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Authors:Agustinus Kristiadi, Felix Strieth-Kalthoff, Sriram Ganapathi Subramanian, Vincent Fortuin, Pascal Poupart, Geoff Pleiss

Abstract:Bayesian optimization (BO) is an integral part of automated scientific discovery -- the so-called self-driving lab -- where human inputs are ideally minimal or at least non-blocking. However, scientists often have strong intuition, and thus human feedback is still useful. Nevertheless, prior works in enhancing BO with expert feedback, such as by incorporating it in an offline or online but blocking (arrives at each BO iteration) manner, are incompatible with the spirit of self-driving labs. In this work, we study whether a small amount of randomly arriving expert feedback that is being incorporated in a non-blocking manner can improve a BO campaign. To this end, we run an additional, independent computing thread on top of the BO loop to handle the feedback-gathering process. The gathered feedback is used to learn a Bayesian preference model that can readily be incorporated into the BO thread, to steer its exploration-exploitation process. Experiments on toy and chemistry datasets suggest that even just a few intermittent, asynchronous expert feedback can be useful for improving or constraining BO. This can especially be useful for its implication in improving self-driving labs, e.g. making them more data-efficient and less costly.

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Abstract:Diffusion models have shown exceptional capabilities in generating realistic videos. Yet, their training has been predominantly confined to offline environments where models can repeatedly train on i.i.d. data to convergence. This work explores the feasibility of training diffusion models from a semantically continuous video stream, where correlated video frames sequentially arrive one at a time. To investigate this, we introduce two novel continual video generative modeling benchmarks, Lifelong Bouncing Balls and Windows 95 Maze Screensaver, each containing over a million video frames generated from navigating stationary environments. Surprisingly, our experiments show that diffusion models can be effectively trained online using experience replay, achieving performance comparable to models trained with i.i.d. samples given the same number of gradient steps.

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Authors:Natalie Maus, Kyurae Kim, Geoff Pleiss, David Eriksson, John P. Cunningham, Jacob R. Gardner

Abstract:High-dimensional Bayesian optimization (BO) tasks such as molecular design often require 10,000 function evaluations before obtaining meaningful results. While methods like sparse variational Gaussian processes (SVGPs) reduce computational requirements in these settings, the underlying approximations result in suboptimal data acquisitions that slow the progress of optimization. In this paper we modify SVGPs to better align with the goals of BO: targeting informed data acquisition rather than global posterior fidelity. Using the framework of utility-calibrated variational inference, we unify GP approximation and data acquisition into a joint optimization problem, thereby ensuring optimal decisions under a limited computational budget. Our approach can be used with any decision-theoretic acquisition function and is compatible with trust region methods like TuRBO. We derive efficient joint objectives for the expected improvement and knowledge gradient acquisition functions in both the standard and batch BO settings. Our approach outperforms standard SVGPs on high-dimensional benchmark tasks in control and molecular design.

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Abstract:In online continual learning, a neural network incrementally learns from a non-i.i.d. data stream. Nearly all online continual learning methods employ experience replay to simultaneously prevent catastrophic forgetting and underfitting on past data. Our work demonstrates a limitation of this approach: networks trained with experience replay tend to have unstable optimization trajectories, impeding their overall accuracy. Surprisingly, these instabilities persist even when the replay buffer stores all previous training examples, suggesting that this issue is orthogonal to catastrophic forgetting. We minimize these instabilities through a simple modification of the optimization geometry. Our solution, Layerwise Proximal Replay (LPR), balances learning from new and replay data while only allowing for gradual changes in the hidden activation of past data. We demonstrate that LPR consistently improves replay-based online continual learning methods across multiple problem settings, regardless of the amount of available replay memory.

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Abstract:This paper is intended to appear as a chapter for the Handbook of Markov Chain Monte Carlo. The goal of this chapter is to unify various problems at the intersection of Markov chain Monte Carlo (MCMC) and machine learning$\unicode{x2014}$which includes black-box variational inference, adaptive MCMC, normalizing flow construction and transport-assisted MCMC, surrogate-likelihood MCMC, coreset construction for MCMC with big data, Markov chain gradient descent, Markovian score climbing, and more$\unicode{x2014}$within one common framework. By doing so, the theory and methods developed for each may be translated and generalized.

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Authors:Agustinus Kristiadi, Felix Strieth-Kalthoff, Marta Skreta, Pascal Poupart, Alán Aspuru-Guzik, Geoff Pleiss

Abstract:Automation is one of the cornerstones of contemporary material discovery. Bayesian optimization (BO) is an essential part of such workflows, enabling scientists to leverage prior domain knowledge into efficient exploration of a large molecular space. While such prior knowledge can take many forms, there has been significant fanfare around the ancillary scientific knowledge encapsulated in large language models (LLMs). However, existing work thus far has only explored LLMs for heuristic materials searches. Indeed, recent work obtains the uncertainty estimate -- an integral part of BO -- from point-estimated, non-Bayesian LLMs. In this work, we study the question of whether LLMs are actually useful to accelerate principled Bayesian optimization in the molecular space. We take a sober, dispassionate stance in answering this question. This is done by carefully (i) viewing LLMs as fixed feature extractors for standard but principled BO surrogate models and by (ii) leveraging parameter-efficient finetuning methods and Bayesian neural networks to obtain the posterior of the LLM surrogate. Our extensive experiments with real-world chemistry problems show that LLMs can be useful for BO over molecules, but only if they have been pretrained or finetuned with domain-specific data.

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Abstract:Gaussian process (GP) hyperparameter optimization requires repeatedly solving linear systems with $n \times n$ kernel matrices. To address the prohibitive $\mathcal{O}(n^3)$ time complexity, recent work has employed fast iterative numerical methods, like conjugate gradients (CG). However, as datasets increase in magnitude, the corresponding kernel matrices become increasingly ill-conditioned and still require $\mathcal{O}(n^2)$ space without partitioning. Thus, while CG increases the size of datasets GPs can be trained on, modern datasets reach scales beyond its applicability. In this work, we propose an iterative method which only accesses subblocks of the kernel matrix, effectively enabling \emph{mini-batching}. Our algorithm, based on alternating projection, has $\mathcal{O}(n)$ per-iteration time and space complexity, solving many of the practical challenges of scaling GPs to very large datasets. Theoretically, we prove our method enjoys linear convergence and empirically we demonstrate its robustness to ill-conditioning. On large-scale benchmark datasets up to four million datapoints our approach accelerates training by a factor of 2$\times$ to 27$\times$ compared to CG.

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Abstract:Many areas of machine learning and science involve large linear algebra problems, such as eigendecompositions, solving linear systems, computing matrix exponentials, and trace estimation. The matrices involved often have Kronecker, convolutional, block diagonal, sum, or product structure. In this paper, we propose a simple but general framework for large-scale linear algebra problems in machine learning, named CoLA (Compositional Linear Algebra). By combining a linear operator abstraction with compositional dispatch rules, CoLA automatically constructs memory and runtime efficient numerical algorithms. Moreover, CoLA provides memory efficient automatic differentiation, low precision computation, and GPU acceleration in both JAX and PyTorch, while also accommodating new objects, operations, and rules in downstream packages via multiple dispatch. CoLA can accelerate many algebraic operations, while making it easy to prototype matrix structures and algorithms, providing an appealing drop-in tool for virtually any computational effort that requires linear algebra. We showcase its efficacy across a broad range of applications, including partial differential equations, Gaussian processes, equivariant model construction, and unsupervised learning.

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Abstract:While Gaussian processes are a mainstay for various engineering and scientific applications, the uncertainty estimates don't satisfy frequentist guarantees, and can be miscalibrated in practice. State-of-the-art approaches for designing calibrated models rely on inflating the Gaussian process posterior variance, which yields confidence intervals that are potentially too coarse. To remedy this, we present a calibration approach that generates predictive quantiles using a computation inspired by the vanilla Gaussian process posterior variance, but using a different set of hyperparameters, chosen to satisfy an empirical calibration constraint. This results in a calibration approach that is considerably more flexible than existing approaches. Our approach is shown to yield a calibrated model under reasonable assumptions. Furthermore, it outperforms existing approaches not only when employed for calibrated regression, but also to inform the design of Bayesian optimization algorithms.

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Abstract:Classical results establish that ensembles of small models benefit when predictive diversity is encouraged, through bagging, boosting, and similar. Here we demonstrate that this intuition does not carry over to ensembles of deep neural networks used for classification, and in fact the opposite can be true. Unlike regression models or small (unconfident) classifiers, predictions from large (confident) neural networks concentrate in vertices of the probability simplex. Thus, decorrelating these points necessarily moves the ensemble prediction away from vertices, harming confidence and moving points across decision boundaries. Through large scale experiments, we demonstrate that diversity-encouraging regularizers hurt the performance of high-capacity deep ensembles used for classification. Even more surprisingly, discouraging predictive diversity can be beneficial. Together this work strongly suggests that the best strategy for deep ensembles is utilizing more accurate, but likely less diverse, component models.

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