1,306 research outputs found
Classification in biological networks with hypergraphlet kernels
MOTIVATION: Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins and drugs) and edges represent relational ties between these objects (binds-to, interacts-with and regulates). This approach has been highly successful owing to the theory, methodology and software that support analysis and learning on graphs. Graphs, however, suffer from information loss when modeling physical systems due to their inability to accurately represent multiobject relationships. Hypergraphs, a generalization of graphs, provide a framework to mitigate information loss and unify disparate graph-based methodologies. RESULTS: We present a hypergraph-based approach for modeling biological systems and formulate vertex classification, edge classification and link prediction problems on (hyper)graphs as instances of vertex classification on (extended, dual) hypergraphs. We then introduce a novel kernel method on vertex- and edge-labeled (colored) hypergraphs for analysis and learning. The method is based on exact and inexact (via hypergraph edit distances) enumeration of hypergraphlets; i.e. small hypergraphs rooted at a vertex of interest. We empirically evaluate this method on fifteen biological networks and show its potential use in a positive-unlabeled setting to estimate the interactome sizes in various species. AVAILABILITY AND IMPLEMENTATION: https://github.com/jlugomar/hypergraphlet-kernels. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online
Analysis of Highly Directive Cavity-Type Configurations Comprising of Low Profile Antennas Covered by Superstrates
In this paper we present a technique for designing antenna/superstrate composites to produce enhanced directivities. As a first step, we study the underlying mechanism that governs the performance of theses antennas by studying the canonical problem of a line source in a rectangular waveguide. The above problem is solved by constructing the Green’s function corresponding to the line source in the rectangular guide, one of whose walls is partially reflecting, that is can leak electromagnetic energy into the space external to the guide. The Green’s function for this problem can be constructed by aggregating the multiple reflections from the two walls. Although the above model is only two-dimensional, we show that it can be used to predict the performance of antenna/superstrate composites. We demonstrate this by modeling several highly directive antennas and show that indeed the required characteristics of this type of antennas can be determined from the analysis of the cutoff behavior of the rectangular guide
Analysis of real time operations control strategies for Tren Urbano
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2000.Includes bibliographical references (leaves 146-148).by Iris N. Ortiz.S.M
Monopoles and Holography
We present a holographic theory in AdS_4 whose zero temperature ground state
develops a crystal structure, spontaneously breaking translational symmetry.
The crystal is induced by a background magnetic field, but requires no chemical
potential. This lattice arises from the existence of 't Hooft-Polyakov monopole
solitons in the bulk which condense to form a classical object known as a
monopole wall. In the infra-red, the magnetic field is screened and there is an
emergent SU(2) global symmetry.Comment: 33 pages, 16 figures; v2: ref adde
Gauge invariant perturbation theory and non-critical string models of Yang-Mills theories
We carry out a gauge invariant analysis of certain perturbations of
-branes solutions of low energy string theories. We get generically a
system of second order coupled differential equations, and show that only in
very particular cases it is possible to reduce it to just one differential
equation. Later, we apply it to a multi-parameter, generically singular family
of constant dilaton solutions of non-critical string theories in
dimensions, a generalization of that recently found in arXiv:0709.0471[hep-th].
According to arguments coming from the holographic gauge theory-gravity
correspondence, and at least in some region of the parameters space, we obtain
glue-ball spectra of Yang-Mills theories in diverse dimensions, putting special
emphasis in the scalar metric perturbations not considered previously in the
literature in the non critical setup. We compare our numerical results to those
studied previously and to lattice results, finding qualitative and in some
cases, tuning properly the parameters, quantitative agreement. These results
seem to show some kind of universality of the models, as well as an irrelevance
of the singular character of the solutions. We also develop the analysis for
the T-dual, non trivial dilaton family of solutions, showing perfect agreement
between them.Comment: A new reference added
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