arXiv subjects

Ilse C. F. Ipsen

Publications and source records attributed to Ilse C. F. Ipsen.

34 records · Page 2Linked to original sources

arXiv2021

SEAGLE: A Scalable Exact Algorithm for Large-Scale Set-Based GxE Tests in Biobank Data

The explosion of biobank data offers immediate opportunities for gene-environment (GxE) interaction studies of complex diseases because of the large sample sizes and the rich collection in genetic and non-genetic information. However, the extremely large sample size also introduces new computational challenges in GxE assessment, especially for set-based GxE variance component (VC) tests, which are a widely used strategy to boost overall GxE signals and to evaluate the joint GxE effect of multiple variants from a biologically meaningful unit (e.g., gene). In this work, we focus on continuous traits and present SEAGLE, a Scalable Exact AlGorithm for Large-scale set-based GxE tests, to permit GxE VC tests for biobank-scale data. SEAGLE employs modern matrix computations to achieve the same "exact" results as the original GxE VC tests without imposing additional assumptions or relying on approximations. SEAGLE can easily accommodate sample sizes in the order of $10^5$, is implementable on standard laptops, and does not require specialized computing equipment. We demonstrate SEAGLE's performance through extensive simulations. We illustrate its utility by conducting genome-wide gene-based GxE analysis on the Taiwan Biobank data to explore the interaction of gene and physical activity status on body mass index.

stat.CO↗

arXiv2021

Probabilistic Iterative Methods for Linear Systems

This paper presents a probabilistic perspective on iterative methods for approximating the solution $\mathbf{x}_* \in \mathbb{R}^d$ of a nonsingular linear system $\mathbf{A} \mathbf{x}_* = \mathbf{b}$. In the approach a standard iterative method on $\mathbb{R}^d$ is lifted to act on the space of probability distributions $\mathcal{P}(\mathbb{R}^d)$. Classically, an iterative method produces a sequence $\mathbf{x}_m$ of approximations that converge to $\mathbf{x}_*$. The output of the iterative methods proposed in this paper is, instead, a sequence of probability distributions $μ_m \in \mathcal{P}(\mathbb{R}^d)$. The distributional output both provides a "best guess" for $\mathbf{x}_*$, for example as the mean of $μ_m$, and also probabilistic uncertainty quantification for the value of $\mathbf{x}_*$ when it has not been exactly determined. Theoretical analysis is provided in the prototypical case of a stationary linear iterative method. In this setting we characterise both the rate of contraction of $μ_m$ to an atomic measure on $\mathbf{x}_*$ and the nature of the uncertainty quantification being provided. We conclude with an empirical illustration that highlights the insight into solution uncertainty that can be provided by probabilistic iterative methods.

stat.ME↗

arXiv2020

A Projector-Based Approach to Quantifying Total and Excess Uncertainties for Sketched Linear Regression

Linear regression is a classic method of data analysis. In recent years, sketching -- a method of dimension reduction using random sampling, random projections, or both -- has gained popularity as an effective computational approximation when the number of observations greatly exceeds the number of variables. In this paper, we address the following question: How does sketching affect the statistical properties of the solution and key quantities derived from it? To answer this question, we present a projector-based approach to sketched linear regression that is exact and that requires minimal assumptions on the sketching matrix. Therefore, downstream analyses hold exactly and generally for all sketching schemes. Additionally, a projector-based approach enables derivation of key quantities from classic linear regression that account for the combined model- and algorithm-induced uncertainties. We demonstrate the usefulness of a projector-based approach in quantifying and enabling insight on excess uncertainties and bias-variance decompositions for sketched linear regression. Finally, we demonstrate how the insights from our projector-based analyses can be used to produce practical sketching diagnostics to aid the design of judicious sketching schemes.

stat.ML↗

arXiv2020

Multiplicative Perturbation Bounds for Multivariate Multiple Linear Regression in Schatten $p$-Norms

Multivariate multiple linear regression (MMLR), which occurs in a number of practical applications, generalizes traditional least squares (multivariate linear regression) to multiple right-hand sides. We extend recent MLR analyses to sketched MMLR in general Schatten $p$-norms by interpreting the sketched problem as a multiplicative perturbation. Our work represents an extension of Maher's results on Schatten $p$-norms. We derive expressions for the exact and perturbed solutions in terms of projectors for easy geometric interpretation. We also present a geometric interpretation of the action of the sketching matrix in terms of relevant subspaces. We show that a key term in assessing the accuracy of the sketched MMLR solution can be viewed as a tangent of a largest principal angle between subspaces under some assumptions. Our results enable additional interpretation of the difference between an orthogonal and oblique projector with the same range.

math.NA↗

arXiv2019

Efficient Computation of Gaussian Likelihoods for Stationary Markov Random Field Models

Rue and Held (2005) proposed a method for efficiently computing the Gaussian likelihood for stationary Markov random field models, when the data locations fall on a complete regular grid, and the model has no additive error term. The calculations rely on the availability of the covariances. We prove a theorem giving the rate of convergence of a spectral method of computing the covariances, establishing that the error decays faster than any polynomial in the size of the computing grid. We extend the exact likelihood calculations to the case of non-rectangular domains and missing values on the interior of the grid and to the case when an additive uncorrelated error term (nugget) is present in the model. We also give an alternative formulation of the likelihood that has a smaller memory burden, parts of which can be computed in parallel. We show in simulations that using the exact likelihood can give far better parameter estimates than using standard Markov random field approximations. Having access to the exact likelihood allows for model comparisons via likelihood ratios on large datasets, so as an application of the methods, we compare several state-of-the-art methods for large spatial datasets on an aerosol optical thickness dataset. We find that simple block independent likelihood and composite likelihood methods outperform stochastic partial differential equation approximations in terms of computation time and returning parameter estimates that nearly maximize the likelihood.

stat.CO↗

arXiv2019

Probabilistic Error Analysis for Inner Products

Probabilistic models are proposed for bounding the forward error in the numerically computed inner product (dot product, scalar product) between of two real $n$-vectors. We derive probabilistic perturbation bounds, as well as probabilistic roundoff error bounds for the sequential accumulation of the inner product. These bounds are non-asymptotic, explicit, and make minimal assumptions on perturbations and roundoffs. The perturbations are represented as independent, bounded, zero-mean random variables, and the probabilistic perturbation bound is based on Azuma's inequality. The roundoffs are also represented as bounded, zero-mean random variables. The first probabilistic bound assumes that the roundoffs are independent, while the second one does not. For the latter, we construct a Martingale that mirrors the sequential order of computations. Numerical experiments confirm that our bounds are more informative, often by several orders of magnitude, than traditional deterministic bounds -- even for small vector dimensions~$n$ and very stringent success probabilities. In particular the probabilistic roundoff error bounds are functions of $\sqrt{n}$ rather than~$n$, thus giving a quantitative confirmation of Wilkinson's intuition. The paper concludes with a critical assessment of the probabilistic approach.

math.NA↗

arXiv2018

Probabilistic Linear Solvers: A Unifying View

Several recent works have developed a new, probabilistic interpretation for numerical algorithms solving linear systems in which the solution is inferred in a Bayesian framework, either directly or by inferring the unknown action of the matrix inverse. These approaches have typically focused on replicating the behavior of the conjugate gradient method as a prototypical iterative method. In this work surprisingly general conditions for equivalence of these disparate methods are presented. We also describe connections between probabilistic linear solvers and projection methods for linear systems, providing a probabilistic interpretation of a far more general class of iterative methods. In particular, this provides such an interpretation of the generalised minimum residual method. A probabilistic view of preconditioning is also introduced. These developments unify the literature on probabilistic linear solvers, and provide foundational connections to the literature on iterative solvers for linear systems.

stat.CO↗

arXiv2018

Low-Rank Matrix Approximations Do Not Need a Singular Value Gap

This is a systematic investigation into the sensitivity of low-rank approximations of real matrices. We show that the low-rank approximation errors, in the two-norm, Frobenius norm and more generally, any Schatten p-norm, are insensitive to additive rank-preserving perturbations in the projector basis; and to matrix perturbations that are additive or change the number of columns (including multiplicative perturbations). Thus, low-rank matrix approximations are always well-posed and do not require a singular value gap. In the presence of a singular value gap, connections are established between low-rank approximations and subspace angles.

math.NA↗

arXiv2018

A Probabilistic Subspace Bound with Application to Active Subspaces

Given a real symmetric positive semi-definite matrix E, and an approximation S that is a sum of n independent matrix-valued random variables, we present bounds on the relative error in S due to randomization. The bounds do not depend on the matrix dimensions but only on the numerical rank (intrinsic dimension) of E. Our approach resembles the low-rank approximation of kernel matrices from random features, but our accuracy measures are more stringent. In the context of parameter selection based on active subspaces, where S is computed via Monte Carlo sampling, we present a bound on the number of samples so that with high probability the angle between the dominant subspaces of E and S is less than a user-specified tolerance. This is a substantial improvement over existing work, as it is a non-asymptotic and fully explicit bound on the sampling amount n, and it allows the user to tune the success probability. It also suggests that Monte Carlo sampling can be efficient in the presence of many parameters, as long as the underlying function f is sufficiently smooth.

math.NA↗

arXiv2017

Randomized Matrix-free Trace and Log-Determinant Estimators

We present randomized algorithms for estimating the trace and deter- minant of Hermitian positive semi-definite matrices. The algorithms are based on subspace iteration, and access the matrix only through matrix vector products. We analyse the error due to randomization, for starting guesses whose elements are Gaussian or Rademacher random variables. The analysis is cleanly separated into a structural (deterministic) part followed by a probabilistic part. Our absolute bounds for the expectation and concentration of the estimators are non-asymptotic and informative even for matrices of low dimension. For the trace estimators, we also present asymptotic bounds on the number of samples (columns of the starting guess) required to achieve a user-specified relative error. Numerical experiments illustrate the performance of the estimators and the tightness of the bounds on low-dimensional matrices; and on a challenging application in uncertainty quantification arising from Bayesian optimal experimental design.

math.NA↗

arXiv2015

Conditioning of Leverage Scores and Computation by QR Decomposition

The leverage scores of a full-column rank matrix A are the squared row norms of any orthonormal basis for range(A). We show that corresponding leverage scores of two matrices A and A + ΔA are close in the relative sense, if they have large magnitude and if all principal angles between the column spaces of A and A + ΔA are small. We also show three classes of bounds that are based on perturbation results of QR decompositions. They demonstrate that relative differences between individual leverage scores strongly depend on the particular type of perturbation ΔA. The bounds imply that the relative accuracy of an individual leverage score depends on: its magnitude and the two-norm condition of A, if ΔA is a general perturbation; the two-norm condition number of A, if ΔA is a perturbation with the same norm-wise row-scaling as A; (to first order) neither condition number nor leverage score magnitude, if ΔA is a component-wise row-scaled perturbation. Numerical experiments confirm the qualitative and quantitative accuracy of our bounds.

math.NA↗

arXiv2014

Randomized Approximation of the Gram Matrix: Exact Computation and Probabilistic Bounds

Given a real matrix A with n columns, the problem is to approximate the Gram product AA^T by c << n weighted outer products of columns of A. Necessary and sufficient conditions for the exact computation of AA^T (in exact arithmetic) from c >= rank(A) columns depend on the right singular vector matrix of A. For a Monte-Carlo matrix multiplication algorithm by Drineas et al. that samples outer products, we present probabilistic bounds for the 2-norm relative error due to randomization. The bounds depend on the stable rank or the rank of A, but not on the matrix dimensions. Numerical experiments illustrate that the bounds are informative, even for stringent success probabilities and matrices of small dimension. We also derive bounds for the smallest singular value and the condition number of matrices obtained by sampling rows from orthonormal matrices.

math.NA↗

arXiv2014

The Effect of Coherence on Sampling from Matrices with Orthonormal Columns, and Preconditioned Least Squares Problems

Motivated by the least squares solver Blendenpik, we investigate three strategies for uniform sampling of rows from m x n matrices Q with orthonormal columns. The goal is to determine, with high probability, how many rows are required so that the sampled matrices have full rank and are well-conditioned with respect to inversion. Extensive numerical experiments illustrate that the three sampling strategies (without replacement, with replacement, and Bernoulli sampling) behave almost identically, for small to moderate amounts of sampling. In particular, sampled matrices of full rank tend to have two-norm condition numbers of at most 10. We derive a bound on the condition number of the sampled matrices in terms of the coherence μ of Q. This bound applies to all three different sampling strategies; it implies a, not necessarily tight, lower bound of O(m μ ln(n)) for the number of sampled rows; and it is realistic and informative even for matrices of small dimension and the stringent requirement of a 99 percent success probability. For uniform sampling with replacement we derive a potentially tighter condition number bound in terms of the leverage scores of Q. To obtain a more easily computable version of this bound, in terms of just the largest leverage scores, we first derive a general bound on the two-norm of diagonally scaled matrices. To facilitate the numerical experiments and test the tightness of the bounds, we present algorithms to generate matrices with user-specified coherence and leverage scores. These algorithms, the three sampling strategies, and a large variety of condition number bounds are implemented in the Matlab toolbox kappa_SQ_v3.

math.NA↗

arXiv2011

Determinant Approximations

A sequence of approximations for the determinant and its logarithm of a complex matrixis derived, along with relative error bounds. The determinant approximations are derived from expansions of det(X)=exp(trace(log(X))), and they apply to non-Hermitian matrices. Examples illustrate that these determinant approximations are efficient for lattice simulations of finite temperature nuclear matter, and that they use significantly less space than Gaussian elimination. The first approximation in the sequence is a block diagonal approximation; it represents an extension of Fischer's and Hadamard's inequalities to non-Hermitian matrices. In the special case of Hermitian positive-definite matrices, block diagonal approximations can be competitive with sparse inverse approximations. At last, a different representation of sparse inverse approximations is given and it is shown that their accuracy increases as more matrix elements are included.

math.NA↗

arXiv2011

La Budde's Method for Computing Characteristic Polynomials

La Budde's method computes the characteristic polynomial of a real matrix A in two stages: first it applies orthogonal similarity transformations to reduce A to upper Hessenberg form H, and second it computes the characteristic polynomial of H from characteristic polynomials of leading principal submatrices of H. If A is symmetric, then H is symmetric tridiagonal, and La Budde's method simplifies to the Sturm sequence method. If A is diagonal then La Budde's method reduces to the Summation Algorithm, a Horner-like scheme used by the MATLAB function POLY to compute characteristic polynomials from eigenvalues. We present recursions to compute the individual coefficients of the characteristic polynomial in the second stage of La Budde's method, and derive running error bounds for symmetric and nonsymmetric matrices. We also show that La Budde's method can be more accurate than POLY, especially for indefinite and nonsymmetric matrices A. Unlike POLY, La Budde's method is not affected by illconditioning of eigenvalues, requires only real arithmetic, and allows the computation of individual coefficients.

math.NA↗

arXiv2003

Zone Determinant Expansions for Nuclear Lattice Simulations

We introduce a new approximation to nucleon matrix determinants that is physically motivated by chiral effective theory. The method involves breaking the lattice into spatial zones and expanding the determinant in powers of the boundary hopping parameter.

nucl-th↗