Achieving robustness to aleatoric uncertainty with heteroscedastic Bayesian optimisation

Bayesian optimisation is a sample-efficient search methodology that holds great promise for accelerating drug and materials discovery programs. A frequently-overlooked modelling consideration in Bayesian optimisation strategies however, is the representation of heteroscedastic aleatoric uncertainty. In many practical applications it is desirable to identify inputs with low aleatoric noise, an example of which might be a material composition which consistently displays robust properties in response to a noisy fabrication process. In this paper, we propose a heteroscedastic Bayesian optimisation scheme capable of representing and minimising aleatoric noise across the input space. Our scheme employs a heteroscedastic Gaussian process (GP) surrogate model in conjunction with two straightforward adaptations of existing acquisition functions. First, we extend the augmented expected improvement (AEI) heuristic to the heteroscedastic setting and second, we introduce the aleatoric noise-penalised expected improvement (ANPEI) heuristic. Both methodologies are capable of penalising aleatoric noise in the suggestions and yield improved performance relative to homoscedastic Bayesian optimisation and random sampling on toy problems as well as on two real-world scientific datasets. Code is available at: \url{https://github.com/Ryan-Rhys/Heteroscedastic-BO

Dirac field in topologically massive gravity

We consider a Dirac field coupled minimally to the Mielke-Baekler model of gravity and investigate cosmological solutions in three dimensions. We arrive at a family of solutions which exists even in the limit of vanishing cosmological constant.Comment: 12 pages. Title changed. Conclusion extended. Appendix added. To appear in Gen. Rel. Gra

Two experiments for the price of one? -- The role of the second oscillation maximum in long baseline neutrino experiments

We investigate the quantitative impact that data from the second oscillation maximum has on the performance of wide band beam neutrino oscillation experiments. We present results for the physics sensitivities to standard three flavor oscillation, as well as results for the sensitivity to non-standard interactions. The quantitative study is performed using an experimental setup similar to the Fermilab to DUSEL Long Baseline Neutrino Experiment (LBNE). We find that, with the single exception of sensitivity to the mass hierarchy, the second maximum plays only a marginal role due to the experimental difficulties to obtain a statistically significant and sufficiently background-free event sample at low energies. This conclusion is valid for both water Cherenkov and liquid argon detectors. Moreover, we confirm that non-standard neutrino interactions are very hard to distinguish experimentally from standard three-flavor effects and can lead to a considerable loss of sensitivity to \theta_{13}, the mass hierarchy and CP violation.Comment: RevTex 4.1, 23 pages, 10 figures; v2: Typos corrected, very minor clarifications; matches published version; v3: Fixed a typo in the first equation in sec. III

MiniBooNE and LSND data: non-standard neutrino interactions in a (3+1) scheme versus (3+2) oscillations

The recently observed event excess in MiniBooNE anti-neutrino data is in agreement with the LSND evidence for electron anti-neutrino appearance. We propose an explanation of these data in terms of a (3+1) scheme with a sterile neutrino including non-standard neutrino interactions (NSI) at neutrino production and detection. The interference between oscillations and NSI provides a source for CP violation which we use to reconcile different results from neutrino and anti-neutrino data. Our best fit results imply NSI at the level of a few percent relative to the standard weak interaction, in agreement with current bounds. We compare the quality of the NSI fit to the one obtained within the (3+1) and (3+2) pure oscillation frameworks. We also briefly comment on using NSI (in an effective two-flavour framework) to address a possible difference in neutrino and anti-neutrino results from the MINOS experiment.Comment: 28 pages, 9 figures, discussion improved, new appendix added, conclusions unchange

An inhibitory pull-push circuit in frontal cortex.

Push-pull is a canonical computation of excitatory cortical circuits. By contrast, we identify a pull-push inhibitory circuit in frontal cortex that originates in vasoactive intestinal polypeptide (VIP)-expressing interneurons. During arousal, VIP cells rapidly and directly inhibit pyramidal neurons; VIP cells also indirectly excite these pyramidal neurons via parallel disinhibition. Thus, arousal exerts a feedback pull-push influence on excitatory neurons-an inversion of the canonical push-pull of feedforward input

Effect of Stocking Density and Sex on Feathering, Body Injury and Breast Meat Quality of Broiler Chikens

The experiment was conducted at the College of Veterinary Medicine and Animal Production of UNESP-Botucatu Campus to evaluate the effect of stocking densities and sex on body injuries and breast meat quality. One thousand nine hundred and fifty day-old Ross chicks were reared until 42 days of age on a randomized factorial arrangement with three stock densities (10, 13 and 16 birds/m²) and two sexes. At 28, 35 and 42 days of age, 15 birds/treatment were sampled to determine feathering percentage related to body weight and 50 birds/treatment to evaluate score feathering. At 42 days of age, all broilers were processed to evaluate body injuries and breast meat quality. Increasing stocking densities decreased feathering and increased body injuries like breast blisters, dermatitis, bruises and scratches. Breast meat yield and breast length width and depth was negatively affected (p<.05) as stocking densities increased.O experimento foi conduzido nas instalações experimentais da Faculdade de Medicina Veterinária e Zootecnia - UNESP, Campus de Botucatu, SP, Brasil, com o objetivo de avaliar o efeito da densidade de criação e do sexo sobre o empenamento, incidência de lesões na carcaça e a qualidade de carne de peito de frangos de corte. Foram utilizados 1950 pintos de corte sexados, da linhagem Ross, distribuídos em um delineamento inteiramente casualizado, com esquema fatorial com 3 densidades (10, 13 e 16 aves/m²) e dois sexos com 5 repetições, sendo que uma foi destinada exclusivamente para reserva, criados até os 42 dias de idade. Aos 28, 35 e 42 dias foram amostradas 3 aves por repetição para a determinação do empenamento através da porcentagem de penas e 10 aves para a determinação do escore de empenamento. Também aos 42 dias de idade todas as aves foram identificadas na pata com anilhas numeradas e submetidas à avaliação da incidência de lesões na pele. Foram escolhidas ao acaso 5 aves por repetição para a determinação da qualidade da carne de peito. Pode-se concluir que o aumento na densidade de criação promoveu uma diminuição na velocidade de empenamento e, conseqüentemente, uma maior incidência de lesões na carcaça. O comprimento, a largura e a espessura do peito foram menores para as aves criadas na maior densidade, e a perda de peso por cozimento foi maior para as aves criadas na maior densidade.000

Helical Chirality: a Link between Local Interactions and Global Topology in DNA

DNA supercoiling plays a major role in many cellular functions. The global DNA conformation is however intimately linked to local DNA-DNA interactions influencing both the physical properties and the biological functions of the supercoiled molecule. Juxtaposition of DNA double helices in ubiquitous crossover arrangements participates in multiple functions such as recombination, gene regulation and DNA packaging. However, little is currently known about how the structure and stability of direct DNA-DNA interactions influence the topological state of DNA. Here, a crystallographic analysis shows that due to the intrinsic helical chirality of DNA, crossovers of opposite handedness exhibit markedly different geometries. While right-handed crossovers are self-fitted by sequence-specific groove-backbone interaction and bridging Mg2+ sites, left-handed crossovers are juxtaposed by groove-groove interaction. Our previous calculations have shown that the different geometries result in differential stabilisation in solution, in the presence of divalent cations. The present study reveals that the various topological states of the cell are associated with different inter-segmental interactions. While the unstable left-handed crossovers are exclusively formed in negatively supercoiled DNA, stable right-handed crossovers constitute the local signature of an unusual topological state in the cell, such as the positively supercoiled or relaxed DNA. These findings not only provide a simple mechanism for locally sensing the DNA topology but also lead to the prediction that, due to their different tertiary intra-molecular interactions, supercoiled molecules of opposite signs must display markedly different physical properties. Sticky inter-segmental interactions in positively supercoiled or relaxed DNA are expected to greatly slow down the slithering dynamics of DNA. We therefore suggest that the intrinsic helical chirality of DNA may have oriented the early evolutionary choices for DNA topology

Impact of inhaled corticosteroids on growth in children with asthma: systematic review and meta-analysis

Background: Long-term inhaled corticosteroids (ICS) may reduce growth velocity and final height of children with asthma. We aimed to evaluate the association between ICS use of >12 months and growth. Methods: We initially searched MEDLINE and EMBASE in July 2013, followed by a PubMed search updated to December 2014. We selected RCTs and controlled observational studies of ICS use in patients with asthma. We conducted random effects meta-analysis of mean differences in growth velocity (cm/year) or final height (cm) between groups. Heterogeneity was assessed using the I2 statistic. Results: We found 23 relevant studies (twenty RCTs and three observational studies) after screening 1882 hits. Meta-analysis of 16 RCTs showed that ICS use significantly reduced growth velocity at one year follow-up (mean difference -0.48 cm/year (95% CI -0.66 to -0.29)). There was evidence of a dose-response effect in three RCTs. Final adult height showed a mean reduction of -1.20 cm (95% CI -1.90 cm to -0.50 cm) with budesonide versus placebo in a high quality RCT. Meta-analysis of two lower quality observational studies revealed uncertainty in the association between ICS use and final adult height, pooled mean difference -0.85 cm (95% CI -3.35 to 1.65). Conclusion: Use of ICS for >12 months in children with asthma has a limited impact on annual growth velocity. In ICS users, there is a slight reduction of about a centimeter in final adult height, which when interpreted in the context of average adult height in England (175 cm for men and 161 cm for women), represents a 0.7% reduction compared to non-ICS users

Examining Potential of Scents for Enhancement of User Performance with Mobile Apps

Intelligent mobile phones, or simply smartphones, have seen a large widespread usage among the entire world population during the last years. These devices are, in fact, considered as an essential tool in our current day to day life activities. Aromatherapy could be defined as the medical usage of essential oils derived from diverse types of vegetables. Although this paper does not look through direct medical usages or benefits, it is focused on one of its main effects, the stimuli to enhance focus. This study makes use of one of the main essential oils, rosemary, as olfactory stimuli over regular users performing a set of tasks with mobile apps. Results of the experimental group, when compared to regular users not affected with olfactory stimuli, aim to suggest that there is not a clear impact on mobile users' performance. Nonetheless, more research is needed to categorize the effects of aromatherapy on mobile users.FPU research staff education program of the “University of Alcala” (UAH), grant no. 30400M000.541.A 640.0