Computing with CodeRunner at Coventry University:Automated summative assessment of Python and C++ code.

CodeRunner is a free open-source Moodle plugin for automatically marking student code. We describe our experience using CodeRunner for summative assessment in our first year undergraduate programming curriculum at Coventry University. We use it to assess both Python3 and C++14 code (CodeRunner supports other languages also). We give examples of our questions and report on how key metrics have changed following its use at Coventry.Comment: 4 pages. Accepted for presentation at CEP2

Reactome: A database of biological pathways

REACTOME is an open-source, open access, manually curated, peer-reviewed and highly reliable pathway database. A new website is currently in preparation, which includes tools for visualising pathway diagrams and analyzing user-supplied data in a pathway context. Reactome provides facilities for exporting its content in BioPax and SBML formats

Semi-automated co-reference identification in digital humanities collections

Locating specific information within museum collections represents a significant challenge for collection users. Even when the collections and catalogues exist in a searchable digital format, formatting differences and the imprecise nature of the information to be searched mean that information can be recorded in a large number of different ways. This variation exists not just between different collections, but also within individual ones. This means that traditional information retrieval techniques are badly suited to the challenges of locating particular information in digital humanities collections and searching, therefore, takes an excessive amount of time and resources. This thesis focuses on a particular search problem, that of co-reference identification. This is the process of identifying when the same real world item is recorded in multiple digital locations. In this thesis, a real world example of a co-reference identification problem for digital humanities collections is identified and explored. In particular the time consuming nature of identifying co-referent records. In order to address the identified problem, this thesis presents a novel method for co-reference identification between digitised records in humanities collections. Whilst the specific focus of this thesis is co-reference identification, elements of the method described also have applications for general information retrieval. The new co-reference method uses elements from a broad range of areas including; query expansion, co-reference identification, short text semantic similarity and fuzzy logic. The new method was tested against real world collections information, the results of which suggest that, in terms of the quality of the co-referent matches found, the new co-reference identification method is at least as effective as a manual search. The number of co-referent matches found however, is higher using the new method. The approach presented here is capable of searching collections stored using differing metadata schemas. More significantly, the approach is capable of identifying potential co-reference matches despite the highly heterogeneous and syntax independent nature of the Gallery, Library Archive and Museum (GLAM) search space and the photo-history domain in particular. The most significant benefit of the new method is, however, that it requires comparatively little manual intervention. A co-reference search using it has, therefore, significantly lower person hour requirements than a manually conducted search. In addition to the overall co-reference identification method, this thesis also presents: • A novel and computationally lightweight short text semantic similarity metric. This new metric has a significantly higher throughput than the current prominent techniques but a negligible drop in accuracy. • A novel method for comparing photographic processes in the presence of variable terminology and inaccurate field information. This is the first computational approach to do so.AHR

Intergalactic Helium Absorption in Cold Dark Matter Models

Observations from the HUT and the HST have recently detected HeII absorption along the lines of sight to two high redshift quasars. We use cosmological simulations with gas dynamics to investigate HeII absorption in the cold dark matter (CDM) theory of structure formation. We consider two Omega=1 CDM models with different normalizations and one Omega_0=0.4 CDM model, all incorporating the photoionizing UV background spectrum computed by Haardt & Madau (1996). The simulated gas distribution, combined with the H&M spectral shape, accounts for the relative observed values of taubar_HI and taubar_HeII, the effective mean optical depths for HI and HeII absorption. If the background intensity is as high as H&M predict, then matching the absolute values of taubar_HI and taubar_HeII requires a baryon abundance larger (by factors between 1.5 and 3 for the various CDM models) than our assumed value of Omega_b h^2=0.0125. The simulations reproduce the evolution of taubar_heII over the observed redshift range, 2.2 < z < 3.3, if the HeII photoionization rate remains roughly constant. HeII absorption in the CDM simulations is produced by a diffuse, fluctuating, intergalactic medium, which also gives rise to the HI ly-alpha forest. Much of the HeII opacity arises in underdense regions where the HI optical depth is very low. We compute statistical properties of the HeII and HI absorption that can be used to test the CDM models and distinguish them from an alternative scenario in which the HeII absorption is caused by discrete, compact clouds. The CDM scenario predicts that a substantial amount of baryonic material resides in underdense regions at high redshift. HeII absorption is the only sensitive probe of such extremely diffuse, intergalactic gas, so it can provide a vital test of this fundamental prediction.Comment: Accepted for publication in ApJ, 36 pages, LaTeX (aaspp4), 12 figures. Changes include addition of more information on statistical uncertainties and on the adopted UV background. Also available at http://www-astronomy.mps.ohio-state.edu/~racc

Characterization of Lyman Alpha Spectra and Predictions of Structure Formation Models: A Flux Statistics Approach

In gravitational instability models, \lya absorption arises from a continuous fluctuating medium, so that spectra provide a non-linear one-dimensional ``map'' of the underlying density field. We characterise this continuous absorption using statistical measures applied to the distribution of absorbed flux. We describe two simple members of a family of statistics which we apply to simulated spectra in order to show their sensitivity as probes of cosmological parameters (H$_{0}$, $\Omega$, the initial power spectrum of matter fluctuations) and the physical state of the IGM. We make use of SPH simulation results to test the flux statistics, as well as presenting a preliminary application to Keck HIRES data.Comment: Contribution to proceedings of the 18th Texas Symposium on Relativistic Astrophysics (eds A. Olinto, J. Frieman and D. Schramm, World Scientific),Chicago, December 1996, 3 pages, LaTeX (sprocl), 2 figures. Also available at http://www-astronomy.mps.ohio-state.edu/~racc

Term Clustering of Syntactic Phrases

Term clustering and syntactic phrase formation are methods for transforming natural language text. Both have had only mixed success as strategies for improving the quality of text representations for document retrieval. Since the strengths of these methods are complementary, we have explored combining them to produce superior representations. In this paper we discuss our implementation of a syntactic phrase generator, as well as our preliminary experiments with producing phrase clusters. These experiments show small improvements in retrieval effectiveness resulting from the use of phrase clusters, but it is clear that corpora much larger than standard information retrieval test collections will be required to thoroughly evaluate the use of this technique

Cross-correlations of the Lyman-alpha forest with weak lensing convergence I: Analytical Estimates of S/N and Implications for Neutrino Mass and Dark Energy

We expect a detectable correlation between two seemingly unrelated quantities: the four point function of the cosmic microwave background (CMB) and the amplitude of flux decrements in quasar (QSO) spectra. The amplitude of CMB convergence in a given direction measures the projected surface density of matter. Measurements of QSO flux decrements trace the small-scale distribution of gas along a given line-of-sight. While the cross-correlation between these two measurements is small for a single line-of-sight, upcoming large surveys should enable its detection. This paper presents analytical estimates for the signal to noise (S/N) for measurements of the cross-correlation between the flux decrement and the convergence and for measurements of the cross-correlation between the variance in flux decrement and the convergence. For the ongoing BOSS (SDSS III) and Planck surveys, we estimate an S/N of 30 and 9.6 for these two correlations. For the proposed BigBOSS and ACTPOL surveys, we estimate an S/N of 130 and 50 respectively. Since the cross-correlation between the variance in flux decrement and the convergence is proportional to the fourth power of $\sigma_8$, the amplitude of these cross-correlations can potentially be used to measure the amplitude of $\sigma_8$ at z~2 to 2.5% with BOSS and Planck and even better with future data sets. These measurements have the potential to test alternative theories for dark energy and to constrain the mass of the neutrino. The large potential signal estimated in our analytical calculations motivate tests with non-linear hydrodynamical simulations and analyses of upcoming data sets.Comment: 24 pages, 9 figure