Implementing Bayesian variable selection for linear Gaussian regression models for analysing high dimensional data sets is of current interest in many fields. In order to make such analysis operational, we propose a new sampling algorithm based upon Evolutionary Monte Carlo and designed to work under the "large p, small n" paradigm, thus making fully Bayesian multivariate analysis feasible, for example, in genetics/genomics experiments. Two real data examples in genomics are presented, demonstrating the performance of the algorithm in a space of up to 10,000 covariates. Finally the methodology is compared with a recently proposed search algorithms in an extensive simulation study.
In the study of life tables the random variable of interest is usually assumed discrete since mortality rates are studied for integer ages. In dynamic life tables a time domain is included to account for the evolution effect of the hazard rates in time. In this article we follow a survival analysis approach and use a nonparametric description of the hazard rates. We construct a discrete time stochastic processes that reflects dependence across age as well as in time. This process is used as a bayesian nonparametric prior distribution for the hazard rates for the study of evolutionary life tabl…
It has long been posited that there is a connection between the dynamical equations describing evolutionary processes in biology and sequential Bayesian learning methods. This manuscript describes new research in which this precise connection is rigorously established in the continuous time setting. Here we focus on a partial differential equation known as the Kushner-Stratonovich equation describing the evolution of the posterior density in time. Of particular importance is a piecewise smooth approximation of the observation path from which the discrete time filtering equations, which are sho…
The Alan Turing Institute（艾伦·图灵研究所）；Imperial College London（帝国理工学院）；Newcastle University（纽卡斯尔大学）
In our previous work, we introduced the rule-based Bayesian Regression, a methodology that leverages two concepts: (i) Bayesian inference, for the general framework and uncertainty quantification and (ii) rule-based systems for the incorporation of expert knowledge and intuition. The resulting method creates a penalty equivalent to a common Bayesian prior, but it also includes information that typically would not be available within a standard Bayesian context. In this work, we extend the aforementioned methodology with grammatical evolution, a symbolic genetic programming technique that we ut…
Bayesian optimization (BO) is a global optimization strategy designed to find the minimum of an expensive black-box function, typically defined on a compact subset of $\mathcal{R}^d$, by using a Gaussian process (GP) as a surrogate model for the objective. Although currently available acquisition functions address this goal with different degree of success, an over-exploration effect of the contour of the search space is typically observed. However, in problems like the configuration of machine learning algorithms, the function domain is conservatively large and with a high probability the glo…
We consider Bayesian optimization of expensive-to-evaluate experiments that generate vector-valued outcomes over which a decision-maker (DM) has preferences. These preferences are encoded by a utility function that is not known in closed form but can be estimated by asking the DM to express preferences over pairs of outcome vectors. To address this problem, we develop Bayesian optimization with preference exploration, a novel framework that alternates between interactive real-time preference learning with the DM via pairwise comparisons between outcomes, and Bayesian optimization with a learne…
Resolving the exploration-exploitation trade-off remains a fundamental problem in the design and implementation of reinforcement learning (RL) algorithms. In this paper, we focus on model-free RL using the epsilon-greedy exploration policy, which despite its simplicity, remains one of the most frequently used forms of exploration. However, a key limitation of this policy is the specification of $\varepsilon$. In this paper, we provide a novel Bayesian perspective of $\varepsilon$ as a measure of the uniformity of the Q-value function. We introduce a closed-form Bayesian model update based on B…
Brigham Young University（杨百翰大学）；Harvard University（哈佛大学）
This paper introduces a probabilistic framework to estimate parameters of an acquisition function given observed human behavior that can be modeled as a collection of sample paths from a Bayesian optimization procedure. The methodology involves defining a likelihood on observed human behavior from an optimization task, where the likelihood is parameterized by a Bayesian optimization subroutine governed by an unknown acquisition function. This structure enables us to make inference on a subject's acquisition function while allowing their behavior to deviate around the solution to the Bayesian o…
Research in reinforcement learning has produced algorithms for optimal decision making under uncertainty that fall within two main types. The first employs a Bayesian framework, where optimality improves with increased computational time. This is because the resulting planning task takes the form of a dynamic programming problem on a belief tree with an infinite number of states. The second type employs relatively simple algorithm which are shown to suffer small regret within a distribution-free framework. This paper presents a lower bound and a high probability upper bound on the optimal valu…
Determination of functions for poorly characterized genes is crucial for understanding biological processes and studying human diseases. Functionally associated genes are often gained and lost together through evolution. Therefore identifying co-evolution of genes can predict functional gene-gene associations. We describe here the full statistical model and computational strategies underlying the original algorithm, CLustering by Inferred Models of Evolution (CLIME 1.0) recently reported by us [Li et al., 2014]. CLIME 1.0 employs a mixture of tree-structured hidden Markov models for gene evolu…
PAC-Bayesian Analysis of the Exploration-Exploitation Trade-off
Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；Università degli Studi di Milano（米兰大学）；Université Laval（拉瓦尔大学）；University of Leoben（莱奥本大学）；University College London（伦敦大学学院）
Optimism about the poorly understood states and actions is the main driving force of exploration for many provably-efficient reinforcement learning algorithms. We propose optimism in the face of sensible value functions (OFVF)- a novel data-driven Bayesian algorithm to constructing Plausibility sets for MDPs to explore robustly minimizing the worst case exploration cost. The method computes policies with tighter optimistic estimates for exploration by introducing two new ideas. First, it is based on Bayesian posterior distributions rather than distribution-free bounds. Second, OFVF does not co…
Balancing exploration and exploitation is a fundamental part of reinforcement learning, yet most state-of-the-art algorithms use a naive exploration protocol like $ε$-greedy. This contributes to the problem of high sample complexity, as the algorithm wastes effort by repeatedly visiting parts of the state space that have already been explored. We introduce a novel method based on Bayesian linear regression and latent space embedding to generate an intrinsic reward signal that encourages the learning agent to seek out unexplored parts of the state space. This method is computationally efficient…
Reinforcement learning studies how to balance exploration and exploitation in real-world systems, optimizing interactions with the world while simultaneously learning how the world operates. One general class of algorithms for such learning is the multi-armed bandit setting. Randomized probability matching, based upon the Thompson sampling approach introduced in the 1930s, has recently been shown to perform well and to enjoy provable optimality properties. It permits generative, interpretable modeling in a Bayesian setting, where prior knowledge is incorporated, and the computed posteriors nat…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and covariates are limited to only a fraction of species. On the other hand, evolutionary relationships, encoded as phylogenetic trees, can act as proxies for underlying traits and historical patterns of parasite sharing among hosts. We show that using a network-based conditional model, phylogenetic information provides strong predictive power in a recently published g…
Duckworth-Lewis (D/L) method is the incumbent rain rule used to decide the result of a limited overs cricket match should it not be able to reach its natural conclusion. Duckworth and Lewis (1998) devised a two factor relationship between the numbers of overs a team had remaining and the number of wickets they had lost in order to quantify the percentage resources a team has at any stage of the match. As number of remaining overs decrease and lost wickets increase the resources are expected to decrease. The resource table which is still being used by ICC (International Cricket Council) for 50 …
The human intrinsic desire to pursue knowledge, also known as curiosity, is considered essential in the process of skill acquisition. With the aid of artificial curiosity, we could equip current techniques for control, such as Reinforcement Learning, with more natural exploration capabilities. A promising approach in this respect has consisted of using Bayesian surprise on model parameters, i.e. a metric for the difference between prior and posterior beliefs, to favour exploration. In this contribution, we propose to apply Bayesian surprise in a latent space representing the agent's current un…
Sorbonne Université（索邦大学）；INSERM（法国国家健康与医学研究院）；CNRS（法国国家科学研究中心）；Institut de la Vision（视觉研究所）
Bayesian optimization (BO) is an effective approach to optimize expensive black-box functions, that seeks to trade-off between exploitation (selecting parameters where the maximum is likely) and exploration (selecting parameters where we are uncertain about the objective function). In many real-world situations, direct measurements of the objective function are not possible, and only binary measurements such as success/failure or pairwise comparisons are available. To perform efficient exploration in this setting, we show that it is important for BO algorithms to distinguish between different …
University of Cambridge（剑桥大学）；Alan Turing Institute（艾伦·图灵研究所）；University College London（伦敦大学学院）
The use of ensembles of neural networks (NNs) for the quantification of predictive uncertainty is widespread. However, the current justification is intuitive rather than analytical. This work proposes one minor modification to the normal ensembling methodology, which we prove allows the ensemble to perform Bayesian inference, hence converging to the corresponding Gaussian Process as both the total number of NNs, and the size of each, tend to infinity. This working paper provides early-stage results in a reinforcement learning setting, analysing the practicality of the technique for an ensemble…
We study reinforcement learning (RL) in high dimensional episodic Markov decision processes (MDP). We consider value-based RL when the optimal Q-value is a linear function of d-dimensional state-action feature representation. For instance, in deep-Q networks (DQN), the Q-value is a linear function of the feature representation layer (output layer). We propose two algorithms, one based on optimism, LINUCB, and another based on posterior sampling, LINPSRL. We guarantee frequentist and Bayesian regret upper bounds of O(d sqrt{T}) for these two algorithms, where T is the number of episodes. We ext…
Massachusetts Institute of Technology, Lincoln Laboratory（麻省理工学院林肯实验室）
Multiple techniques for producing calibrated predictive probabilities using deep neural networks in supervised learning settings have emerged that leverage approaches to ensemble diverse solutions discovered during cyclic training or training from multiple random starting points (deep ensembles). However, only a limited amount of work has investigated the utility of exploring the local region around each diverse solution (posterior mode). Using three well-known deep architectures on the CIFAR-10 dataset, we evaluate several simple methods for exploring local regions of the weight space with re…
Microorganisms play a critical role in host health. The advancement of high-throughput sequencing technology provides opportunities for a deeper understanding of microbial interactions. However, due to the limitations of 16S ribosomal RNA sequencing, microbiome data are zero-inflated, and a quantitative comparison of microbial abundances cannot be made across subjects. By leveraging a recent microbiome profiling technique that quantifies 16S ribosomal RNA microbial counts, we propose a novel Bayesian graphical model that incorporates microorganisms' evolutionary history through a phylogenetic …
Northeastern University（东北大学）；Mitsubishi Electric Research Laboratories (MERL)（三菱电机研究实验室（MERL））
Learning data representations that capture task-related features, but are invariant to nuisance variations remains a key challenge in machine learning. We introduce an automated Bayesian inference framework, called AutoBayes, that explores different graphical models linking classifier, encoder, decoder, estimator and adversarial network blocks to optimize nuisance-invariant machine learning pipelines. AutoBayes also enables learning disentangled representations, where the latent variable is split into multiple pieces to impose various relationships with the nuisance variation and task labels. …
Bayesian optimization (BO) and its batch extensions are successful for optimizing expensive black-box functions. However, these traditional BO approaches are not yet ideal for optimizing less expensive functions when the computational cost of BO can dominate the cost of evaluating the blackbox function. Examples of these less expensive functions are cheap machine learning models, inexpensive physical experiment through simulators, and acquisition function optimization in Bayesian optimization. In this paper, we consider a batch BO setting for situations where function evaluations are less expe…
Bayesian Optimization by Kernel Regression and Density-based Exploration
Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, P. R. China（上海交通大学紫阳学院）；School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, P. R. China（上海交通大学数学科学学院）；Shanghai Institute of Aerospace Systems Engineering, Shanghai 201109, P. R. China（上海航天系统工程研究院）；Department of Mathematics, Shanghai University, Shanghai 200444, P. R. China（上海大学数学系）；Newtouch Center for Mathematics of Shanghai University, Shanghai University, Shanghai 200444, P. R. China（上海大学数学中心）
University of Exeter（埃克塞特大学）；Swansea University（斯旺西大学）
The performance of acquisition functions for Bayesian optimisation to locate the global optimum of continuous functions is investigated in terms of the Pareto front between exploration and exploitation. We show that Expected Improvement (EI) and the Upper Confidence Bound (UCB) always select solutions to be expensively evaluated on the Pareto front, but Probability of Improvement is not guaranteed to do so and Weighted Expected Improvement does so only for a restricted range of weights. We introduce two novel $ε$-greedy acquisition functions. Extensive empirical evaluation of these together wi…
We propose a framework based on distributional reinforcement learning and recent attempts to combine Bayesian parameter updates with deep reinforcement learning. We show that our proposed framework conceptually unifies multiple previous methods in exploration. We also derive a practical algorithm that achieves efficient exploration on challenging control tasks.
We are often interested in identifying the feasible subset of a decision space under multiple constraints to permit effective design exploration. If determining feasibility required computationally expensive simulations, the cost of exploration would be prohibitive. Bayesian search is data-efficient for such problems: starting from a small dataset, the central concept is to use Bayesian models of constraints with an acquisition function to locate promising solutions that may improve predictions of feasibility when the dataset is augmented. At the end of this sequential active learning approach…
Evolutionary Structural Shift in Security Screening Sensitivity within the U.S. Aviation Network: A 15-Year Longitudinal Bayesian Assessment (2010-2024)
Recent advances in deep reinforcement learning have made significant strides in performance on applications such as Go and Atari games. However, developing practical methods to balance exploration and exploitation in complex domains remains largely unsolved. Thompson Sampling and its extension to reinforcement learning provide an elegant approach to exploration that only requires access to posterior samples of the model. At the same time, advances in approximate Bayesian methods have made posterior approximation for flexible neural network models practical. Thus, it is attractive to consider a…
Chalmers University of Technology（查尔姆斯理工大学）；ENS（巴黎高等师范学院）；CNRS（法国国家科学研究中心）；PSL University（巴黎文理研究大学）；Inria（法国国家信息与自动化研究所）；National University of Singapore（新加坡国立大学）
We propose a generic, Bayesian, information geometric approach to the exploration--exploitation trade-off in multi-armed bandit problems. Our approach, BelMan, uniformly supports pure exploration, exploration--exploitation, and two-phase bandit problems. The knowledge on bandit arms and their reward distributions is summarised by the barycentre of the joint distributions of beliefs and rewards of the arms, the \emph{pseudobelief-reward}, within the beliefs-rewards manifold. BelMan alternates \emph{information projection} and \emph{reverse information projection}, i.e., projection of the pseudo…
This paper describes a new library for learning Bayesian networks from data containing discrete and continuous variables (mixed data). In addition to the classical learning methods on discretized data, this library proposes its algorithm that allows structural learning and parameters learning from mixed data without discretization since data discretization leads to information loss. This algorithm based on mixed MI score function for structural learning, and also linear regression and Gaussian distribution approximation for parameters learning. The library also offers two algorithms for enumer…
Designing efficient exploration is central to Reinforcement Learning due to the fundamental problem posed by the exploration-exploitation dilemma. Bayesian exploration strategies like Thompson Sampling resolve this trade-off in a principled way by modeling and updating the distribution of the parameters of the action-value function, the outcome model of the environment. However, this technique becomes infeasible for complex environments due to the computational intractability of maintaining probability distributions over parameters of outcome models of corresponding complexity. Moreover, the a…
The Mars Curiosity rover carries an instrument, ChemCam, designed to measure the composition of surface rocks and soil using laser-induced breakdown spectroscopy (LIBS). The measured spectra from this instrument must be analyzed to identify the component elements in the target sample, as well as their relative proportions. This process, which we call disaggregation, is complicated by so-called matrix effects, which describe nonlinear changes in the relative heights of emission lines as an unknown function of composition due to atomic interactions within the LIBS plasma. In this work we explore…
