Why Can Large Language Models Generate Correct Chain-of-Thoughts?

This paper delves into the capabilities of large language models (LLMs), specifically focusing on advancing the theoretical comprehension of chain-of-thought prompting. We investigate how LLMs can be effectively induced to generate a coherent chain of thoughts. To achieve this, we introduce a two-level hierarchical graphical model tailored for natural language generation. Within this framework, we establish a compelling geometrical convergence rate that gauges the likelihood of an LLM-generated chain of thoughts compared to those originating from the true language. Our findings provide a theoretical justification for the ability of LLMs to produce the correct sequence of thoughts (potentially) explaining performance gains in tasks demanding reasoning skills.

Framework and Benchmarks for Combinatorial and Mixed-variable Bayesian Optimization

This paper introduces a modular framework for Mixed-variable and Combinatorial Bayesian Optimization (MCBO) to address the lack of systematic benchmarking and standardized evaluation in the field. Current MCBO papers often introduce non-diverse or non-standard benchmarks to evaluate their methods, impeding the proper assessment of different MCBO primitives and their combinations. Additionally, papers introducing a solution for a single MCBO primitive often omit benchmarking against baselines that utilize the same methods for the remaining primitives. This omission is primarily due to the significant implementation overhead involved, resulting in a lack of controlled assessments and an inability to showcase the merits of a contribution effectively. To overcome these challenges, our proposed framework enables an effortless combination of Bayesian Optimization components, and provides a diverse set of synthetic and real-world benchmarking tasks. Leveraging this flexibility, we implement 47 novel MCBO algorithms and benchmark them against seven existing MCBO solvers and five standard black-box optimization algorithms on ten tasks, conducting over 4000 experiments. Our findings reveal a superior combination of MCBO primitives outperforming existing approaches and illustrate the significance of model fit and the use of a trust region. We make our MCBO library available under the MIT license at \url{https://github.com/huawei-noah/HEBO/tree/master/MCBO}.

End-to-End Meta-Bayesian Optimisation with Transformer Neural Processes

Meta-Bayesian optimisation (meta-BO) aims to improve the sample efficiency of Bayesian optimisation by leveraging data from related tasks. While previous methods successfully meta-learn either a surrogate model or an acquisition function independently, joint training of both components remains an open challenge. This paper proposes the first end-to-end differentiable meta-BO framework that generalises neural processes to learn acquisition functions via transformer architectures. We enable this end-to-end framework with reinforcement learning (RL) to tackle the lack of labelled acquisition data. Early on, we notice that training transformer-based neural processes from scratch with RL is challenging due to insufficient supervision, especially when rewards are sparse. We formalise this claim with a combinatorial analysis showing that the widely used notion of regret as a reward signal exhibits a logarithmic sparsity pattern in trajectory lengths. To tackle this problem, we augment the RL objective with an auxiliary task that guides part of the architecture to learn a valid probabilistic model as an inductive bias. We demonstrate that our method achieves state-of-the-art regret results against various baselines in experiments on standard hyperparameter optimisation tasks and also outperforms others in the real-world problems of mixed-integer programming tuning, antibody design, and logic synthesis for electronic design automation.

Contextual Causal Bayesian Optimisation

Causal Bayesian optimisation (CaBO) combines causality with Bayesian optimisation (BO) and shows that there are situations where the optimal reward is not achievable if causal knowledge is ignored. While CaBO exploits causal relations to determine the set of controllable variables to intervene on, it does not exploit purely observational variables and marginalises them. We show that, in general, utilising a subset of observational variables as a context to choose the values of interventional variables leads to lower cumulative regrets. We propose a general framework of contextual causal Bayesian optimisation that efficiently searches through combinations of controlled and contextual variables, known as policy scopes, and identifies the one yielding the optimum. We highlight the difficulties arising from the application of the causal acquisition function currently used in CaBO to select the policy scope in contextual settings and propose a multi-armed bandits based selection mechanism. We analytically show that well-established methods, such as contextual BO (CoBO) or CaBO, are not able to achieve the optimum in some cases, and empirically show that the proposed method achieves sub-linear regret in various environments and under different configurations.

Sample-Efficient Optimisation with Probabilistic Transformer Surrogates

Faced with problems of increasing complexity, recent research in Bayesian Optimisation (BO) has focused on adapting deep probabilistic models as flexible alternatives to Gaussian Processes (GPs). In a similar vein, this paper investigates the feasibility of employing state-of-the-art probabilistic transformers in BO. Upon further investigation, we observe two drawbacks stemming from their training procedure and loss definition, hindering their direct deployment as proxies in black-box optimisation. First, we notice that these models are trained on uniformly distributed inputs, which impairs predictive accuracy on non-uniform data - a setting arising from any typical BO loop due to exploration-exploitation trade-offs. Second, we realise that training losses (e.g., cross-entropy) only asymptotically guarantee accurate posterior approximations, i.e., after arriving at the global optimum, which generally cannot be ensured. At the stationary points of the loss function, however, we observe a degradation in predictive performance especially in exploratory regions of the input space. To tackle these shortcomings we introduce two components: 1) a BO-tailored training prior supporting non-uniformly distributed points, and 2) a novel approximate posterior regulariser trading-off accuracy and input sensitivity to filter favourable stationary points for improved predictive performance. In a large panel of experiments, we demonstrate, for the first time, that one transformer pre-trained on data sampled from random GP priors produces competitive results on 16 benchmark black-boxes compared to GP-based BO. Since our model is only pre-trained once and used in all tasks without any retraining and/or fine-tuning, we report an order of magnitude time-reduction, while matching and sometimes outperforming GPs.

AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation

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 to combat harmful pathogens. However, the combinatorial nature of CDRH3 sequence space makes it impossible to search for an optimal binding sequence exhaustively and efficiently, especially not experimentally. Here, we present AntBO: a Combinatorial Bayesian Optimisation framework enabling efficient in silico design of the CDRH3 region. Ideally, antibodies should bind to their target antigen and be free from any harmful outcomes. Therefore, we introduce the CDRH3 trust region that restricts the search to sequences with feasible developability scores. To benchmark AntBO, we use the Absolut! software suite as a black-box oracle because it can score the target specificity and affinity of designed antibodies in silico in an unconstrained fashion. The results across 188 antigens demonstrate the benefit of AntBO in designing CDRH3 regions with diverse biophysical properties. In under 200 protein designs, AntBO can suggest antibody sequences that outperform the best binding sequence drawn from 6.9 million experimentally obtained CDRH3s and a commonly used genetic algorithm baseline. Additionally, AntBO finds very-high affinity CDRH3 sequences in only 38 protein designs whilst requiring no domain knowledge. We conclude AntBO brings automated antibody design methods closer to what is practically viable for in vitro experimentation.

BOiLS: Bayesian Optimisation for Logic Synthesis

Optimising the quality-of-results (QoR) of circuits during logic synthesis is a formidable challenge necessitating the exploration of exponentially sized search spaces. While expert-designed operations aid in uncovering effective sequences, the increase in complexity of logic circuits favours automated procedures. Inspired by the successes of machine learning, researchers adapted deep learning and reinforcement learning to logic synthesis applications. However successful, those techniques suffer from high sample complexities preventing widespread adoption. To enable efficient and scalable solutions, we propose BOiLS, the first algorithm adapting modern Bayesian optimisation to navigate the space of synthesis operations. BOiLS requires no human intervention and effectively trades-off exploration versus exploitation through novel Gaussian process kernels and trust-region constrained acquisitions. In a set of experiments on EPFL benchmarks, we demonstrate BOiLS's superior performance compared to state-of-the-art in terms of both sample efficiency and QoR values.

High-Dimensional Bayesian Optimisation with Variational Autoencoders and Deep Metric Learning

We introduce a method based on deep metric learning to perform Bayesian optimisation over high-dimensional, structured input spaces using variational autoencoders (VAEs). By extending ideas from supervised deep metric learning, we address a longstanding problem in high-dimensional VAE Bayesian optimisation, namely how to enforce a discriminative latent space as an inductive bias. Importantly, we achieve such an inductive bias using just 1% of the available labelled data relative to previous work, highlighting the sample efficiency of our approach. As a theoretical contribution, we present a proof of vanishing regret for our method. As an empirical contribution, we present state-of-the-art results on real-world high-dimensional black-box optimisation problems including property-guided molecule generation. It is the hope that the results presented in this paper can act as a guiding principle for realising effective high-dimensional Bayesian optimisation.