Verifying the fully “Laplacianised” posterior Naïve Bayesian approach and more

Mussa and Glen would like to thank Unilever for financial support, whereas Mussa and Mitchell thank the BBSRC for funding this research through grant BB/I00596X/1. Mitchell thanks the Scottish Universities Life Sciences Alliance (SULSA) for financial support.Background In a recent paper, Mussa, Mitchell and Glen (MMG) have mathematically demonstrated that the “Laplacian Corrected Modified Naïve Bayes” (LCMNB) algorithm can be viewed as a variant of the so-called Standard Naïve Bayes (SNB) scheme, whereby the role played by absence of compound features in classifying/assigning the compound to its appropriate class is ignored. MMG have also proffered guidelines regarding the conditions under which this omission may hold. Utilising three data sets, the present paper examines the validity of these guidelines in practice. The paper also extends MMG’s work and introduces a new version of the SNB classifier: “Tapered Naïve Bayes” (TNB). TNB does not discard the role of absence of a feature out of hand, nor does it fully consider its role. Hence, TNB encapsulates both SNB and LCMNB. Results LCMNB, SNB and TNB performed differently on classifying 4,658, 5,031 and 1,149 ligands (all chosen from the ChEMBL Database) distributed over 31 enzymes, 23 membrane receptors, and one ion-channel, four transporters and one transcription factor as their target proteins. When the number of features utilised was equal to or smaller than the “optimal” number of features for a given data set, SNB classifiers systematically gave better classification results than those yielded by LCMNB classifiers. The opposite was true when the number of features employed was markedly larger than the “optimal” number of features for this data set. Nonetheless, these LCMNB performances were worse than the classification performance achieved by SNB when the “optimal” number of features for the data set was utilised. TNB classifiers systematically outperformed both SNB and LCMNB classifiers. Conclusions The classification results obtained in this study concur with the mathematical based guidelines given in MMG’s paper—that is, ignoring the role of absence of a feature out of hand does not necessarily improve classification performance of the SNB approach; if anything, it could make the performance of the SNB method worse. The results obtained also lend support to the rationale, on which the TNB algorithm rests: handled judiciously, taking into account absence of features can enhance (not impair) the discriminatory classification power of the SNB approach.Publisher PDFPeer reviewe

Characterization of Alkali Metal Dispensers and Non-Evaporable Getter Pumps in Ultra-High Vacuum Systems for Cold Atomic Sensors

A glass ultrahigh vacuum chamber with rubidium alkali metal dispensers and non-evaporable getter pumps has been developed and used to create a cold atomic sample in a chamber that operates with only passive vacuum pumps. The ion-mass spectrum of evaporated gases from the alkali metal dispenser has been recorded as a function of dispenser current. The efficacy of the non-evaporable getter pumps in promoting and maintaining vacuum has been characterized by observation of the Rb vapor optical absorption on the D2 transition at 780 nm and vacuum chamber pressure rate of rise tests. We have demonstrated a sample of laser-cooled Rb atoms in this chamber when isolated and operating without active vacuum pumps

Polarisation structuring of broadband light

Spatial structuring of the intensity, phase and polarisation of light is useful in a wide variety of modern applications, from microscopy to optical communications. This shaping is most commonly achieved using liquid crystal spatial light modulators (LC-SLMs). However, the inherent chromatic dispersion of LC-SLMs when used as diffractive elements presents a challenge to the extension of such techniques from monochromatic to broadband light. In this work we demonstrate a method of generating broadband vector beams with dynamically tunable intensity, phase and polarisation over a bandwidth of 100 nm. We use our system to generate radially and azimuthally polarised vector vortex beams carrying orbital angular momentum, and beams whose polarisation states span the majority of the Poincaré sphere. We characterise these broadband vector beams using spatially and spectrally resolved Stokes measurements, and detail the technical and fundamental limitations of our technique, including beam generation fidelity and efficiency. The broadband vector beam shaper that we demonstrate here may find use in applications such as ultrafast beam shaping and white light microscopy

Polarisation structuring of broadband light

Spatial structuring of the intensity, phase and polarisation of light is useful in a wide variety of modern applications, from microscopy to optical communications. This shaping is most commonly achieved using liquid crystal spatial light modulators (LC-SLMs). However, the inherent chromatic dispersion of LC-SLMs when used as diffractive elements presents a challenge to the extension of such techniques from monochromatic to broadband light. In this work we demonstrate a method of generating broadband vector beams with dynamically tunable intensity, phase and polarisation over a bandwidth of 100 nm. We use our system to generate radially and azimuthally polarised vector vortex beams carrying orbital angular momentum, and beams whose polarisation states span the majority of the Poincaré sphere. We characterise these broadband vector beams using spatially and spectrally resolved Stokes measurements, and detail the technical and fundamental limitations of our technique, including beam generation fidelity and efficiency. The broadband vector beam shaper that we demonstrate here may find use in applications such as ultrafast beam shaping and white light microscopy

A Classroom Experiment on Exchange Rate Determination with Purchasing Power Parity

We develop a classroom experiment on exchange rate determination appropriate for undergraduate courses in macroeconomics and international economics. Students represent citizens from different countries and need to obtain currency to purchase goods. By participating in a sealed bid auction to buy currency, students gain a better understanding of currency markets and the determination of exchange rates. The implicit framework for exchange rate determination is one in which prices are perfectly flexible (in the long run) so that purchasing power parity (PPP) prevails. Additional treatments allow students to examine the impact of transport costs, nontradable goods and tariffs on the exchange rate and to explore possible deviations from PPP.

The effectiveness of incarceration-based drug treatment on criminal behavior.

Background - Many, if not most, incarcerated offenders have substance abuse problems. Without effective treatment, these substance-abusing offenders are likely to persist in non-drug offending. The period of incarceration offers an opportunity to intervene in the cycle of drug abuse and crime. Although many types of incarceration-based drug treatment programs are available (e.g., therapeutic communities and group counseling), the effectiveness of these programs is unclear. Objectives - The objective of this research synthesis is to systematically review quasi-experimental and experimental (RCT) evaluations of the effectiveness of incarceration-based drug treatment programs in reducing post-release recidivism and drug relapse. A secondary objective of this synthesis is to examine variation in effectiveness by programmatic, sample, and methodological features. In this update of the original 2006 review (see Mitchell, Wilson, and MacKenzie, 2006), studies made available since the original review were included in an effort to keep current with emerging research. Main results - Seventy-four evaluations met our eligibility criteria. The overall average effect of these programs was approximately a 15 to 17% reduction in recidivism and drug relapse. The effectiveness of such programs, however, varied by program type. Therapeutic communities had relatively consistent but modest reductions in recidivism and drug relapse. Counseling and narcotic maintenance programs had mixed effects. Specifically, counseling programs on average reduced recidivism but not drug relapse, narcotic maintenance programs had sizeable reductions in drug relapse but not recidivism, and boot camps had negligible effects on both recidivism and drug relapse. Conclusions - This synthesis of evaluations of incarceration-based drug treatment programs found that such programs are modestly effective in reducing recidivism. These findings most strongly support the effectiveness of therapeutic communities, as these programs produced relatively consistent reductions in recidivism and drug use. Both counseling and incarceration-based narcotic maintenance programs had mixed effects. Counseling programs were associated with reductions in recidivism but not drug use; whereas, incarceration-based narcotic maintenance programs were associated with reductions in drug use but not recidivism. Note that our findings regarding the effectiveness of incarceration-based narcotic maintenance programs differ from a larger review of community-based narcotic maintenance programs (see Egli, Pina, Christensen, Aebi, and Killias, 2009). Finally, boot camp programs for drug offenders had negligible effects on both recidivism and drug use