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We consider a Bayesian functional data analysis for observations measured as extremely long sequences. Splitting the sequence into a number of small windows with manageable length, the windows may not be independent especially when they are neighboring to each other. We propose to utilize Bayesian smoothing splines to estimate individual functional patterns within each window and to establish transition models for parameters involved in each window to address the dependent structure between windows. The functional difference of groups of individuals at each window can be evaluated by Bayes Factor based on Markov Chain Monte Carlo samples in the analysis. In this paper, we examine the proposed method through simulation studies and apply it to identify differentially methylated genetic regions in TCGA lung adenocarcinoma data.

Most physical processes posses structural properties such as constant energies, volumes, and other invariants over time. When learning models of such dynamical systems, it is critical to respect these invariants to ensure accurate predictions and physically meaningful behavior. Strikingly, state-of-the-art methods in Gaussian process (GP) dynamics model learning are not addressing this issue. On the other hand, classical numerical integrators are specifically designed to preserve these crucial properties through time. We propose to combine the advantages of GPs as function approximators with structure preserving numerical integrators for dynamical systems, such as Runge-Kutta methods. These integrators assume access to the ground truth dynamics and require evaluations of intermediate and future time steps that are unknown in a learning-based scenario. This makes direct inference of the GP dynamics, with embedded numerical scheme, intractable. Our key technical contribution is the evaluation of the implicitly defined Runge-Kutta transition probability. In a nutshell, we introduce an implicit layer for GP regression, which is embedded into a variational inference-based model learning scheme.

Safe autonomous navigation in unknown environments is an important problem for ground, aerial, and underwater robots. This paper proposes techniques to learn the dynamics models of a mobile robot from trajectory data and synthesize a tracking controller with safety and stability guarantees. The state of a mobile robot usually contains its position, orientation, and generalized velocity and satisfies Hamilton's equations of motion. Instead of a hand-derived dynamics model, we use a dataset of state-control trajectories to train a translation-equivariant nonlinear Hamiltonian model represented as a neural ordinary differential equation (ODE) network. The learned Hamiltonian model is used to synthesize an energy-shaping passivity-based controller and derive conditions which guarantee safe regulation to a desired reference pose. Finally, we enable adaptive tracking of a desired path, subject to safety constraints obtained from obstacle distance measurements. The trade-off between the system's energy level and the distance to safety constraint violation is used to adaptively govern the reference pose along the desired path. Our safe adaptive controller is demonstrated on a simulated hexarotor robot navigating in unknown complex environments.

Background: It has long been advised to account for baseline covariates in the analysis of confirmatory randomised trials, with the main statistical justifications being that this increases power and, when a randomisation scheme balanced covariates, permits a valid estimate of experimental error. There are various methods available to account for covariates but it is not clear how to choose among them. Methods: Taking the perspective of writing a statistical analysis plan, we consider how to choose between the three most promising broad approaches: direct adjustment, standardisation and inverse-probability-of-treatment weighting. Results: The three approaches are similar in being asymptotically efficient, in losing efficiency with mis-specified covariate functions, and in handling designed balance. If a marginal estimand is targeted (for example, a risk difference or survival difference), then direct adjustment should be avoided because it involves fitting non-standard models that are subject to convergence issues. Convergence is most likely with IPTW. Robust standard errors used by IPTW are anti-conservative at small sample sizes. All approaches can use similar methods to handle missing covariate data. With missing outcome data, each method has its own way to estimate a treatment effect in the all-randomised population. We illustrate some issues in a reanalysis of GetTested, a randomised trial designed to assess the effectiveness of an electonic sexually-transmitted-infection testing and results service. Conclusions: No single approach is always best: the choice will depend on the trial context. We encourage trialists to consider all three methods more routinely.

We investigate data-driven forward-inverse problems for Yajima-Oikawa system by employing two technologies which improve the performance of PINN in deep physics-informed neural network (PINN), namely neuron-wise locally adaptive activation functions and L2 norm parameter regularization. In particular, we not only recover three different forms of vector rogue waves (RWs) in the forward problem of Yajima-Oikawa (YO) system, including bright-bright RWs, intermediatebright RWs and dark-bright RWs, but also study the inverse problem of YO system by data-driven with noise of different intensity. Compared with PINN method using only locally adaptive activation function, the PINN method with two strategies shows amazing robustness when studying the inverse problem of YO system with noisy training data, that is, the improved PINN model proposed by us has excellent noise immunity. The asymptotic analysis of wavenumber k and the MI analysis for YO system with unknown parameters are derived systematically by applying the linearized instability analysis on plane wave.

We propose optimal Bayesian two-sample tests for testing equality of high-dimensional mean vectors and covariance matrices between two populations. In many applications including genomics and medical imaging, it is natural to assume that only a few entries of two mean vectors or covariance matrices are different. Many existing tests that rely on aggregating the difference between empirical means or covariance matrices are not optimal or yield low power under such setups. Motivated by this, we develop Bayesian two-sample tests employing a divide-and-conquer idea, which is powerful especially when the difference between two populations is sparse but large. The proposed two-sample tests manifest closed forms of Bayes factors and allow scalable computations even in high-dimensions. We prove that the proposed tests are consistent under relatively mild conditions compared to existing tests in the literature. Furthermore, the testable regions from the proposed tests turn out to be optimal in terms of rates. Simulation studies show clear advantages of the proposed tests over other state-of-the-art methods in various scenarios. Our tests are also applied to the analysis of the gene expression data of two cancer data sets.

Optimization of hyperparameters of Gaussian process regression (GPR) determines success or failure of the application of the method. Such optimization is difficult with sparse data, in particular in high-dimensional spaces where the data sparsity issue cannot be resolved by adding more data. We show that parameter optimization is facilitated by rectangularization of the defining equation of GPR. On the example of a 15-dimensional molecular potential energy surface we demonstrate that this approach allows effective hyperparameter tuning even with very sparse data.

In the context of Bayesian inversion for scientific and engineering modeling, Markov chain Monte Carlo sampling strategies are the benchmark due to their flexibility and robustness in dealing with arbitrary posterior probability density functions (PDFs). However, these algorithms been shown to be inefficient when sampling from posterior distributions that are high-dimensional or exhibit multi-modality and/or strong parameter correlations. In such contexts, the sequential Monte Carlo technique of transitional Markov chain Monte Carlo (TMCMC) provides a more efficient alternative. Despite the recent applicability for Bayesian updating and model selection across a variety of disciplines, TMCMC may require a prohibitive number of tempering stages when the prior PDF is significantly different from the target posterior. Furthermore, the need to start with an initial set of samples from the prior distribution may present a challenge when dealing with implicit priors, e.g. based on feasible regions. Finally, TMCMC can not be used for inverse problems with improper prior PDFs that represent lack of prior knowledge on all or a subset of parameters. In this investigation, a generalization of TMCMC that alleviates such challenges and limitations is proposed, resulting in a tempering sampling strategy of enhanced robustness and computational efficiency. Convergence analysis of the proposed sequential Monte Carlo algorithm is presented, proving that the distance between the intermediate distributions and the target posterior distribution monotonically decreases as the algorithm proceeds. The enhanced efficiency associated with the proposed generalization is highlighted through a series of test inverse problems and an engineering application in the oil and gas industry.

Dynamic treatment regimes (DTRs) consist of a sequence of decision rules, one per stage of intervention, that finds effective treatments for individual patients according to patient information history. DTRs can be estimated from models which include the interaction between treatment and a small number of covariates which are often chosen a priori. However, with increasingly large and complex data being collected, it is difficult to know which prognostic factors might be relevant in the treatment rule. Therefore, a more data-driven approach of selecting these covariates might improve the estimated decision rules and simplify models to make them easier to interpret. We propose a variable selection method for DTR estimation using penalized dynamic weighted least squares. Our method has the strong heredity property, that is, an interaction term can be included in the model only if the corresponding main terms have also been selected. Through simulations, we show our method has both the double robustness property and the oracle property, and the newly proposed methods compare favorably with other variable selection approaches.

Matter evolved under influence of gravity from minuscule density fluctuations. Non-perturbative structure formed hierarchically over all scales, and developed non-Gaussian features in the Universe, known as the Cosmic Web. To fully understand the structure formation of the Universe is one of the holy grails of modern astrophysics. Astrophysicists survey large volumes of the Universe and employ a large ensemble of computer simulations to compare with the observed data in order to extract the full information of our own Universe. However, to evolve trillions of galaxies over billions of years even with the simplest physics is a daunting task. We build a deep neural network, the Deep Density Displacement Model (hereafter D$^3$M), to predict the non-linear structure formation of the Universe from simple linear perturbation theory. Our extensive analysis, demonstrates that D$^3$M outperforms the second order perturbation theory (hereafter 2LPT), the commonly used fast approximate simulation method, in point-wise comparison, 2-point correlation, and 3-point correlation. We also show that D$^3$M is able to accurately extrapolate far beyond its training data, and predict structure formation for significantly different cosmological parameters. Our study proves, for the first time, that deep learning is a practical and accurate alternative to approximate simulations of the gravitational structure formation of the Universe.