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We consider the simultaneously fast and in-place computation of the Euclidean polynomial modular remainder $R(X) $\not\equiv$ A(X) \mod B(X)$ with $A$ and $B$ of respective degrees $n$ and $m $\le$ n$. But fast algorithms for this usually come at the expense of (potentially large) extra temporary space. To remain in-place a further issue is to avoid the storage of the whole quotient $Q(X)$ such that $A=BQ+R$. If the multiplication of two polynomials of degree $k$ can be performed with $M(k)$ operations and $O(k)$ extra space, and if it is allowed to use the input space of $A$ or $B$ for intermediate computations, but putting $A$ and $B$ back to their initial states after the completion of the remainder computation, we here propose an in-place algorithm (that is with its extra required space reduced to $O(1)$ only) using at most $O(n/m M(m)\log(m)$ arithmetic operations, if $\M(m)$ is quasi-linear, or $O(n/m M(m)}$ otherwise. We also propose variants that compute -- still in-place and with the same kind of complexity bounds -- the over-place remainder $A(X) $\not\equiv$ A(X) \mod B(X)$, the accumulated remainder $R(X) += A(X) \mod B(X)$ and the accumulated modular multiplication $R(X) += A(X)C(X) \mod B(X)$. To achieve this, we develop techniques for Toeplitz matrix operations which output is also part of the input. Fast and in-place accumulating versions are obtained for the latter, and thus for convolutions, and then used for polynomial remaindering. This is realized via further reductions to accumulated polynomial multiplication, for which fast in-place algorithms have recently been developed.

We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of which are the values realized by a function $\Gamma$. $\Gamma$ acts on neighborhoods of arbitrary radius that are located at strategic positions within the DNA sequence and carries complete information about the local distribution of frequencies of the nucleotides as a consequence of the uniqueness of prime factorization of integer. The algorithm exhibits linear time complexity and turns out to consume significantly small memory. The two natural parameters characterizing the radius and location of the neighbourhoods are fixed by comparing the phylogenetic tree with the benchmark for full genome sequences of fish mtDNA datasets. Using these fitting parameters, the method is applied to analyze a number of genome sequences from benchmark and other standard datasets. The algorithm proves to be computationally efficient compared to Co-phylog and CD-MAWS when applied over a certain range of a simulated dataset.

We present a new and straightforward derivation of a family $\mathcal{F}(h,\tau)$ of exponential splittings of Strang-type for the general linear evolutionary equation with two linear components. One component is assumed to be a time-independent, unbounded operator, while the other is a bounded one with explicit time dependence. The family $\mathcal{F}(h,\tau)$ is characterized by the length of the time-step $h$ and a continuous parameter $\tau$, which defines each member of the family. It is shown that the derivation and error analysis follows from two elementary arguments: the variation of constants formula and specific quadratures for integrals over simplices. For these Strang-type splittings, we prove their convergence which, depending on some commutators of the relevant operators, may be of first or second order. As a result, error bounds appear in terms of commutator bounds. Based on the explicit form of the error terms, we establish the influence of $\tau$ on the accuracy of $\mathcal{F}(h,\tau)$, allowing us to investigate the optimal value of $\tau$. This simple yet powerful approach establishes the connection between exponential integrators and splitting methods. Furthermore, the present approach can be easily applied to the derivation of higher-order splitting methods under similar considerations. Needless to say, the obtained results also apply to Strang-type splittings in the case of time independent-operators. To complement rigorous results, we present numerical experiments with various values of $\tau$ based on the linear Schr\"odinger equation.

Subshifts are colorings of $\mathbb{Z}^d$ defined by families of forbidden patterns. Given a subshift and a finite pattern, its extender set is the set of admissible completions of this pattern. It has been conjectured that the behavior of extender sets, and in particular their growth called extender entropy (arXiv:1711.07515), could provide a way to separate the classes of sofic and effective subshifts. We prove here that both classes have the same possible extender entropies: exactly the $\Pi_3$ real numbers of $[0,+\infty)$. We also consider computational properties of extender entropies for subshifts with some language or dynamical properties: computable language, minimal and some mixing properties.

We propose a Lawson-time-splitting extended Fourier pseudospectral (LTSeFP) method for the numerical integration of the Gross-Pitaevskii equation with time-dependent potential that is of low regularity in space. For the spatial discretization of low regularity potential, we use an extended Fourier pseudospectral (eFP) method, i.e., we compute the discrete Fourier transform of the low regularity potential in an extended window. For the temporal discretization, to efficiently implement the eFP method for time-dependent low regularity potential, we combine the standard time-splitting method with a Lawson-type exponential integrator to integrate potential and nonlinearity differently. The LTSeFP method is both accurate and efficient: it achieves first-order convergence in time and optimal-order convergence in space in $L^2$-norm under low regularity potential, while the computational cost is comparable to the standard time-splitting Fourier pseudospectral method. Theoretically, we also prove such convergence orders for a large class of spatially low regularity time-dependent potential. Extensive numerical results are reported to confirm the error estimates and to demonstrate the superiority of our method.

The hazard function represents one of the main quantities of interest in the analysis of survival data. We propose a general approach for parametrically modelling the dynamics of the hazard function using systems of autonomous ordinary differential equations (ODEs). This modelling approach can be used to provide qualitative and quantitative analyses of the evolution of the hazard function over time. Our proposal capitalises on the extensive literature of ODEs which, in particular, allow for establishing basic rules or laws on the dynamics of the hazard function via the use of autonomous ODEs. We show how to implement the proposed modelling framework in cases where there is an analytic solution to the system of ODEs or where an ODE solver is required to obtain a numerical solution. We focus on the use of a Bayesian modelling approach, but the proposed methodology can also be coupled with maximum likelihood estimation. A simulation study is presented to illustrate the performance of these models and the interplay of sample size and censoring. Two case studies using real data are presented to illustrate the use of the proposed approach and to highlight the interpretability of the corresponding models. We conclude with a discussion on potential extensions of our work and strategies to include covariates into our framework.

We consider nonlinear solvers for the incompressible, steady (or at a fixed time step for unsteady) Navier-Stokes equations in the setting where partial measurement data of the solution is available. The measurement data is incorporated/assimilated into the solution through a nudging term addition to the the Picard iteration that penalized the difference between the coarse mesh interpolants of the true solution and solver solution, analogous to how continuous data assimilation (CDA) is implemented for time dependent PDEs. This was considered in the paper [Li et al. {\it CMAME} 2023], and we extend the methodology by improving the analysis to be in the $L^2$ norm instead of a weighted $H^1$ norm where the weight depended on the coarse mesh width, and to the case of noisy measurement data. For noisy measurement data, we prove that the CDA-Picard method is stable and convergent, up to the size of the noise. Numerical tests illustrate the results, and show that a very good strategy when using noisy data is to use CDA-Picard to generate an initial guess for the classical Newton iteration.

Due to the lack of a canonical ordering in ${\mathbb R}^d$ for $d>1$, defining multivariate generalizations of the classical univariate ranks has been a long-standing open problem in statistics. Optimal transport has been shown to offer a solution in which multivariate ranks are obtained by transporting data points to a grid that approximates a uniform reference measure (Chernozhukov et al., 2017; Hallin, 2017; Hallin et al., 2021), thereby inducing ranks, signs, and a data-driven ordering of ${\mathbb R}^d$. We take up this new perspective to define and study multivariate analogues of the sign covariance/quadrant statistic, Spearman's rho, Kendall's tau, and van der Waerden covariances. The resulting tests of multivariate independence are fully distribution-free, hence uniformly valid irrespective of the actual (absolutely continuous) distribution of the observations. Our results provide the asymptotic distribution theory for these new test statistics, with asymptotic approximations to critical values to be used for testing independence between random vectors, as well as a power analysis of the resulting tests in an extension of the so-called Konijn model. For the van der Waerden tests, this power analysis includes a multivariate Chernoff--Savage property guaranteeing that, under elliptical generalized Konijn models, the asymptotic relative efficiency with respect to Wilks' classical (pseudo-)Gaussian procedure of our van der Waerden tests is strictly larger than or equal to one, where equality is achieved under Gaussian distributions only. We similarly provide a lower bound for the asymptotic relative efficiency of our Spearman procedure with respect to Wilks' test, thus extending the classical result by Hodges and Lehmann on the asymptotic relative efficiency, in univariate location models, of Wilcoxon tests with respect to the Student ones.

Nurmuhammad et al. developed the Sinc-Nystr\"{o}m methods for initial value problems in which the solutions exhibit exponential decay end behavior. In these methods, the Single-Exponential (SE) transformation or the Double-Exponential (DE) transformation is combined with the Sinc approximation. Hara and Okayama improved on these transformations to attain a better convergence rate, which was later supported by theoretical error analyses. However, these methods have a computational drawback owing to the inclusion of a special function in the basis functions. To address this issue, Okayama and Hara proposed Sinc-collocation methods, which do not include any special function in the basis functions. This study conducts error analyses of these methods.

The starting point for much of multivariate analysis (MVA) is an $n\times p$ data matrix whose $n$ rows represent observations and whose $p$ columns represent variables. Some multivariate data sets, however, may be best conceptualized not as $n$ discrete $p$-variate observations, but as $p$ curves or functions defined on a common time interval. We introduce a framework for extending techniques of multivariate analysis to such settings. The proposed framework rests on the assumption that the curves can be represented as linear combinations of basis functions such as B-splines. This is formally identical to the Ramsay-Silverman representation of functional data; but whereas functional data analysis extends MVA to the case of observations that are curves rather than vectors -- heuristically, $n\times p$ data with $p$ infinite -- we are instead concerned with what happens when $n$ is infinite. We describe how to translate the classical MVA methods of covariance and correlation estimation, principal component analysis, Fisher's linear discriminant analysis, and $k$-means clustering to the continuous-time setting. We illustrate the methods with a novel perspective on a well-known Canadian weather data set, and with applications to neurobiological and environmetric data. The methods are implemented in the publicly available R package \texttt{ctmva}.