constant amount of additional memory. The technique was inspired from one…
The intention of this note is two-fold. First, we study integer optimization problems in standard form defined by $A \in\mathbb{Z}^{m\times{}n}$ and present an algorithm to solve such problems in polynomial-time provided that both the…
In this paper, we study a fundamental problem in submodular optimization, which is called sequential submodular maximization. Specifically, we aim to select and rank a group of $k$ items from a ground set $V$ such that the weighted…
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…
Many real-world networks can be modeled as graphs. Finding dense subgraphs is a key problem in graph mining with applications in diverse domains. In this paper, we consider two variants of the densest subgraph problem where multiple graph…