Related papers: Minimum Segmentation for Pan-genomic Founder Recon…
The sequence reconstruction problem involves a model where a sequence is transmitted over several identical channels. This model investigates the minimum number of channels required for the unique reconstruction of the transmitted sequence.…
We give an algorithm that, given graphs $G$ and $H$, tests whether $H$ is a minor of $G$ in time ${\cal O}_H(n^{1+o(1)})$; here, $n$ is the number of vertices of $G$ and the ${\cal O}_H(\cdot)$-notation hides factors that depend on $H$ and…
In this paper, we consider the problems for covering multiple intervals on a line. Given a set $B$ of $m$ line segments (called "barriers") on a horizontal line $L$ and another set $S$ of $n$ horizontal line segments of the same length in…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
In this work, we obtain the following new results. 1. Given a sequence $D=((h_1,s_1), (h_2,s_2) ..., (h_n,s_n))$ of number pairs, where $s_i>0$ for all $i$, and a number $L_h$, we propose an O(n)-time algorithm for finding an index interval…
We provide a general framework to exclude parameterized running times of the form $O(\ell^\beta+ n^\gamma)$ for problems that have polynomial running time lower bounds under hypotheses from fine-grained complexity. Our framework is based on…
In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string $x$ given random "traces" of $x$ where each trace is generated by deleting each coordinate of $x$ independently with…
For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…
We study graph ordering problems with a min-max objective. A classical problem of this type is cutwidth, where given a graph we want to order its vertices such that the number of edges crossing any point is minimized. We give a $…
In this paper we consider the problem of segmenting $n$ aligned random sequences of equal length $m$, into a finite number of independent blocks. We propose to use a penalized maximum likelihood criterion to infer simultaneously the number…
In this note, we consider the problem of finding a step-by-step transformation between two longest increasing subsequences in a sequence, namely Longest Increasing Subsequence Reconfiguration. We give a polynomial-time algorithm for…
Exponential-time approximation has recently gained attention as a practical way to deal with the bitter NP-hardness of well-known optimization problems. We study for the first time the $(1 + \varepsilon)$-approximate min-sum subset…
Given an undirected edge-weighted graph $G=(V,E)$ with $m$ edges and $n$ vertices, the minimum cut problem asks to find a subset of vertices $S$ such that the total weight of all edges between $S$ and $V \setminus S$ is minimized. Karger's…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
We propose a parameter-minimal neural architecture for solving differential equations by restricting the hypothesis class to Horner-factorized polynomials, yielding an implicit, differentiable trial solution with only a small set of…
The $k$-cut problem asks, given a connected graph $G$ and a positive integer $k$, to find a minimum-weight set of edges whose removal splits $G$ into $k$ connected components. We give the first polynomial-time algorithm with approximation…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
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…
We investigate the problem of partitioning a rectilinear polygon $P$ with $n$ vertices and no holes % with no holes into rectangles using disjoint line segments drawn inside $P$ under two optimality criteria. In the minimum ink partition,…