Related papers: Efficient Computation of Sequence Mappability

We study the problem of finding a minimum homology basis, that is, a lightest set of cycles that generates the $1$-dimensional homology classes with $\mathbb{Z}_2$ coefficients in a given simplicial complex $K$. This problem has been…

The problem of approximately computing the $k$ dominant Fourier coefficients of a vector $X$ quickly, and using few samples in time domain, is known as the Sparse Fourier Transform (sparse FFT) problem. A long line of work on the sparse FFT…

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 study a problem where k autonomous mobile agents are initially located on distinct nodes of a weighted graph (with n nodes and m edges). Each autonomous mobile agent has a predefined velocity and is only allowed to move along the edges…

Background: Short sequence substrings of a fixed length k, called k-mers, are a ubiquitous computational primitive in bioinformatics, used across sequence indexing, read mapping, genome assembly, metagenomic classification, and comparative…

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…

We study the allocation problem in the Massively Parallel Computation (MPC) model. This problem is a special case of $b$-matching, in which the input is a bipartite graph with capacities greater than $1$ in only one part of the bipartition.…

Knapsack is one of the most fundamental problems in theoretical computer science. In the $(1 - \epsilon)$-approximation setting, although there is a fine-grained lower bound of $(n + 1 / \epsilon) ^ {2 - o(1)}$ based on the $(\min,…

Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…

Sampling edges from a graph in sublinear time is a fundamental problem and a powerful subroutine for designing sublinear-time algorithms. Suppose we have access to the vertices of the graph and know a constant-factor approximation to the…

We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a…

We consider the problem of sorting $n$ items, given the outcomes of $m$ pre-existing comparisons. We present a simple and natural deterministic algorithm that runs in $O(m + \log T)$ time and does $O(\log T)$ comparisons, where $T$ is the…

Min-plus matrix multiplication is used in many problems operating on distances in graphs or solvable by dynamic programming. Assuming the APSP hypothesis, there is no subcubic-time algorithm for the min-plus product of two general $n\times…

A fundamental problem arising in many applications in Web science and social network analysis is, given an arbitrary approximation factor $c>1$, to output a set $S$ of nodes that with high probability contains all nodes of PageRank at least…

In-place associative integer sorting technique was proposed for integer lists which requires only constant amount of additional memory replacing bucket sort, distribution counting sort and address calculation sort family of algorithms.…

Maximizing a non-negative, monontone, submodular function $f$ over $n$ elements under a cardinality constraint $k$ (SMCC) is a well-studied NP-hard problem. It has important applications in, e.g., machine learning and influence…

An orientable sequence of order $n$ is a cyclic binary sequence such that each length-$n$ substring appears at most once \emph{in either direction}. Maximal length orientable sequences are known only for $n\leq 7$, and a trivial upper bound…

A distance matrix $A \in \mathbb R^{n \times m}$ represents all pairwise distances, $A_{ij}=\mathrm{d}(x_i,y_j)$, between two point sets $x_1,...,x_n$ and $y_1,...,y_m$ in an arbitrary metric space $(\mathcal Z, \mathrm{d})$. Such matrices…

In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…

Given a collection of $m$ sets from a universe $\mathcal{U}$, the Maximum Set Coverage problem consists of finding $k$ sets whose union has largest cardinality. This problem is NP-Hard, but the solution can be approximated by a polynomial…