Avoiding spurious feedback loops in the reconstruction of gene regulatory networks with dynamic bayesian networks

Feedback loops and recurrent structures are essential to the regulation and stable control of complex biological systems. The application of dynamic as opposed to static Bayesian networks is promising in that, in principle, these feedback loops can be learned. However, we show that the widely applied BGe score is susceptible to learning spurious feedback loops, which are a consequence of non-linear regulation and autocorrelation in the data. We propose a non-linear generalisation of the BGe model, based on a mixture model, and demonstrate that this approach successfully represses spurious feedback loops

PDF and scale uncertainties of various DY distributions in ADD and RS models at hadron colliders

In the extra dimension models of ADD and RS we study the dependence of the various parton distribution functions on observable of Drell-Yan process to NLO in QCD at LHC and Tevatron energies. Uncertainties at LHC due to factorisation scales in going from leading to next-to-leading order in QCD for the various distributions get reduced by about 2.75 times for a $\mu_F$ range $0.5 ~Q < \mu_F < 1.5 ~Q$. Further uncertainties arising from the error on experimental data are estimated using the MRST parton distribution functions.Comment: 27 pages, 11 figures, the version to appear in European Physical Journal

80-річчя члена-кореспондента НАН України А.Ф. Фролова

26 листопада виповнилося 80 років відомому вченому-медику членові-кореспондентові НАН України і НАМН України Аркадію Федоровичу Фролову

Free expansion of lowest Landau level states of trapped atoms: a wavefunction microscope

We show that for any lowest-Landau-level state of a trapped, rotating, interacting Bose gas, the particle distribution in coordinate space in a free expansion (time of flight) experiment is related to that in the trap at the time it is turned off by a simple rescaling and rotation. When the lowest-Landau-level approximation is valid, interactions can be neglected during the expansion, even when they play an essential role in the ground state when the trap is present. The correlations in the density in a single snapshot can be used to obtain information about the fluid, such as whether a transition to a quantum Hall state has occurred.Comment: 5 pages, no figures. v2: discussion of neglect of interactions during expansion improved, refs adde

Schwinger-Dyson approach to non-equilibrium classical field theory

In this paper we discuss a Schwinger-Dyson [SD] approach for determining the time evolution of the unequal time correlation functions of a non-equilibrium classical field theory, where the classical system is described by an initial density matrix at time $t=0$. We focus on $\lambda \phi^4$ field theory in 1+1 space time dimensions where we can perform exact numerical simulations by sampling an ensemble of initial conditions specified by the initial density matrix. We discuss two approaches. The first, the bare vertex approximation [BVA], is based on ignoring vertex corrections to the SD equations in the auxiliary field formalism relevant for 1/N expansions. The second approximation is a related approximation made to the SD equations of the original formulation in terms of $\phi$ alone. We compare these SD approximations as well as a Hartree approximation with exact numerical simulations. We find that both approximations based on the SD equations yield good agreement with exact numerical simulations and cure the late time oscillation problem of the Hartree approximation. We also discuss the relationship between the quantum and classical SD equations.Comment: 36 pages, 5 figure

Impact of Bayesian network model structure on the accuracy of medical diagnostic systems

While Bayesian network models may contain a handful of numerical parameters that are important for their quality, several empirical studies have confirmed that overall precision of their probabilities is not crucial. In this paper, we study the impact of the structure of a Bayesian network on the precision of medical diagnostic systems. We show that also the structure is not that important - diagnostic accuracy of several medical diagnostic models changes minimally when we subject their structures to such transformations as arc removal and arc reversal. © 2014 Springer International Publishing

Quantum Hall ferromagnets, cooperative transport anisotropy, and the random field Ising model

We discuss the behaviour of a quantum Hall system when two Landau levels with opposite spin and combined filling factor near unity are brought into energetic coincidence using an in-plane component of magnetic field. We focus on the interpretation of recent experiments under these conditions [Zeitler et al, Phys. Rev. Lett. 86, 866 (2001); Pan et al, Phys. Rev. B 64, 121305 (2001)], in which a large resistance anisotropy develops at low temperatures. Modelling the systems involved as Ising quantum Hall ferromagnets, we suggest that this transport anisotropy reflects domain formation induced by a random field arising from isotropic sample surface roughness.Comment: 4 pages, submitted to Physical Review

Effects of sildenafil on symptoms and exercise capacity for heart failure with reduced ejection fraction and pulmonary hypertension (the SilHF study): a randomized placebo-controlled multicentre trial

Aims: Pulmonary hypertension (PHT) may complicate heart failure with reduced ejection fraction (HFrEF) and is associated with a substantial symptom burden and poor prognosis. Sildenafil, a phosphodiesterase-5 (PDE-5) inhibitor, might have beneficial effects on pulmonary haemodynamics, cardiac function and exercise capacity in HFrEF and PHT. The aim of this study was to determine the safety, tolerability, and efficacy of sildenafil in patients with HFrEF and indirect evidence of PHT. Methods and results: The Sildenafil in Heart Failure (SilHF) trial was an investigator-led, randomized, multinational trial in which patients with HFrEF and a pulmonary artery systolic pressure (PASP) ≥40 mmHg by echocardiography were randomly assigned in a 2:1 ratio to receive sildenafil (up to 40 mg three times/day) or placebo. The co-primary endpoints were improvement in patient global assessment by visual analogue scale and in the 6-min walk test at 24 weeks. The planned sample size was 210 participants but, due to problems with supplying sildenafil/placebo and recruitment, only 69 patients (11 women, median age 68 (interquartile range [IQR] 62–74) years, median left ventricular ejection fraction 29% (IQR 24–35), median PASP 45 (IQR 42–55) mmHg) were included. Compared to placebo, sildenafil did not improve symptoms, quality of life, PASP or walk test distance. Sildenafil was generally well tolerated, but those assigned to sildenafil had numerically more serious adverse events (33% vs. 21%). Conclusion: Compared to placebo, sildenafil did not improve symptoms, quality of life or exercise capacity in patients with HFrEF and PHT.publishedVersio