Community detection algorithms: a comparative analysis

Uncovering the community structure exhibited by real networks is a crucial step towards an understanding of complex systems that goes beyond the local organization of their constituents. Many algorithms have been proposed so far, but none of them has been subjected to strict tests to evaluate their performance. Most of the sporadic tests performed so far involved small networks with known community structure and/or artificial graphs with a simplified structure, which is very uncommon in real systems. Here we test several methods against a recently introduced class of benchmark graphs, with heterogeneous distributions of degree and community size. The methods are also tested against the benchmark by Girvan and Newman and on random graphs. As a result of our analysis, three recent algorithms introduced by Rosvall and Bergstrom, Blondel et al. and Ronhovde and Nussinov, respectively, have an excellent performance, with the additional advantage of low computational complexity, which enables one to analyze large systems.Comment: 12 pages, 8 figures. The software to compute the values of our general normalized mutual information is available at http://santo.fortunato.googlepages.com/inthepress

Global existence of solutions for a multi-phase flow: a drop in a gas-tube

In this paper we study the flow of an inviscid fluid composed by three different phases. The model is a simple hyperbolic system of three conservation laws, in Lagrangian coordinates, where the phase interfaces are stationary. Our main result concerns the global existence of weak entropic solutions to the initial-value problem for large initial data

Global weak solutions for a model of two-phase flow with a single interface

We consider a simple nonlinear hyperbolic system modeling the flow of an inviscid fluid. The model includes as state variable the mass density fraction of the vapor in the fluid and then phase transitions can be taken into consideration; moreover, phase interfaces are contact discontinuities for the system. We focus on the special case of initial data consisting of two different phases separated by an interface. We find explicit bounds on the (possibly large) initial data in order that weak entropic solutions exist for all times. The proof exploits a carefully tailored version of the front tracking scheme

Global existence of solutions for a multi-phase flow: a bubble in a liquid tube and related cases

In this paper we study the problem of the global existence (in time) of weak, entropic solutions to a system of three hyperbolic conservation laws, in one space dimension, for large initial data. The system models the dynamics of phase transitions in an isothermal fluid; in Lagrangian coordinates, the phase interfaces are represented as stationary contact discontinuities. We focus on the persistence of solutions consisting in three bulk phases separated by two interfaces. Under some stability conditions on the phase configuration and by a suitable front tracking algorithm we show that, if the BV-norm of the initial data is less than an explicit (large) threshold, then the Cauchy problem has global solutions

Seed mucilage effect on water uptake and germination in five species from the hyper-arid Arabian desert

© 2016 Elsevier Ltd. The effect of mucilage removal on germination percentages and velocity (Timson\u27s index) was studied for five Arabian desert species (Lavandula subnuda, Lepidium aucheri, Boerhavia elegans, Plantago ciliata and Plantago amplexicaulis) under two photoperiods (0, 12 h of light daily) and three thermoperiods (night/day temperatures of 15/25, 20/30 and 25/35 °C). Mucilage presence increased water uptake in all species, and was associated with higher germination percentages in L. subnuda, B. elegans and P. ciliata, but not L. aucheri and P. amplexicaulis. Germination velocity response to mucilage presence was mixed, being increased in L. aucheri and reduced in L. subnuda. In all species germination was increased by light and affected by temperature, but species\u27 response to temperature varied. Interactions of mucilage presence with temperature were more frequent than with light. Seed mucilage plays a role in germination regulation of these species, but the effects are species-specific. Mucilage presence inhibited germination at lower temperatures in L. subnuda and P. ciliata, at higher temperatures in B. elegans, and increased germination velocity but not percentage in L. aucheri. It had no influence on germination in P. amplexicaulis. The differences detected demonstrate as perhaps mucilage in seeds of some desert species serves also to other ecological purposes

Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities

Many complex networks display a mesoscopic structure with groups of nodes sharing many links with the other nodes in their group and comparatively few with nodes of different groups. This feature is known as community structure and encodes precious information about the organization and the function of the nodes. Many algorithms have been proposed but it is not yet clear how they should be tested. Recently we have proposed a general class of undirected and unweighted benchmark graphs, with heterogenous distributions of node degree and community size. An increasing attention has been recently devoted to develop algorithms able to consider the direction and the weight of the links, which require suitable benchmark graphs for testing. In this paper we extend the basic ideas behind our previous benchmark to generate directed and weighted networks with built-in community structure. We also consider the possibility that nodes belong to more communities, a feature occurring in real systems, like, e. g., social networks. As a practical application, we show how modularity optimization performs on our new benchmark.Comment: 9 pages, 13 figures. Final version published in Physical Review E. The code to create the benchmark graphs can be freely downloaded from http://santo.fortunato.googlepages.com/inthepress

Seed germination requirements and salt stress tolerance of coastal rare species in Sardinia

To survive to adverse factors that characterize coastal environments, plant species often require special physiological or metabolic adaptations to overcome environmental stresses. Stress may be physical (e.g. temperature) or chemical (e.g. salinity). Many communities comprise highly specialized species, which have comparatively restricted geographical distributions. The coastal species investigated in this Ph.D. program were chosen accordingly to their habitat: Phleum sardoum (Hackel) Hackel and Rouya polygama (Desf.) Coincy for sandy dunes; Brassica insularis Moris and Lavatera triloba L. ssp. pallescens (Moris) Nyman for coastal cliffs; Lavatera triloba L. ssp. triloba and Halopeplis amplexicaulis (Vahl) Ces., Pass. & Gibelli for ultra-saline environments. Moreover, seed germination ecology of L. agrigentina Tineo, a species growing in clayey-chalky plains of South Italy, was also investigated for a comparative study within the Lavatera genus. For all the studied species, light and temperature requirements for seed germination were evaluated; their germination responses to salt stress (NaCl) and their germination recovery. Interpopulation variability on germination patterns was also evaluated for R. polygama, B. insularis and L. triloba ssp. triloba. Salt spray tolerance on the vegetative growth and biomass production during the early seedling developmental stages was evaluated for B. insularis, L. triloba ssp. pallescens, L. triloba ssp. triloba and H. amplexicaulis. Light did not affect germination percentages in any of the studied species enabling seed germination also under soil surface and highlighting that seeds were not photo-inhibited for germination. Seed germination of P. sardoum and R. polygama, as well as that of L. agrigentina, L. triloba ssp. pallescens and L. triloba ssp. triloba, reflected the optimal range of temperatures of “typical” Mediterranean species, suggesting germination in autumn-winter, when water availability, soil moisture and rainfalls are high, and temperatures are not excessively prohibitive for germination and consequent seedlings establishment. B. insularis differed from other “typical” Mediterranean plants, for which germination at low temperatures is a widely extended trait, demonstrating that germination of this species may occur in a wide time window during the year. H. amplexicaulis seed germination was highly promoted by the daily fluctuation of temperatures, while germination at constant temperatures was sensibly lower. Salinity tests showed higher germination percentages in the non-saline conditions, with seed mortality increasing proportionally with NaCl concentrations and temperatures. Salt tolerance limits varied among species, from a minimum of 100 mM NaCl for P. sardoum to 600 mM for H. amplexicaulis and L. triloba ssp. pallescens, without a clear habitat related pattern. The species for which salt spray experiments were conducted showed different responses on seedling growth to salt aerosol tolerance, with these differences being related to the habitat of each species and their distance from the sea. Populations of B. insularis and L. triloba ssp. pallescens, growing in coastal cliffs highly influenced by wind and salt spray, showed the lowest seedling mortality. High interpopulation variability in salt spray tolerance was detected for B. insularis, between a coastal and an inland population, with the latter resulting not adapted to this abiotic environmental factor. Seedling survival of the two inland species (L. triloba ssp. triloba and H. amplexicaulis) was inversely proportional to the increase of nebulization frequency, demonstrating a low adaptation to salt spray, likely due to their distance from the sea coast and/or to interposed vegetation that may determine a lower impact of marine aerosol. The results of this study lead to a better knowledge on the autoecology of the investigated species and to their limits of tolerance to abiotic factors such as temperature, soil salinity and salt spray

Empirical fragility assessment using conditional GMPE-based ground shaking fields: application to damage data for 2016 Amatrice Earthquake

AbstractRecent earthquakes have exposed the vulnerability of existing buildings; this is demonstrated by damage incurred after moderate-to-high magnitude earthquakes. This stresses the need to exploit available data from different sources to develop reliable seismic risk components. As far as it regards empirical fragility assessment, accurate estimation of ground-shaking at the location of buildings of interest is as crucial as the accurate evaluation of observed damage for these buildings. This implies that explicit consideration of the uncertainties in the prediction of ground shaking leads to more robust empirical fragility curves. In such context, the simulation-based methods can be employed to provide fragility estimates that integrate over the space of plausible ground-shaking fields. These ground-shaking fields are generated according to the joint probability distribution of ground-shaking at the location of the buildings of interest considering the spatial correlation structure in the ground motion prediction residuals and updated based on the registered ground shaking data and observed damage. As an alternative to the embedded coefficients in the ground motion prediction equations accounting for subsoil categories, stratigraphic coefficients can be applied directly to the ground motion fields at the engineering bedrock level. Empirical fragility curves obtained using the observed damage in the aftermath of Amatrice Earthquake for residential masonry buildings show that explicit consideration of the uncertainty in the prediction of ground-shaking significantly affects the results