Related papers: Sequence Searching Allowing for Non-Overlapping Ad…
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…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between…
We present a near-optimal polynomial-time approximation algorithm for the asymmetric traveling salesman problem for graphs of bounded orientable or non-orientable genus. Our algorithm achieves an approximation factor of O(f(g)) on graphs…
The SetCover problem has been extensively studied in many different models of computation, including parallel and distributed settings. From an approximation point of view, there are two standard guarantees: an $O(\log…
String Edit Distance is a more-than-classical problem whose behavior in the dynamic setting, where the strings are updated over time, is well studied. A single-character substitution, insertion, or deletion can be processed in time…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…
Near-duplicate text alignment is the task of identifying, among the texts in a corpus, all the subsequences (substrings) that are similar to a given query. Traditional approaches rely on seeding-extension-filtering heuristics, which lack…
We consider the isomorphism problem for hypergraphs taking as input two hypergraphs over the same set of vertices $V$ and a permutation group $\Gamma$ over domain $V$, and asking whether there is a permutation $\gamma \in \Gamma$ that…
In semi-supervised segmentation, capturing meaningful semantic structures from unlabeled data is essential. This is particularly challenging in histopathology image analysis, where objects are densely distributed. To address this issue, we…
We consider the problem of makespan minimization on unrelated machines when job sizes are stochastic. The goal is to find a fixed assignment of jobs to machines, to minimize the expected value of the maximum load over all the machines. For…
We study a generalization of the recently introduced order-preserving pattern matching, where instead of looking for an exact copy of the pattern, we only require that the relative order between the elements is the same. In our variant, we…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
We describe approximation algorithms in Linial's classic LOCAL model of distributed computing to find maximum-weight matchings in a hypergraph of rank $r$. Our main result is a deterministic algorithm to generate a matching which is an…
The stochastic matching problem deals with finding a maximum matching in a graph whose edges are unknown but can be accessed via queries. This is a special case of stochastic $k$-set packing, where the problem is to find a maximum packing…
While neural machine translation (NMT) has achieved state-of-the-art translation performance, it is unable to capture the alignment between the input and output during the translation process. The lack of alignment in NMT models leads to…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
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…
Sublinear time algorithms for approximating maximum matching size have long been studied. Much of the progress over the last two decades on this problem has been on the algorithmic side. For instance, an algorithm of Behnezhad [FOCS'21]…