A Cluster Elastic Net for Multivariate Regression

We propose a method for estimating coefficients in multivariate regression when there is a clustering structure to the response variables. The proposed method includes a fusion penalty, to shrink the difference in fitted values from responses in the same cluster, and an L1 penalty for simultaneous variable selection and estimation. The method can be used when the grouping structure of the response variables is known or unknown. When the clustering structure is unknown the method will simultaneously estimate the clusters of the response and the regression coefficients. Theoretical results are presented for the penalized least squares case, including asymptotic results allowing for p >> n. We extend our method to the setting where the responses are binomial variables. We propose a coordinate descent algorithm for both the normal and binomial likelihood, which can easily be extended to other generalized linear model (GLM) settings. Simulations and data examples from business operations and genomics are presented to show the merits of both the least squares and binomial methods.Comment: 37 Pages, 11 Figure

Male-biased operational sex ratios and the Viking phenomenon : an evolutionary anthropological perspective on Late Iron Age Scandinavian raiding

Acknowledgements We would like to thank Laura Whitehouse, John Carman, Oliver Grimm, Julie Lund, Bjørnar Olsen, two anonymous reviewers, and the editor for their comments and suggestions on earlier versions of this paper. We also thank Alex Woolf for providing us with a copy of his forthcoming article on the Vikings in Ireland. Lastly, we are grateful to Luke Glowacki, Shane McFarlane, and Ryan Schacht for their insights about raiding and OSRs. Needless to say, all remaining errors are our own. Funding BR and MC are supported by the Social Sciences and Humanities Research Council of Canada through a Partnership Grant (895-2011-1009) awarded to the Cultural Evolution of Religion Research Consortium (www.ubc/hecc/cerc). MC is also supported by the Canada Research Chairs Program, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, and Simon Fraser University. NP is supported by a Swedish Research Council grant for "The Viking Phenomenon" project (2015-00466).Peer reviewedPublisher PD

Ambipolar diffusion in smoothed particle magnetohydrodynamics

In partially ionised plasmas, the magnetic field can become decoupled from the neutral gas and diffuse through it in a process known as ambipolar diffusion. Although ambipolar diffusion has been implemented in several grid codes, we here provide an implementation in smoothed particle magnetohydrodynamics (SPMHD). We use the strong coupling approximation in which the ion density is negligible, allowing a single fluid approach. The equations are derived to conserve energy, and to provide a positive definite contribution to the entropy. We test the implementation in both a simple 1D SPMHD code and the fully 3D code PHANTOM. The wave damping test yields agreement within 0.03-2 per cent of the analytical result, depending on the value of the collisional coupling constant. The oblique C-shocks test yields results that typically agree within 4 per cent of the semi-analytical result. Our algorithm is therefore suitable for exploring the effect ambipolar diffusion has on physical processes, such as the formation of stars from molecular clouds.Comment: Accepted for publication by MNRA

Natural selection maximizes Fisher information

In biology, information flows from the environment to the genome by the process of natural selection. But it has not been clear precisely what sort of information metric properly describes natural selection. Here, I show that Fisher information arises as the intrinsic metric of natural selection and evolutionary dynamics. Maximizing the amount of Fisher information about the environment captured by the population leads to Fisher's fundamental theorem of natural selection, the most profound statement about how natural selection influences evolutionary dynamics. I also show a relation between Fisher information and Shannon information (entropy) that may help to unify the correspondence between information and dynamics. Finally, I discuss possible connections between the fundamental role of Fisher information in statistics, biology, and other fields of science.Comment: Published version freely available at DOI listed her

Superfluid vortices in four spatial dimensions

Quantum vortices in superfluids have been an important research area for many decades. Naturally, research on this topic has focused on two and three-dimensional superfluids, in which vortex cores form points and lines, respectively. Very recently, however, there has been growing interest in the quantum simulation of systems with four spatial dimensions; this raises the question of how vortices would behave in a higher-dimensional superfluid. In this paper, we begin to establish the phenomenology of vortices in 4D superfluids under rotation, where the vortex core can form a plane. In 4D, the most generic type of rotation is a "double rotation" with two angles (or frequencies). We show, by solving the Gross-Pitaesvkii equation, that the simplest case of equal-frequency double rotation can stabilise a pair of vortex planes intersecting at a point. This opens up a wide number of future research topics, including unequal-frequency double rotations; the stability and reconnection dynamics of intersecting vortex surfaces; and the possibility of closed vortex surfaces

Curved vortex surfaces in four-dimensional superfluids. II. Equal-frequency double rotations

As is well known, two-dimensional and three-dimensional superfluids under rotation can support topological excitations such as quantized point vortices and line vortices, respectively. Recently, we have studied how, in a hypothetical four-dimensional (4D) superfluid, such excitations can be generalized to vortex planes and surfaces. In this paper we continue our analysis of skewed and curved vortex surfaces based on the 4D Gross-Pitaevskii equation and show that certain types of such states can be stabilized by equal-frequency double rotations for suitable parameters. This work extends the rich phenomenology of vortex surfaces in four dimensions and raises interesting questions about vortex reconnections and the competition between various vortex structures which have no direct analog in lower dimensions

Confirmation that mrub_1751 is homologous to \u3cem\u3eE. coli\u3c/em\u3e xylF, mrub_1752 is homologous to \u3cem\u3eE. coli\u3c/em\u3e xylH, and mrub_1753 is homologous to \u3cem\u3eE. coli\u3c/em\u3e xylG

In this project we investigated the biological function of the genes Mrub_1751, Mrub_1752 and Mrub_1753 (KEGG map number 02010). We predict these genes encode components of a D-xylose ATP Binding Cassette (ABC) transporter: 1) Mrub_1752 (DNA coordinates 1809004-1810224 on the forward strand) encodes the permease component (aka transmembrane domain), predicted to be an ortholog and 2) Mrub_1753 (DNA coordinates 1810227-1811000 on the forward strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1751 (DNA coordinates 1807855-1808892 on the forward strand) encodes the solute binding protein. The ABC-transporter for M. ruber to transport D-xylose is homologous with the transporter found in E. coli, allowing for the transport of D-xylose into the cell. Of interest is the finding that Mrub_1753 and E. coli xylG appear to be partly embedded in the cell membrane, unlike most ATP-binding domains. This project is part of the Meiothermus ruber genome analysis project, which predicts gene function using the bioinformatics tools collected under the umbrella of the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT)

Curved vortex surfaces in four-dimensional superfluids. I. Unequal-frequency double rotations

The study of superfluid quantum vortices has long been an important area of research, with previous work naturally focusing on two-dimensional and three-dimensional systems, where rotation stabilizes point vortices and line vortices respectively. Interestingly, this physics generalizes for a hypothetical four-dimensional (4D) superfluid to include vortex planes, which can have a much richer phenomenology. In this paper we study the possibility of skewed and curved vortex planes, which have no direct analog in lower dimensions. By analytically and numerically studying the 4D Gross-Pitaevskii equation, we show that such vortex surfaces can be stabilized and favored by double rotation with unequal rotation frequencies. Our work raises open questions for further research into the physics of these vortex surfaces and suggests interesting future extensions to tilted vortex surfaces under equal-frequency double rotation and to more realistic 4D models

On the Use of Minimum Penalties in Statistical Learning

Modern multivariate machine learning and statistical methodologies estimate parameters of interest while leveraging prior knowledge of the association between outcome variables. The methods that do allow for estimation of relationships do so typically through an error covariance matrix in multivariate regression which does not scale to other types of models. In this article we proposed the MinPEN framework to simultaneously estimate regression coefficients associated with the multivariate regression model and the relationships between outcome variables using mild assumptions. The MinPen framework utilizes a novel penalty based on the minimum function to exploit detected relationships between responses. An iterative algorithm that generalizes current state of the art methods is proposed as a solution to the non-convex optimization that is required to obtain estimates. Theoretical results such as high dimensional convergence rates, model selection consistency, and a framework for post selection inference are provided. We extend the proposed MinPen framework to other exponential family loss functions, with a specific focus on multiple binomial responses. Tuning parameter selection is also addressed. Finally, simulations and two data examples are presented to show the finite sample properties of this framewok

The introduction, deployment and impact of assistant practitioners in diagnostic radiography in Scotland

This article describes the outcomes of an evaluation of the impact of introducing Assistant Practitioners (AP) roles into imaging departments in 13 of the 14 NHS Boards in Scotland. Between 2006 and 2009 some 34 individuals were trained as APs in diagnostic radiography with 33 subsequently taking up AP posts. In 2010 NHS Education for Scotland commissioned an evaluation of the impact brought about through introduction of the diagnostic imaging AP role in imaging departments. The research found that a minority of the managers had considered the workforce implications of introducing the new roles or the supervisory arrangements that would be required. In some sites implementation of the roles had resulted in the release of radiographers for additional training and higher level activities, but in others financial constraints had limited such initiatives. Managers believed that APs had helped maintain or improve service capacity and quality