Efficient chaining of seeds in ordered trees

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space

Uniform random generation of large acyclic digraphs

Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory networks, not only the estimation of model parameters but the reconstruction of the structure itself is of great interest. As well as for the assessment of different structure learning algorithms in simulation studies, a uniform sample from the space of directed acyclic graphs is required to evaluate the prevalence of certain structural features. Here we analyse how to sample acyclic digraphs uniformly at random through recursive enumeration, an approach previously thought too computationally involved. Based on complexity considerations, we discuss in particular how the enumeration directly provides an exact method, which avoids the convergence issues of the alternative Markov chain methods and is actually computationally much faster. The limiting behaviour of the distribution of acyclic digraphs then allows us to sample arbitrarily large graphs. Building on the ideas of recursive enumeration based sampling we also introduce a novel hybrid Markov chain with much faster convergence than current alternatives while still being easy to adapt to various restrictions. Finally we discuss how to include such restrictions in the combinatorial enumeration and the new hybrid Markov chain method for efficient uniform sampling of the corresponding graphs.Comment: 15 pages, 2 figures. To appear in Statistics and Computin

Robust Henderson III estimators of variance components in the nested error model

Common methods for estimating variance components in Linear Mixed Models include Maximum Likelihood (ML) and Restricted Maximum Likelihood (REML). These methods are based on the strong assumption of multivariate normal distribution and it is well know that they are very sensitive to outlying observations with respect to any of the random components. Several robust altematives of these methods have been proposed (e.g. Fellner 1986, Richardson and Welsh 1995). In this work we present several robust alternatives based on the Henderson method III which do not rely on the normality assumption and provide explicit solutions for the variance components estimators. These estimators can later be used to derive robust estimators of regression coefficients. Finally, we describe an application of this procedure to small area estimation, in which the main target is the estimation of the means of areas or domains when the within-area sample sizes are small

Local density of states in superconductor-strong ferromagnet structures

We study the dependence of the local density of states (LDOS) on coordinates for a superconductor-ferromagnet (S/F) bilayer and a S/F/S structure assuming that the exchange energy h in the ferromagnet is sufficiently large: $>>1,$ where $\tau$ is the elastic relaxation time. This limit cannot be described by the Usadel equation and we solve the more general Eilenberger equation. We demonstrate that, in the main approximation in the parameter $(h\tau)^{-1}$, the proximity effect does not lead to a modification of the LDOS in the S/F system and a non-trivial dependence on coordinates shows up in next orders in $(h\tau) ^{-1}.$ In the S/F/S sandwich the correction to the LDOS is nonzero in the main approximation and depends on the phase difference between the superconductors. We also calculate the superconducting critical temperature $T_{c}$ for the bilayered system and show that it does not depend on the exchange energy of the ferromagnet in the limit of large h and a thick F layer.Comment: 9 pages, 5 figure

A Complete Set of In-plane Spin-transfer Coefficients for Small Angle pp Elastic Scattering at 200 MeV

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

Effects of surface plasma treatment on threshold voltage hysteresis and instability in metal-insulator-semiconductor (MIS) AlGaN/GaN heterostructure HEMTs

In a bid to understand the commonly observed hysteresis in the threshold voltage (VTH) in AlGaN/GaN metal-insulator-semiconductor high electron mobility transistors during forward gate bias stress, we have analyzed a series of measurements on devices with no surface treatment and with two different plasma treatments before the in-situ Al2O3 deposition. The observed changes between samples were quasi-equilibrium VTH, forward bias related VTH hysteresis, and electrical response to reverse bias stress. To explain these effects, a disorder induced gap state model, combined with a discrete level donor, at the dielectric/semiconductor interface was employed. Technology Computer-Aided Design modeling demonstrated the possible differences in the interface state distributions that could give a consistent explanation for the observations

Cryptoferromagnetic state in superconductor-ferromagnet multilayers

We study a possibility of a non-homogeneous magnetic order (cryptoferromagnetic state) in heterostructures consisting of a bulk superconductor and a ferromagnetic thin layer that can be due to the influence of the superconductor. The exchange field in the ferromagnet may be strong and exceed the inverse mean free time. A new approach based on solving the Eilenberger equations in the ferromagnet and the Usadel equations in the superconductor is developed. We derive a phase diagram between the cryptoferromagnetic and ferromagnetic states and discuss the possibility of an experimental observation of the CF state in different materials.Comment: 4 pages, 1 figur