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 for Combinatorial Bayesian Optimization (MerCBO). The key idea behind MerCBO is to provide explicit feature maps for diffusion kernels over discrete objects by exploiting the structure of their combinatorial graph representation. These Mercer features combined with Thompson sampling as the acquisition function allows us to employ tractable solvers to find next structures for evaluation. Experiments on diverse real-world benchmarks demonstrate that MerCBO performs similarly or better than prior methods. The source code is available at https://github.com/aryandeshwal/MerCBO .
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 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…
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…
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）
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…
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）
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. …
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…
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 …
Divide and Learn: Multi-Objective Combinatorial Optimization at Scale
Department of Computer Science & Engineering UC San Diego（计算机科学与工程系，圣地亚哥大学）；Department of Statistics Stanford University（统计学系，斯坦福大学）；Halıcıoğlu Data Science Institute UC San Diego（Halıcıoğlu数据科学研究所，圣地亚哥大学）
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. …
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）
Optimizing expensive to evaluate black-box functions over an input space consisting of all permutations of d objects is an important problem with many real-world applications. For example, placement of functional blocks in hardware design to optimize performance via simulations. The overall goal is to minimize the number of function evaluations to find high-performing permutations. The key challenge in solving this problem using the Bayesian optimization (BO) framework is to trade-off the complexity of statistical model and tractability of acquisition function optimization. In this paper, we p…
TagBO: LLM-Driven Task-Aware Graph Bayesian Optimization for Scientific Discovery
Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）；Harbin Institute of Technology（哈尔滨工业大学）；Fudan University（复旦大学）；Shenzhen Loop Area Institute（深圳河套学院）；Shanghai Jiao Tong University（上海交通大学）；Central South University（中南大学）；Huazhong Agricultural University（华中农业大学）
Sequential assembly with geometric primitives has drawn attention in robotics and 3D vision since it yields a practical blueprint to construct a target shape. However, due to its combinatorial property, a greedy method falls short of generating a sequence of volumetric primitives. To alleviate this consequence induced by a huge number of feasible combinations, we propose a combinatorial 3D shape generation framework. The proposed framework reflects an important aspect of human generation processes in real life -- we often create a 3D shape by sequentially assembling unit primitives with geomet…
Bayesian optimization (BO) is a powerful approach for optimizing black-box, expensive-to-evaluate functions. To enable a flexible trade-off between the cost and accuracy, many applications allow the function to be evaluated at different fidelities. In order to reduce the optimization cost while maximizing the benefit-cost ratio, in this paper, we propose Batch Multi-fidelity Bayesian Optimization with Deep Auto-Regressive Networks (BMBO-DARN). We use a set of Bayesian neural networks to construct a fully auto-regressive model, which is expressive enough to capture strong yet complex relationsh…
In the machine learning algorithms, the choice of the hyperparameter is often an art more than a science, requiring labor-intensive search with expert experience. Therefore, automation on hyperparameter optimization to exclude human intervention is a great appeal, especially for the black-box functions. Recently, there have been increasing demands of solving such concealed tasks for better generalization, though the task-dependent issue is not easy to solve. The Black-Box Optimization challenge (NeurIPS 2020) required competitors to build a robust black-box optimizer across different domains o…
Centrum Wiskunde & Informatica（荷兰国家数学与计算机科学研究中心）；Leiden University Medical Center（莱顿大学医学中心）；TU Delft（代尔夫特理工大学）
We propose a novel surrogate-assisted Evolutionary Algorithm for solving expensive combinatorial optimization problems. We integrate a surrogate model, which is used for fitness value estimation, into a state-of-the-art P3-like variant of the Gene-Pool Optimal Mixing Algorithm (GOMEA) and adapt the resulting algorithm for solving non-binary combinatorial problems. We test the proposed algorithm on an ensemble learning problem. Ensembling several models is a common Machine Learning technique to achieve better performance. We consider ensembles of several models trained on disjoint subsets of a …
University of Amsterdam（阿姆斯特丹大学）；Qualcomm AI Research（高通人工智能研究院）；QT Technologies Ireland Limited（QT技术爱尔兰有限公司）；QUALCOMM India Private Limited（高通印度私人有限公司）
Macro placement is the problem of placing memory blocks on a chip canvas. It can be formulated as a combinatorial optimization problem over sequence pairs, a representation which describes the relative positions of macros. Solving this problem is particularly challenging since the objective function is expensive to evaluate. In this paper, we develop a novel approach to macro placement using Bayesian optimization (BO) over sequence pairs. BO is a machine learning technique that uses a probabilistic surrogate model and an acquisition function that balances exploration and exploitation to effici…
Graph Bayesian Optimization for Multiplex Influence Maximization
School of New Media and Communication, Tianjin University（天津大学新媒体与传播学院）；Department of Computer Science and Engineering, Mississippi State University（密西西比州立大学计算机科学与工程系）
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 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…
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…
Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (MCMC) or Combinatorial Sequential Monte Carlo (CSMC). However, when MCMC is used for evolutionary parameter learning, convergence requires long runs with inefficient exploration of the state space. We introduce Variational Combinatorial Sequential Monte Carlo (VCSMC), a powerful framework that establishes variational sequential search to learn distributions over intricate combinatorial structures. We then develop nes…
Mahidol University（玛希隆大学）；Idiap Research Institute（Idiap研究所）；University of Bern（伯尔尼大学）；Centre of Excellence in Mathematics（数学卓越中心）
We focus on kernel methods for set-valued inputs and their application to Bayesian set optimization, notably combinatorial optimization. We investigate two classes of set kernels that both rely on Reproducing Kernel Hilbert Space embeddings, namely the ``Double Sum'' (DS) kernels recently considered in Bayesian set optimization, and a class introduced here called ``Deep Embedding'' (DE) kernels that essentially consists in applying a radial kernel on Hilbert space on top of the canonical distance induced by another kernel such as a DS kernel. We establish in particular that while DS kernels ty…
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…
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…
Bilkent University（比尔肯特大学）；University of Cambridge（剑桥大学）
Influence maximization, adaptive routing, and dynamic spectrum allocation all require choosing the right action from a large set of alternatives. Thanks to the advances in combinatorial optimization, these and many similar problems can be efficiently solved given an environment with known stochasticity. In this paper, we take this one step further and focus on combinatorial optimization in unknown environments. We consider a very general learning framework called combinatorial multi-armed bandit with probabilistically triggered arms and a very powerful Bayesian algorithm called Combinatorial T…
Real-world decision-making systems are often subject to uncertainties that have to be resolved through observational data. Therefore, we are frequently confronted with combinatorial optimization problems of which the objective function is unknown and thus has to be debunked using empirical evidence. In contrast to the common practice that relies on a learning-and-optimization strategy, we consider the regression between combinatorial spaces, aiming to infer high-quality optimization solutions from samples of input-solution pairs -- without the need to learn the objective function. Our main del…
DynGFN: Towards Bayesian Inference of Gene Regulatory Networks with GFlowNets
University of Toronto（多伦多大学）；Vector Institute（向量研究所）；Mila - Quebec AI Institute（Mila-魁北克人工智能研究所）；University Health Network（大学健康网络）；Université de Montréal（蒙特利尔大学）；Valence Labs（Valence实验室）
Queen Mary University of London（伦敦玛丽女王大学）；The Alan Turing Institute（艾伦·图灵研究所）
Score-based algorithms that learn Bayesian Network (BN) structures provide solutions ranging from different levels of approximate learning to exact learning. Approximate solutions exist because exact learning is generally not applicable to networks of moderate or higher complexity. In general, approximate solutions tend to sacrifice accuracy for speed, where the aim is to minimise the loss in accuracy and maximise the gain in speed. While some approximate algorithms are optimised to handle thousands of variables, these algorithms may still be unable to learn such high dimensional structures. S…
Peking University（北京大学）；University of Minnesota（明尼苏达大学）；Microsoft Research（微软研究院）；Carnegie Mellon University（卡内基梅隆大学）
Consider a bandit algorithm that recommends actions to self-interested users in a recommendation system. The users are free to choose other actions and need to be incentivized to follow the algorithm's recommendations. While the users prefer to exploit, the algorithm can incentivize them to explore by leveraging the information collected from the previous users. All published work on this problem, known as incentivized exploration, focuses on small, unstructured action sets and mainly targets the case when the users' beliefs are independent across actions. However, realistic exploration proble…
Bayesian Optimisation (BO) refers to a suite of techniques for global optimisation of expensive black box functions, which use introspective Bayesian models of the function to efficiently search for the optimum. While BO has been applied successfully in many applications, modern optimisation tasks usher in new challenges where conventional methods fail spectacularly. In this work, we present Dragonfly, an open source Python library for scalable and robust BO. Dragonfly incorporates multiple recently developed methods that allow BO to be applied in challenging real world settings; these include…
Volvo Car Corporation（沃尔沃汽车公司）；Chalmers University of Technology（查尔姆斯理工大学）
In this work, we address the problem of long-distance navigation for battery electric vehicles (BEVs), where one or more charging sessions are required to reach the intended destination. We consider the availability and performance of the charging stations to be unknown and stochastic, and develop a combinatorial semi-bandit framework for exploring the road network to learn the parameters of the queue time and charging power distributions. Within this framework, we first outline a pre-processing for the road network graph to handle the constrained combinatorial optimization problem in an effic…
