The ranking of experiments by expected information gain (EIG) in Bayesian experimental design is sensitive to changes in the model's prior distribution, and the approximation of EIG yielded by sampling will have errors similar to the use of a perturbed prior. We define and analyze \emph{robust expected information gain} (REIG), a modification of the objective in EIG maximization by minimizing an affine relaxation of EIG over an ambiguity set of distributions that are close to the original prior in KL-divergence. We show that, when combined with a sampling-based approach to estimating EIG, REIG corresponds to a `log-sum-exp' stabilization of the samples used to estimate EIG, meaning that it can be efficiently implemented in practice. Numerical tests combining REIG with variational nested Monte Carlo (VNMC), adaptive contrastive estimation (ACE) and mutual information neural estimation (MINE) suggest that in practice REIG also compensates for the variability of under-sampled estimators.

As a relatively new field, network neuroscience has tended to focus on aggregate behaviours of the brain averaged over many successive experiments or over long recordings in order to construct robust brain models. These models are limited in their ability to explain dynamic state changes in the brain which occurs spontaneously as a result of normal brain function. Hidden Markov Models (HMMs) trained on neuroimaging time series data have since arisen as a method to produce dynamical models that are easy to train but can be difficult to fully parametrise or analyse. We propose an interpretation of these neural HMMs as multiplex brain state graph models we term Hidden Markov Graph Models (HMGMs). This interpretation allows for dynamic brain activity to be analysed using the full repertoire of network analysis techniques. Furthermore, we propose a general method for selecting HMM hyperparameters in the absence of external data, based on the principle of maximum entropy, and use this to select the number of layers in the multiplex model. We produce a new tool for determining important communities of brain regions using a spatiotemporal random walk-based procedure that takes advantage of the underlying Markov structure of the model. Our analysis of real multi-subject fMRI data provides new results that corroborate the modular processing hypothesis of the brain at rest as well as contributing new evidence of functional overlap between and within dynamic brain state communities. Our analysis pipeline provides a way to characterise dynamic network activity of the brain under novel behaviours or conditions.

We propose a new approach, called as functional deep neural network (FDNN), for classifying multi-dimensional functional data. Specifically, a deep neural network is trained based on the principle components of the training data which shall be used to predict the class label of a future data function. Unlike the popular functional discriminant analysis approaches which rely on Gaussian assumption, the proposed FDNN approach applies to general non-Gaussian multi-dimensional functional data. Moreover, when the log density ratio possesses a locally connected functional modular structure, we show that FDNN achieves minimax optimality. The superiority of our approach is demonstrated through both simulated and real-world datasets.

Hierarchical multi-label classification (HMC) has drawn increasing attention in the past few decades. It is applicable when hierarchical relationships among classes are available and need to be incorporated along with the multi-label classification whereby each object is assigned to one or more classes. There are two key challenges in HMC: i) optimizing the classification accuracy, and meanwhile ii) ensuring the given class hierarchy. To address these challenges, in this article, we introduce a new statistic called the multidimensional local precision rate (mLPR) for each object in each class. We show that classification decisions made by simply sorting objects across classes in descending order of their true mLPRs can, in theory, ensure the class hierarchy and lead to the maximization of CATCH, an objective function we introduce that is related to the area under a hit curve. This approach is the first of its kind that handles both challenges in one objective function without additional constraints, thanks to the desirable statistical properties of CATCH and mLPR. In practice, however, true mLPRs are not available. In response, we introduce HierRank, a new algorithm that maximizes an empirical version of CATCH using estimated mLPRs while respecting the hierarchy. The performance of this approach was evaluated on a synthetic data set and two real data sets; ours was found to be superior to several comparison methods on evaluation criteria based on metrics such as precision, recall, and $F_1$ score.

This paper uses Gaussian mixture model instead of linear Gaussian model to fit the distribution of every node in Bayesian network. We will explain why and how we use Gaussian mixture models in Bayesian network. Meanwhile we propose a new method, called double iteration algorithm, to optimize the mixture model, the double iteration algorithm combines the expectation maximization algorithm and gradient descent algorithm, and it performs perfectly on the Bayesian network with mixture models. In experiments we test the Gaussian mixture model and the optimization algorithm on different graphs which is generated by different structure learning algorithm on real data sets, and give the details of every experiment.

Solving general Markov decision processes (MDPs) is a computationally hard problem. Solving finite-horizon MDPs, on the other hand, is highly tractable with well known polynomial-time algorithms. What drives this extreme disparity, and do problems exist that lie between these diametrically opposed complexities? In this paper we identify and analyse a sub-class of stochastic shortest path problems (SSPs) for general state-action spaces whose dynamics satisfy a particular drift condition. This construction generalises the traditional, temporal notion of a horizon via decreasing reachability: a property called reductivity. It is shown that optimal policies can be recovered in polynomial-time for reductive SSPs -- via an extension of backwards induction -- with an efficient analogue in reductive MDPs. The practical considerations of the proposed approach are discussed, and numerical verification provided on a canonical optimal liquidation problem.

Markov chains are used to model probabilities using information that can be encoded in the current state. Each state has a certain probability of transitioning to each other state, so each time you are in a state and want to transition, a markov chain can predict outcomes based on pre-existing probability data. More technically, information is put into a matrix and a vector - also called a column matrix - and with many iterations, a collection of probability vectors makes up Markov chains. To determine the transition probabilities, you have to "train" your Markov Chain on some input corpus.

Physics-informed extreme learning machine (PIELM) has recently received significant attention as a rapid version of physics-informed neural network (PINN) for solving partial differential equations (PDEs). The key characteristic is to fix the input layer weights with random values and use Moore-Penrose generalized inverse for the output layer weights. The framework is effective, but it easily suffers from overfitting noisy data and lacks uncertainty quantification for the solution under noise scenarios.To this end, we develop the Bayesian physics-informed extreme learning machine (BPIELM) to solve both forward and inverse linear PDE problems with noisy data in a unified framework. In our framework, a prior probability distribution is introduced in the output layer for extreme learning machine with physic laws and the Bayesian method is used to estimate the posterior of parameters. Besides, for inverse PDE problems, problem parameters considered as new output layer weights are unified in a framework with forward PDE problems. Finally, we demonstrate BPIELM considering both forward problems, including Poisson, advection, and diffusion equations, as well as inverse problems, where unknown problem parameters are estimated. The results show that, compared with PIELM, BPIELM quantifies uncertainty arising from noisy data and provides more accurate predictions. In addition, BPIELM is considerably cheaper than PINN in terms of the computational cost.

Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages. Thus, there is a need for computational host prediction. Despite some promising results, computational host prediction remains a challenge because of the limited known interactions and the sheer amount of sequenced phages by high-throughput sequencing technologies. The state-of-the-art methods can only achieve 43\% accuracy at the species level. In this work, we formulate host prediction as link prediction in a knowledge graph that integrates multiple protein and DNA-based sequence features. Our implementation named CHERRY can be applied to predict hosts for newly discovered viruses and to identify viruses infecting targeted bacteria. We demonstrated the utility of CHERRY for both applications and compared its performance with 11 popular host prediction methods. To our best knowledge, CHERRY has the highest accuracy in identifying virus-prokaryote interactions. It outperforms all the existing methods at the species level with an accuracy increase of 37\%. In addition, CHERRY's performance on short contigs is more stable than other tools.

A new Bayesian modelling framework is introduced for piece-wise homogeneous variable-memory Markov chains, along with a collection of effective algorithmic tools for change-point detection and segmentation of discrete time series. Building on the recently introduced Bayesian Context Trees (BCT) framework, the distributions of different segments in a discrete time series are described as variable-memory Markov chains. Inference for the presence and location of change-points is then performed via Markov chain Monte Carlo sampling. The key observation that facilitates effective sampling is that, using one of the BCT algorithms, the prior predictive likelihood of the data can be computed exactly, integrating out all the models and parameters in each segment. This makes it possible to sample directly from the posterior distribution of the number and location of the change-points, leading to accurate estimates and providing a natural quantitative measure of uncertainty in the results. Estimates of the actual model in each segment can also be obtained, at essentially no additional computational cost. Results on both simulated and real-world data indicate that the proposed methodology performs better than or as well as state-of-the-art techniques.