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We study the complexity of Maximum Clique in intersection graphs of convex objects in the plane. On the algorithmic side, we extend the polynomial-time algorithm for unit disks [Clark '90, Raghavan and Spinrad '03] to translates of any…
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…
Representing graphs by their homomorphism counts has led to the beautiful theory of homomorphism indistinguishability in recent years. Moreover, homomorphism counts have promising applications in database theory and machine learning, where…
We consider the computational complexity of reconfiguration problems, in which one is given two combinatorial configurations satisfying some constraints, and is asked to transform one into the other using elementary transformations, while…
We study the weighted token swapping problem, in which we are given a graph on $n$ vertices, $n$ weighted tokens, an initial assignment of one token to each vertex, and a final assignment of one token to each vertex. The goal is to find a…
A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
We study the computational complexity of estimating local observables for Gibbs distributions. A simple combinatorial example is the average size of an independent set in a graph. In a recent work, we established NP-hardness of…
Non-parametric two-sample tests based on energy distance or maximum mean discrepancy are widely used statistical tests for comparing multivariate data from two populations. While these tests enjoy desirable statistical properties, their…
We study the visual complexity of animated transitions between point sets. Although there exist many metrics for point set similarity, these metrics are not adequate for this purpose, as they typically treat each point separately. Instead,…
A dominating set of a graph $G=(V,E)$ is a subset of vertices $S\subseteq V$ such that every vertex $v\in V\setminus S$ has at least one neighbor in set $S$. The corresponding optimization problem is known to be NP-hard. The best known…
Gibbons and Korach studied a fundamental problem in 1997: given an observed sequence of reads and writes of a multi-threaded program, does there exist an interleaving which is sequentially consistent? Apart from applications in testing…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
We address the problem of finding the minimal number of block interchanges (exchange of two intervals) required to transform a duplicated linear genome into a tandem duplicated linear genome. We provide a formula for the distance as well as…
We call a matrix completely mixable if the entries in its columns can be permuted so that all row sums are equal. If it is not completely mixable, we want to determine the smallest maximal and largest minimal row sum attainable. These…
This paper presents the following results on sets that are complete for NP. 1. If there is a problem in NP that requires exponential time at almost all lengths, then every many-one NP-complete set is complete under length-increasing…