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We provide a class of diffusion processes for continuous time-varying multivariate angular data with explicit transition probability densities, enabling exact likelihood inference. The presented diffusions are time-reversible and can be constructed for any pre-specified stationary distribution on the torus, including highly-multimodal mixtures. We give results on asymptotic likelihood theory allowing one-sample inference and tests of linear hypotheses for $k$ groups of diffusions, including homogeneity. We show that exact and direct diffusion bridge simulation is possible too. A class of circular jump processes with similar properties is also proposed. Several numerical experiments illustrate the methodology for the circular and two-dimensional torus cases. The new family of diffusions is applied (i) to test several homogeneity hypotheses on the movement of ants and (ii) to simulate bridges between the three-dimensional backbones of two related proteins., Comment: 23 pages, 7 figures, 2 tables

Stochastic differential equations provide a powerful tool for modelling dynamic phenomena affected by random noise. In case of repeated observations of time series for several experimental units, it is often the case that some of the parameters vary between the individual experimental units, which has motivated a considerable interest in stochastic differential equations with mixed effects, where a subset of the parameters are random. These models enable simultaneous representation of randomness in the dynamics and variability between experimental units. When the data are observations at discrete time points, the likelihood function is only rarely explicitly available, so for likelihood-based inference to be feasible, numerical methods are needed. We present Gibbs samplers and stochastic EM-algorithms based on augmented data obtained by the simple method for simulation of diffusion bridges in Bladt and S{\o}rensen (2014). This method is easy to implement and has no tuning parameters. The method is, moreover, computationally efficient at low sampling frequencies because the computing time increases linearly with the time between observations. The algorithms can be extended to models with measurement errors. The Gibbs sampler as well as the EM-algorithm are shown to simplify considerably for exponential families of diffusion processes, including many models used in practice. In a simulation study, the estimation methods are shown to work well for Ornstein-Uhlenbeck processes and t-diffusions with mixed effects. Finally, the Gibbs sampler is applied to neuronal data.

A general theory of efficient estimation for ergodic diffusion processes sampled at high frequency with an infinite time horizon is presented. High frequency sampling is common in many applications, with finance as a prominent example. The theory is formulated in term of approximate martingale estimating functions and covers a large class of estimators including most of the previously proposed estimators for diffusion processes. Easily checked conditions ensuring that an estimating function is an approximate martingale are derived, and general conditions ensuring consistency and asymptotic normality of estimators are given. Most importantly, simple conditions are given that ensure rate optimality and efficiency. Rate optimal estimators of parameters in the diffusion coefficient converge faster than estimators of drift coefficient parameters because they take advantage of the information in the quadratic variation. The conditions facilitate the choice among the multitude of estimators that have been proposed for diffusion models. Optimal martingale estimating functions in the sense of Godambe and Heyde and their high frequency approximations are, under weak conditions, shown to satisfy the conditions for rate optimality and efficiency. This provides a natural feasible method of constructing explicit rate optimal and efficient estimating functions by solving a linear equation.

Control of magnetization and electric polarization is attractive in relation to tailoring materials for data storage and devices such as sensors or antennae. In magnetoelectric materials, these degrees of freedom are closely coupled, allowing polarization to be controlled by a magnetic field, and magnetization by an electric field, but the magnitude of the effect remains a challenge in the case of single-phase magnetoelectrics for application. We demonstrate that the magnetoelectric properties of the mixed-anisotropy antiferromagnet LiNi$_{1-x}$Fe$_x$PO$_4$ are profoundly affected by replacing a fraction of the Ni$^{2+}$ ions with Fe$^{2+}$ on the transition metal site. This introduces random site-dependent single-ion anisotropy energies and causes a lowering of the magnetic symmetry of the system. In turn, magnetoelectric couplings that are symmetry-forbidden in the parent compounds, LiNiPO$_4$ and LiFePO$_4$, are unlocked and the dominant coupling is enhanced by two orders of magnitude. Our results demonstrate the potential of mixed-anisotropy magnets for tuning magnetoelectric properties.

We present a method to manipulate the final morphology of roll-to-roll slot-die coated poly(3-hexylthiophene) (P3HT) by optically exciting the p-type polymer in solution while coating. Our results provide a comprehensive picture of the entire knowledge chain, from demonstrating how to apply our method to a fundamental understanding of the changes in morphology and physical properties induced by exciting P3HT while coating. By combining results from density functional theory and molecular dynamics simulations with a variety of X-ray experiments, absorption spectroscopy, and THz spectroscopy, we demonstrate the relationship between morphology and physical properties of the thin film. Specifically, in P3HT films excited with light during deposition, we observe changes in crystallinity and texture with more face-on orientation and increased out-of-plane charge mobility.

This paper obtains asymptotic results for parametric inference using prediction-based estimating functions when the data are high frequency observations of a diffusion process with an infinite time horizon. Specifically, the data are observations of a diffusion process at $n$ equidistant time points $\Delta_n i$, and the asymptotic scenario is $\Delta_n \to 0$ and $n\Delta_n \to \infty$. For a useful and tractable classes of prediction-based estimating functions, existence of a consistent estimator is proved under standard weak regularity conditions on the diffusion process and the estimating function. Asymptotic normality of the estimator is established under the additional rate condition $n\Delta_n^3 \to 0$. The prediction-based estimating functions are approximate martingale estimating functions to a smaller order than what has previously been studied, and new non-standard asymptotic theory is needed. A Monte Carlo method for calculating the asymptotic variance of the estimators is proposed., Comment: 26 pages

Neutron diffraction with static and pulsed magnetic fields is used to directly probe the magnetic structures in LiNiPO$_4$ up to 25T and 42T, respectively. By combining these results with magnetometry and electric polarization measurements under pulsed fields, the magnetic and magnetoelectric phases are investigated up to 56T applied along the easy $c$-axis. In addition to the already known transitions at lower fields, three new ones are reported at 37.6, 39.4 and 54T. Ordering vectors are identified with ${\bf Q}_{\mathrm{VI}}$ = (0, 1/3, 0) in the interval 37.6--39.4T and ${\bf Q}_{\mathrm{VII}}$ = (0, 0, 0) in the interval 39.4-54T. A quadratic magnetoelectric effect is discovered in the ${\bf Q}_{\mathrm{VII}}$ = (0, 0, 0) phase and the field-dependence of the induced electric polarization is described using a simple mean-field model. The observed magnetic structure and magnetoelectric tensor elements point to a change in the lattice symmetry in this phase. We speculate on the possible physical mechanism responsible for the magnetoelectric effect in LiNiPO4.

Diffusions are a fundamental class of models in many fields, including finance, engineering, and biology. Simulating diffusions is challenging as their sample paths are infinite-dimensional and their transition functions are typically intractable. In statistical settings such as parameter inference for discretely observed diffusions, we require simulation techniques for diffusions conditioned on hitting a given endpoint, which introduces further complication. In this paper we introduce a Markov chain Monte Carlo algorithm for simulating bridges of ergodic diffusions which (i) is exact in the sense that there is no discretisation error, (ii) has computational cost that is linear in the duration of the bridges, and (iii) provides bounds on local maxima and minima of the simulated trajectory. Our approach works directly on diffusion path space, by constructing a proposal (which we term a confluence) that is then corrected with an accept/reject step in a pseudo-marginal algorithm. Our method requires only the simulation of unconditioned diffusion sample paths. We apply our approach to the simulation of Langevin diffusion bridges, a practical problem arising naturally in many situations, such as statistical inference in distributed settings., Comment: Significant revision of prior submission, with an improved methodology which is far broader in its applicability. Updated author listing. 19 pages, 5 figures

Magnetic structures are investigated by means of neutron diffraction to shine a light on the intricate details that are believed to be key to understanding the magnetoelectric effect in LiCoPO$_4$ . At zero field, a spontaneous spin canting of $\varphi = 7(1)^{\circ}$ is found. The spins tilt away from the easy $b$-axis toward $c$. Symmetry considerations lead to the magnetic point group $m'_z$, which is consistent with the previously observed magnetoelectric tensor form and weak ferromagnetic moment along $b$. For magnetic fields applied along $a$, the induced ferromagnetic moment couples via the Dzyaloshinskii-Moriya interaction to yield an additional field-induced spin canting. An upper limit to the size of the interaction is estimated from the canting angle.

This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction of ergodic diffusions with stationary distributions equal to well-known directional distributions, which can be regarded as toroidal analogues of the Ornstein-Uhlenbeck process. The important challenges that arise in the estimation of the diffusion parameters require the consideration of tractable approximate likelihoods and, among the several approaches introduced, the one yielding a specific approximation to the transition density of the wrapped normal process is shown to give the best empirical performance on average. This provides the methodological building block for Evolutionary Torus Dynamic Bayesian Network (ETDBN), a hidden Markov model for protein evolution that emits a wrapped normal process and two continuous-time Markov chains per hidden state. The chapter describes the main features of ETDBN, which allows for both "smooth" conformational changes and "catastrophic" conformational jumps, and several empirical benchmarks. The insights into the relationship between sequence and structure evolution that ETDBN provides are illustrated in a case study., Comment: 26 pages, 13 figures

Asymptotic statistical theory for estimating functions is reviewed in a generality suitable for stochastic processes. Conditions concerning existence of a consistent estimator, uniqueness, rate of convergence, and the asymptotic distribution are treated separately. Our conditions are not minimal, but can be verified for many interesting stochastic process models. Several examples illustrate the wide applicability of the theory and why the generality is needed.

Asymptotic theory for approximate martingale estimating functions is generalised to diffusions with finite-activity jumps, when the sampling frequency and terminal sampling time go to infinity. Rate optimality and efficiency are of particular concern. Under mild assumptions, it is shown that estimators of drift, diffusion, and jump parameters are consistent and asymptotically normal, as well as rate-optimal for the drift and jump parameters. Additional conditions are derived, which ensure rate-optimality for the diffusion parameter as well as efficiency for all parameters. The findings indicate a potentially fruitful direction for the further development of estimation for jump-diffusions.

We introduce stochastic models for continuous-time evolution of angles and develop their estimation. We focus on studying Langevin diffusions with stationary distributions equal to well-known distributions from directional statistics, since such diffusions can be regarded as toroidal analogues of the Ornstein-Uhlenbeck process. Their likelihood function is a product of transition densities with no analytical expression, but that can be calculated by solving the Fokker-Planck equation numerically through adequate schemes. We propose three approximate likelihoods that are computationally tractable: (i) a likelihood based on the stationary distribution; (ii) toroidal adaptations of the Euler and Shoji-Ozaki pseudo-likelihoods; (iii) a likelihood based on a specific approximation to the transition density of the wrapped normal process. A simulation study compares, in dimensions one and two, the approximate transition densities to the exact ones, and investigates the empirical performance of the approximate likelihoods. Finally, two diffusions are used to model the evolution of the backbone angles of the protein G (PDB identifier 1GB1) during a molecular dynamics simulation. The software package sdetorus implements the estimation methods and applications presented in the paper., Comment: 29 pages, 8 figures, 5 tables

Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. The evolutionary trajectory between the two structures in the protein pair is treated as a random walk in dihedral angle space, which is modelled using a novel angular diffusion process on the two-dimensional torus. Coupling sequence and structure evolution in our model allows for modelling both "smooth" conformational changes and "catastrophic" conformational jumps, conditioned on the amino acid changes. The model has interpretable parameters and is comparatively more realistic than previous stochastic models, providing new insights into the relationship between sequence and structure evolution. For example, using the trained model we were able to identify an apparent sequence-structure evolutionary motif present in a large number of homologous protein pairs. The generative nature of our model enables us to evaluate its validity and its ability to simulate aspects of protein evolution conditioned on an amino acid sequence, a related amino acid sequence, a related structure or any combination thereof., Comment: 23 pages, 10 figures. Supplementary material: 5 pages, 4 figures

Parametric estimation for diffusion processes is considered for high frequency observations over a fixed time interval. The processes solve stochastic differential equations with an unknown parameter in the diffusion coefficient. We find easily verified conditions on approximate martingale estimating functions under which estimators are consistent, rate optimal, and efficient under high frequency (in-fill) asymptotics. The asymptotic distributions of the estimators are shown to be normal variance-mixtures, where the mixing distribution generally depends on the full sample path of the diffusion process over the observation time interval. Utilising the concept of stable convergence, we also obtain the more easily applicable result that for a suitable data dependent normalisation, the estimators converge in distribution to a standard normal distribution. The theory is illustrated by a simulation study comparing an efficient and a non-efficient estimating function for an ergodic and a non-ergodic model., Comment: Published at http://projecteuclid.org/euclid.bj/1489737628 in the Bernoulli Journal ( see http://www.bernoulli-society.org/index.php/publications/bernoulli-journal/bernoulli-journal ) by the International Statistical Institute/Bernoulli Society ( see http://www.bernoulli-society.org )

We propose simple methods for multivariate diffusion bridge simulation, which plays a fundamental role in simulation-based likelihood and Bayesian inference for stochastic differential equations. By a novel application of classical coupling methods, the new approach generalizes a previously proposed simulation method for one-dimensional bridges to the multi-variate setting. First a method of simulating approximate, but often very accurate, diffusion bridges is proposed. These approximate bridges are used as proposal for easily implementable MCMC algorithms that produce exact diffusion bridges. The new method is much more generally applicable than previous methods. Another advantage is that the new method works well for diffusion bridges in long intervals because the computational complexity of the method is linear in the length of the interval. In a simulation study the new method performs well, and its usefulness is illustrated by an application to Bayesian estimation for the multivariate hyperbolic diffusion model., Comment: arXiv admin note: text overlap with arXiv:1403.1762

With a view to statistical inference for discretely observed diffusion models, we propose simple methods of simulating diffusion bridges, approximately and exactly. Diffusion bridge simulation plays a fundamental role in likelihood and Bayesian inference for diffusion processes. First a simple method of simulating approximate diffusion bridges is proposed and studied. Then these approximate bridges are used as proposal for an easily implemented Metropolis-Hastings algorithm that produces exact diffusion bridges. The new method utilizes time-reversibility properties of one-dimensional diffusions and is applicable to all one-dimensional diffusion processes with finite speed-measure. One advantage of the new approach is that simple simulation methods like the Milstein scheme can be applied to bridge simulation. Another advantage over previous bridge simulation methods is that the proposed method works well for diffusion bridges in long intervals because the computational complexity of the method is linear in the length of the interval. For $\rho$-mixing diffusions the approximate method is shown to be particularly accurate for long time intervals. In a simulation study, we investigate the accuracy and efficiency of the approximate method and compare it to exact simulation methods. In the study, our method provides a very good approximation to the distribution of a diffusion bridge for bridges that are likely to occur in applications to statistical inference. To illustrate the usefulness of the new method, we present an EM-algorithm for a discretely observed diffusion process., Comment: Published in at http://dx.doi.org/10.3150/12-BEJ501 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm)

This article demonstrates that flexible and statistically tractable multi-modal diffusion models can be attained by transformation of simple well-known diffusion models such as the Ornstein-Uhlenbeck model, or more generally a Pearson diffusion. The transformed diffusion inherits many properties of the underlying simple diffusion including its mixing rates and distributions of first passage times. Likelihood inference and martingale estimating functions are considered in the case of a discretely observed bimodal diffusion. It is further demonstrated that model parameters can be identified and estimated when the diffusion is observed with additional measurement error. The new approach is applied to molecular dynamics data in form of a reaction coordinate of the small Trp-zipper protein, for which the folding and unfolding rates are estimated. The new models provide a better fit to this type of protein folding data than previous models because the diffusion coefficient is state-dependent., Comment: 18 pages

Statistical inference for discrete time observations of an affine stochastic delay differential equation is considered. The main focus is on maximum pseudo-likelihood estimators, which are easy to calculate in practice. A more general class of prediction-based estimating functions is investigated as well. In particular, the optimal prediction-based estimating function and the asymptotic properties of the estimators are derived. The maximum pseudo-likelihood estimator is a particular case, and an expression is found for the efficiency loss when using the maximum pseudo-likelihood estimator, rather than the computationally more involved optimal prediction-based estimator. The distribution of the pseudo-likelihood estimator is investigated in a simulation study. Two examples of affine stochastic delay equation are considered in detail., Comment: Published in at http://dx.doi.org/10.3150/11-BEJ411 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm)