We consider the problem of optimizing expensive black-box functions over high-dimensional combinatorial spaces which arises in many science, engineering, and ML applications. We use Bayesian Optimization (BO) and propose a novel surrogate modeling approach for efficiently handling a large number of binary and categorical parameters. The key idea is to select a number of discrete structures from the input space (the dictionary) and use them to define an ordinal embedding for high-dimensional combinatorial structures. This allows us to use existing Gaussian process models for continuous spaces. We develop a principled approach based on binary wavelets to construct dictionaries for binary spaces, and propose a randomized construction method that generalizes to categorical spaces. We provide theoretical justification to support the effectiveness of the dictionary-based embeddings. Our experiments on diverse real-world benchmarks demonstrate the effectiveness of our proposed surrogate modeling approach over state-of-the-art BO methods.
ARM Machine Learning Research Lab（ARM机器学习研究实验室）；University of California, San Diego（加州大学圣地亚哥分校）
This paper addresses the problem of learning dictionaries for multimodal datasets, i.e. datasets collected from multiple data sources. We present an algorithm called multimodal sparse Bayesian dictionary learning (MSBDL). MSBDL leverages information from all available data modalities through a joint sparsity constraint. The underlying framework offers a considerable amount of flexibility to practitioners and addresses many of the shortcomings of existing multimodal dictionary learning approaches. In particular, the procedure includes the automatic tuning of hyperparameters and is unique in tha…
Naively trained neural networks tend to experience catastrophic forgetting in sequential task settings, where data from previous tasks are unavailable. A number of methods, using various model expansion strategies, have been proposed recently as possible solutions. However, determining how much to expand the model is left to the practitioner, and often a constant schedule is chosen for simplicity, regardless of how complex the incoming task is. Instead, we propose a principled Bayesian nonparametric approach based on the Indian Buffet Process (IBP) prior, letting the data determine how much to…
Nonnegative matrix factorization (NMF) with group sparsity constraints is formulated as a probabilistic graphical model and, assuming some observed data have been generated by the model, a feasible variational Bayesian algorithm is derived for learning model parameters. When used in a supervised learning scenario, NMF is most often utilized as an unsupervised feature extractor followed by classification in the obtained feature subspace. Having mapped the class labels to a more general concept of groups which underlie sparsity of the coefficients, what the proposed group sparse NMF model allows…
Joint space-time wind field data extrapolation and uncertainty quantification using nonparametric Bayesian dictionary learning
Department of Civil and Systems Engineering, Johns Hopkins University, United States of America（约翰霍普金斯大学土木与系统工程系）；Department of Civil Engineering and Engineering Mechanics, Columbia University（哥伦比亚大学土木工程与工程力学系）
Bayesian optimization is a popular method for solving the problem of global optimization of an expensive-to-evaluate black-box function. It relies on a probabilistic surrogate model of the objective function, upon which an acquisition function is built to determine where next to evaluate the objective function. In general, Bayesian optimization with Gaussian process regression operates on a continuous space. When input variables are categorical or discrete, an extra care is needed. A common approach is to use one-hot encoded or Boolean representation for categorical variables which might yield…
The Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳））
In high-dimensional settings, sparse structures are critical for efficiency in term of memory and computation complexity. For a linear system, to find the sparsest solution provided with an over-complete dictionary of features directly is typically NP-hard, and thus alternative approximate methods should be considered. In this paper, our choice for alternative method is sparse Bayesian learning, which, as empirical Bayesian approaches, uses a parameterized prior to encourage sparsity in solution, rather than the other methods with fixed priors such as LASSO. Screening test, however, aims at qu…
We consider a learning problem of identifying a dictionary matrix D (M times N dimension) from a sample set of M dimensional vectors Y = N^{-1/2} DX, where X is a sparse matrix (N times P dimension) in which the density of non-zero entries is 0<rho< 1. In particular, we focus on the minimum sample size P_c (sample complexity) necessary for perfectly identifying D of the optimal learning scheme when D and X are independently generated from certain distributions. By using the replica method of statistical mechanics, we show that P_c=O(N) holds as long as alpha = M/N >rho is satisfied in the limi…
University of Hawaii Manoa（夏威夷大学马诺阿分校）；Coveo Solutions Inc.（Coveo解决方案公司）
We present a proof of a combinatorial conjecture from the second author's Ph.D. thesis. The proof relies on binomial and multinomial sums identities. We also discuss the relevance of the conjecture in the context of PAC-Bayesian machine learning.
University of Amsterdam（阿姆斯特丹大学）；Qualcomm AI Research（高通人工智能研究院）；CIFAR（加拿大高等研究院）
This paper focuses on Bayesian Optimization (BO) for objectives on combinatorial search spaces, including ordinal and categorical variables. Despite the abundance of potential applications of Combinatorial BO, including chipset configuration search and neural architecture search, only a handful of methods have been proposed. We introduce COMBO, a new Gaussian Process (GP) BO. COMBO quantifies "smoothness" of functions on combinatorial search spaces by utilizing a combinatorial graph. The vertex set of the combinatorial graph consists of all possible joint assignments of the variables, while ed…
Massachusetts Institute of Technology（麻省理工学院）；The University of Arizona（亚利桑那大学）
The optimization of expensive-to-evaluate black-box functions over combinatorial structures is an ubiquitous task in machine learning, engineering and the natural sciences. The combinatorial explosion of the search space and costly evaluations pose challenges for current techniques in discrete optimization and machine learning, and critically require new algorithmic ideas. This article proposes, to the best of our knowledge, the first algorithm to overcome these challenges, based on an adaptive, scalable model that identifies useful combinatorial structure even when data is scarce. Our acquisi…
A generative Bayesian model is developed for deep (multi-layer) convolutional dictionary learning. A novel probabilistic pooling operation is integrated into the deep model, yielding efficient bottom-up and top-down probabilistic learning. After learning the deep convolutional dictionary, testing is implemented via deconvolutional inference. To speed up this inference, a new statistical approach is proposed to project the top-layer dictionary elements to the data level. Following this, only one layer of deconvolution is required during testing. Experimental results demonstrate powerful capabil…
We introduce a neural-network architecture, termed the constrained recurrent sparse autoencoder (CRsAE), that solves convolutional dictionary learning problems, thus establishing a link between dictionary learning and neural networks. Specifically, we leverage the interpretation of the alternating-minimization algorithm for dictionary learning as an approximate Expectation-Maximization algorithm to develop autoencoders that enable the simultaneous training of the dictionary and regularization parameter (ReLU bias). The forward pass of the encoder approximates the sufficient statistics of the E…
University of Toronto（多伦多大学）；Vector Institute（向量研究所）
This paper focuses on Bayesian Optimization in combinatorial spaces. In many applications in the natural science. Broad applications include the study of molecules, proteins, DNA, device structures and quantum circuit designs, a on optimization over combinatorial categorical spaces is needed to find optimal or pareto-optimal solutions. However, only a limited amount of methods have been proposed to tackle this problem. Many of them depend on employing Gaussian Process for combinatorial Bayesian Optimizations. Gaussian Processes suffer from scalability issues for large data sizes as their scali…
University of Amsterdam（阿姆斯特丹大学）；Qualcomm AI Research（高通人工智能研究院）
In this work we propose a batch Bayesian optimization method for combinatorial problems on permutations, which is well suited for expensive-to-evaluate objectives. We first introduce LAW, an efficient batch acquisition method based on determinantal point processes using the acquisition weighted kernel. Relying on multiple parallel evaluations, LAW enables accelerated search on combinatorial spaces. We then apply the framework to permutation problems, which have so far received little attention in the Bayesian Optimization literature, despite their practical importance. We call this method LAW2…
In many high-throughput experimental design settings, such as those common in biochemical engineering, batched queries are more cost effective than one-by-one sequential queries. Furthermore, it is often not possible to directly choose items to query. Instead, the experimenter specifies a set of constraints that generates a library of possible items, which are then selected stochastically. Motivated by these considerations, we investigate \emph{Batched Stochastic Bayesian Optimization} (BSBO), a novel Bayesian optimization scheme for choosing the constraints in order to guide exploration towar…
We study the problem of optimizing expensive blackbox functions over combinatorial spaces (e.g., sets, sequences, trees, and graphs). BOCS (Baptista and Poloczek, 2018) is a state-of-the-art Bayesian optimization method for tractable statistical models, which performs semi-definite programming based acquisition function optimization (AFO) to select the next structure for evaluation. Unfortunately, BOCS scales poorly for large number of binary and/or categorical variables. Based on recent advances in submodular relaxation (Ito and Fujimaki, 2016) for solving Binary Quadratic Programs, we study …
School of EECS, Washington State University（华盛顿州立大学电气工程与计算机科学学院）
Bayesian optimization (BO) is an efficient framework for solving black-box optimization problems with expensive function evaluations. This paper addresses the BO problem setting for combinatorial spaces (e.g., sequences and graphs) that occurs naturally in science and engineering applications. A prototypical example is molecular optimization guided by expensive experiments. The key challenge is to balance the complexity of statistical models and tractability of search to select combinatorial structures for evaluation. In this paper, we propose an efficient approach referred as Mercer Features …
Virginia Polytechnic Institute and State University（弗吉尼亚理工大学）
We develop the necessary theory in computational algebraic geometry to place Bayesian networks into the realm of algebraic statistics. We present an algebra{statistics dictionary focused on statistical modeling. In particular, we link the notion of effiective dimension of a Bayesian network with the notion of algebraic dimension of a variety. We also obtain the independence and non{independence constraints on the distributions over the observable variables implied by a Bayesian network with hidden variables, via a generating set of an ideal of polynomials associated to the network. These resul…
This paper introduces a method for efficiently inferring a high-dimensional distributed quantity from a few observations. The quantity of interest (QoI) is approximated in a basis (dictionary) learned from a training set. The coefficients associated with the approximation of the QoI in the basis are determined by minimizing the misfit with the observations. To obtain a probabilistic estimate of the quantity of interest, a Bayesian approach is employed. The QoI is treated as a random field endowed with a hierarchical prior distribution so that closed-form expressions can be obtained for the pos…
Omnipresent Yet Overlooked: Heat Kernels in Combinatorial Bayesian Optimization
ETH Zürich（苏黎世联邦理工学院）；Secondmind；University of Cambridge（剑桥大学）；Tübingen AI Center（蒂宾根人工智能中心）；University of Edinburgh（爱丁堡大学）；Lancaster University（兰卡斯特大学）
Super-resolution methods form high-resolution images from low-resolution images. In this paper, we develop a new Bayesian nonparametric model for super-resolution. Our method uses a beta-Bernoulli process to learn a set of recurring visual patterns, called dictionary elements, from the data. Because it is nonparametric, the number of elements found is also determined from the data. We test the results on both benchmark and natural images, comparing with several other models from the research literature. We perform large-scale human evaluation experiments to assess the visual quality of the res…
Although there is a rich literature on methods for allowing the variance in a univariate regression model to vary with predictors, time and other factors, relatively little has been done in the multivariate case. Our focus is on developing a class of nonparametric covariance regression models, which allow an unknown p x p covariance matrix to change flexibly with predictors. The proposed modeling framework induces a prior on a collection of covariance matrices indexed by predictors through priors for predictor-dependent loadings matrices in a factor model. In particular, the predictor-dependen…
When a black-box optimization objective can only be evaluated with costly or noisy measurements, most standard optimization algorithms are unsuited to find the optimal solution. Specialized algorithms that deal with exactly this situation make use of surrogate models. These models are usually continuous and smooth, which is beneficial for continuous optimization problems, but not necessarily for combinatorial problems. However, by choosing the basis functions of the surrogate model in a certain way, we show that it can be guaranteed that the optimal solution of the surrogate model is integer. …
Microsoft Research（微软研究院）；Stanford University（斯坦福大学）
We address online combinatorial optimization when the player has a prior over the adversary's sequence of losses. In this framework, Russo and Van Roy proposed an information-theoretic analysis of Thompson Sampling based on the information ratio, resulting in optimal worst-case regret bounds. In this paper we introduce three novel ideas to this line of work. First we propose a new quantity, the scale-sensitive information ratio, which allows us to obtain more refined first-order regret bounds (i.e., bounds of the form $\sqrt{L^*}$ where $L^*$ is the loss of the best combinatorial action). Seco…
This paper addresses the problem of identifying a lower dimensional space where observed data can be sparsely represented. This under-complete dictionary learning task can be formulated as a blind separation problem of sparse sources linearly mixed with an unknown orthogonal mixing matrix. This issue is formulated in a Bayesian framework. First, the unknown sparse sources are modeled as Bernoulli-Gaussian processes. To promote sparsity, a weighted mixture of an atom at zero and a Gaussian distribution is proposed as prior distribution for the unobserved sources. A non-informative prior distrib…
Combinatorial Bandit Bayesian Optimization for Tensor Outputs
Department of Industrial Engineering, Tsinghua University, Beijing 100084, China（清华大学工业工程系）；College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China（南京航空航天大学经济管理学院）
Learning the structure of Bayesian networks is a difficult combinatorial optimization problem. In this paper, we consider learning of tree-augmented naive Bayes (TAN) structures for Bayesian network classifiers with discrete input features. Instead of performing a combinatorial optimization over the space of possible graph structures, the proposed method learns a distribution over graph structures. After training, we select the most probable structure of this distribution. This allows for a joint training of the Bayesian network parameters along with its TAN structure using gradient-based opti…
University of Zurich（苏黎世大学）；ETH Zurich（苏黎世联邦理工学院）；ETH AI Center（苏黎世联邦理工学院人工智能中心）
We study the combinatorial assignment domain, which includes combinatorial auctions and course allocation. The main challenge in this domain is that the bundle space grows exponentially in the number of items. To address this, several papers have recently proposed machine learning-based preference elicitation algorithms that aim to elicit only the most important information from agents. However, the main shortcoming of this prior work is that it does not model a mechanism's uncertainty over values for not yet elicited bundles. In this paper, we address this shortcoming by presenting a Bayesian…
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…
An ideal cognitively-inspired memory system would compress and organize incoming items. The Kanerva Machine (Wu et al, 2018) is a Bayesian model that naturally implements online memory compression. However, the organization of the Kanerva Machine is limited by its use of a single Gaussian random matrix for storage. Here we introduce the Product Kanerva Machine, which dynamically combines many smaller Kanerva Machines. Its hierarchical structure provides a principled way to abstract invariant features and gives scaling and capacity advantages over single Kanerva Machines. We show that it can ex…
Analyzing multiple studies allows leveraging data from a range of sources and populations, but until recently, there have been limited methodologies to approach the joint unsupervised analysis of multiple high-dimensional studies. A recent method, Bayesian Multi-Study Factor Analysis (BMSFA), identifies latent factors common to all studies, as well as latent factors specific to individual studies. However, BMSFA does not allow for partially shared factors, i.e. latent factors shared by more than one but less than all studies. We extend BMSFA by introducing a new method, Tetris, for Bayesian co…
Among the many ways to model signals, a recent approach that draws considerable attention is sparse representation modeling. In this model, the signal is assumed to be generated as a random linear combination of a few atoms from a pre-specified dictionary. In this work we analyze two Bayesian denoising algorithms -- the Maximum-Aposteriori Probability (MAP) and the Minimum-Mean-Squared-Error (MMSE) estimators, under the assumption that the dictionary is unitary. It is well known that both these estimators lead to a scalar shrinkage on the transformed coefficients, albeit with a different respo…
Criteo AI Lab（Criteo人工智能实验室）；IRIT（图卢兹计算机科学研究所）；Université de Toulouse（图卢兹大学）；CNRS（法国国家科学研究中心）
Binary data matrices can represent many types of data such as social networks, votes, or gene expression. In some cases, the analysis of binary matrices can be tackled with nonnegative matrix factorization (NMF), where the observed data matrix is approximated by the product of two smaller nonnegative matrices. In this context, probabilistic NMF assumes a generative model where the data is usually Bernoulli-distributed. Often, a link function is used to map the factorization to the $[0,1]$ range, ensuring a valid Bernoulli mean parameter. However, link functions have the potential disadvantage …
University of Edinburgh（爱丁堡大学）；Technische Universität Darmstadt（达姆施塔特工业大学）；Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；University of Oslo（奥斯陆大学）；American University of Beirut Medical Centre（贝鲁特美国大学医学中心）；University College London（伦敦大学学院）
Antibodies are canonically Y-shaped multimeric proteins capable of highly specific molecular recognition. The CDRH3 region located at the tip of variable chains of an antibody dominates antigen-binding specificity. Therefore, it is a priority to design optimal antigen-specific CDRH3 regions to develop therapeutic antibodies. However, the combinatorial nature of CDRH3 sequence space makes it impossible to search for an optimal binding sequence exhaustively and efficiently using computational approaches. Here, we present \texttt{AntBO}: a combinatorial Bayesian optimisation framework enabling ef…
The l1-regularization is very popular in high dimensional statistics -- it changes a combinatorial problem of choosing which subset of the parameter are zero, into a simple continuous optimization. Using a continuous prior concentrated near zero, the Bayesian counterparts are successful in quantifying the uncertainty in the variable selection problems; nevertheless, the lack of exact zeros makes it difficult for broader problems such as the change-point detection and rank selection. Inspired by the duality of the l1-regularization as a constraint onto an l1-ball, we propose a new prior by proj…
We propose a Bayesian approach to learn discriminative dictionaries for sparse representation of data. The proposed approach infers probability distributions over the atoms of a discriminative dictionary using a Beta Process. It also computes sets of Bernoulli distributions that associate class labels to the learned dictionary atoms. This association signifies the selection probabilities of the dictionary atoms in the expansion of class-specific data. Furthermore, the non-parametric character of the proposed approach allows it to infer the correct size of the dictionary. We exploit the aforeme…
University of Electronic Science and Technology of China（电子科技大学）；Stevens Institute of Technology（史蒂文斯理工学院）
We consider a dictionary learning problem whose objective is to design a dictionary such that the signals admits a sparse or an approximate sparse representation over the learned dictionary. Such a problem finds a variety of applications such as image denoising, feature extraction, etc. In this paper, we propose a new hierarchical Bayesian model for dictionary learning, in which a Gaussian-inverse Gamma hierarchical prior is used to promote the sparsity of the representation. Suitable priors are also placed on the dictionary and the noise variance such that they can be reasonably inferred from…
Chennai Mathematical Institute（金奈数学研究所）；University of Southampton（南安普顿大学）
Statistical Machine Learning (SML) refers to a body of algorithms and methods by which computers are allowed to discover important features of input data sets which are often very large in size. The very task of feature discovery from data is essentially the meaning of the keyword `learning' in SML. Theoretical justifications for the effectiveness of the SML algorithms are underpinned by sound principles from different disciplines, such as Computer Science and Statistics. The theoretical underpinnings particularly justified by statistical inference methods are together termed as statistical le…
We propose a construction for joint feature learning and clustering of multichannel extracellular electrophysiological data across multiple recording periods for action potential detection and discrimination ("spike sorting"). Our construction improves over the previous state-of-the art principally in four ways. First, via sharing information across channels, we can better distinguish between single-unit spikes and artifacts. Second, our proposed "focused mixture model" (FMM) elegantly deals with units appearing, disappearing, or reappearing over multiple recording days, an important considera…
One of the focal points of the modern literature on Bayesian nonparametrics has been the problem of clustering, or partitioning, where each data point is modeled as being associated with one and only one of some collection of groups called clusters or partition blocks. Underlying these Bayesian nonparametric models are a set of interrelated stochastic processes, most notably the Dirichlet process and the Chinese restaurant process. In this paper we provide a formal development of an analogous problem, called feature modeling, for associating data points with arbitrary nonnegative integer numbe…
The Institute of Statistical Mathematics, Research Organization of Information and Systems（信息系统研究机构统计数学研究所）；Daicel Corporation（大赛璐公司）
The identification of synthetic routes that end with a desired product has been an inherently time-consuming process that is largely dependent on expert knowledge regarding a limited fraction of the entire reaction space. At present, emerging machine-learning technologies are overturning the process of retrosynthetic planning. The objective of this study is to discover synthetic routes backwardly from a given desired molecule to commercially available compounds. The problem is reduced to a combinatorial optimization task with the solution space subject to the combinatorial complexity of all po…
Extracting the underlying low-dimensional space where high-dimensional signals often reside has long been at the center of numerous algorithms in the signal processing and machine learning literature during the past few decades. At the same time, working with incomplete (partly observed) large scale datasets has recently been commonplace for diverse reasons. This so called {\it big data era} we are currently living calls for devising online subspace learning algorithms that can suitably handle incomplete data. Their envisaged objective is to {\it recursively} estimate the unknown subspace by p…
