FooPar: A Functional Object Oriented Parallel Framework in Scala

We present FooPar, an extension for highly efficient Parallel Computing in the multi-paradigm programming language Scala. Scala offers concise and clean syntax and integrates functional programming features. Our framework FooPar combines these features with parallel computing techniques. FooPar is designed modular and supports easy access to different communication backends for distributed memory architectures as well as high performance math libraries. In this article we use it to parallelize matrix matrix multiplication and show its scalability by a isoefficiency analysis. In addition, results based on a empirical analysis on two supercomputers are given. We achieve close-to-optimal performance wrt. theoretical peak performance. Based on this result we conclude that FooPar allows to fully access Scala's design features without suffering from performance drops when compared to implementations purely based on C and MPI

Propagation Failure in Excitable Media

We study a mechanism of pulse propagation failure in excitable media where stable traveling pulse solutions appear via a subcritical pitchfork bifurcation. The bifurcation plays a key role in that mechanism. Small perturbations, externally applied or from internal instabilities, may cause pulse propagation failure (wave breakup) provided the system is close enough to the bifurcation point. We derive relations showing how the pitchfork bifurcation is unfolded by weak curvature or advective field perturbations and use them to demonstrate wave breakup. We suggest that the recent observations of wave breakup in the Belousov-Zhabotinsky reaction induced either by an electric field or a transverse instability are manifestations of this mechanism.Comment: 8 pages. Aric Hagberg: http://cnls.lanl.gov/~aric; Ehud Meron:http://www.bgu.ac.il/BIDR/research/staff/meron.htm

SentiBench - a benchmark comparison of state-of-the-practice sentiment analysis methods

In the last few years thousands of scientific papers have investigated sentiment analysis, several startups that measure opinions on real data have emerged and a number of innovative products related to this theme have been developed. There are multiple methods for measuring sentiments, including lexical-based and supervised machine learning methods. Despite the vast interest on the theme and wide popularity of some methods, it is unclear which one is better for identifying the polarity (i.e., positive or negative) of a message. Accordingly, there is a strong need to conduct a thorough apple-to-apple comparison of sentiment analysis methods, \textit{as they are used in practice}, across multiple datasets originated from different data sources. Such a comparison is key for understanding the potential limitations, advantages, and disadvantages of popular methods. This article aims at filling this gap by presenting a benchmark comparison of twenty-four popular sentiment analysis methods (which we call the state-of-the-practice methods). Our evaluation is based on a benchmark of eighteen labeled datasets, covering messages posted on social networks, movie and product reviews, as well as opinions and comments in news articles. Our results highlight the extent to which the prediction performance of these methods varies considerably across datasets. Aiming at boosting the development of this research area, we open the methods' codes and datasets used in this article, deploying them in a benchmark system, which provides an open API for accessing and comparing sentence-level sentiment analysis methods

Linking forest cover, soil erosion and mire hydrology to late-Holocene human activity and climate in NW Spain

This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 3.0 License (http://www.creativecommons.org/licenses/by-nc/3.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page (http://www.uk.sagepub.com/aboutus/openaccess.htm).This article has been made available through the Brunel Open Access Publishing Fund.Forest clearance is one of the main drivers of soil erosion and hydrological changes in mires, although climate may also play a significant role. Because of the wide range of factors involved, understanding these complex links requires long-term multi-proxy approaches and research on the best proxies to focus. A peat core from NW Spain (Cruz do Bocelo mire), spanning the last ~3000 years, has been studied at high resolution by physical (density and loss on ignition (LOI)), geochemical (elemental composition) and palynological (pollen and non-pollen palynomorphs) analyses. Proxies related to mineral matter fluxes from the catchment (lithogenic tracers, Glomus and Entorrhiza), rainfall (Bromine), mire hydrology (HdV-18), human pressure (Cerealia-type, nitrophilous taxa and coprophilous fungi) and forest cover (mesophilous tree taxa) were the most useful to reconstruct the evolution of the mire and its catchment. Forest clearance for farming was one of the main drivers of environmental change from at least the local Iron Age (~2685 cal. yr BP) onwards. The most intense phase of deforestation occurred during Roman and Germanic times and the late Middle Ages. During these phases, the entire catchment was affected, resulting in enhanced soil erosion and severe hydrological modifications of the mire. Climate, especially rainfall, may have also accelerated these processes during wetter periods. However, it is noteworthy that the hydrology of the mire seems to have been insensitive to rainfall variations when mesophilous forest dominated. Abrupt changes were only detected once intense forest clearance commenced during the Iron Age/Roman transition (~2190 cal. yr BP) phase, which represented a tipping point in catchment's ability to buffer impacts. Overall, our findings highlight the importance of studying ecosystems' long-term trajectories and catchment-wide processes when implementing mire habitat protection measures.This work was funded by the projects CGL2010-20672 (Plan Nacional I+D+i, Spanish Ministry of Science and Innovation) and 10PXIB200182PR (General Directorate of I+D, Xunta de Galicia). N Silva-Sánchez and L López-Merino are currently supported by a FPU predoctoral scholarship (AP2010-3264) funded by the Spanish Government and a MINT postdoctoral fellowship funded by the Brunel Institute for the Environment, respectively

Controlling domain patterns far from equilibrium

A high degree of control over the structure and dynamics of domain patterns in nonequilibrium systems can be achieved by applying nonuniform external fields near parity breaking front bifurcations. An external field with a linear spatial profile stabilizes a propagating front at a fixed position or induces oscillations with frequency that scales like the square root of the field gradient. Nonmonotonic profiles produce a variety of patterns with controllable wavelengths, domain sizes, and frequencies and phases of oscillations.Comment: Published version, 4 pages, RevTeX. More at http://t7.lanl.gov/People/Aric

Some Like It Fat: Comparative Ultrastructure of the Embryo in Two Demosponges of the Genus Mycale (Order Poecilosclerida) from Antarctica and the Caribbean

0000-0002-7993-1523© 2015 Riesgo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License [4.0], which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Using Synchronic and Diachronic Relations for Summarizing Multiple Documents Describing Evolving Events

In this paper we present a fresh look at the problem of summarizing evolving events from multiple sources. After a discussion concerning the nature of evolving events we introduce a distinction between linearly and non-linearly evolving events. We present then a general methodology for the automatic creation of summaries from evolving events. At its heart lie the notions of Synchronic and Diachronic cross-document Relations (SDRs), whose aim is the identification of similarities and differences between sources, from a synchronical and diachronical perspective. SDRs do not connect documents or textual elements found therein, but structures one might call messages. Applying this methodology will yield a set of messages and relations, SDRs, connecting them, that is a graph which we call grid. We will show how such a grid can be considered as the starting point of a Natural Language Generation System. The methodology is evaluated in two case-studies, one for linearly evolving events (descriptions of football matches) and another one for non-linearly evolving events (terrorist incidents involving hostages). In both cases we evaluate the results produced by our computational systems.Comment: 45 pages, 6 figures. To appear in the Journal of Intelligent Information System

Order Parameter Equations for Front Transitions: Planar and Circular Fronts

Near a parity breaking front bifurcation, small perturbations may reverse the propagation direction of fronts. Often this results in nonsteady asymptotic motion such as breathing and domain breakup. Exploiting the time scale differences of an activator-inhibitor model and the proximity to the front bifurcation, we derive equations of motion for planar and circular fronts. The equations involve a translational degree of freedom and an order parameter describing transitions between left and right propagating fronts. Perturbations, such as a space dependent advective field or uniform curvature (axisymmetric spots), couple these two degrees of freedom. In both cases this leads to a transition from stationary to oscillating fronts as the parity breaking bifurcation is approached. For axisymmetric spots, two additional dynamic behaviors are found: rebound and collapse.Comment: 9 pages. Aric Hagberg: http://t7.lanl.gov/People/Aric/; Ehud Meron: http://www.bgu.ac.il/BIDR/research/staff/meron.htm

Force transmission in a packing of pentagonal particles

We perform a detailed analysis of the contact force network in a dense confined packing of pentagonal particles simulated by means of the contact dynamics method. The effect of particle shape is evidenced by comparing the data from pentagon packing and from a packing with identical characteristics except for the circular shape of the particles. A counterintuitive finding of this work is that, under steady shearing, the pentagon packing develops a lower structural anisotropy than the disk packing. We show that this weakness is compensated by a higher force anisotropy, leading to enhanced shear strength of the pentagon packing. We revisit "strong" and "weak" force networks in the pentagon packing, but our simulation data provide also evidence for a large class of "very weak" forces carried mainly by vertex-to-edge contacts. The strong force chains are mostly composed of edge-to-edge contacts with a marked zig-zag aspect and a decreasing exponential probability distribution as in a disk packing

Collective emotions online and their influence on community life

E-communities, social groups interacting online, have recently become an object of interdisciplinary research. As with face-to-face meetings, Internet exchanges may not only include factual information but also emotional information - how participants feel about the subject discussed or other group members. Emotions are known to be important in affecting interaction partners in offline communication in many ways. Could emotions in Internet exchanges affect others and systematically influence quantitative and qualitative aspects of the trajectory of e-communities? The development of automatic sentiment analysis has made large scale emotion detection and analysis possible using text messages collected from the web. It is not clear if emotions in e-communities primarily derive from individual group members' personalities or if they result from intra-group interactions, and whether they influence group activities. We show the collective character of affective phenomena on a large scale as observed in 4 million posts downloaded from Blogs, Digg and BBC forums. To test whether the emotions of a community member may influence the emotions of others, posts were grouped into clusters of messages with similar emotional valences. The frequency of long clusters was much higher than it would be if emotions occurred at random. Distributions for cluster lengths can be explained by preferential processes because conditional probabilities for consecutive messages grow as a power law with cluster length. For BBC forum threads, average discussion lengths were higher for larger values of absolute average emotional valence in the first ten comments and the average amount of emotion in messages fell during discussions. Our results prove that collective emotional states can be created and modulated via Internet communication and that emotional expressiveness is the fuel that sustains some e-communities.Comment: 23 pages including Supporting Information, accepted to PLoS ON