Related papers: Minimum Segmentation for Pan-genomic Founder Recon…
We consider the classical Minimum Balanced Cut problem: given a graph $G$, compute a partition of its vertices into two subsets of roughly equal volume, while minimizing the number of edges connecting the subsets. We present the first {\em…
We present an algorithm that takes as input an $n$-vertex planar graph $G$ and a $k$-vertex pattern graph $P$, and computes the number of (induced) copies of $P$ in $G$ in $2^{O(k/\log k)}n^{O(1)}$ time. If $P$ is a matching, independent…
In numerical linear algebra, considerable effort has been devoted to obtaining faster algorithms for linear systems whose underlying matrices exhibit structural properties. A prominent success story is the method of generalized nested…
In the classic Minimum Bisection problem we are given as input a graph $G$ and an integer $k$. The task is to determine whether there is a partition of $V(G)$ into two parts $A$ and $B$ such that $||A|-|B|| \leq 1$ and there are at most $k$…
The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein's work in 2001, this number is determined by the…
Prototype learning and decoder construction are the keys for few-shot segmentation. However, existing methods use only a single prototype generation mode, which can not cope with the intractable problem of objects with various scales.…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
Traditionally, reconfiguration problems ask the question whether a given solution of an optimization problem can be transformed to a target solution in a sequence of small steps that preserve feasibility of the intermediate solutions. In…
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…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
The restoration lemma by Afek, Bremler-Barr, Kaplan, Cohen, and Merritt [Dist. Comp. '02] proves that, in an undirected unweighted graph, any replacement shortest path avoiding a failing edge can be expressed as the concatenation of two…
Short integer linear programs are programs with a relatively small number of constraints. We show how recent improvements on the running-times of solvers for such programs can be used to obtain fast pseudo-polynomial time algorithms for…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
We investigate the sample size requirement for exact recovery of a high order tensor of low rank from a subset of its entries. In the Tucker decomposition framework, we show that the Riemannian optimization algorithm with initial value…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We consider a basic computational task of finding $s$ planted rank-1 $m \times n$ matrices in a linear subspace $\mathcal{U} \subseteq \mathbb{R}^{m \times n}$ where $\dim(\mathcal{U}) = R \ge s$. The work of Johnston-Lovitz-Vijayaraghavan…
V. Levenshtein first proposed the sequence reconstruction problem in 2001. This problem studies the model where the same sequence from some set is transmitted over multiple channels, and the decoder receives the different outputs. Assume…
We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with…
Minimum $k$-Section denotes the NP-hard problem to partition the vertex set of a graph into $k$ sets of sizes as equal as possible while minimizing the cut width, which is the number of edges between these sets. When $k$ is an input…