Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach.

We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population. Most existing approaches for local ancestry estimation ignore the latent genetic relatedness between ancestral populations and treat them as independent. In this article, we exploit such information by building an inheritance model that describes both the ancestral populations and the admixed population jointly in a unified framework. Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each ancestral population and further extend it to generate the admixed population. Through an effective utilization of the population structural information under a principled nonparametric Bayesian framework, the resulting model is significantly less sensitive to the choice and the amount of training data for ancestral populations than state-of-the-art algorithms. We also improve the robustness under deviation from common modeling assumptions by incorporating population-specific scale parameters that allow variable recombination rates in different populations. Our method is applicable to an admixed population from an arbitrary number of ancestral populations and also performs competitively in terms of spurious ancestry proportions under a general multiway admixture assumption. We validate the proposed method by simulation under various admixing scenarios and present empirical analysis results from a worldwide-distributed dataset from the Human Genome Diversity Project.

Extended VTS for noise-robust speech recognition

Model compensation is a standard way of improving the robustness of speech recognition systems to noise. A number of popular schemes are based on vector Taylor series (VTS) compensation, which uses a linear approximation to represent the influence of noise on the clean speech. To compensate the dynamic parameters, the continuous time approximation is often used. This approximation uses a point estimate of the gradient, which fails to take into account that dynamic coefficients are a function of a number of consecutive static coefficients. In this paper, the accuracy of dynamic parameter compensation is improved by representing the dynamic features as a linear transformation of a window of static features. A modified version of VTS compensation is applied to the distribution of the window of static features and, importantly, their correlations. These compensated distributions are then transformed to distributions over standard static and dynamic features. With this improved approximation, it is also possible to obtain full-covariance corrupted speech distributions. This addresses the correlation changes that occur in noise. The proposed scheme outperformed the standard VTS scheme by 10% to 20% relative on a range of tasks. © 2006 IEEE.

Factor analysis based VTS and JUD noise estimation and compensation

Model based compensation schemes are a powerful approach for noise robust speech recognition. Recently there have been a number of investigations into adaptive training, and estimating the noise models used for model adaptation. This paper examines the use of EM-based schemes for both canonical models and noise estimation, including discriminative adaptive training. One issue that arises when estimating the noise model is a mismatch between the noise estimation approximation and final model compensation scheme. This paper proposes FA-style compensation where this mismatch is eliminated, though at the expense of a sensitivity to the initial noise estimates. EM-based discriminative adaptive training is evaluated on in-car and Aurora4 tasks. FA-style compensation is then evaluated in an incremental mode on the in-car task. © 2011 IEEE.

Structured discriminative models for noise robust continuous speech recognition

Recently there has been interest in structured discriminative models for speech recognition. In these models sentence posteriors are directly modelled, given a set of features extracted from the observation sequence, and hypothesised word sequence. In previous work these discriminative models have been combined with features derived from generative models for noise-robust speech recognition for continuous digits. This paper extends this work to medium to large vocabulary tasks. The form of the score-space extracted using the generative models, and parameter tying of the discriminative model, are both discussed. Update formulae for both conditional maximum likelihood and minimum Bayes' risk training are described. Experimental results are presented on small and medium to large vocabulary noise-corrupted speech recognition tasks: AURORA 2 and 4. © 2011 IEEE.

Improving reverberant VTS for hands-free robust speech recognition

Model-based approaches to handling additive background noise and channel distortion, such as Vector Taylor Series (VTS), have been intensively studied and extended in a number of ways. In previous work, VTS has been extended to handle both reverberant and background noise, yielding the Reverberant VTS (RVTS) scheme. In this work, rather than assuming the observation vector is generated by the reverberation of a sequence of background noise corrupted speech vectors, as in RVTS, the observation vector is modelled as a superposition of the background noise and the reverberation of clean speech. This yields a new compensation scheme RVTS Joint (RVTSJ), which allows an easy formulation for joint estimation of both additive and reverberation noise parameters. These two compensation schemes were evaluated and compared on a simulated reverberant noise corrupted AURORA4 task. Both yielded large gains over VTS baseline system, with RVTSJ outperforming the previous RVTS scheme. © 2011 IEEE.

Extending noise robust structured support vector machines to larger vocabulary tasks

This paper describes a structured SVM framework suitable for noise-robust medium/large vocabulary speech recognition. Several theoretical and practical extensions to previous work on small vocabulary tasks are detailed. The joint feature space based on word models is extended to allow context-dependent triphone models to be used. By interpreting the structured SVM as a large margin log-linear model, illustrates that there is an implicit assumption that the prior of the discriminative parameter is a zero mean Gaussian. However, depending on the definition of likelihood feature space, a non-zero prior may be more appropriate. A general Gaussian prior is incorporated into the large margin training criterion in a form that allows the cutting plan algorithm to be directly applied. To further speed up the training process, 1-slack algorithm, caching competing hypothesis and parallelization strategies are also proposed. The performance of structured SVMs is evaluated on noise corrupted medium vocabulary speech recognition task: AURORA 4. © 2011 IEEE.

The parameter space of graphene chemical vapor deposition on polycrystalline Cu

A systematic study of the parameter space of graphene chemical vapor deposition (CVD) on polycrystalline Cu foils is presented, aiming at a more fundamental process rationale in particular regarding the choice of carbon precursor and mitigation of Cu sublimation. CH 4 as precursor requires H 2 dilution and temperatures ≥1000 °C to keep the Cu surface reduced and yield a high-quality, complete monolayer graphene coverage. The H 2 atmosphere etches as-grown graphene; hence, maintaining a balanced CH 4/H 2 ratio is critical. Such balance is more easily achieved at low-pressure conditions, at which however Cu sublimation reaches deleterious levels. In contrast, C 6H 6 as precursor requires no reactive diluent and consistently gives similar graphene quality at 100-150 °C lower temperatures. The lower process temperature and more robust processing conditions allow the problem of Cu sublimation to be effectively addressed. Graphene formation is not inherently self-limited to a monolayer for any of the precursors. Rather, the higher the supplied carbon chemical potential, the higher the likelihood of film inhomogeneity and primary and secondary multilayer graphene nucleation. For the latter, domain boundaries of the inherently polycrystalline CVD graphene offer pathways for a continued carbon supply to the catalyst. Graphene formation is significantly affected by the Cu crystallography; i.e., the evolution of microstructure and texture of the catalyst template form an integral part of the CVD process. © 2012 American Chemical Society.

Robust network reconstruction in polynomial time

This paper presents an efficient algorithm for robust network reconstruction of Linear Time-Invariant (LTI) systems in the presence of noise, estimation errors and unmodelled nonlinearities. The method here builds on previous work [1] on robust reconstruction to provide a practical implementation with polynomial computational complexity. Following the same experimental protocol, the algorithm obtains a set of structurally-related candidate solutions spanning every level of sparsity. We prove the existence of a magnitude bound on the noise, which if satisfied, guarantees that one of these structures is the correct solution. A problem-specific model-selection procedure then selects a single solution from this set and provides a measure of confidence in that solution. Extensive simulations quantify the expected performance for different levels of noise and show that significantly more noise can be tolerated in comparison to the original method. © 2012 IEEE.

Stable multivariate rational interpolation for parameter-dependent aerospace models

A multivariate, robust, rational interpolation method for propagating uncertainties in several dimensions is presented. The algorithm for selecting numerator and denominator polynomial orders is based on recent work that uses a singular value decomposition approach. In this paper we extend this algorithm to higher dimensions and demonstrate its efficacy in terms of convergence and accuracy, both as a method for response suface generation and interpolation. To obtain stable approximants for continuous functions, we use an L2 error norm indicator to rank optimal numerator and denominator solutions. For discontinous functions, a second criterion setting an upper limit on the approximant value is employed. Analytical examples demonstrate that, for the same stencil, rational methods can yield more rapid convergence compared to pseudospectral or collocation approaches for certain problems. © 2012 AIAA.

What is the weakest topology in which feedback stability is robust?

Mathematical theorems in control theory are only of interest in so far as their assumptions relate to practical situations. The space of systems with transfer functions in ℋ∞, for example, has many advantages mathematically, but includes large classes of non-physical systems, and one must be careful in drawing inferences from results in that setting. Similarly, the graph topology has long been known to be the weakest, or coarsest, topology in which (1) feedback stability is a robust property (i.e. preserved in small neighbourhoods) and (2) the map from open-to-closed-loop transfer functions is continuous. However, it is not known whether continuity is a necessary part of this statement, or only required for the existing proofs. It is entirely possible that the answer depends on the underlying classes of systems used. The class of systems we concern ourselves with here is the set of systems that can be approximated, in the graph topology, by real rational transfer function matrices. That is, lumped parameter models, or those distributed systems for which it makes sense to use finite element methods. This is precisely the set of systems that have continuous frequency responses in the extended complex plane. For this class, we show that there is indeed a weaker topology; in which feedback stability is robust but for which the maps from open-to-closed-loop transfer functions are not necessarily continuous. © 2013 Copyright Taylor and Francis Group, LLC.

Single event molecular signalling for estimation and control

Cell biology is characterised by low molecule numbers and coupled stochastic chemical reactions with intrinsic noise permeating and dominating the interactions between molecules. Recent work [9] has shown that in such environments there are hard limits on the accuracy with which molecular populations can be controlled and estimated. These limits are predicated on a continuous diffusion approximation of the target molecule (although the remainder of the system is non-linear and discrete). The principal result of [9] assumes that the birth rate of the signalling species is linearly dependent on the target molecule population size. In this paper, we investigate the situation when the entire system is kept discrete, and arbitrary non-linear coupling is allowed between the target molecule and downstream signalling molecules. In this case it is possible, by relying solely on the event triggered nature of control and signalling reactions, to define non-linear reaction rate modulation schemes that achieve improved performance in certain parameter regimes. These schemes would not appear to be biologically relevant, raising the question of what are an appropriate set of assumptions for obtaining biologically meaningful results. © 2013 EUCA.