Quantifying loopy network architectures

Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of methods have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the Asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes) from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.Comment: 17 pages, 8 figures. During preparation of this manuscript the authors became aware of the work of Mileyko at al., concurrently submitted for publicatio

Visualizing Multivariate Hierarchic Data Using Enhanced Radial Space-Filling Layout

Currently, visualization tools for large ontologies (e.g., pathway and gene ontologies) result in a very flat wide tree that is difficult to fit on a single display. This paper develops the concept of using an enhanced radial space-filling (ERSF) layout to show biological ontologies efficiently. The ERSF technique represents ontology terms as circular regions in 3D. Orbital connections in a third dimension correspond to non-tree edges in the ontology that exist when an ontology term belongs to multiple categories. Biologists can use the ERSF layout to identify highly activated pathway or gene ontology categories by mapping experimental statistics such as coefficient of variation and overrepresentation values onto the visualization. This paper illustrates the use of the ERSF layout to explore pathway and gene ontologies using a gene expression dataset from E. coli

From the web of data to a world of action

This is the author’s version of a work that was accepted for publication in Web Semantics: Science, Services and Agents on the World Wide Web. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Web Semantics: Science, Services and Agents on the World Wide Web 8.4 (2010): 10.1016/j.websem.2010.04.007This paper takes as its premise that the web is a place of action, not just information, and that the purpose of global data is to serve human needs. The paper presents several component technologies, which together work towards a vision where many small micro-applications can be threaded together using automated assistance to enable a unified and rich interaction. These technologies include data detector technology to enable any text to become a start point of semantic interaction; annotations for web-based services so that they can link data to potential actions; spreading activation over personal ontologies, to allow modelling of context; algorithms for automatically inferring 'typing' of web-form input data based on previous user inputs; and early work on inferring task structures from action traces. Some of these have already been integrated within an experimental web-based (extended) bookmarking tool, Snip!t, and a prototype desktop application On Time, and the paper discusses how the components could be more fully, yet more openly, linked in terms of both architecture and interaction. As well as contributing to the goal of an action and activity-focused web, the work also exposes a number of broader issues, theoretical, practical, social and economic, for the Semantic Web.Parts of this work were supported by the Information Society Technologies (IST) Program of the European Commission as part of the DELOS Network of Excellence on Digital Libraries (Contract G038- 507618). Thanks also to Emanuele Tracanna, Marco Piva, and Raffaele Giuliano for their work on On Time

Collapse and folding of pressurized rings in two dimensions

Hydrostatically pressurized circular rings confined to two dimensions (or cylinders constrained to have only z-independent deformations) undergo Euler type buckling when the outside pressure exceeds a critical value. We perform a stability analysis of rings with arc-length dependent bending moduli and determine how weakened bending modulus segments affect the buckling critical pressure. Rings with a 4-fold symmetric modulation are particularly susceptible to collapse. In addition we study the initial post-buckling stages of the pressurized rings to determine possible ring folding patterns

The usability of description logics: understanding the cognitive difficulties presented by description logics

Description Logics have been extensively studied from the viewpoint of decidability and computational tractability. Less attention has been given to their usability and the cognitive difficulties they present, in particular for those who are not specialists in logic. This paper reports on a study into the difficulties associated with the most commonly used Description Logic features. Psychological theories are used to take account of these. Whilst most of the features presented no difficulty to participants, the comprehension of some was affected by commonly occurring misconceptions. The paper proposes explanations and remedies for some of these difficulties. In addition, the time to confirm stated inferences was found to depend both on the maximum complexity of the relations involved and the number of steps in the argument

Thermal Evolution of the Non Supersymmetric Metastable Vacua in N=2 SU(2) SYM Softly Broken to N=1

It has been shown that four dimensional N=2 gauge theories, softly broken to N=1 by a superpotential term, can accommodate metastable non-supersymmetric vacua in their moduli space. We study the SU(2) theory at high temperatures in order to determine whether a cooling universe settles in the metastable vacuum at zero temperature. We show that the corrections to the free energy because of the BPS dyons are such that may destroy the existence of the metastable vacuum at high temperatures. Nevertheless we demonstrate the universe can settle in the metastable vacuum, provided that the following two conditions are hold: first the superpotential term is not arbitrarily small in comparison to the strong coupling scale of the gauge theory, and second the metastable vacuum lies in the strongly coupled region of the moduli space.Comment: 32 pages, 30 figure

Limited Urban Growth: London's Street Network Dynamics since the 18th Century

We investigate the growth dynamics of Greater London defined by the administrative boundary of the Greater London Authority, based on the evolution of its street network during the last two centuries. This is done by employing a unique dataset, consisting of the planar graph representation of nine time slices of Greater London's road network spanning 224 years, from 1786 to 2010. Within this time-frame, we address the concept of the metropolitan area or city in physical terms, in that urban evolution reveals observable transitions in the distribution of relevant geometrical properties. Given that London has a hard boundary enforced by its long-standing green belt, we show that its street network dynamics can be described as a fractal space-filling phenomena up to a capacitated limit, whence its growth can be predicted with a striking level of accuracy. This observation is confirmed by the analytical calculation of key topological properties of the planar graph, such as the topological growth of the network and its average connectivity. This study thus represents an example of a strong violation of Gibrat's law. In particular, we are able to show analytically how London evolves from a more loop-like structure, typical of planned cities, toward a more tree-like structure, typical of self-organized cities. These observations are relevant to the discourse on sustainable urban planning with respect to the control of urban sprawl in many large cities, which have developed under the conditions of spatial constraints imposed by green belts and hard urban boundaries.Comment: PlosOne, in publicatio

Distributed flow optimization and cascading effects in weighted complex networks

We investigate the effect of a specific edge weighting scheme $\sim (k_i k_j)^{\beta}$ on distributed flow efficiency and robustness to cascading failures in scale-free networks. In particular, we analyze a simple, yet fundamental distributed flow model: current flow in random resistor networks. By the tuning of control parameter $\beta$ and by considering two general cases of relative node processing capabilities as well as the effect of bandwidth, we show the dependence of transport efficiency upon the correlations between the topology and weights. By studying the severity of cascades for different control parameter $\beta$, we find that network resilience to cascading overloads and network throughput is optimal for the same value of $\beta$ over the range of node capacities and available bandwidth

From Interactive Open Learner Modelling to Intelligent Mentoring: STyLE-OLM and Beyond

STyLE-OLM (Dimitrova 2003 International Journal of Artificial Intelligence in Education, 13, 35–78) presented a framework for interactive open learner modelling which entails the development of the means by which learners can inspect, discuss and alter the learner model that has been jointly constructed by themselves and the system. This paper outlines the STyLE-OLM framework and reflects on the key challenges it addressed: (a) the design of an appropriate communication medium; this was addressed by proposing a structured language using diagrammatic presentations of conceptual graphs; (b) the management of the interaction with the learner; this was addressed by designing a framework for interactive open learner modelling dialogue utilising dialogue games; (c) the accommodation of different beliefs about the learner’s domain model; this was addressed with a mechanism for maintaining different views about the learner beliefs which adapted belief modal logic operators; and (d) the assessment of any resulting improvements in learner model accuracy and learner reflection; this was addressed in a user study with an instantiation of STyLE-OLM for diagnosing a learner’s knowledge of finance concept, as part of a larger project that developed an intelligent system to assist with learning domain terminology in a foreign language. Reviewing follow on work, we refer to projects by the authors’ students and colleagues leading to further extension and adoption of STyLE-OLM, as well as relevant approaches in open learner modelling which have cited the STyLE-OLM framework. The paper points at outstanding research challenges and outlines future a research direction to extend interactive open learner modelling towards mentor-like intelligent learning systems