The increasing availability of structured but high dimensional data has opened new opportunities for optimization. One emerging and promising avenue is the exploration of unsupervised methods for projecting structured high dimensional data into low dimensional continuous representations, simplifying the optimization problem and enabling the application of traditional optimization methods. However, this line of research has been purely methodological with little connection to the needs of practitioners so far. In this paper, we study the effect of different search space design choices for performing Bayesian Optimization in high dimensional structured datasets. In particular, we analyse the influence of the dimensionality of the latent space, the role of the acquisition function and evaluate new methods to automatically define the optimization bounds in the latent space. Finally, based on experimental results using synthetic and real datasets, we provide recommendations for the practitioners.
University of Pennsylvania（宾夕法尼亚大学）；Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）；University College London（伦敦大学学院）；Massachusetts Institute of Technology（麻省理工学院）
Bayesian optimization over the latent spaces of deep autoencoder models (DAEs) has recently emerged as a promising new approach for optimizing challenging black-box functions over structured, discrete, hard-to-enumerate search spaces (e.g., molecules). Here the DAE dramatically simplifies the search space by mapping inputs into a continuous latent space where familiar Bayesian optimization tools can be more readily applied. Despite this simplification, the latent space typically remains high-dimensional. Thus, even with a well-suited latent space, these approaches do not necessarily provide a …
Bayesian optimization (BO) is a sample-efficient global optimization algorithm for black-box functions which are expensive to evaluate. Existing literature on model based optimization in conditional parameter spaces are usually built on trees. In this work, we generalize the additive assumption to tree-structured functions and propose an additive tree-structured covariance function, showing improved sample-efficiency, wider applicability and greater flexibility. Furthermore, by incorporating the structure information of parameter spaces and the additive assumption in the BO loop, we develop a …
Bayesian optimization (BO) is a sample-efficient global optimization algorithm for black-box functions which are expensive to evaluate. Existing literature on model based optimization in conditional parameter spaces are usually built on trees. In this work, we generalize the additive assumption to tree-structured functions and propose an additive tree-structured covariance function, showing improved sample-efficiency, wider applicability and greater flexibility. Furthermore, by incorporating the structure information of parameter spaces and the additive assumption in the BO loop, we develop a …
Mines ParisTech – PSL（巴黎高等矿业学院——巴黎文理研究大学）；Inria（法国国家信息与自动化研究所）；Sorbonne Université（索邦大学）；University College London（伦敦大学学院）
Many practical machine learning tasks can be framed as Structured prediction problems, where several output variables are predicted and considered interdependent. Recent theoretical advances in structured prediction have focused on obtaining fast rates convergence guarantees, especially in the Implicit Loss Embedding (ILE) framework. PAC-Bayes has gained interest recently for its capacity of producing tight risk bounds for predictor distributions. This work proposes a novel PAC-Bayes perspective on the ILE Structured prediction framework. We present two generalization bounds, on the risk and e…
Finding an optimal parameter of a black-box function is important for searching stable material structures and finding optimal neural network structures, and Bayesian optimization algorithms are widely used for the purpose. However, most of existing Bayesian optimization algorithms can only handle vector data and cannot handle complex structured data. In this paper, we propose the topological Bayesian optimization, which can efficiently find an optimal solution from structured data using \emph{topological information}. More specifically, in order to apply Bayesian optimization to structured da…
University of Cambridge（剑桥大学）；The Alan Turing Institute（阿兰·图灵研究所）
Current auto-tuning frameworks struggle with tuning computer systems configurations due to their large parameter space, complex interdependencies, and high evaluation cost. Utilizing probabilistic models, Structured Bayesian Optimization (SBO) has recently overcome these difficulties. SBO decomposes the parameter space by utilizing contextual information provided by system experts leading to fast convergence. However, the complexity of building probabilistic models has hindered its wider adoption. We propose BoAnon, a SBO framework that learns the system structure from its logs. BoAnon provide…
The engineering of machine learning systems is still a nascent field; relying on a seemingly daunting collection of quickly evolving tools and best practices. It is our hope that this guidebook will serve as a useful resource for machine learning practitioners looking to take advantage of Bayesian optimization techniques. We outline four example machine learning problems that can be solved using open source machine learning libraries, and highlight the benefits of using Bayesian optimization in the context of these common machine learning applications.
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；Alan Turing Institute（艾伦·图灵研究所）
Clinical prognostic models derived from largescale healthcare data can inform critical diagnostic and therapeutic decisions. To enable off-theshelf usage of machine learning (ML) in prognostic research, we developed AUTOPROGNOSIS: a system for automating the design of predictive modeling pipelines tailored for clinical prognosis. AUTOPROGNOSIS optimizes ensembles of pipeline configurations efficiently using a novel batched Bayesian optimization (BO) algorithm that learns a low-dimensional decomposition of the pipelines high-dimensional hyperparameter space in concurrence with the BO procedure.…
National University of Singapore（新加坡国立大学）；Indian Institute of Technology (BHU) Varanasi（印度理工学院（巴纳拉斯印度教大学）瓦拉纳西分校）
Bayesian Optimization (BO) has shown significant success in tackling expensive low-dimensional black-box optimization problems. Many optimization problems of interest are high-dimensional, and scaling BO to such settings remains an important challenge. In this paper, we consider generalized additive models in which low-dimensional functions with overlapping subsets of variables are composed to model a high-dimensional target function. Our goal is to lower the computational resources required and facilitate faster model learning by reducing the model complexity while retaining the sample-effici…
Washington State University（华盛顿州立大学）；Microsoft Research（微软研究院）
The rising growth of deep neural networks (DNNs) and datasets in size motivates the need for efficient solutions for simultaneous model selection and training. Many methods for hyperparameter optimization (HPO) of iterative learners, including DNNs, attempt to solve this problem by querying and learning a response surface while searching for the optimum of that surface. However, many of these methods make myopic queries, do not consider prior knowledge about the response structure, and/or perform a biased cost-aware search, all of which exacerbate identifying the best-performing model when a t…
We consider the problem of optimizing combinatorial spaces (e.g., sequences, trees, and graphs) using expensive black-box function evaluations. For example, optimizing molecules for drug design using physical lab experiments. Bayesian optimization (BO) is an efficient framework for solving such problems by intelligently selecting the inputs with high utility guided by a learned surrogate model. A recent BO approach for combinatorial spaces is through a reduction to BO over continuous spaces by learning a latent representation of structures using deep generative models (DGMs). The selected inpu…
Bayesian Optimization (BO) has shown great promise for the global optimization of functions that are expensive to evaluate, but despite many successes, standard approaches can struggle in high dimensions. To improve the performance of BO, prior work suggested incorporating gradient information into a Gaussian process surrogate of the objective, giving rise to kernel matrices of size $nd \times nd$ for $n$ observations in $d$ dimensions. Naïvely multiplying with (resp. inverting) these matrices requires $\mathcal{O}(n^2d^2)$ (resp. $\mathcal{O}(n^3d^3$)) operations, which becomes infeasible for…
This paper presents a Bayesian optimization method with exponential convergence without the need of auxiliary optimization and without the delta-cover sampling. Most Bayesian optimization methods require auxiliary optimization: an additional non-convex global optimization problem, which can be time-consuming and hard to implement in practice. Also, the existing Bayesian optimization method with exponential convergence requires access to the delta-cover sampling, which was considered to be impractical. Our approach eliminates both requirements and achieves an exponential convergence rate.
VinAI Research（VinAI研究院）；University of Texas, Austin（德克萨斯大学奥斯汀分校）；Hanoi University of Science and Technology（河内科技大学）
Approximate inference in Bayesian deep networks exhibits a dilemma of how to yield high fidelity posterior approximations while maintaining computational efficiency and scalability. We tackle this challenge by introducing a novel variational structured approximation inspired by the Bayesian interpretation of Dropout regularization. Concretely, we focus on the inflexibility of the factorized structure in Dropout posterior and then propose an improved method called Variational Structured Dropout (VSD). VSD employs an orthogonal transformation to learn a structured representation on the variation…
We introduce a Bayesian Gaussian process latent variable model that explicitly captures spatial correlations in data using a parameterized spatial kernel and leveraging structure-exploiting algebra on the model covariance matrices for computational tractability. Inference is made tractable through a collapsed variational bound with similar computational complexity to that of the traditional Bayesian GP-LVM. Inference over partially-observed test cases is achieved by optimizing a "partially-collapsed" bound. Modeling high-dimensional time series systems is enabled through use of a dynamical GP …
University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Koc University（科奇大学）
We introduce a Bayesian perspective for the structured matrix factorization problem. The proposed framework provides a probabilistic interpretation for existing geometric methods based on determinant minimization. We model input data vectors as linear transformations of latent vectors drawn from a distribution uniform over a particular domain reflecting structural assumptions, such as the probability simplex in Nonnegative Matrix Factorization and polytopes in Polytopic Matrix Factorization. We represent the rows of the linear transformation matrix as vectors generated independently from a nor…
We introduce a methodology for nonlinear inverse problems using a variational Bayesian approach where the unknown quantity is a spatial field. A structured Bayesian Gaussian process latent variable model is used both to construct a low-dimensional generative model of the sample-based stochastic prior as well as a surrogate for the forward evaluation. Its Bayesian formulation captures epistemic uncertainty introduced by the limited number of input and output examples, automatically selects an appropriate dimensionality for the learned latent representation of the data, and rigorously propagates…
Zhejiang University（浙江大学）；Zhejiang University - University of Illinois at Urbana-Champaign Institute（浙江大学伊利诺伊大学厄巴纳香槟校区联合学院）
Class imbalance has a detrimental effect on the predictive performance of most supervised learning algorithms as the imbalanced distribution can lead to a bias preferring the majority class. To solve this problem, we propose a Supervised Contrastive Learning (SCL) method with Tree-structured Parzen Estimator (TPE) technique for imbalanced tabular datasets. Contrastive learning (CL) can extract the information hidden in data even without labels and has shown some potential for imbalanced learning tasks. SCL further considers the label information based on CL, which also addresses the insufficie…
IBM research（IBM研究院）；MIT-IBM Watson AI Lab（麻省理工学院-IBM沃森人工智能实验室）；Harvard University（哈佛大学）
Bayesian Neural Networks (BNNs) have recently received increasing attention for their ability to provide well-calibrated posterior uncertainties. However, model selection---even choosing the number of nodes---remains an open question. Recent work has proposed the use of a horseshoe prior over node pre-activations of a Bayesian neural network, which effectively turns off nodes that do not help explain the data. In this work, we propose several modeling and inference advances that consistently improve the compactness of the model learned while maintaining predictive performance, especially in sm…
RIKEN AIP（理化学研究所人工智能研究中心）；Nagoya Institute of Technology（名古屋工业大学）；Nagoya University（名古屋大学）；AIST（产业技术综合研究所）
In this paper, we propose an active learning method for an inverse problem that aims to find an input that achieves a desired structured-output. The proposed method provides new acquisition functions for minimizing the error between the desired structured-output and the prediction of a Gaussian process model, by effectively incorporating the correlation between multiple outputs of the underlying multi-valued black box output functions. The effectiveness of the proposed method is verified by applying it to two synthetic shape search problem and real data. In the real data experiment, we tackle …
IBM Research（IBM研究（中心））；Dublin, Ireland（爱尔兰都柏林（注意：Dublin, Ireland是地址，非机构，按要求不应提取，此处原数据中可能存在格式错误，正确机构应为IBM Research，而Dublin, Ireland是地点信息，根据提取规则，不应提取地址，因此仅保留IBM Research））
We introduce a new Bayesian multi-class support vector machine by formulating a pseudo-likelihood for a multi-class hinge loss in the form of a location-scale mixture of Gaussians. We derive a variational-inference-based training objective for gradient-based learning. Additionally, we employ an inducing point approximation which scales inference to large data sets. Furthermore, we develop hybrid Bayesian neural networks that combine standard deep learning components with the proposed model to enable learning for unstructured data. We provide empirical evidence that our model outperforms the co…
Return of the Latent Space COWBOYS: Re-thinking the use of VAEs for Bayesian Optimisation of Structured Spaces
School of Mathematical Sciences, Lancaster University, UK（数学科学学院，兰卡斯特大学）；Department of Applied Maths and Theoretical Physics, University of Cambridge, UK（应用数学与理论物理系，剑桥大学）
Sparse Bayesian Deep Functional Learning with Structured Region Selection
School of Statistics and Data Science, Shanghai University of Finance and Economics（上海金融学院统计与数据科学学院）；School of Statistics（统计学院）；Data Science, Shanghai University of Finance（金融大学数据科学学院）；Department of Biostatistics, Yale School of Public Health（耶鲁大学公共卫生学院生物统计学系）
Despite recent advances in its theoretical understanding, there still remains a significant gap in the ability of existing PAC-Bayesian theories on meta-learning to explain performance improvements in the few-shot learning setting, where the number of training examples in the target tasks is severely limited. This gap originates from an assumption in the existing theories which supposes that the number of training examples in the observed tasks and the number of training examples in the target tasks follow the same distribution, an assumption that rarely holds in practice. By relaxing this ass…
Variational Bayesian Methods for a Tree-Structured Stick-Breaking Process Mixture of Gaussians by Application of the Bayes Codes for Context Tree Models
Center for Data Science Waseda University（早稻田大学数据科学中心）
German Cancer Research Center (DKFZ)（德国癌症研究中心（DKFZ））；German Cancer Consortium (DKTK)（德国癌症联盟（DKTK））；Goethe University Frankfurt（法兰克福歌德大学）；Frankfurt Cancer Institute（法兰克福癌症研究所）
Many real-world systems are described not only by data from a single source but via multiple data views. In genomic medicine, for instance, patients can be characterized by data from different molecular layers. Latent variable models with structured sparsity are a commonly used tool for disentangling variation within and across data views. However, their interpretability is cumbersome since it requires a direct inspection and interpretation of each factor from domain experts. Here, we propose MuVI, a novel multi-view latent variable model based on a modified horseshoe prior for modeling struct…
UC San Diego（加州大学圣地亚哥分校）；University of Amsterdam（阿姆斯特丹大学）
Bayesian inference has great promise for the privacy-preserving analysis of sensitive data, as posterior sampling automatically preserves differential privacy, an algorithmic notion of data privacy, under certain conditions (Dimitrakakis et al., 2014; Wang et al., 2015). While this one posterior sample (OPS) approach elegantly provides privacy "for free," it is data inefficient in the sense of asymptotic relative efficiency (ARE). We show that a simple alternative based on the Laplace mechanism, the workhorse of differential privacy, is as asymptotically efficient as non-private posterior infe…
Bottom-Up Hidden Tree Markov Model is a highly expressive model for tree-structured data. Unfortunately, it cannot be used in practice due to the intractable size of its state-transition matrix. We propose a new approximation which lies on the Tucker factorisation of tensors. The probabilistic interpretation of such approximation allows us to define a new probabilistic model for tree-structured data. Hence, we define the new approximated model and we derive its learning algorithm. Then, we empirically assess the effective power of the new model evaluating it on two different tasks. In both cas…
University of British Columbia（英属哥伦比亚大学）；Ecole Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）；RIKEN Center for AI Project（理化学研究所人工智能项目中心）
Uncertainty estimation in large deep-learning models is a computationally challenging task, where it is difficult to form even a Gaussian approximation to the posterior distribution. In such situations, existing methods usually resort to a diagonal approximation of the covariance matrix despite, the fact that these matrices are known to result in poor uncertainty estimates. To address this issue, we propose a new stochastic, low-rank, approximate natural-gradient (SLANG) method for variational inference in large, deep models. Our method estimates a "diagonal plus low-rank" structure based sole…
Continuous latent time series models are prevalent in Bayesian modeling; examples include the Kalman filter, dynamic collaborative filtering, or dynamic topic models. These models often benefit from structured, non mean field variational approximations that capture correlations between time steps. Black box variational inference with reparameterization gradients (BBVI) allows us to explore a rich new class of Bayesian non-conjugate latent time series models; however, a naive application of BBVI to such structured variational models would scale quadratically in the number of time steps. We desc…
We introduce an individual claims forecasting framework utilizing Bayesian mixture density networks that can be used for claims analytics tasks such as case reserving and triaging. The proposed approach enables incorporating claims information from both structured and unstructured data sources, producing multi-period cash flow forecasts, and generating different scenarios of future payment patterns. We implement and evaluate the modeling framework using publicly available data.
In classification applications, we often want probabilistic predictions to reflect confidence or uncertainty. Dropout, a commonly used training technique, has recently been linked to Bayesian inference, yielding an efficient way to quantify uncertainty in neural network models. However, as previously demonstrated, confidence estimates computed with a naive implementation of dropout can be poorly calibrated, particularly when using convolutional networks. In this paper, through the lens of ensemble learning, we associate calibration error with the correlation between the models sampled with dro…
