Extracting few representative reconciliations with Host-Switches (Extended Abstract)

Phylogenetic tree reconciliation is the approach commonly used to in- vestigate the coevolution of sets of organisms such as hosts and symbionts. Given a phylogenetic tree for each such set, respectively denoted by H and S, together with a mapping φ of the leaves of S to the leaves of H, a reconciliation is a mapping ρ of the internal vertices of S to the vertices of H which extends φ with some constraints. Given a cost for each reconciliation, a huge number of most parsimonious ones are possible, even exponential in the dimension of the trees. Without further information, any biological interpretation of the underlying coevolution would require that all optimal solutions are enumerated and examined. The latter is however impossible without pro- viding some sort of high level view of the situation. One approach would be to extract a small number of representatives, based on some notion of similarity or of equivalence between the reconciliations. In this paper, we define two equivalence relations that allow one to identify many reconciliations with a single one, thereby reducing their number. Extensive experiments indicate that the number of output solutions greatly decreases in general. By how much clearly depends on the constraints that are given as input

Push & Pull: autonomous deployment of mobile sensors for a complete coverage

Mobile sensor networks are important for several strategic applications devoted to monitoring critical areas. In such hostile scenarios, sensors cannot be deployed manually and are either sent from a safe location or dropped from an aircraft. Mobile devices permit a dynamic deployment reconfiguration that improves the coverage in terms of completeness and uniformity. In this paper we propose a distributed algorithm for the autonomous deployment of mobile sensors called Push&Pull. According to our proposal, movement decisions are made by each sensor on the basis of locally available information and do not require any prior knowledge of the operating conditions or any manual tuning of key parameters. We formally prove that, when a sufficient number of sensors are available, our approach guarantees a complete and uniform coverage. Furthermore, we demonstrate that the algorithm execution always terminates preventing movement oscillations. Numerous simulations show that our algorithm reaches a complete coverage within reasonable time with moderate energy consumption, even when the target area has irregular shapes. Performance comparisons between Push&Pull and one of the most acknowledged algorithms show how the former one can efficiently reach a more uniform and complete coverage under a wide range of working scenarios.Comment: Technical Report. This paper has been published on Wireless Networks, Springer. Animations and the complete code of the proposed algorithm are available for download at the address: http://www.dsi.uniroma1.it/~novella/mobile_sensors

A Realistic Model to Support Rescue Operations after an Earthquake via UAVs

In this paper, we consider the problem of completely flying over an area just hit by an earthquake with a fleet of Unmanned Aerial Vehicles (UAVs) to opportunely direct rescue teams. The cooperation between UAVs ensures that the search for possible survivors can be faster and more effective than the solutions currently implemented by civil protection. To study this scenario, we introduce the Cover by Multitrips with Priorities (CMP) problem, which tries to keep into account all the main real-life issues connected to the flight and coordination of the UAVs. We conduct a theoretical study to estimate the best number of UAVs and additional batteries, to give indications to the organization that leads the rescue teams to be able to guarantee rapid and effective rescue. Finally, based on some theoretical considerations, we propose some heuristics that tackle the problem of flying over the whole area with a fleet of UAVs in the shortest possible time. Simulations show that they work efficiently in both the proposed scenarios and provide better performance than previous solutions once they are arranged to work in our scenarios. The main advantages of our approach w.r.t. the current drone-based solutions used by the civil defense are that UAVs do not need drivers so the time of all available rescue workers can be invested in doing something else. In our model, we take into account that some sites (e.g. buildings with a high fire risk or schools and hospitals) have a higher priority and must be inspected first, and the possibility that UAVs can make a decision based on what they detect. Finally, our approach allows UAVs to collaborate so that the same sites will be flown over exactly once in order to speed up the rescue mission

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility

Cytoplasmic incompatibility (CI) relates to the manipulation by the parasite Wolbachia of its host reproduction. Despite its widespread occurrence, the molecular basis of CI remains unclear and theoretical models have been proposed to understand the phenomenon. We consider in this paper the quantitative Lock-Key model which currently represents a good hypothesis that is consistent with the data available. CI is in this case modelled as the problem of covering the edges of a bipartite graph with the minimum number of chain subgraphs. This problem is already known to be NP-hard, and we provide an exponential algorithm with a non trivial complexity. It is frequent that depending on the dataset, there may be many optimal solutions which can be biologically quite different among them. To rely on a single optimal solution may therefore be problematic. To this purpose, we address the problem of enumerating (listing) all minimal chain subgraph covers of a bipartite graph and show that it can be solved in quasi-polynomial time. Interestingly, in order to solve the above problems, we considered also the problem of enumerating all the maximal chain subgraphs of a bipartite graph and improved on the current results in the literature for the latter. Finally, to demonstrate the usefulness of our methods we show an application on a real dataset

A Book of Generations – Writing at the Frontier

We address the problem of finding viewpoints that preserve the relational structure of a three-dimensional graph drawing under orthographic parallel projection. Previously, algorithms for finding the best viewpoints under two natural models of viewpoint “goodness” were proposed. Unfortunately, the inherent combinatorial complexity of the problem makes finding exact solutions is impractical. In this paper, we propose two approximation algorithms for the problem, commenting on their design, and presenting results on their performance

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

Upward Three-Dimensional Grid Drawings of Graphs

A \emph{three-dimensional grid drawing} of a graph is a placement of the vertices at distinct points with integer coordinates, such that the straight line segments representing the edges do not cross. Our aim is to produce three-dimensional grid drawings with small bounding box volume. We prove that every $n$-vertex graph with bounded degeneracy has a three-dimensional grid drawing with $O(n^{3/2})$ volume. This is the broadest class of graphs admiting such drawings. A three-dimensional grid drawing of a directed graph is \emph{upward} if every arc points up in the z-direction. We prove that every directed acyclic graph has an upward three-dimensional grid drawing with $(n^3)$ volume, which is tight for the complete dag. The previous best upper bound was $O(n^4)$. Our main result is that every $c$-colourable directed acyclic graph ($c$ constant) has an upward three-dimensional grid drawing with $O(n^2)$ volume. This result matches the bound in the undirected case, and improves the best known bound from $O(n^3)$ for many classes of directed acyclic graphs, including planar, series parallel, and outerplanar