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

Gravitating sphalerons and sphaleron black holes in asymptotically anti-de Sitter spacetime

Numerical arguments are presented for the existence of spherically symmetric regular and black hole solutions of the EYMH equations with a negative cosmological constant. These solutions approach asymptotically the anti-de Sitter spacetime. The main properties of the solutions and the differences with respect to the asymptotically flat case are discussed. The instability of the gravitating sphaleron solutions is also proven.Comment: 30 pages, LaTeX, 8 Encapsulated PostScript figure

Monopoles, Dyons and Black Holes in the Four-Dimensional Einstein-Yang-Mills Theory

A continuum of monopole, dyon and black hole solutions exist in the Einstein-Yang-Mills theory in asymptotically anti-de Sitter space. Their structure is studied in detail. The solutions are classified by non-Abelian electric and magnetic charges and the ADM mass. The stability of the solutions which have no node in non-Abelian magnetic fields is established. There exist critical spacetime solutions which terminate at a finite radius, and have universal behavior. The moduli space of the solutions exhibits a fractal structure as the cosmological constant approaches zero.Comment: 36 Pages, 16 Figures. Minor typos corrected and one figure modifie

Gauge invariant perturbation theory and non-critical string models of Yang-Mills theories

We carry out a gauge invariant analysis of certain perturbations of $D-2$-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 $D$ 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

Edge Currents in Non-commutative Chern-Simons Theory from a New Matrix Model

This paper discusses the formulation of the non-commutative Chern-Simons (CS) theory where the spatial slice, an infinite strip, is a manifold with boundaries. As standard star products are not correct for such manifolds, the standard non-commutative CS theory is not also appropriate here. Instead we formulate a new finite-dimensional matrix CS model as an approximation to the CS theory on the strip. A work which has points of contact with ours is due to Lizzi, Vitale and Zampini where the authors obtain a description for the fuzzy disc. The gauge fields in our approach are operators supported on a subspace of finite dimension N+\eta of the Hilbert space of eigenstates of a simple harmonic oscillator with N, \eta \in Z^+ and N \neq 0. This oscillator is associated with the underlying Moyal plane. The resultant matrix CS theory has a fuzzy edge. It becomes the required sharp edge when N and \eta goes to infinity in a suitable sense. The non-commutative CS theory on the strip is defined by this limiting procedure. After performing the canonical constraint analysis of the matrix theory, we find that there are edge observables in the theory generating a Lie algebra with properties similar to that of a non-abelian Kac-Moody algebra. Our study shows that there are (\eta+1)^2 abelian charges (observables) given by the matrix elements (\cal A_i)_{N-1 N-1} and (\cal A_i)_{nm} (where n or m \geq N) of the gauge fields, that obey certain standard canonical commutation relations. In addition, the theory contains three unique non-abelian charges, localized near the N^th level. We show that all non-abelian edge observables except these three can be constructed from the abelian charges above. Using the results of this analysis we discuss the large N and \eta limit.Comment: LaTeX, 16 pages and 2 figures. Comments added in sections 4 and 5. A minor error corrected in section 4. Figures replaced for clarity. Typos correcte

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

Digitalization of Aeronautic Painting Shop Floors for Improved Commissioning Activities

Industrial commissioning plays a critical role in ensuring the safe and efficient operation of facilities and minimizes downtime and maintenance costs over their lifetime. To extend and adjust commissioning capabilities, Virtual Commissioning uses digital models of devices and processes to verify, validate, and optimize code programming, and component selection. To perform the validation process, a simulation involving control devices and process digital twins is required, leading to inherent computational complexity. Distributed simulation approach allows for simulation of complex systems by breaking down a large simulation into smaller, manageable parts that can be run simultaneously on separate processors, while still preserving the overall behavior and interactions of the system being simulated. This paper presents a distributed Virtual Commissioning solution for a spray paint process presented in UAV painting shop floor. The methodology for developing the implementation is described in detail: greenfield scenario generation, automation process, software toolchain development, selection of communication protocols, re-use of digital twins for extended applications, and complexity analysis. A set of 3d scenarios is used to demonstrate the result’s performance

Guaiacol and its mixtures: New data and predictive models. Part 2: Gibbs energy of solvation

© 2018 Elsevier B.V. Guaiacol is a model molecule for lignocellulosic biomass processing, and thus understanding its interactions with solvents is an important step when developing units for processing lignocellulosic biomass. In this work, activity coefficient measurements of different solvents (acetonitrile, ethanol, tetrahydrofuran) in guaiacol have been performed at different concentrations and temperatures. These measurements have been used to estimate the infinite dilution activity coefficients and the Gibbs energy of solvation of guaiacol in the different solvents, and of each solvent in guaiacol. These estimated values were compared to those obtained with different predictive models: UNIFAC DMD, Monte Carlo Molecular Simulation, COSMO-SAC and GC-PPC-SAFT. The predictions are in very good agreement with the Gibbs energies of solvation derived from experimental data. Some conclusions are also drawn regarding the inter- and intramolecular hydrogen bonding in guaiacol and about its affinity with different solvents on the basis of the inter- and intramolecular interactions taking place

How Malthusian Ideology crept into the Newsroom: British tabloids and the coverage of the ‘underclass’

This article argues that Malthusianism as a series of discursive regimes, developed in the Victorian-era, serves in times of austerity to reproduce an elite understanding of social exclusion in which those in a state of poverty are to blame for their own situation. It highlights that Malthusianism is present in the public discourse, becoming an underlining feature in news coverage of the so-called ‘underclass’. Our findings broadly contradict the normative claim that journalism ‘speaks truth to power’, and suggest instead that overall as a political practice, journalism tends to reproduce and reinforce hegemonic discourses of power. The piece is based on critical discourse analysis (CDA), which has been applied to a significant sample of news articles published by tabloid newspapers in Britain which focussed on the concept of the ‘underclass’. By looking at the evidence, the authors argue that the ‘underclass’ is a concept used by some journalists to cast people living in poverty as ‘undeserving’ of public and state support. In so doing, these journalists help create a narrative which supports cuts in welfare provisions and additional punitive measures against some of the most vulnerable members of society