Mixed-Variable Bayesian Optimization

The optimization of expensive to evaluate, black-box, mixed-variable functions, i.e. functions that have continuous and discrete inputs, is a difficult and yet pervasive problem in science and engineering. In Bayesian optimization (BO), special cases of this problem that consider fully continuous or fully discrete domains have been widely studied. However, few methods exist for mixed-variable domains and none of them can handle discrete constraints that arise in many real-world applications. In this paper, we introduce MiVaBo, a novel BO algorithm for the efficient optimization of mixed-variable functions combining a linear surrogate model based on expressive feature representations with Thompson sampling. We propose an effective method to optimize its acquisition function, a challenging problem for mixed-variable domains, making MiVaBo the first BO method that can handle complex constraints over the discrete variables. Moreover, we provide the first convergence analysis of a mixed-variable BO algorithm. Finally, we show that MiVaBo is significantly more sample efficient than state-of-the-art mixed-variable BO algorithms on several hyperparameter tuning tasks, including the tuning of deep generative models.Comment: IJCAI 2020 camera-ready; 17 pages, extended version with supplementary materia

Bayesian optimization under mixed constraints with a slack-variable augmented Lagrangian

An augmented Lagrangian (AL) can convert a constrained optimization problem into a sequence of simpler (e.g., unconstrained) problems, which are then usually solved with local solvers. Recently, surrogate-based Bayesian optimization (BO) sub-solvers have been successfully deployed in the AL framework for a more global search in the presence of inequality constraints; however, a drawback was that expected improvement (EI) evaluations relied on Monte Carlo. Here we introduce an alternative slack variable AL, and show that in this formulation the EI may be evaluated with library routines. The slack variables furthermore facilitate equality as well as inequality constraints, and mixtures thereof. We show how our new slack "ALBO" compares favorably to the original. Its superiority over conventional alternatives is reinforced on several mixed constraint examples.Comment: 24 pages, 5 figure

Hybrid Models for Mixed Variables in Bayesian Optimization

This paper presents a new type of hybrid models for Bayesian optimization (BO) adept at managing mixed variables, encompassing both quantitative (continuous and integer) and qualitative (categorical) types. Our proposed new hybrid models merge Monte Carlo Tree Search structure (MCTS) for categorical variables with Gaussian Processes (GP) for continuous ones. Addressing efficiency in searching phase, we juxtapose the original (frequentist) upper confidence bound tree search (UCTS) and the Bayesian Dirichlet search strategies, showcasing the tree architecture's integration into Bayesian optimization. Central to our innovation in surrogate modeling phase is online kernel selection for mixed-variable BO. Our innovations, including dynamic kernel selection, unique UCTS (hybridM) and Bayesian update strategies (hybridD), position our hybrid models as an advancement in mixed-variable surrogate models. Numerical experiments underscore the hybrid models' superiority, highlighting their potential in Bayesian optimization.Comment: 32 pages, 8 Figure

A general mathematical framework for constrained mixed-variable blackbox optimization problems with meta and categorical variables

A mathematical framework for modelling constrained mixed-variable optimization problems is presented in a blackbox optimization context. The framework introduces a new notation and allows solution strategies. The notation framework allows meta and categorical variables to be explicitly and efficiently modelled, which facilitates the solution of such problems. The new term meta variables is used to describe variables that influence which variables are acting or nonacting: meta variables may affect the number of variables and constraints. The flexibility of the solution strategies supports the main blackbox mixed-variable optimization approaches: direct search methods and surrogate-based methods (Bayesian optimization). The notation system and solution strategies are illustrated through an example of a hyperparameter optimization problem from the machine learning community

Uncertainty-Aware Mixed-Variable Machine Learning for Materials Design

Data-driven design shows the promise of accelerating materials discovery but is challenging due to the prohibitive cost of searching the vast design space of chemistry, structure, and synthesis methods. Bayesian Optimization (BO) employs uncertainty-aware machine learning models to select promising designs to evaluate, hence reducing the cost. However, BO with mixed numerical and categorical variables, which is of particular interest in materials design, has not been well studied. In this work, we survey frequentist and Bayesian approaches to uncertainty quantification of machine learning with mixed variables. We then conduct a systematic comparative study of their performances in BO using a popular representative model from each group, the random forest-based Lolo model (frequentist) and the latent variable Gaussian process model (Bayesian). We examine the efficacy of the two models in the optimization of mathematical functions, as well as properties of structural and functional materials, where we observe performance differences as related to problem dimensionality and complexity. By investigating the machine learning models' predictive and uncertainty estimation capabilities, we provide interpretations of the observed performance differences. Our results provide practical guidance on choosing between frequentist and Bayesian uncertainty-aware machine learning models for mixed-variable BO in materials design

Bayesian Optimization for Materials Design with Mixed Quantitative and Qualitative Variables

Although Bayesian Optimization (BO) has been employed for accelerating materials design in computational materials engineering, existing works are restricted to problems with quantitative variables. However, real designs of materials systems involve both qualitative and quantitative design variables representing material compositions, microstructure morphology, and processing conditions. For mixed-variable problems, existing Bayesian Optimization (BO) approaches represent qualitative factors by dummy variables first and then fit a standard Gaussian process (GP) model with numerical variables as the surrogate model. This approach is restrictive theoretically and fails to capture complex correlations between qualitative levels. We present in this paper the integration of a novel latent-variable (LV) approach for mixed-variable GP modeling with the BO framework for materials design. LVGP is a fundamentally different approach that maps qualitative design variables to underlying numerical LV in GP, which has strong physical justification. It provides flexible parameterization and representation of qualitative factors and shows superior modeling accuracy compared to the existing methods. We demonstrate our approach through testing with numerical examples and materials design examples. It is found that in all test examples the mapped LVs provide intuitive visualization and substantial insight into the nature and effects of the qualitative factors. Though materials designs are used as examples, the method presented is generic and can be utilized for other mixed variable design optimization problems that involve expensive physics-based simulations.Comment: 29 pages, 9 figures, 3 table

Bayesian Deep Net GLM and GLMM

Deep feedforward neural networks (DFNNs) are a powerful tool for functional approximation. We describe flexible versions of generalized linear and generalized linear mixed models incorporating basis functions formed by a DFNN. The consideration of neural networks with random effects is not widely used in the literature, perhaps because of the computational challenges of incorporating subject specific parameters into already complex models. Efficient computational methods for high-dimensional Bayesian inference are developed using Gaussian variational approximation, with a parsimonious but flexible factor parametrization of the covariance matrix. We implement natural gradient methods for the optimization, exploiting the factor structure of the variational covariance matrix in computation of the natural gradient. Our flexible DFNN models and Bayesian inference approach lead to a regression and classification method that has a high prediction accuracy, and is able to quantify the prediction uncertainty in a principled and convenient way. We also describe how to perform variable selection in our deep learning method. The proposed methods are illustrated in a wide range of simulated and real-data examples, and the results compare favourably to a state of the art flexible regression and classification method in the statistical literature, the Bayesian additive regression trees (BART) method. User-friendly software packages in Matlab, R and Python implementing the proposed methods are available at https://github.com/VBayesLabComment: 35 pages, 7 figure, 10 table

Parallel Mixed Bayesian Optimization Algorithm: A Scaleup Analysis

Estimation of Distribution Algorithms have been proposed as a new paradigm for evolutionary optimization. This paper focuses on the parallelization of Estimation of Distribution Algorithms. More specifically, the paper discusses how to predict performance of parallel Mixed Bayesian Optimization Algorithm (MBOA) that is based on parallel construction of Bayesian networks with decision trees. We determine the time complexity of parallel Mixed Bayesian Optimization Algorithm and compare this complexity with experimental results obtained by solving the spin glass optimization problem. The empirical results fit well the theoretical time complexity, so the scalability and efficiency of parallel Mixed Bayesian Optimization Algorithm for unknown instances of spin glass benchmarks can be predicted. Furthermore, we derive the guidelines that can be used to design effective parallel Estimation of Distribution Algorithms with the speedup proportional to the number of variables in the problem.Comment: Optimization by Building and Using Probabilistic Models OBUPM-200

Inference in Hybrid Bayesian Networks Using Mixtures of Gaussians

The main goal of this paper is to describe a method for exact inference in general hybrid Bayesian networks (BNs) (with a mixture of discrete and continuous chance variables). Our method consists of approximating general hybrid Bayesian networks by a mixture of Gaussians (MoG) BNs. There exists a fast algorithm by Lauritzen-Jensen (LJ) for making exact inferences in MoG Bayesian networks, and there exists a commercial implementation of this algorithm. However, this algorithm can only be used for MoG BNs. Some limitations of such networks are as follows. All continuous chance variables must have conditional linear Gaussian distributions, and discrete chance nodes cannot have continuous parents. The methods described in this paper will enable us to use the LJ algorithm for a bigger class of hybrid Bayesian networks. This includes networks with continuous chance nodes with non-Gaussian distributions, networks with no restrictions on the topology of discrete and continuous variables, networks with conditionally deterministic variables that are a nonlinear function of their continuous parents, and networks with continuous chance variables whose variances are functions of their parents.Comment: Appears in Proceedings of the Twenty-Second Conference on Uncertainty in Artificial Intelligence (UAI2006

Consistent Second-Order Conic Integer Programming for Learning Bayesian Networks

Bayesian Networks (BNs) represent conditional probability relations among a set of random variables (nodes) in the form of a directed acyclic graph (DAG), and have found diverse applications in knowledge discovery. We study the problem of learning the sparse DAG structure of a BN from continuous observational data. The central problem can be modeled as a mixed-integer program with an objective function composed of a convex quadratic loss function and a regularization penalty subject to linear constraints. The optimal solution to this mathematical program is known to have desirable statistical properties under certain conditions. However, the state-of-the-art optimization solvers are not able to obtain provably optimal solutions to the existing mathematical formulations for medium-size problems within reasonable computational times. To address this difficulty, we tackle the problem from both computational and statistical perspectives. On the one hand, we propose a concrete early stopping criterion to terminate the branch-and-bound process in order to obtain a near-optimal solution to the mixed-integer program, and establish the consistency of this approximate solution. On the other hand, we improve the existing formulations by replacing the linear "big-$M$" constraints that represent the relationship between the continuous and binary indicator variables with second-order conic constraints. Our numerical results demonstrate the effectiveness of the proposed approaches