Related papers: Minimum Segmentation for Pan-genomic Founder Recon…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
We consider the problem of computing a sequence of range minimum queries. We assume a sequence of commands that contains values and queries. Our goal is to quickly determine the minimum value that exists between the current position and a…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
We consider the problem of recovering a low-multilinear-rank tensor from a small amount of linear measurements. We show that the Riemannian gradient algorithm initialized by one step of iterative hard thresholding can reconstruct an…
Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…
Kimelfeld and Sagiv [Kimelfeld and Sagiv, PODS 2006], [Kimelfeld and Sagiv, Inf. Syst. 2008] pointed out the problem of enumerating $K$-fragments is of great importance in a keyword search on data graphs. In a graph-theoretic term, the…
We present a \emph{deterministic exact algorithm} for the \emph{minimum $k$-cut problem} on simple graphs. Our approach combines the \emph{principal sequence of partitions (PSP)}, derived canonically from ideal loads, with a single level of…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
Let $P$ be a path graph of $n$ vertices embedded in a metric space. We consider the problem of adding a new edge to $P$ to minimize the radius of the resulting graph. Previously, a similar problem for minimizing the diameter of the graph…
Suppose $\mathcal{F}$ is a finite family of graphs. We consider the following meta-problem, called $\mathcal{F}$-Immersion Deletion: given a graph $G$ and integer $k$, decide whether the deletion of at most $k$ edges of $G$ can result in a…
In this work, we carry out structural and algorithmic studies of a problem of barrier forming: selecting theminimum number of straight line segments (barriers) that separate several sets of mutually disjoint objects in the plane. The…
Given a graph $G=(V,E)$ with two distinguished vertices $s,t\in V$ and an integer parameter $L>0$, an {\em $L$-bounded cut} is a subset $F$ of edges (vertices) such that the every path between $s$ and $t$ in $G\setminus F$ has length more…
We study three fundamental problems of Linear Algebra, lying in the heart of various Machine Learning applications, namely: 1)"Low-rank Column-based Matrix Approximation". We are given a matrix A and a target rank k. The goal is to select a…
The Minimum Linear Arrangement problem (MLA) consists of finding a mapping $\pi$ from vertices of a graph to distinct integers that minimizes $\sum_{\{u,v\}\in E}|\pi(u) - \pi(v)|$. In that setting, vertices are often assumed to lie on a…
For a string $S$, a palindromic substring $S[i..j]$ is said to be a \emph{shortest unique palindromic substring} ($\mathit{SUPS}$) for an interval $[s, t]$ in $S$, if $S[i..j]$ occurs exactly once in $S$, the interval $[i, j]$ contains $[s,…
Block-structured integer linear programs (ILPs) play an important role in various application fields. We address $n$-fold ILPs where the matrix $\mathcal{A}$ has a specific structure, i.e., where the blocks in the lower part of…
We develop a randomized approximation algorithm for the classical maximum coverage problem, which given a list of sets $A_1,A_2,\cdots, A_m$ and integer parameter $k$, select $k$ sets $A_{i_1}, A_{i_2},\cdots, A_{i_k}$ for maximum union…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…