arXiv subjects

Manuel Lafond

Publications and source records attributed to Manuel Lafond.

49 records · Page 3Linked to original sources

arXiv2019

Distributed Pattern Formation in a Ring

Motivated by concerns about diversity in social networks, we consider the following pattern formation problems in rings. Assume $n$ mobile agents are located at the nodes of an $n$-node ring network. Each agent is assigned a colour from the set $\{c_1, c_2, \ldots, c_q \}$. The ring is divided into $k$ contiguous {\em blocks} or neighbourhoods of length $p$. The agents are required to rearrange themselves in a distributed manner to satisfy given diversity requirements: in each block $j$ and for each colour $c_i$, there must be exactly $n_i(j) >0$ agents of colour $c_i$ in block $j$. Agents are assumed to be able to see agents in adjacent blocks, and move to any position in adjacent blocks in one time step. When the number of colours $q=2$, we give an algorithm that terminates in time $N_1/n^*_1 + k + 4$ where $N_1$ is the total number of agents of colour $c_1$ and $n^*_1$ is the minimum number of agents of colour $c_1$ required in any block. When the diversity requirements are the same in every block, our algorithm requires $3k+4$ steps, and is asymptotically optimal. Our algorithm generalizes for an arbitrary number of colours, and terminates in $O(nk)$ steps. We also show how to extend it to achieve arbitrary specific final patterns, provided there is at least one agent of every colour in every pattern.

cs.DC↗

arXiv2019

Time-Energy Tradeoffs for Evacuation by Two Robots in the Wireless Model

Two robots stand at the origin of the infinite line and are tasked with searching collaboratively for an exit at an unknown location on the line. They can travel at maximum speed $b$ and can change speed or direction at any time. The two robots can communicate with each other at any distance and at any time. The task is completed when the last robot arrives at the exit and evacuates. We study time-energy tradeoffs for the above evacuation problem. The evacuation time is the time it takes the last robot to reach the exit. The energy it takes for a robot to travel a distance $x$ at speed $s$ is measured as $xs^2$. The total and makespan evacuation energies are respectively the sum and maximum of the energy consumption of the two robots while executing the evacuation algorithm. Assuming that the maximum speed is $b$, and the evacuation time is at most $cd$, where $d$ is the distance of the exit from the origin, we study the problem of minimizing the total energy consumption of the robots. We prove that the problem is solvable only for $bc \geq 3$. For the case $bc=3$, we give an optimal algorithm, and give upper bounds on the energy for the case $bc>3$. We also consider the problem of minimizing the evacuation time when the available energy is bounded by $Δ$. Surprisingly, when $Δ$ is a constant, independent of the distance $d$ of the exit from the origin, we prove that evacuation is possible in time $O(d^{3/2}\log d)$, and this is optimal up to a logarithmic factor. When $Δ$ is linear in $d$, we give upper bounds on the evacuation time.

cs.DS↗

arXiv2019

Energy Consumption of Group Search on a Line

Consider two robots that start at the origin of the infinite line in search of an exit at an unknown location on the line. The robots can only communicate if they arrive at the same location at exactly the same time, i.e. they use the so-called face-to-face communication model. The group search time is defined as the worst-case time as a function of $d$, the distance of the exit from the origin, when both robots can reach the exit. It has long been known that for a single robot traveling at unit speed, the search time is at least $9d-o(d)$. It was shown recently that $k\geq2$ robots traveling at unit speed also require at least $9d$ group search time. We investigate energy-time trade-offs in group search by two robots, where the energy loss experienced by a robot traveling a distance $x$ at constant speed $s$ is given by $s^2 x$. Specifically, we consider the problem of minimizing the total energy used by the robots, under the constraints that the search time is at most a multiple $c$ of the distance $d$ and the speed of the robots is bounded by $b$. Motivation for this study is that for the case when robots must complete the search in $9d$ time with maximum speed one, a single robot requires at least $9d$ energy, while for two robots, all previously proposed algorithms consume at least $28d/3$ energy. When the robots have bounded memory, we generalize existing algorithms to obtain a family of optimal (and in some cases nearly optimal) algorithms parametrized by pairs of $b,c$ values that can solve the problem for the entire spectrum of these pairs for which the problem is solvable. We also propose a novel search algorithm, with unbounded memory, that simultaneously achieves search time $9d$ and consumes energy $8.42588d$. Our result shows that two robots can search on the line in optimal time $9d$ while consuming less total energy than a single robot within the same search time.

cs.DM↗

arXiv2018

Reconciling Multiple Genes Trees via Segmental Duplications and Losses

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost $δ$ and $λ$, respectively. We show that the problem is polynomial-time solvable when $δ\leq λ$ (via LCA-mapping), while if $δ> λ$ the problem is NP-hard, even when $λ= 0$ and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are $δ/λ$ and the number $d$ of segmental duplications, of time complexity $O(\lceil \fracδλ \rceil^{d} \cdot n \cdot \fracδλ)$. Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.

q-bio.PE↗

arXiv2018

The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics

A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in biogeographical studies, to study the evolution of gene families, and also within approaches to construct phylogenetic networks. A multilabelled tree in which no leaf-labels are repeated is called a phylogenetic tree, and one in which every label is the same is also known as a tree-shape. In this paper, we consider the complexity of computing metrics on MUL-trees that are obtained by extending metrics on phylogenetic trees. In particular, by restricting our attention to tree shapes, we show that computing the metric extension on MUL-trees is NP complete for two well-known metrics on phylogenetic trees, namely, the path-difference and Robinson Foulds distances. We also show that the extension of the Robinson Foulds distance is fixed parameter tractable with respect to the distance parameter. The path distance complexity result allows us to also answer an open problem concerning the complexity of solving the quadratic assignment problem for two matrices that are a Robinson similarity and a Robinson dissimilarity, which we show to be NP-complete. We conclude by considering the maximum agreement subtree (MAST) distance on phylogenetic trees to MUL-trees. Although its extension to MUL-trees can be computed in polynomial time, we show that computing its natural generalization to more than two MUL-trees is NP-complete, although fixed-parameter tractable in the maximum degree when the number of given trees is bounded.

q-bio.PE↗

arXiv2017

Reconstructing protein and gene phylogenies by extending the framework of reconciliation

The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on alternative protein isoforms. These methods often lead to inaccurate gene tree reconstructions that require to be corrected before being used in phylogenetic tree reconciliation analyses or gene products phylogeny reconstructions. Here, we propose a new approach for the reconstruction of accurate gene trees and protein trees accounting for the production of alternative protein isoforms by the genes of a gene family. We extend the concept of reconciliation to protein trees, and we define a new reconciliation problem called MinDRGT that consists in finding a gene tree that minimizes a double reconciliation cost with a given protein tree and a given species tree. We define a second problem called MinDRPGT that consists in finding a protein tree and a gene tree minimizing a double reconciliation cost, given a species tree and a set of protein subtrees. We provide algorithmic exact and heuristic solutions for some versions of the problems, and we present the results of an application to the correction of gene trees from the Ensembl database. An implementation of the heuristic method is available at https://github.com/UdeS-CoBIUS/Protein2GeneTree.

cs.DS↗

arXiv2017

On strongly chordal graphs that are not leaf powers

A common task in phylogenetics is to find an evolutionary tree representing proximity relationships between species. This motivates the notion of leaf powers: a graph G = (V, E) is a leaf power if there exist a tree T on leafset V and a threshold k such that uv is an edge if and only if the distance between u and v in T is at most k. Characterizing leaf powers is a challenging open problem, along with determining the complexity of their recognition. This is in part due to the fact that few graphs are known to not be leaf powers, as such graphs are difficult to construct. Recently, Nevries and Rosenke asked if leaf powers could be characterized by strong chordality and a finite set of forbidden subgraphs. In this paper, we provide a negative answer to this question, by exhibiting an infinite family \G of (minimal) strongly chordal graphs that are not leaf powers. During the process, we establish a connection between leaf powers, alternating cycles and quartet compatibility. We also show that deciding if a chordal graph is \G-free is NP-complete, which may provide insight on the complexity of the leaf power recognition problem.

cs.DM↗

arXiv2017

On the Weighted Quartet Consensus problem

In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on the Weighted Quartet Consensus problem, a problem with unknown complexity status so far. Here we prove that the Weighted Quartet Consensus problem is NP-hard and we give a 1/2-factor approximation for this problem. During the process, we propose a derandomization procedure of a previously known randomized 1/3-factor approximation. We also investigate the fixed-parameter tractability of this problem.

cs.DS↗

arXiv2017

Weak Coverage of a Rectangular Barrier

Assume n wireless mobile sensors are initially dispersed in an ad hoc manner in a rectangular region. They are required to move to final locations so that they can detect any intruder crossing the region in a direction parallel to the sides of the rectangle, and thus provide weak barrier coverage of the region. We study three optimization problems related to the movement of sensors to achieve weak barrier coverage: minimizing the number of sensors moved (MinNum), minimizing the average distance moved by the sensors (MinSum), and minimizing the maximum distance moved by the sensors (MinMax). We give an O(n^{3/2}) time algorithm for the MinNum problem for sensors of diameter 1 that are initially placed at integer positions; in contrast we show that the problem is NP-hard even for sensors of diameter 2 that are initially placed at integer positions. We show that the MinSum problem is solvable in O(n log n) time for homogeneous range sensors in arbitrary initial positions, while it is NP-hard for heterogeneous sensor ranges. Finally, we prove that even very restricted homogeneous versions of the MinMax problem are NP-hard.

cs.DC↗

arXiv2016

Whom to befriend to influence people

Alice wants to join a new social network, and influence its members to adopt a new product or idea. Each person $v$ in the network has a certain threshold $t(v)$ for {\em activation}, i.e adoption of the product or idea. If $v$ has at least $t(v)$ activated neighbors, then $v$ will also become activated. If Alice wants to activate the entire social network, whom should she befriend? More generally, we study the problem of finding the minimum number of links that a set of external influencers should form to people in the network, in order to activate the entire social network. This {\em Minimum Links} Problem has applications in viral marketing and the study of epidemics. Its solution can be quite different from the related and widely studied Target Set Selection problem. We prove that the Minimum Links problem cannot be approximated to within a ratio of $O(2^{\log^{1-ε} n})$, for any fixed $ε>0$, unless $NP\subseteq DTIME(n^{polylog(n)})$, where $n$ is the number of nodes in the network. On the positive side, we give linear time algorithms to solve the problem for trees, cycles, and cliques, for any given set of external influencers, and give precise bounds on the number of links needed. For general graphs, we design a polynomial time algorithm to compute size-efficient link sets that can activate the entire graph.

cs.DS↗

arXiv2016

Gene Tree Construction and Correction using SuperTree and Reconciliation

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a set of input gene trees on partial data. In this perspective, the phylogenetic tree for the species containing the genes of interest can be used to choose among the many possible compatible "supergenetrees", the most natural criteria being to minimize a reconciliation cost. We develop a variety of algorithmic solutions for the construction and correction of gene trees using the supertree framework. A dynamic programming supertree algorithm for constructing or correcting gene trees, exponential in the number of input trees, is first developed for the less constrained version of the problem. It is then adapted to gene trees with nodes labeled as duplication or speciation, the additional constraint being to preserve the orthology and paralogy relations between genes. Then, a quadratic time algorithm is developed for efficiently correcting an initial gene tree while preserving a set of "trusted" subtrees, as well as the relative phylogenetic distance between them, in both cases of labeled or unlabeled input trees. By applying these algorithms to the set of Ensembl gene trees, we show that this new correction framework is particularly useful to correct weaklysupported duplication nodes. The C++ source code for the algorithms and simulations described in the paper are available at https://github.com/UdeM-LBIT/SuGeT.

cs.DS↗

arXiv2016

The SCJ small parsimony problem for weighted gene adjacencies (Extended version)

Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a single ancestral genome, use a scaffolding approach to select a subset of ancestral gene adjacencies, generally aiming at reducing the fragmentation of the reconstructed ancestral genome. In this paper, we describe an exact algorithm for the Small Parsimony Problem that combines both approaches. We consider that gene adjacencies at internal nodes of the species phylogeny are weighted, and we introduce an objective function defined as a convex combination of these weights and the evolutionary cost under the Single-Cut-or-Join (SCJ) model. The weights of ancestral gene adjacencies can e.g. be obtained through the recent availability of ancient DNA sequencing data, which provide a direct hint at the genome structure of the considered ancestor, or through probabilistic analysis of gene adjacencies evolution. We show the NP-hardness of our problem variant and propose a Fixed-Parameter Tractable algorithm based on the Sankoff-Rousseau dynamic programming algorithm that also allows to sample co-optimal solutions. We apply our approach to mammalian and bacterial data providing different degrees of complexity. We show that including adjacency weights in the objective has a significant impact in reducing the fragmentation of the reconstructed ancestral gene orders.

cs.DS↗

arXiv2014

Hamiltonian chordal graphs are not cycle extendible

In 1990, Hendry conjectured that every Hamiltonian chordal graph is cycle extendible; that is, the vertices of any non-Hamiltonian cycle are contained in a cycle of length one greater. We disprove this conjecture by constructing counterexamples on $n$ vertices for any $n \geq 15$. Furthermore, we show that there exist counterexamples where the ratio of the length of a non-extendible cycle to the total number of vertices can be made arbitrarily small. We then consider cycle extendibility in Hamiltonian chordal graphs where certain induced subgraphs are forbidden, notably $P_n$ and the bull.

math.CO↗