Related papers: The Hybrid k-Deck Problem: Reconstructing Sequence…

In this paper, we study $k$-Way Min-cost Perfect Matching with Delays - the $k$-MPMD problem. This problem considers a metric space with $n$ nodes. Requests arrive at these nodes in an online fashion. The task is to match these requests…

A graph is distance-hereditary if for any pair of vertices, their distance in every connected induced subgraph containing both vertices is the same as their distance in the original graph. The Distance-Hereditary Vertex Deletion problem…

Sequence partition problems arise in many fields, such as sequential data analysis, information transmission, and parallel computing. In this paper, we study the following partition problem variant: given a sequence of $n$ items…

Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…

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…

Suppose that we are given two independent sets I_b and I_r of a graph such that |I_b|=|I_r|, and imagine that a token is placed on each vertex in |I_b|. Then, the sliding token problem is to determine whether there exists a sequence of…

In this work, we consider a restricted case of the well studied Sorting by Block Interchanges problem. We put an upper bound k on the length of the blocks (substrings) to be interchanged at each step. We call the problem Sorting by k-Block…

We study the problem of reconfiguring one minimum $s$-$t$-separator $A$ into another minimum $s$-$t$-separator $B$ in some $n$-vertex graph $G$ containing two non-adjacent vertices $s$ and $t$. We consider several variants of the problem as…

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 the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is transmitted through a probabilistic \emph{deletion channel} which independently deletes each bit with some fixed probability $\delta$ and concatenates…

The minimum spanning tree clustering algorithm is capable of detecting clusters with irregular boundaries. In this paper we propose two minimum spanning trees based clustering algorithm. The first algorithm produces k clusters with center…

We consider the densest $k$-subgraph problem, which seeks to identify the $k$-node subgraph of a given input graph with maximum number of edges. This problem is well-known to be NP-hard, by reduction to the maximum clique problem. We…

We study a problem of reconstruction of connected graphs where the input gives all subsets of size k that induce a connected subgraph. Originally introduced by Bastide et al. (WG 2023) for triples ($k=3$), this problem received…

Generation of an (arbitrarily) long string of bits unique to a given finite-length numerical seed is of great value in the field of random number generation, computer simulations, and other areas of computer science. Extending this idea…

In the $k$-mismatch problem we are given a pattern of length $n$ and a text and must find all locations where the Hamming distance between the pattern and the text is at most $k$. A series of recent breakthroughs have resulted in an…

We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…

In this paper we study a natural generalization of both {\sc $k$-Path} and {\sc $k$-Tree} problems, namely, the {\sc Subgraph Isomorphism} problem. In the {\sc Subgraph Isomorphism} problem we are given two graphs $F$ and $G$ on $k$ and $n$…

The deletion channel takes as input a bit string $\mathbf{x} \in \{0,1\}^n$, and deletes each bit independently with probability $q$, yielding a shorter string. The trace reconstruction problem is to recover an unknown string $\mathbf{x}$…

This paper addresses the Data-Diff problem: given a dataset and a subsequent version of the dataset, find the shortest sequence of operations that transforms the dataset to the subsequent version, under a restricted family of operations. We…

Minimum Bisection denotes the NP-hard problem to partition the vertex set of a graph into two sets of equal sizes while minimizing the width of the bisection, which is defined as the number of edges between these two sets. We first consider…