Bayesian variable selection in structured high-dimensional covariate spaces with applications in genomics

We consider the problem of variable selection in regression modeling in high-dimensional spaces where there is known structure among the covariates. This is an unconventional variable selection problem for two reasons: (1) The dimension of the covariate space is comparable, and often much larger, than the number of subjects in the study, and (2) the covariate space is highly structured, and in some cases it is desirable to incorporate this structural information in to the model building process. We approach this problem through the Bayesian variable selection framework, where we assume that the covariates lie on an undirected graph and formulate an Ising prior on the model space for incorporating structural information. Certain computational and statistical problems arise that are unique to such high-dimensional, structured settings, the most interesting being the phenomenon of phase transitions. We propose theoretical and computational schemes to mitigate these problems. We illustrate our methods on two different graph structures: the linear chain and the regular graph of degree k. Finally, we use our methods to study a specific application in genomics: the modeling of transcription factor binding sites in DNA sequences. © 2010 American Statistical Association.

Trends in hospital librarianship and hospital library services: 1989 to 2006.

OBJECTIVE: The research studied the status of hospital librarians and library services to better inform the Medical Library Association's advocacy activities. METHODS: The Vital Pathways Survey Subcommittee of the Task Force on Vital Pathways for Hospital Librarians distributed a web-based survey to hospital librarians and academic health sciences library directors. The survey results were compared to data collected in a 1989 survey of hospital libraries by the American Hospital Association in order to identify any trends in hospital libraries, roles of librarians, and library services. A web-based hospital library report form based on the survey questions was also developed to more quickly identify changes in the status of hospital libraries on an ongoing basis. RESULTS: The greatest change in library services between 1989 and 2005/06 was in the area of access to information, with 40% more of the respondents providing access to commercial online services, 100% more providing access to Internet resources, and 28% more providing training in database searching and use of information resources. Twenty-nine percent (n = 587) of the 2005/06 respondents reported a decrease in staff over the last 5 years. CONCLUSIONS: Survey data support reported trends of consolidation of hospitals and hospital libraries and additions of new services. These services have likely required librarians to acquire new skills. It is hoped that future surveys will be undertaken to continue to study these trends.

TEACHING HIGH SCHOOL STUDENTS THE BEST CHORAL REPERTOIRE FROM THE GREAT COMPOSERS: MASTERWORKS AVAILABLE FOR IMMEDIATE, FREE ACCESS FROM THE CHORAL PUBLIC DOMAIN LIBRARY

Studying the choral works of the great composers of the past is always a worthy endeavor. For those aspiring to create an excellent high school choral program, it is critical to a student's musical foundation and heritage. Choral educators who teach high school are often bombarded with the most recently published new choral works, when they have a trove of excellent pieces right at their fingertips through websites like the Choral Public Domain Library (CPDL), all available at no cost. This project will explore the pedagogical reasons why this canon of public domain choral music should be taught at the high school level. A thorough guide to CPDL and an anthology of 200 works available on CPDL will provide the conductor with resources for programming this music. Though choral music in the public domain is free to all, publishers still publish this music and adhere copyright claims. This can create mistrust of legitimate editions on CPDL; why are they available at no cost when publishers are claiming copyright on similar editions? These issues will be thoroughly discussed in this project. For any given work on CPDL, there may be multiple editions available on the site. Choosing the right edition requires knowledge about basic editorial principles, especially for works written during the Renaissance period. A detailed discussion of these principles will provide the conductor with the tools needed to choose the best edition for his or her ensemble.

Iterative inversion of experimental data in weighted spaces

We present iterative algorithms for solving linear inverse problems with discrete data and compare their performances with the method of singular function expansion, in view of applications in optical imaging and particle sizing.

The Use of Singular Systems and other Inversion Methods in Weighted L2- spaces

info:eu-repo/semantics/published

Dynamic load-balancing of finite element applications with the DRAMA library

The DRAMA library, developed within the European Commission funded (ESPRIT) project DRAMA, supports dynamic load-balancing for parallel (message-passing) mesh-based applications. The target applications are those with dynamic and solution-adaptive features. The focus within the DRAMA project was on finite element simulation codes for structural mechanics. An introduction to the DRAMA library will illustrate that the very general cost model and the interface designed specifically for application requirements provide simplified and effective access to a range of parallel partitioners. The main body of the paper will demonstrate the ability to provide dynamic load-balancing for parallel FEM problems that include: adaptive meshing, re-meshing, the need for multi-phase partitioning.

CAPLib - A 'thin layer' message passing library to support computational mechanics codes on distributed memory parallel systems

The Computer Aided Parallelisation Tools (CAPTools) [Ierotheou, C, Johnson SP, Cross M, Leggett PF, Computer aided parallelisation tools (CAPTools)-conceptual overview and performance on the parallelisation of structured mesh codes, Parallel Computing, 1996;22:163±195] is a set of interactive tools aimed to provide automatic parallelisation of serial FORTRAN Computational Mechanics (CM) programs. CAPTools analyses the user's serial code and then through stages of array partitioning, mask and communication calculation, generates parallel SPMD (Single Program Multiple Data) messages passing FORTRAN. The parallel code generated by CAPTools contains calls to a collection of routines that form the CAPTools communications Library (CAPLib). The library provides a portable layer and user friendly abstraction over the underlying parallel environment. CAPLib contains optimised message passing routines for data exchange between parallel processes and other utility routines for parallel execution control, initialisation and debugging. By compiling and linking with different implementations of the library, the user is able to run on many different parallel environments. Even with today's parallel systems the concept of a single version of a parallel application code is more of an aspiration than a reality. However for CM codes the data partitioning SPMD paradigm requires a relatively small set of message-passing communication calls. This set can be implemented as an intermediate `thin layer' library of message-passing calls that enables the parallel code (especially that generated automatically by a parallelisation tool such as CAPTools) to be as generic as possible. CAPLib is just such a `thin layer' message passing library that supports parallel CM codes, by mapping generic calls onto machine specific libraries (such as CRAY SHMEM) and portable general purpose libraries (such as PVM an MPI). This paper describe CAPLib together with its three perceived advantages over other routes: - as a high level abstraction, it is both easy to understand (especially when generated automatically by tools) and to implement by hand, for the CM community (who are not generally parallel computing specialists); - the one parallel version of the application code is truly generic and portable; - the parallel application can readily utilise whatever message passing libraries on a given machine yield optimum performance.

The collection of pre-evacuation times from evacuation trials involving a Hospital Outpatient area and a University Library facility

This paper presents data relating to occupant pre-evacuation times from a university and a hospital outpatient facility. Although the two structures are entirely different they do employ relatively similar procedures: members of staff sweeping areas of the structure to encourage individuals to evacuate. However, the manner in which the dependent population reacts to these procedures is quite different. In the hospital case the patients only evacuated once a member of the nursing staff had instructed them to do so while in the university evacuation the students were less dependent upon the actions of the staff with over 50% of them evacuating with no prior prompting. Although this data may be useful in a variety of areas, it was collected primarily for use within evacuation models.

A policy-definition language and prototype implementation library for policy-based autonomic systems

This paper presents work towards generic policy toolkit support for autonomic computing systems in which the policies themselves can be adapted dynamically and automatically. The work is motivated by three needs: the need for longer-term policy-based adaptation where the policy itself is dynamically adapted to continually maintain or improve its effectiveness despite changing environmental conditions; the need to enable non autonomics-expert practitioners to embed self-managing behaviours with low cost and risk; and the need for adaptive policy mechanisms that are easy to deploy into legacy code. A policy definition language is presented; designed to permit powerful expression of self-managing behaviours. The language is very flexible through the use of simple yet expressive syntax and semantics, and facilitates a very diverse policy behaviour space through both hierarchical and recursive uses of language elements. A prototype library implementation of the policy support mechanisms is described. The library reads and writes policies in well-formed XML script. The implementation extends the state of the art in policy-based autonomics through innovations which include support for multiple policy versions of a given policy type, multiple configuration templates, and meta-policies to dynamically select between policy instances and templates. Most significantly, the scheme supports hot-swapping between policy instances. To illustrate the feasibility and generalised applicability of these tools, two dissimilar example deployment scenarios are examined. The first is taken from an exploratory implementation of self-managing parallel processing, and is used to demonstrate the simple and efficient use of the tools. The second example demonstrates more-advanced functionality, in the context of an envisioned multi-policy stock trading scheme which is sensitive to environmental volatility

Collection and analysis of pre-evacuation time data collected from evacuation trials conducted in library facilities in Brazil

Two evacuation trials were conducted within Brazilian library facilities by FSEG staff in January 2005. These trials represent one of the first such trials conducted in Brazil. The purpose of these evacuation trials was to collect pre-evacuation time data from a population with a cultural background different to that found in western Europe. In total some 34 pre-evacuation times were collected from the experiments and these ranged from 5 to 98 seconds with a mean pre-evacuation time of 46.7 seconds

Spaces of observation and obscurity: cinematic prisons of light and dark

In The Eye of Power, Foucault delineated the key concerns surrounding hospital architecture in the latter half of the eighteenth century as being the ‘visibility of bodies, individuals and things'. As such, the ‘new form of hospital' that came to be developed ‘was at once the effect and support of a new type of gaze'. This was a gaze that was not simply concerned with ways of minimising overcrowding or cross-contamination. Rather, this was a surveillance intended to produce knowledge about the pathological bodies contained within the hospital walls. This would then allow for their appropriate classification. Foucault went on to describe how these principles came to be applied to the architecture of prisons. This was exemplified for him in the distinct shape of Bentham's panopticon. This circular design, which has subsequently become an often misused synonym for a contemporary culture of surveillance, was premised on a binary of the seen and the not-seen. An individual observer could stand at the central point of the circle and observe the cells (and their occupants) on the perimeter whilst themselves remaining unseen. The panopticon in its purest form was never constructed, yet it conveys the significance of the production of knowledge through observation that became central to institutional design at this time and modern thought more broadly. What is curious though is that whilst the aim of those late eighteenth century buildings was to produce wellventilated spaces suffused with light, this provoked an interest in its opposite. The gothic movement in literature that was developing in parallel conversely took a ‘fantasy world of stone walls, darkness, hideouts and dungeons…' as its landscape (Vidler, 1992: 162). Curiously, despite these modern developments in prison design, the façade took on these characteristics. The gothic imagination came to describe that unseen world that lay behind the outer wall. This is what Evans refers to as an architectural ‘hoax'. The façade was taken to represent the world within the prison walls and it was the façade that came to inform the popular imagination about what occurred behind it. The rational, modern principles ordering the prison became conflated with the meanings projected by and onto the façade. This confusion of meanings have then been repeated and reenforced in the subsequent representations of the prison. This is of paramount importance since it is the cinematic and televisual representation of the prison, as I argue here and elsewhere, that maintain this erroneous set of meanings, this ‘hoax'.

Safe spaces and sense of identity: views and experiences of lesbian, gay and bisexual young people

Empirical data on the life experiences of contemporary school-age lesbian, gay and bisexual (LGB) young people in Britain remains somewhat sparse. This paper reports the preliminary findings of a study conducted at a recently-initiated LGB youth Summer School. To further an appreciation of issues of concern to today's LGB teenagers, in-depth interviews were conducted with 10 Summer School participants (five female and five male, aged 15-18 years). The aim was to elicit their views and experiences relating to their need for support such as that offered by the Summer School. Themes drawn from participants' interviews are presented. Key issues included: being positioned as different by their majority heterosexual peers; feelings of isolation and loneliness in their peer groups and families; difficulties in finding others like themselves for companionship; and the importance of meeting more LGB people of their own age.

Data processing of remotely sensed airborne hyperspectral data using the Airborne Processing Library (APL): Geocorrection algorithm descriptions and spatial accuracy assessment

Remote sensing airborne hyperspectral data are routinely used for applications including algorithm development for satellite sensors, environmental monitoring and atmospheric studies. Single flight lines of airborne hyperspectral data are often in the region of tens of gigabytes in size. This means that a single aircraft can collect terabytes of remotely sensed hyperspectral data during a single year. Before these data can be used for scientific analyses, they need to be radiometrically calibrated, synchronised with the aircraft's position and attitude and then geocorrected. To enable efficient processing of these large datasets the UK Airborne Research and Survey Facility has recently developed a software suite, the Airborne Processing Library (APL), for processing airborne hyperspectral data acquired from the Specim AISA Eagle and Hawk instruments. The APL toolbox allows users to radiometrically calibrate, geocorrect, reproject and resample airborne data. Each stage of the toolbox outputs data in the common Band Interleaved Lines (BILs) format, which allows its integration with other standard remote sensing software packages. APL was developed to be user-friendly and suitable for use on a workstation PC as well as for the automated processing of the facility; to this end APL can be used under both Windows and Linux environments on a single desktop machine or through a Grid engine. A graphical user interface also exists. In this paper we describe the Airborne Processing Library software, its algorithms and approach. We present example results from using APL with an AISA Eagle sensor and we assess its spatial accuracy using data from multiple flight lines collected during a campaign in 2008 together with in situ surveyed ground control points.