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This paper reports on the historical development of the Runge-Kutta methods beginning with the simple Euler method up to an embedded 13-stage method. Moreover, the design and the use of those methods under error order, stability and computation time conditions is edited for students of numerical analysis at undergraduate level. The second part presents applications in natural sciences, compares different methods and illustrates some of the difficulties of numerical solutions.
The estimation of a log-concave density on R is a canonical problem in the area of shape-constrained nonparametric inference. We present a Bayesian nonparametric approach to this problem based on an exponentiated Dirichlet process mixture prior and show that the posterior distribution converges to the log-concave truth at the (near-) minimax rate in Hellinger distance. Our proof proceeds by establishing a general contraction result based on the log-concave maximum likelihood estimator that prevents the need for further metric entropy calculations. We further present computationally more feasible approximations and both an empirical and hierarchical Bayes approach. All priors are illustrated numerically via simulations.
In 1914 Bohr proved that there is an r ∈ (0, 1) such that if a power series converges in the unit disk and its sum has modulus less than 1 then, for |z| < r, the sum of absolute values of its terms is again less than 1. Recently analogous results were obtained for functions of several variables. The aim of this paper is to comprehend the theorem of Bohr in the context of solutions to second order elliptic equations meeting the maximum principle.
The paper is devoted to pseudodifferential boundary value problems in domains with singular points on the boundary. The tangent cone at a singular point is allowed to degenerate. In particular, the boundary may rotate and oscillate in a neighbourhood of such a point. We show a criterion for the Fredholm property of a boundary value problem and derive estimates of solutions close to singular points.
We study the Cauchy problem for a nonlinear elliptic equation with data on a piece S of the boundary surface partial derivative X. By the Cauchy problem is meant any boundary value problem for an unknown function u in a domain X with the property that the data on S, if combined with the differential equations in X, allows one to determine all derivatives of u on S by means of functional equations. In the case of real analytic data of the Cauchy problem, the existence of a local solution near S is guaranteed by the Cauchy-Kovalevskaya theorem. We discuss a variational setting of the Cauchy problem which always possesses a generalized solution.
Let v be a valuation of terms of type tau, assigning to each term t of type tau a value v(t) greater than or equal to 0. Let k greater than or equal to 1 be a natural number. An identity s approximate to t of type tau is called k- normal if either s = t or both s and t have value greater than or equal to k, and otherwise is called non-k-normal. A variety V of type tau is said to be k-normal if all its identities are k-normal, and non-k-normal otherwise. In the latter case, there is a unique smallest k-normal variety N-k(A) (V) to contain V , called the k-normalization of V. Inthe case k = 1, for the usual depth valuation of terms, these notions coincide with the well-known concepts of normal identity, normal variety, and normalization of a variety. I. Chajda has characterized the normalization of a variety by means of choice algebras. In this paper we generalize his results to a characterization of the k-normalization of a variety, using k-choice algebras. We also introduce the concept of a k-inflation algebra, and for the case that v is the usual depth valuation of terms, we prove that a variety V is k-normal iff it is closed under the formation of k- inflations, and that the k-normalization of V consists precisely of all homomorphic images of k-inflations of algebras in V
The generalized hybrid Monte Carlo (GHMC) method combines Metropolis corrected constant energy simulations with a partial random refreshment step in the particle momenta. The standard detailed balance condition requires that momenta are negated upon rejection of a molecular dynamics proposal step. The implication is a trajectory reversal upon rejection, which is undesirable when interpreting GHMC as thermostated molecular dynamics. We show that a modified detailed balance condition can be used to implement GHMC without momentum flips. The same modification can be applied to the generalized shadow hybrid Monte Carlo (GSHMC) method. Numerical results indicate that GHMC/GSHMC implementations with momentum flip display a favorable behavior in terms of sampling efficiency, i.e., the traditional GHMC/GSHMC implementations with momentum flip got the advantage of a higher acceptance rate and faster decorrelation of Monte Carlo samples. The difference is more pronounced for GHMC. We also numerically investigate the behavior of the GHMC method as a Langevin-type thermostat. We find that the GHMC method without momentum flip interferes less with the underlying stochastic molecular dynamics in terms of autocorrelation functions and it to be preferred over the GHMC method with momentum flip. The same finding applies to GSHMC.
The Net Reclassification Improvement (NRI) has become a popular metric for evaluating improvement in disease prediction models through the past years. The concept is relatively straightforward but usage and interpretation has been different across studies. While no thresholds exist for evaluating the degree of improvement, many studies have relied solely on the significance of the NRI estimate. However, recent studies recommend that statistical testing with the NRI should be avoided. We propose using confidence ellipses around the estimated values of event and non-event NRIs which might provide the best measure of variability around the point estimates. Our developments are illustrated using practical examples from EPIC-Potsdam study.
We consider a class of ergodic Hamilton-Jacobi-Bellman (HJB) equations, related to large time asymptotics of non-smooth multiplicative functional of difusion processes. Under suitable ergodicity assumptions on the underlying difusion, we show existence of these asymptotics, and that they solve the related HJB equation in the viscosity sense.
Model-informed precision dosing (MIPD) is a quantitative dosing framework that combines prior knowledge on the drug-disease-patient system with patient data from therapeutic drug/ biomarker monitoring (TDM) to support individualized dosing in ongoing treatment. Structural models and prior parameter distributions used in MIPD approaches typically build on prior clinical trials that involve only a limited number of patients selected according to some exclusion/inclusion criteria. Compared to the prior clinical trial population, the patient population in clinical practice can be expected to also include altered behavior and/or increased interindividual variability, the extent of which, however, is typically unknown. Here, we address the question of how to adapt and refine models on the level of the model parameters to better reflect this real-world diversity. We propose an approach for continued learning across patients during MIPD using a sequential hierarchical Bayesian framework. The approach builds on two stages to separate the update of the individual patient parameters from updating the population parameters. Consequently, it enables continued learning across hospitals or study centers, because only summary patient data (on the level of model parameters) need to be shared, but no individual TDM data. We illustrate this continued learning approach with neutrophil-guided dosing of paclitaxel. The present study constitutes an important step toward building confidence in MIPD and eventually establishing MIPD increasingly in everyday therapeutic use.
Transition path theory (TPT) for diffusion processes is a framework for analyzing the transitions of multiscale ergodic diffusion processes between disjoint metastable subsets of state space. Most methods for applying TPT involve the construction of a Markov state model on a discretization of state space that approximates the underlying diffusion process. However, the assumption of Markovianity is difficult to verify in practice, and there are to date no known error bounds or convergence results for these methods. We propose a Monte Carlo method for approximating the forward committor, probability current, and streamlines from TPT for diffusion processes. Our method uses only sample trajectory data and partitions of state space based on Voronoi tessellations. It does not require the construction of a Markovian approximating process. We rigorously prove error bounds for the approximate TPT objects and use these bounds to show convergence to their exact counterparts in the limit of arbitrarily fine discretization. We illustrate some features of our method by application to a process that solves the Smoluchowski equation on a triple-well potential.
For each compact subset K of the complex plane C which does not surround zero, the Riemann surface Sζ of the Riemann zeta function restricted to the critical half-strip 0 < Rs < 1/2 contains infinitely many schlicht copies of K lying ‘over’ K. If Sζ also contains at least one such copy, for some K which surrounds zero, then the Riemann hypothesis fails.
A function has vanishing mean oscillation (VMO) on R up(n) if its mean oscillation - the local average of its pointwise deviation from its mean value - both is uniformly bounded over all cubes within R up(n) and converges to zero with the volume of the cube. The more restrictive class of functions with vanishing lower oscillation (VLO) arises when the mean value is replaced by the minimum value in this definition. It is shown here that each VMO function is the difference of two functions in VLO.
We study those nonlinear partial differential equations which appear as Euler-Lagrange equations of variational problems. On defining weak boundary values of solutions to such equations we initiate the theory of Lagrangian boundary value problems in spaces of appropriate smoothness. We also analyse if the concept of mapping degree of current importance applies to Lagrangian problems.
We consider the problem of discrete time filtering (intermittent data assimilation) for differential equation models and discuss methods for its numerical approximation. The focus is on methods based on ensemble/particle techniques and on the ensemble Kalman filter technique in particular. We summarize as well as extend recent work on continuous ensemble Kalman filter formulations, which provide a concise dynamical systems formulation of the combined dynamics-assimilation problem. Possible extensions to fully nonlinear ensemble/particle based filters are also outlined using the framework of optimal transportation theory.
A new efficient algorithm is presented for joint diagonalization of several matrices. The algorithm is based on the Frobenius-norm formulation of the joint diagonalization problem, and addresses diagonalization with a general, non- orthogonal transformation. The iterative scheme of the algorithm is based on a multiplicative update which ensures the invertibility of the diagonalizer. The algorithm's efficiency stems from the special approximation of the cost function resulting in a sparse, block-diagonal Hessian to be used in the computation of the quasi-Newton update step. Extensive numerical simulations illustrate the performance of the algorithm and provide a comparison to other leading diagonalization methods. The results of such comparison demonstrate that the proposed algorithm is a viable alternative to existing state-of-the-art joint diagonalization algorithms. The practical use of our algorithm is shown for blind source separation problems
We show a Lefschetz fixed point formula for holomorphic functions in a bounded domain D with smooth boundary in the complex plane. To introduce the Lefschetz number for a holomorphic map of D, we make use of the Bergman kernal of this domain. The Lefschetz number is proved to be the sum of usual contributions of fixed points of the map in D and contributions of boundary fixed points, these latter being different for attracting and repulsing fixed points.
We generalize the popular ensemble Kalman filter to an ensemble transform filter, in which the prior distribution can take the form of a Gaussian mixture or a Gaussian kernel density estimator. The design of the filter is based on a continuous formulation of the Bayesian filter analysis step. We call the new filter algorithm the ensemble Gaussian-mixture filter (EGMF). The EGMF is implemented for three simple test problems (Brownian dynamics in one dimension, Langevin dynamics in two dimensions and the three-dimensional Lorenz-63 model). It is demonstrated that the EGMF is capable of tracking systems with non-Gaussian uni- and multimodal ensemble distributions.
Parallel File Systems like PVFS2 are a necessary compo nent for high-performance computing. The design of ef ;cient communication layers for these systems is still of great research interest. This paper presents a low- latency messaging method for PVFS2 dedicated for Gigabit Ether net networks and discusses relevant design issues. In con trast to other approaches, we argue that zero-copying can be achieved also for big messages without use of a rendez vous protocol. Further, ef;ciency within the communica tion layer like a small call stack plays an important role.
We elaborate a boundary Fourier method for studying an analogue of the Hilbert problem for analytic functions within the framework of generalised Cauchy-Riemann equations. The boundary value problem need not satisfy the Shapiro-Lopatinskij condition and so it fails to be Fredholm in Sobolev spaces. We show a solvability condition of the Hilbert problem, which looks like those for ill-posed
problems, and construct an explicit formula for approximate solutions.
We prove a homology vanishing theorem for graphs with positive Bakry-' Emery curvature, analogous to a classic result of Bochner on manifolds [3]. Specifically, we prove that if a graph has positive curvature at every vertex, then its first homology group is trivial, where the notion of homology that we use for graphs is the path homology developed by Grigor'yan, Lin, Muranov, and Yau [11]. We moreover prove that the fundamental group is finite for graphs with positive Bakry-' Emery curvature, analogous to a classic result of Myers on manifolds [22]. The proofs draw on several separate areas of graph theory, including graph coverings, gain graphs, and cycle spaces, in addition to the Bakry-Emery curvature, path homology, and graph homotopy. The main results follow as a consequence of several different relationships developed among these different areas. Specifically, we show that a graph with positive curvature cannot have a non-trivial infinite cover preserving 3-cycles and 4-cycles, and give a combinatorial interpretation of the first path homology in terms of the cycle space of a graph. Furthermore, we relate gain graphs to graph homotopy and the fundamental group developed by Grigor'yan, Lin, Muranov, and Yau [12], and obtain an alternative proof of their result that the abelianization of the fundamental group of a graph is isomorphic to the first path homology over the integers.
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in these individuals. The ecological parameters of the individual dynamics depend on the number of cells of each type contained by the individual and the cell dynamics depends on the trait of the invaded individual. Our models are rooted in the microscopic description of a random (discrete) population of individuals characterized by one or several adaptive traits and cells characterized by their type. The population is modeled as a stochastic point process whose generator captures the probabilistic dynamics over continuous time of birth, mutation and death for individuals and birth and death for cells. The interaction between individuals (resp. between cells) is described by a competition between individual traits (resp. between cell types). We look for tractable large population approximations. By combining various scalings on population size, birth and death rates and mutation step, the single microscopic model is shown to lead to contrasting nonlinear macroscopic limits of different nature: deterministic approximations, in the form of ordinary, integro- or partial differential equations, or probabilistic ones, like stochastic partial differential equations or superprocesses. The study of the long time behavior of these processes seems very hard and we only develop some simple cases enlightening the difficulties involved.