Reweighting for Nonequilibrium Markov Processes Using Sequential Importance Sampling Methods

We present a generic reweighting method for nonequilibrium Markov processes. With nonequilibrium Monte Carlo simulations at a single temperature, one calculates the time evolution of physical quantities at different temperatures, which greatly saves the computational time. Using the dynamical finite-size scaling analysis for the nonequilibrium relaxation, one can study the dynamical properties of phase transitions together with the equilibrium ones. We demonstrate the procedure for the Ising model with the Metropolis algorithm, but the present formalism is general and can be applied to a variety of systems as well as with different Monte Carlo update schemes.Comment: accepted for publication in Phys. Rev. E (Rapid Communications

Presurgical thalamic hubness predicts surgical outcome in temporal lobe epilepsy.

OBJECTIVE: To characterize the presurgical brain functional architecture presented in patients with temporal lobe epilepsy (TLE) using graph theoretical measures of resting-state fMRI data and to test its association with surgical outcome. METHODS: Fifty-six unilateral patients with TLE, who subsequently underwent anterior temporal lobectomy and were classified as obtaining a seizure-free (Engel class I, n = 35) vs not seizure-free (Engel classes II-IV, n = 21) outcome at 1 year after surgery, and 28 matched healthy controls were enrolled. On the basis of their presurgical resting-state functional connectivity, network properties, including nodal hubness (importance of a node to the network; degree, betweenness, and eigenvector centralities) and integration (global efficiency), were estimated and compared across our experimental groups. Cross-validations with support vector machine (SVM) were used to examine whether selective nodal hubness exceeded standard clinical characteristics in outcome prediction. RESULTS: Compared to the seizure-free patients and healthy controls, the not seizure-free patients displayed a specific increase in nodal hubness (degree and eigenvector centralities) involving both the ipsilateral and contralateral thalami, contributed by an increase in the number of connections to regions distributed mostly in the contralateral hemisphere. Simulating removal of thalamus reduced network integration more dramatically in not seizure-free patients. Lastly, SVM models built on these thalamic hubness measures produced 76% prediction accuracy, while models built with standard clinical variables yielded only 58% accuracy (both were cross-validated). CONCLUSIONS: A thalamic network associated with seizure recurrence may already be established presurgically. Thalamic hubness can serve as a potential biomarker of surgical outcome, outperforming the clinical characteristics commonly used in epilepsy surgery centers

Recent developments of MCViNE and its applications at SNS

MCViNE is an open source, object-oriented Monte Carlo neutron ray-tracing simulation software package. Its design allows for flexible, hierarchical representations of sophisticated instrument components such as detector systems, and samples with a variety of shapes and scattering kernels. Recently this flexible design has enabled several applications of MCViNE simulations at the Spallation Neutron Source (SNS) at Oak Ridge National Lab, including assisting design of neutron instruments at the second target station and design of novel sample environments, as well as studying effects of instrument resolution and multiple scattering. Here we provide an overview of the recent developments and new features of MCViNE since its initial introduction (Jiao et al 2016 Nucl. Instrum. Methods Phys. Res., Sect. A 810, 86–99), and some example applications

Convergence of the SMC implementation of the PHD filter

The probability hypothesis density (PHD) filter is a first moment approximation to the evolution of a dynamic point process which can be used to approximate the optimal filtering equations of the multiple-object tracking problem. We show that, under reasonable assumptions, a sequential Monte Carlo (SMC) approximation of the PHD filter converges in mean of order p ≥ 1, and hence almost surely, to the true PHD filter. We also present a central limit theorem for the SMC approximation, show that the variance is finite under similar assumptions and establish a recursion for the asymptotic variance. This provides a theoretical justification for this implementation of a tractable multiple-object filtering methodology and generalises some results from sequential Monte Carlo theory

A population Monte Carlo scheme with transformed weights and its application to stochastic kinetic models

This paper addresses the problem of Monte Carlo approximation of posterior probability distributions. In particular, we have considered a recently proposed technique known as population Monte Carlo (PMC), which is based on an iterative importance sampling approach. An important drawback of this methodology is the degeneracy of the importance weights when the dimension of either the observations or the variables of interest is high. To alleviate this difficulty, we propose a novel method that performs a nonlinear transformation on the importance weights. This operation reduces the weight variation, hence it avoids their degeneracy and increases the efficiency of the importance sampling scheme, specially when drawing from a proposal functions which are poorly adapted to the true posterior. For the sake of illustration, we have applied the proposed algorithm to the estimation of the parameters of a Gaussian mixture model. This is a very simple problem that enables us to clearly show and discuss the main features of the proposed technique. As a practical application, we have also considered the popular (and challenging) problem of estimating the rate parameters of stochastic kinetic models (SKM). SKMs are highly multivariate systems that model molecular interactions in biological and chemical problems. We introduce a particularization of the proposed algorithm to SKMs and present numerical results.Comment: 35 pages, 8 figure

Taxonomic studies on the genus Aorolaimus Sher, 1963 (Nemata : Hoplolaimidae) : 1. Bibliographic analysis and tentative key to species

L'analyse bibliographique des descriptions d'espèces ou de populations dans le genre #Aorolaimus permet d'évaluer la variabilité intraspécifique des 39 caractères utilisés pour les diagnoses spécifiques ou les relations entre taxons dans ce genre. Trois caractères (aréolations au niveau de la phasmide dans les champs latéraux, position de la phasmide antérieure, existence de mâles) sont bien définis et présentent une variabilité intraspécifique faible et intragénérique suffisante pour proposer six groupes d'espèces à l'intérieur desquels les autres caractères morpho-biométriques ne permettent pas une séparation claire de toutes les espèces. Plusieurs espèces du genre #Aorolaimus apparaissent donc douteuses et leur réexamen de microscopie optique est nécessaire. #Peltamigratus regularis Siddiqi, 1985 est transféré au genre #Aorolaimus comme #Aorolaimus regularis (Siddiqi, 1985) n. comb. #A. brevicaudatus, A. conicori et #A. triticeus sont considérés comme synonymes mineurs de #A. longistylus et #A. thornei comme synonyme mineur de #A. pachyurus. (Résumé d'auteur

Adaptive Importance Sampling in General Mixture Classes

In this paper, we propose an adaptive algorithm that iteratively updates both the weights and component parameters of a mixture importance sampling density so as to optimise the importance sampling performances, as measured by an entropy criterion. The method is shown to be applicable to a wide class of importance sampling densities, which includes in particular mixtures of multivariate Student t distributions. The performances of the proposed scheme are studied on both artificial and real examples, highlighting in particular the benefit of a novel Rao-Blackwellisation device which can be easily incorporated in the updating scheme.Comment: Removed misleading comment in Section

The role of large trees in the biomass production of heterogeneous forest

In heterogeneous forests, large trees retain a substantial amount of above ground biomass, but their annual contribution to biomass accumulation remains unclear. A modal relationship between tree growth and tree size is traditionally expected. But recently, it has been demonstrated that the rate of tree biomass accumulation continuously increases with tree size supporting the metabolic theory of ecology. To clarify the role of large trees in biomass production of heterogeneous forest, we used data of tree growth, mortality and recruitment monitored during 20 years in 10×4-ha plots in a species rich and structurally complex tropical forest (Central African Republic). Biomass gains and losses were analyzed in relation to the abundance of large trees and by tree size classes using a bootstrap procedure. At the plot level, the accumulation of biomass in large trees was generally lower than that accumulated in small trees. The high mass growth rate of few large trees was therefore outbalanced by the growth of the numerous small trees. Moreover, the loss of biomass due to the mortality of few large trees could be substantial, and rarely outbalanced by the accumulation of biomass in these large trees. The annual net accumulation of biomass significantly decreases with the initial abundance of large trees. (Résumé d'auteur

High Water Contents in the Siberian Cratonic Mantle: An FTIR Study of Udachnaya Peridotite Xenoliths

Water is believed to be a key factor controlling the long-term stability of cratonic lithosphere, but mechanisms responsible for the water content distribution in the mantle remain poorly constrained. Water contents were obtained by FTIR in olivine, pyroxene and garnet for 20 well-characterized peridotite xenoliths from the Udachnaya kimberlite (central Siberian craton) and equilibrated at 2-7 GPa. Water contents in minerals do not appear to be related to interaction with the host kimberlite. Diffusion modeling indicates that the core of olivines preserved their original water contents. The Udachnaya peridotites show a broad range of water contents in olivine (6.5 +/- 1.1 to 323 +- 65 ppm H2O (2 sigma)), and garnet (0 - 23 +/- 6 ppm H2O). The water contents of olivine and garnet are positively correlated with modal clinopyroxene, garnet and FeO in olivine. Water-rich garnets are also rich in middle rare earth elements. This is interpreted as the result of interaction between residual peridotites and water rich-melts, consistent with modal and cryptic metasomatism evidenced in the Siberian cratonic mantle. The most water-rich Udachnaya minerals contain 2 to 3 times more water than those from the Kaapvaal craton, the only craton with an intact mantle root for which water data is available. The highest water contents in olivine and orthopyroxene in this study (>= 300 ppm) are found at the bottom of the lithosphere (> 6.5 GPa). This is in contrast with the Kaapvaal craton where the olivines of peridotites equilibrated at > 6.4 GPa have 6 GPa is lower or similar (8.4 10(exp 16) to 8.0 10(exp 18) Pa./s) to that of the asthenosphere (<= 3.7x10(exp 18) Pa./s ). Such lithologies would not be able to resist delamination by the convecting asthenosphere. However, seismology studies as well as the high equilibration pressures of our samples indicate that the Udachnaya cratonic lithosphere is 220-250 km thick. Consequently, the water-rich peridotites are likely not representative of the overall Siberian cratonic lithosphere. Their composition is linked to spatially limited melt metasomatism in mantle regions above asthenospheric upwellings responsible for the kimberlite magmatism prior to their ascent and eruption

A Halomethane thermochemical network from iPEPICO experiments and quantum chemical calculations

Internal energy selected halomethane cations CH3Cl+, CH2Cl2+, CHCl3+, CH3F+, CH2F2+, CHClF2+ and CBrClF2+ were prepared by vacuum ultraviolet photoionization, and their lowest energy dissociation channel studied using imaging photoelectron photoion coincidence spectroscopy (iPEPICO). This channel involves hydrogen atom loss for CH3F+, CH2F2+ and CH3Cl+, chlorine atom loss for CH2Cl2+, CHCl3+ and CHClF2+, and bromine atom loss for CBrClF2+. Accurate 0 K appearance energies, in conjunction with ab initio isodesmic and halogen exchange reaction energies, establish a thermochemical network, which is optimized to update and confirm the enthalpies of formation of the sample molecules and their dissociative photoionization products. The ground electronic states of CHCl3+, CHClF2+ and CBrClF2+ do not confirm to the deep well assumption, and the experimental breakdown curve deviates from the deep well model at low energies. Breakdown curve analysis of such shallow well systems supplies a satisfactorily succinct route to the adiabatic ionization energy of the parent molecule, particularly if the threshold photoelectron spectrum is not resolved and a purely computational route is unfeasible. The ionization energies have been found to be 11.47 ± 0.01 eV, 12.30 ± 0.02 eV and 11.23 ± 0.03 eV for CHCl3, CHClF2 and CBrClF2, respectively. The updated 0 K enthalpies of formation, ∆fHo0K(g) for the ions CH2F+, CHF2+, CHCl2+, CCl3+, CCl2F+ and CClF2+ have been derived to be 844.4 ± 2.1, 601.6 ± 2.7, 890.3 ± 2.2, 849.8 ± 3.2, 701.2 ± 3.3 and 552.2 ± 3.4 kJ mol–1, respectively. The ∆fHo0K(g) values for the neutrals CCl4, CBrClF2, CClF3, CCl2F2 and CCl3F and have been determined to be –94.0 ± 3.2, –446.6 ± 2.7, –702.1 ± 3.5, –487.8 ± 3.4 and –285.2 ± 3.2 kJ mol–1, respectively