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In the area of query complexity of Boolean functions, the most widely studied cost measure of an algorithm is the worst-case number of queries made by it on an input. Motivated by the most natural cost measure studied in online algorithms, the competitive ratio, we consider a different cost measure for query algorithms for Boolean functions that captures the ratio of the cost of the algorithm and the cost of an optimal algorithm that knows the input in advance. The cost of an algorithm is its largest cost over all inputs. Grossman, Komargodski and Naor [ITCS'20] introduced this measure for Boolean functions, and dubbed it instance complexity. Grossman et al. showed, among other results, that monotone Boolean functions with instance complexity 1 are precisely those that depend on one or two variables. We complement the above-mentioned result of Grossman et al. by completely characterizing the instance complexity of symmetric Boolean functions. As a corollary we conclude that the only symmetric Boolean functions with instance complexity 1 are the Parity function and its complement. We also study the instance complexity of some graph properties like Connectivity and k-clique containment. In all the Boolean functions we study above, and those studied by Grossman et al., the instance complexity turns out to be the ratio of query complexity to minimum certificate complexity. It is a natural question to ask if this is the correct bound for all Boolean functions. We show a negative answer in a very strong sense, by analyzing the instance complexity of the Greater-Than and Odd-Max-Bit functions. We show that the above-mentioned ratio is linear in the input size for both of these functions, while we exhibit algorithms for which the instance complexity is a constant.

For an approximate solution of the non-stationary nonlinear Navier-Stokes equations for the flow of an incompressible viscous fluid, depending on the set of input data and the geometry of the domain, the area of optimal parameters in the variables $\nu$ and $\nu^{\ast}$ is experimentally determined depending on $\delta$ included in the definition of the $R_{\nu}$-generalized solution of the problem and the degree of the weight function in the basis of the finite element method. To discretize the problem in time, the Runge-Kutta methods of the first and second orders were used. The areas of optimal parameters for various values of the incoming angles are established.

Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate gradient enables scaling of sampling-based inference, namely Bayesian inference via Hamiltonian Monte Carlo, under random-effects substitution models across large trees and state-spaces. Applied to a dataset of 583 SARS-CoV-2 sequences, an HKY model with random-effects shows strong signals of nonreversibility in the substitution process, and posterior predictive model checks clearly show that it is a more adequate model than a reversible model. When analyzing the pattern of phylogeographic spread of 1441 influenza A virus (H3N2) sequences between 14 regions, a random-effects phylogeographic substitution model infers that air travel volume adequately predicts almost all dispersal rates. A random-effects state-dependent substitution model reveals no evidence for an effect of arboreality on the swimming mode in the tree frog subfamily Hylinae. Simulations reveal that random-effects substitution models can accommodate both negligible and radical departures from the underlying base substitution model. We show that our gradient-based inference approach is over an order of magnitude more time efficient than conventional approaches.

Miura surfaces are the solutions of a constrained nonlinear elliptic system of equations. This system is derived by homogenization from the Miura fold, which is a type of origami fold with multiple applications in engineering. A previous inquiry, gave suboptimal conditions for existence of solutions and proposed an $H^2$-conformal finite element method to approximate them. In this paper, the existence of Miura surfaces is studied using a mixed formulation. It is also proved that the constraints propagate from the boundary to the interior of the domain for well-chosen boundary conditions. Then, a numerical method based on a least-squares formulation, Taylor--Hood finite elements and a Newton method is introduced to approximate Miura surfaces. The numerical method is proved to converge at order one in space and numerical tests are performed to demonstrate its robustness.

When a system of first order linear ordinary differential equations has eigenvalues of large magnitude, its solutions exhibit complicated behaviour, such as high-frequency oscillations, rapid growth or rapid decay. The cost of representing such solutions using standard techniques typically grows with the magnitudes of the eigenvalues. As a consequence, the running times of standard solvers for ordinary differential equations also grow with the size of these eigenvalues. The solutions of scalar equations with slowly-varying coefficients, however, can be efficiently represented via slowly-varying phase functions, regardless of the magnitudes of the eigenvalues of the corresponding coefficient matrix. Here, we couple an existing solver for scalar equations which exploits this observation with a well-known technique for transforming a system of linear ordinary differential equations into scalar form. The result is a method for solving a large class of systems of linear ordinary differential equations in time independent of the magnitudes of the eigenvalues of their coefficient matrices. We discuss the results of numerical experiments demonstrating the properties of our algorithm.

Multi-level modeling is an important approach for analyzing complex survey data using multi-stage sampling. However, estimation of multi-level models can be challenging when we combine several datasets with distinct hierarchies with sampling weights. This paper presents a method for combining multiple datasets with different hierarchical structures due to distinct informative sampling designs for the same survey. To develop an approach with complete generality, we propose to define a pseudo-cluster, a cluster containing only a singleton observation, to unify the data structure and thereby enable estimation of multi-level models incorporating sampling weights across the combined sample. We justify incorporating sampling weights at each level of the hierarchical model and in doing-so define a pseudo-likelihood estimation procedure. Simulation studies are used to illustrate the effect of incorporating sampling designs in this challenging multi-level modeling scenario. We demonstrate in the simulation studies that considering a linear mixed model with sampling weights provides unbiased estimates of model parameters and enhances the estimation of the variance components of the random effects. The proposed method is illustrated through a novel application from the National Survey of Healthcare Organizations and Systems that sought to determine which organizational characteristics or traits, as measured in the surveys, have the strongest average relationship to the percentage of depression and anxiety diagnoses in physician practices in the US.

It is known that difference equations generated as the Newton-Raphson iteration for quadratic equations are solvable in closed form, and the solution can be constructed from linear three-term recurrence relations with constant coefficients. We show that the same construction for four-term recurrence relations gives the solution to the initial value problem of difference equations similar to the Newton-Raphson iteration for cubic equations. In many cases, the solution converges to a root of the cubic equation and the convergence rate is quadratic.

In this paper, a high-order approximation to Caputo-type time-fractional diffusion equations involving an initial-time singularity of the solution is proposed. At first, we employ a numerical algorithm based on the Lagrange polynomial interpolation to approximate the Caputo derivative on the non-uniform mesh. Then truncation error rate and the optimal grading constant of the approximation on a graded mesh are obtained as $\min\{4-\alpha,r\alpha\}$ and $\frac{4-\alpha}{\alpha}$, respectively, where $\alpha\in(0,1)$ is the order of fractional derivative and $r\geq 1$ is the mesh grading parameter. Using this new approximation, a difference scheme for the Caputo-type time-fractional diffusion equation on graded temporal mesh is formulated. The scheme proves to be uniquely solvable for general $r$. Then we derive the unconditional stability of the scheme on uniform mesh. The convergence of the scheme, in particular for $r=1$, is analyzed for non-smooth solutions and concluded for smooth solutions. Finally, the accuracy of the scheme is verified by analyzing the error through a few numerical examples.

Over the last two decades, the field of geometric curve evolutions has attracted significant attention from scientific computing. One of the most popular numerical methods for solving geometric flows is the so-called BGN scheme, which was proposed by Barrett, Garcke, and Nurnberg (J. Comput. Phys., 222 (2007), pp. 441{467), due to its favorable properties (e.g., its computational efficiency and the good mesh property). However, the BGN scheme is limited to first-order accuracy in time, and how to develop a higher-order numerical scheme is challenging. In this paper, we propose a fully discrete, temporal second-order parametric finite element method, which incorporates a mesh regularization technique when necessary, for solving geometric flows of curves. The scheme is constructed based on the BGN formulation and a semi-implicit Crank-Nicolson leap-frog time stepping discretization as well as a linear finite element approximation in space. More importantly, we point out that the shape metrics, such as manifold distance and Hausdorff distance, instead of function norms, should be employed to measure numerical errors. Extensive numerical experiments demonstrate that the proposed BGN-based scheme is second-order accurate in time in terms of shape metrics. Moreover, by employing the classical BGN scheme as a mesh regularization technique when necessary, our proposed second-order scheme exhibits good properties with respect to the mesh distribution.

Dye experimentation is a widely used method in experimental fluid mechanics for flow analysis or for the study of the transport of particles within a fluid. This technique is particularly useful in biomedical diagnostic applications ranging from hemodynamic analysis of cardiovascular systems to ocular circulation. However, simulating dyes governed by convection-diffusion partial differential equations (PDEs) can also be a useful post-processing analysis approach for computational fluid dynamics (CFD) applications. Such simulations can be used to identify the relative significance of different spatial subregions in particular time intervals of interest in an unsteady flow field. Additionally, dye evolution is closely related to non-discrete particle residence time (PRT) calculations that are governed by similar PDEs. This contribution introduces a pseudo-spectral method based on Fourier continuation (FC) for conducting dye simulations and non-discrete particle residence time calculations without numerical diffusion errors. Convergence and error analyses are performed with both manufactured and analytical solutions. The methodology is applied to three distinct physical/physiological cases: 1) flow over a two-dimensional (2D) cavity; 2) pulsatile flow in a simplified partially-grafted aortic dissection model; and 3) non-Newtonian blood flow in a Fontan graft. Although velocity data is provided in this work by numerical simulation, the proposed approach can also be applied to velocity data collected through experimental techniques such as from particle image velocimetry.