arXiv subjects

Guillaume Fertin

Publications and source records attributed to Guillaume Fertin.

13 recordsLinked to original sources

arXiv2026

Resolving Envy by Adding Goods with Bounded Supply: A Type-Count Dichotomy and Two-Agent Hardness

We study envy elimination by adding goods (EEAG) when the additional pool has bounded supply and no separate budget bound. We establish a sharp type-count dichotomy for binary additive valuations. With one additional item type, EEAG is polynomial-time solvable for any number of agents. More generally, our algorithm permits arbitrary nonnegative integer per-copy values. The envy constraints form a system of difference constraints, and Bellman--Ford returns the componentwise least feasible extension. In contrast, with exactly two additional item types, EEAG is \textsf{NP}-complete even when both types have positive finite supply and the approvers of one type form a subset of the approvers of the other. This closes the two-type case left open by Bentert et al. Separately, we prove weak \textsf{NP}-completeness even for two agents with identical additive valuations, one initially endowed good, and a growing number of unit-supply item types. Thus, bounded-supply hardness appears both with two item-types and many agents and with two agents and many item-types.

cs.GT↗

arXiv2022

Sorting Genomes by Prefix Double-Cut-and-Joins

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and recombine the severed endpoints in one of two possible ways: one of these options corresponds to a prefix reversal, which reverses the order of elements between the two cuts (as well as their signs in the signed case). Depending on whether we consider both options or reversals only, our main results are: (1) new structural lower bounds based on the breakpoint graph for sorting by unsigned prefix reversals, unsigned prefix DCJs, or signed prefix DCJs; (2) a polynomial-time algorithm for sorting by signed prefix DCJs, thus answering an open question in [8]; (3) a 3/2-approximation for sorting by unsigned prefix DCJs, which is, to the best of our knowledge, the first sorting by {\em prefix} rearrangements problem that admits an approximation ratio strictly smaller than 2 (with the obvious exception of the polynomial-time solvable problems); and finally, (4) an FPT algorithm for sorting by unsigned prefix DCJs parameterised by the number of breakpoints in the genome.

cs.DS↗

arXiv2019

Graph Motif Problems Parameterized by Dual

Let $G=(V,E)$ be a vertex-colored graph, where $C$ is the set of colors used to color $V$. The Graph Motif (or GM) problem takes as input $G$, a multiset $M$ of colors built from $C$, and asks whether there is a subset $S\subseteq V$ such that (i) $G[S]$ is connected and (ii) the multiset of colors obtained from $S$ equals $M$. The Colorful Graph Motif (or CGM) problem is the special case of GM in which $M$ is a set, and the List-Colored Graph Motif (or LGM) problem is the extension of GM in which each vertex $v$ of $V$ may choose its color from a list $\mathcal{L}(v)\subseteq C$ of colors. We study the three problems GM, CGM, and LGM, parameterized by the dual parameter $\ell:=|V|-|M|$. For general graphs, we show that, assuming the strong exponential time hypothesis, CGM has no $(2-ε)^\ell\cdot |V|^{\mathcal{O}(1)}$-time algorithm, which implies that a previous algorithm, running in $\mathcal{O}(2^\ell\cdot |E|)$ time is optimal [Betzler et al., IEEE/ACM TCBB 2011]. We also prove that LGM is W[1]-hard with respect to $\ell$ even if we restrict ourselves to lists of at most two colors. If we constrain the input graph to be a tree, then we show that GM can be solved in $\mathcal{O}(3^\ell\cdot |V|)$ time but admits no polynomial-size problem kernel, while CGM can be solved in $\mathcal{O}(\sqrt{2}^{\ell} + |V|)$ time and admits a polynomial-size problem kernel.

cs.CC↗

arXiv2018

Finding a Small Number of Colourful Components

A partition $(V_1,\ldots,V_k)$ of the vertex set of a graph $G$ with a (not necessarily proper) colouring $c$ is colourful if no two vertices in any $V_i$ have the same colour and every set $V_i$ induces a connected graph. The COLOURFUL PARTITION problem is to decide whether a coloured graph $(G,c)$ has a colourful partition of size at most $k$. This problem is closely related to the COLOURFUL COMPONENTS problem, which is to decide whether a graph can be modified into a graph whose connected components form a colourful partition by deleting at most $p$ edges. Nevertheless we show that COLOURFUL PARTITION and COLOURFUL COMPONENTS may have different complexities for restricted instances. We tighten known NP-hardness results for both problems and in addition we prove new hardness and tractability results for COLOURFUL PARTITION. Using these results we complete our paper with a thorough parameterized study of COLOURFUL PARTITION.

cs.DS↗

arXiv2018

The Maximum Colorful Arborescence problem parameterized by the structure of its color hierarchy graph

Let G=(V,A) be a vertex-colored arc-weighted directed acyclic graph (DAG) rooted in some vertex r, and let H be its color hierarchy graph, defined as follows: V(H) is the color set C of G, and an arc from color c to color c' exists in H if there is an arc in G from a vertex of color c to a vertex of color c'. In this paper, we study the MAXIMUM COLORFUL ARBORESCENCE problem (or MCA), which takes as input a DAG G with the additional constraint that H is also a DAG, and aims at finding in G an arborescence rooted in r, of maximum weight, and in which no color appears more than once. The MCA problem is motivated by the inference of unknown metabolites from mass spectrometry experiments. However, whereas the problem has been studied for roughly ten years, the crucial property that H is necessarily a DAG has only been pointed out and exploited very recently. In this paper, we further investigate MCA under this new light, by providing algorithmic results for the problem, with a specific focus on fixed-parameterized tractability (FPT) issues, and relatively to different structural parameters of H. In particular, we provide an O*(3^{nhs}) time algorithm for solving MCA, where nhs is the number of vertices of indegree at least two in H, thereby improving the O*(3^{|C|}) algorithm from [Böcker et al. 2008]. We also prove that MCA is W[2]-hard relatively to the treewidth Ht of H, and further show that it is FPT relatively to Ht+lc, where lc = |V| - |C|.

cs.CC↗

arXiv2016

Decomposing Cubic Graphs into Connected Subgraphs of Size Three

Let $S=\{K_{1,3},K_3,P_4\}$ be the set of connected graphs of size 3. We study the problem of partitioning the edge set of a graph $G$ into graphs taken from any non-empty $S'\subseteq S$. The problem is known to be NP-complete for any possible choice of $S'$ in general graphs. In this paper, we assume that the input graph is cubic, and study the computational complexity of the problem of partitioning its edge set for any choice of $S'$. We identify all polynomial and NP-complete problems in that setting, and give graph-theoretic characterisations of $S'$-decomposable cubic graphs in some cases.

cs.DS↗

arXiv2013

A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications

Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced strings, so that some elements may not be covered by any block. We present an efficient fixed-parameter algorithm for the parameters number k of blocks and maximum occurrence d of a letter in either string. We then evaluate this algorithm on bacteria genomes and synthetic data.

cs.DS↗

arXiv2011

Pancake Flipping is Hard

Pancake Flipping is the problem of sorting a stack of pancakes of different sizes (that is, a permutation), when the only allowed operation is to insert a spatula anywhere in the stack and to flip the pancakes above it (that is, to perform a prefix reversal). In the burnt variant, one side of each pancake is marked as burnt, and it is required to finish with all pancakes having the burnt side down. Computing the optimal scenario for any stack of pancakes and determining the worst-case stack for any stack size have been challenges over more than three decades. Beyond being an intriguing combinatorial problem in itself, it also yields applications, e.g. in parallel computing and computational biology. In this paper, we show that the Pancake Flipping problem, in its original (unburnt) variant, is NP-hard, thus answering the long-standing question of its computational complexity.

cs.CC↗

arXiv2010

Sorting by Transpositions is Difficult

In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is, according to numerous studies, a relevant evolutionary distance. The problem of computing this distance when genomes are represented by permutations, called the Sorting by Transpositions problem, has been introduced by Bafna and Pevzner in 1995. It has naturally been the focus of a number of studies, but the computational complexity of this problem has remained undetermined for 15 years. In this paper, we answer this long-standing open question by proving that the Sorting by Transpositions problem is NP-hard. As a corollary of our result, we also prove that the following problem is NP-hard: given a permutation pi, is it possible to sort pi using db(pi)/3 permutations, where db(pi) is the number of breakpoints of pi?

cs.DS↗

arXiv2008

On the Approximability of Comparing Genomes with Duplicates

A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know that genes can be duplicated within the same genome. One possible approach to overcome this difficulty is to establish a one-to-one correspondence (i.e. a matching) between genes of both genomes, where the correspondence is chosen in order to optimize the studied measure. In this paper, we are interested in three measures (number of breakpoints, number of common intervals and number of conserved intervals) and three models of matching (exemplar, intermediate and maximum matching models). We prove that, for each model and each measure M, computing a matching between two genomes that optimizes M is APX-hard. We also study the complexity of the following problem: is there an exemplarization (resp. an intermediate/maximum matching) that induces no breakpoint? We prove the problem to be NP-Complete in the exemplar model for a new class of instances, and we show that the problem is in P in the maximum matching model. We also focus on a fourth measure: the number of adjacencies, for which we give several approximation algorithms in the maximum matching model, in the case where genomes contain the same number of duplications of each gene.

q-bio.QM↗

arXiv2006

Vertex labeling and routing in expanded Apollonian networks

We present a family of networks, expanded deterministic Apollonian networks, which are a generalization of the Apollonian networks and are simultaneously scale-free, small-world, and highly clustered. We introduce a labeling of their vertices that allows to determine a shortest path routing between any two vertices of the network based only on the labels.

physics.soc-ph↗

arXiv2005

High Dimensional Apollonian Networks

We propose a simple algorithm which produces high dimensional Apollonian networks with both small-world and scale-free characteristics. We derive analytical expressions for the degree distribution, the clustering coefficient and the diameter of the networks, which are determined by their dimension.

cond-mat.other↗

arXiv2004

Recursive graphs with small-world scale-free properties

We discuss a category of graphs, recursive clique trees, which have small-world and scale-free properties and allow a fine tuning of the clustering and the power-law exponent of their discrete degree distribution. We determine relevant characteristics of those graphs: the diameter, degree distribution, and clustering parameter. The graphs have also an interesting recursive property, and generalize recent constructions with fixed degree distributions.

cond-mat.stat-mech↗