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Register a new userFast and Accurate Detection of Multiple QTL
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We present a new computational scheme that enables efficient and reliable Quantitative Trait Loci (QTL) scans for experimental populations. Using a standard brute-force exhaustive search effectively prohibits accurate QTL scans involving more than two loci to be performed in practice, at least if permutation testing is used to determine significance. Some more elaborate global optimization approaches, e.g. DIRECT, have earlier been adopted to QTL search problems. Dramatic speedups have been reported for high-dimensional scans. However, since a heuristic termination criterion must be used in these types of algorithms the accuracy of the optimization process cannot be guaranteed. Indeed, earlier results show that a small bias in the significance thresholds is sometimes introduced. Our new optimization scheme, PruneDIRECT, is based on an analysis leading to a computable (Lipschitz) bound on the slope of a transformed objective function. The bound is derived for both infinite size and finite size populations. Introducing a Lipschitz bound in DIRECT leads to an algorithm related to classical Lipschitz optimization. Regions in the search space can be permanently excluded (pruned) during the optimization process. Heuristic termination criteria can thus be avoided. Hence, PruneDIRECT has a well-defined error bound and can in practice be guaranteed to be equivalent to a corresponding exhaustive search. We present simulation results that show that for simultaneous mapping of three QTL using permutation testing, PruneDIRECT is typically more than 50 times faster than exhaustive search. The speedup is higher for stronger QTL. This could be used to quickly detect strong candidate eQTL networks.
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The estimation of the frequencies of multiple superimposed exponentials in noise is an important research problem due to its various applications from engineering to chemistry. In this paper, we propose an efficient and accurate algorithm that estimates the frequency of each component iteratively and consecutively by combining an estimator with a leakage subtraction scheme. During the iterative process, the proposed method gradually reduces estimation error and improves the frequency estimation accuracy. We give theoretical analysis where we derive the theoretical bias and variance of the frequency estimates and discuss the convergence behaviour of the estimator. We show that the algorithm converges to the asymptotic fixed point where the estimation is asymptotically unbiased and the variance is just slightly above the Cramer-Rao lower bound. We then verify the theoretical results and estimation performance using extensive simulation. The simulation results show that the proposed algorithm is capable of obtaining more accurate estimates than state-of-art methods with only a few iterations.
Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid microscale dynamics the dynamical systems approach constructs accurate closures of macroscale discretisations of the microscale system. Here we specifically explore reaction-diffusion problems in two spatial dimensions as a prototype of generic systems in multiple dimensions. Our approach unifies into one the modelling of systems by a type of finite elements, and the `equation free macroscale modelling of microscale simulators efficiently executing only on small patches of the spatial domain. Centre manifold theory ensures that a closed model exist on the macroscale grid, is emergent, and is systematically approximated. Dividing space either into overlapping finite elements or into spatially separated small patches, the specially crafted inter-element/patch coupling also ensures that the constructed discretisations are consistent with the microscale system/PDE to as high an order as desired. Computer algebra handles the considerable algebraic details as seen in the specific application to the Ginzburg--Landau PDE. However, higher order models in multiple dimensions require a mixed numerical and algebraic approach that is also developed. The modelling here may be straightforwardly adapted to a wide class of reaction-diffusion PDEs and lattice equations in multiple space dimensions. When applied to patches of microscopic simulations our coupling conditions promise efficient macroscale simulation.
Low-rank Tucker and CP tensor decompositions are powerful tools in data analytics. The widely used alternating least squares (ALS) method, which solves a sequence of over-determined least squares subproblems, is costly for large and sparse tensors. We propose a fast and accurate sketched ALS algorithm for Tucker decomposition, which solves a sequence of sketched rank-constrained linear least squares subproblems. Theoretical sketch size upper bounds are provided to achieve $O(epsilon)$ relative error for each subproblem with two sketching techniques, TensorSketch and leverage score sampling. Experimental results show that this new ALS algorithm, combined with a new initialization scheme based on randomized range finder, yields up to $22.0%$ relative decomposition residual improvement compared to the state-of-the-art sketched randomized algorithm for Tucker decomposition of various synthetic and real datasets. This Tucker-ALS algorithm is further used to accelerate CP decomposition, by using randomized Tucker compression followed by CP decomposition of the Tucker core tensor. Experimental results show that this algorithm not only converges faster, but also yields more accurate CP decompositions.
In this article, we present an $O(N log N)$ rapidly convergent algorithm for the numerical approximation of the convolution integral with radially symmetric weakly singular kernels and compactly supported densities. To achieve the reduced computational complexity, we utilize the Fast Fourier Transform (FFT) on a uniform grid of size $N$ for approximating the convolution. To facilitate this and maintain the accuracy, we primarily rely on a periodic Fourier extension of the density with a suitably large period depending on the support of the density. The rate of convergence of the method increases with increasing smoothness of the periodic extension and, in fact, approximations exhibit super-algebraic convergence when the extension is infinitely differentiable. Furthermore, when the density has jump discontinuities, we utilize a certain Fourier smoothing technique to accelerate the convergence to achieve the quadratic rate in the overall approximation. Finally, we apply the integration scheme for numerical solution of certain partial differential equations. Moreover, we apply the quadrature to obtain a fast and high-order Nystom solver for the solution of the Lippmann-Schwinger integral equation. We validate the performance of the proposed scheme in terms of accuracy as well as computational efficiency through a variety of numerical experiments.
We solve Poissons equation using new multigrid algorithms that converge rapidly. The novel feature of the 2D and 3D algorithms are the use of extra diagonal grids in the multigrid hierarchy for a much richer and effective communication between the levels of the multigrid. Numerical experiments solving Poissons equation in the unit square and unit cube show simpl
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