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May 21

Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design

Bayesian optimization (BO) is a powerful framework to optimize black-box expensive-to-evaluate functions via sequential interactions. In several important problems (e.g. drug discovery, circuit design, neural architecture search, etc.), though, such functions are defined over large combinatorial and unstructured spaces. This makes existing BO algorithms not feasible due to the intractable maximization of the acquisition function over these domains. To address this issue, we propose GameOpt, a novel game-theoretical approach to combinatorial BO. GameOpt establishes a cooperative game between the different optimization variables, and selects points that are game equilibria of an upper confidence bound acquisition function. These are stable configurations from which no variable has an incentive to deviate- analog to local optima in continuous domains. Crucially, this allows us to efficiently break down the complexity of the combinatorial domain into individual decision sets, making GameOpt scalable to large combinatorial spaces. We demonstrate the application of GameOpt to the challenging protein design problem and validate its performance on four real-world protein datasets. Each protein can take up to 20^{X} possible configurations, where X is the length of a protein, making standard BO methods infeasible. Instead, our approach iteratively selects informative protein configurations and very quickly discovers highly active protein variants compared to other baselines.

Human Alignment of Large Language Models through Online Preference Optimisation

Ensuring alignment of language models' outputs with human preferences is critical to guarantee a useful, safe, and pleasant user experience. Thus, human alignment has been extensively studied recently and several methods such as Reinforcement Learning from Human Feedback (RLHF), Direct Policy Optimisation (DPO) and Sequence Likelihood Calibration (SLiC) have emerged. In this paper, our contribution is two-fold. First, we show the equivalence between two recent alignment methods, namely Identity Policy Optimisation (IPO) and Nash Mirror Descent (Nash-MD). Second, we introduce a generalisation of IPO, named IPO-MD, that leverages the regularised sampling approach proposed by Nash-MD. This equivalence may seem surprising at first sight, since IPO is an offline method whereas Nash-MD is an online method using a preference model. However, this equivalence can be proven when we consider the online version of IPO, that is when both generations are sampled by the online policy and annotated by a trained preference model. Optimising the IPO loss with such a stream of data becomes then equivalent to finding the Nash equilibrium of the preference model through self-play. Building on this equivalence, we introduce the IPO-MD algorithm that generates data with a mixture policy (between the online and reference policy) similarly as the general Nash-MD algorithm. We compare online-IPO and IPO-MD to different online versions of existing losses on preference data such as DPO and SLiC on a summarisation task.

Optimistic Online Mirror Descent for Bridging Stochastic and Adversarial Online Convex Optimization

Stochastically Extended Adversarial (SEA) model is introduced by Sachs et al. [2022] as an interpolation between stochastic and adversarial online convex optimization. Under the smoothness condition, they demonstrate that the expected regret of optimistic follow-the-regularized-leader (FTRL) depends on the cumulative stochastic variance sigma_{1:T}^2 and the cumulative adversarial variation Sigma_{1:T}^2 for convex functions. They also provide a slightly weaker bound based on the maximal stochastic variance sigma_{max}^2 and the maximal adversarial variation Sigma_{max}^2 for strongly convex functions. Inspired by their work, we investigate the theoretical guarantees of optimistic online mirror descent (OMD) for the SEA model. For convex and smooth functions, we obtain the same O(sigma_{1:T^2}+Sigma_{1:T^2}) regret bound, without the convexity requirement of individual functions. For strongly convex and smooth functions, we establish an O(min{log (sigma_{1:T}^2+Sigma_{1:T}^2), (sigma_{max}^2 + Sigma_{max}^2) log T}) bound, better than their O((sigma_{max}^2 + Sigma_{max}^2) log T) bound. For exp-concave and smooth functions, we achieve a new O(dlog(sigma_{1:T}^2+Sigma_{1:T}^2)) bound. Owing to the OMD framework, we can further extend our result to obtain dynamic regret guarantees, which are more favorable in non-stationary online scenarios. The attained results allow us to recover excess risk bounds of the stochastic setting and regret bounds of the adversarial setting, and derive new guarantees for many intermediate scenarios.

JaColBERTv2.5: Optimising Multi-Vector Retrievers to Create State-of-the-Art Japanese Retrievers with Constrained Resources

Neural Information Retrieval has advanced rapidly in high-resource languages, but progress in lower-resource ones such as Japanese has been hindered by data scarcity, among other challenges. Consequently, multilingual models have dominated Japanese retrieval, despite their computational inefficiencies and inability to capture linguistic nuances. While recent multi-vector monolingual models like JaColBERT have narrowed this gap, they still lag behind multilingual methods in large-scale evaluations. This work addresses the suboptimal training methods of multi-vector retrievers in lower-resource settings, focusing on Japanese. We systematically evaluate and improve key aspects of the inference and training settings of JaColBERT, and more broadly, multi-vector models. We further enhance performance through a novel checkpoint merging step, showcasing it to be an effective way of combining the benefits of fine-tuning with the generalization capabilities of the original checkpoint. Building on our analysis, we introduce a novel training recipe, resulting in the JaColBERTv2.5 model. JaColBERTv2.5, with only 110 million parameters and trained in under 15 hours on 4 A100 GPUs, significantly outperforms all existing methods across all common benchmarks, reaching an average score of 0.754, significantly above the previous best of 0.720. To support future research, we make our final models, intermediate checkpoints and all data used publicly available.

Understanding Likelihood Over-optimisation in Direct Alignment Algorithms

Direct Alignment Algorithms (DAAs), such as Direct Preference Optimisation (DPO) and Identity Preference Optimisation (IPO), have emerged as alternatives to online Reinforcement Learning from Human Feedback (RLHF) algorithms such as Proximal Policy Optimisation (PPO) for aligning language models to human preferences, without the need for explicit reward modelling. These methods generally aim to increase the likelihood of generating better (preferred) completions while discouraging worse (non-preferred) ones, while staying close to the original model's behaviour. In this work, we explore the relationship between completion likelihood and model performance in state-of-the-art DAAs, and identify a critical issue of likelihood over-optimisation. Contrary to expectations, we find that higher likelihood of better completions and larger margins between better and worse completion likelihoods do not necessarily lead to better performance, and may even degrade it. Our analysis reveals that while higher likelihood correlates with better memorisation of factual knowledge patterns, a slightly lower completion likelihood tends to improve output diversity, thus leading to better generalisation to unseen scenarios. Moreover, we identify two key indicators that signal when over-optimised output diversity begins to harm performance: Decreasing Entropy over Top-k Tokens and Diminishing Top-k Probability Mass. Our experimental results validate that these indicators are reliable signs of declining performance under different regularisations, helping prevent over-optimisation and improve alignment with human preferences.

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.

AgentCoder: Multi-Agent-based Code Generation with Iterative Testing and Optimisation

The advancement of natural language processing (NLP) has been significantly boosted by the development of transformer-based large language models (LLMs). These models have revolutionized NLP tasks, particularly in code generation, aiding developers in creating software with enhanced efficiency. Despite their advancements, challenges in balancing code snippet generation with effective test case generation and execution persist. To address these issues, this paper introduces Multi-Agent Assistant Code Generation (AgentCoder), a novel solution comprising a multi-agent framework with specialized agents: the programmer agent, the test designer agent, and the test executor agent. During the coding procedure, the programmer agent will focus on the code generation and refinement based on the test executor agent's feedback. The test designer agent will generate test cases for the generated code, and the test executor agent will run the code with the test cases and write the feedback to the programmer. This collaborative system ensures robust code generation, surpassing the limitations of single-agent models and traditional methodologies. Our extensive experiments on 9 code generation models and 12 enhancement approaches showcase AgentCoder's superior performance over existing code generation models and prompt engineering techniques across various benchmarks. For example, AgentCoder achieves 77.4% and 89.1% pass@1 in HumanEval-ET and MBPP-ET with GPT-3.5, while SOTA baselines obtain only 69.5% and 63.0%.

Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

COPlanner: Plan to Roll Out Conservatively but to Explore Optimistically for Model-Based RL

Dyna-style model-based reinforcement learning contains two phases: model rollouts to generate sample for policy learning and real environment exploration using current policy for dynamics model learning. However, due to the complex real-world environment, it is inevitable to learn an imperfect dynamics model with model prediction error, which can further mislead policy learning and result in sub-optimal solutions. In this paper, we propose COPlanner, a planning-driven framework for model-based methods to address the inaccurately learned dynamics model problem with conservative model rollouts and optimistic environment exploration. COPlanner leverages an uncertainty-aware policy-guided model predictive control (UP-MPC) component to plan for multi-step uncertainty estimation. This estimated uncertainty then serves as a penalty during model rollouts and as a bonus during real environment exploration respectively, to choose actions. Consequently, COPlanner can avoid model uncertain regions through conservative model rollouts, thereby alleviating the influence of model error. Simultaneously, it explores high-reward model uncertain regions to reduce model error actively through optimistic real environment exploration. COPlanner is a plug-and-play framework that can be applied to any dyna-style model-based methods. Experimental results on a series of proprioceptive and visual continuous control tasks demonstrate that both sample efficiency and asymptotic performance of strong model-based methods are significantly improved combined with COPlanner.

Exploring Public Attention in the Circular Economy through Topic Modelling with Twin Hyperparameter Optimisation

To advance the circular economy (CE), it is crucial to gain insights into the evolution of public attention, cognitive pathways of the masses concerning circular products, and to identify primary concerns. To achieve this, we collected data from diverse platforms, including Twitter, Reddit, and The Guardian, and utilised three topic models to analyse the data. Given the performance of topic modelling may vary depending on hyperparameter settings, this research proposed a novel framework that integrates twin (single and multi-objective) hyperparameter optimisation for the CE. We conducted systematic experiments to ensure that topic models are set with appropriate hyperparameters under different constraints, providing valuable insights into the correlations between CE and public attention. In summary, our optimised model reveals that public remains concerned about the economic impacts of sustainability and circular practices, particularly regarding recyclable materials and environmentally sustainable technologies. The analysis shows that the CE has attracted significant attention on The Guardian, especially in topics related to sustainable development and environmental protection technologies, while discussions are comparatively less active on Twitter. These insights highlight the need for policymakers to implement targeted education programs, create incentives for businesses to adopt CE principles, and enforce more stringent waste management policies alongside improved recycling processes.