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Jacob Gardner

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19 papers

1 author row

NeurIPS Conference 2025 Conference Paper

A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design

Haydn Jones
Natalie Maus
Josh magnus Ludan
Maggie Huan
Jiaming Liang
Marcelo Der Torossian Torres
Jiatao Liang
Zachary Ives

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis across diverse models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had a high probability of being mutagenic. In this work, we introduce Medex, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. Medex consists of 32. 3 million pairs of natural language facts, and appropriate entity representations (i. e. SMILES or RefSeq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLaVA architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). Medex is highly effective for creating models with strong priors: in supervised prediction problems that use our data for pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with Medex can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset on HuggingFace at https: //huggingface. co/datasets/DocAndDesign/Medex, and will provide expanded versions as the available literature grows.

NeurIPS Conference 2025 Conference Paper

Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization

Natalie Maus
Kyurae Kim
Yimeng Zeng
Haydn Jones
Fangping Wan
Marcelo Der Torossian Torres
Cesar de la Fuente-Nunez
Jacob Gardner

In multi-objective black-box optimization, the goal is typically to find solutions that optimize a set of $T$ black-box objective functions, $f_1, \ldots f_T$, simultaneously. Traditional approaches often seek a single Pareto-optimal set that balances trade-offs among all objectives. In contrast, we consider a problem setting that departs from this paradigm: finding a small set of $K < T$ solutions, that collectively "cover" the $T$ objectives. A set of solutions is defined as "covering" if, for each objective $f_1, \ldots f_T$, there is at least one good solution. A motivating example for this problem setting occurs in drug design. For example, we may have $T$ pathogens and aim to identify a set of $K < T$ antibiotics such that at least one antibiotic can be used to treat each pathogen. This problem, known as coverage optimization, has yet to be tackled with the Bayesian optimization (BO) framework. To fill this void, we develop Multi-Objective Coverage Bayesian Optimization (MOCOBO), a BO algorithm for solving coverage optimization. Our approach is based on a new acquisition function reminiscent of expected improvement in the vanilla BO setup. We demonstrate the performance of our method on high-dimensional black-box optimization tasks, including applications in peptide and molecular design. Results show that the coverage of the $K < T$ solutions found by MOCOBO matches or nearly matches the coverage of $T$ solutions obtained by optimizing each objective individually. Furthermore, in *in vitro* experiments, the peptides found by MOCOBO exhibited high potency against drug-resistant pathogens, further demonstrating the potential of MOCOBO for drug discovery. All of our code is publicly available at the following link: https: //github. com/nataliemaus/mocobo.

NeurIPS Conference 2025 Conference Paper

Nearly Dimension-Independent Convergence of Mean-Field Black-Box Variational Inference

Kyurae Kim
Yian Ma
Trevor Campbell
Jacob Gardner

We prove that, given a mean-field location-scale variational family, black-box variational inference (BBVI) with the reparametrization gradient converges at a rate that is nearly independent of explicit dimension dependence. Specifically, for a $d$-dimensional strongly log-concave and log-smooth target, the number of iterations for BBVI with a sub-Gaussian family to obtain a solution $\epsilon$-close to the global optimum has a dimension dependence of $\mathrm{O}(\log d)$. This is a significant improvement over the $\mathrm{O}(d)$ dependence of full-rank location-scale families. For heavy-tailed families, we prove a weaker $\mathrm{O}(d^{2/k})$ dependence, where $k$ is the number of finite moments of the family. Additionally, if the Hessian of the target log-density is constant, the complexity is free of any explicit dimension dependence. We also prove that our bound on the gradient variance, which is key to our result, cannot be improved using only spectral bounds on the Hessian of the target log-density.

NeurIPS Conference 2024 Conference Paper

Generative Adversarial Model-Based Optimization via Source Critic Regularization

Michael S. Yao
Yimeng Zeng
Hamsa Bastani
Jacob Gardner
James C. Gee
Osbert Bastani

Offline model-based optimization seeks to optimize against a learned surrogate model without querying the true oracle objective function during optimization. Such tasks are commonly encountered in protein design, robotics, and clinical medicine where evaluating the oracle function is prohibitively expensive. However, inaccurate surrogate model predictions are frequently encountered along offline optimization trajectories. To address this limitation, we propose generative adversarial model-based optimization using adaptive source critic regularization (aSCR) —a task- and optimizer- agnostic framework for constraining the optimization trajectory to regions of the design space where the surrogate function is reliable. We propose a computationally tractable algorithm to dynamically adjust the strength of this constraint, and show how leveraging aSCR with standard Bayesian optimization outperforms existing methods on a suite of offline generative design tasks. Our code is available at https: //github. com/michael-s-yao/gabo.

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AAAI Conference 2023 Conference Paper

Learning to Select Pivotal Samples for Meta Re-weighting

Yinjun Wu
Adam Stein
Jacob Gardner
Mayur Naik

Sample re-weighting strategies provide a promising mechanism to deal with imperfect training data in machine learning, such as noisily labeled or class-imbalanced data. One such strategy involves formulating a bi-level optimization problem called the meta re-weighting problem, whose goal is to optimize performance on a small set of perfect pivotal samples, called meta samples. Many approaches have been proposed to efficiently solve this problem. However, all of them assume that a perfect meta sample set is already provided while we observe that the selections of meta sample set is performance-critical. In this paper, we study how to learn to identify such a meta sample set from a large, imperfect training set, that is subsequently cleaned and used to optimize performance in the meta re-weighting setting. We propose a learning framework which reduces the meta samples selection problem to a weighted K-means clustering problem through rigorously theoretical analysis. We propose two clustering methods within our learning framework, Representation-based clustering method (RBC) and Gradient-based clustering method (GBC), for balancing performance and computational efficiency. Empirical studies demonstrate the performance advantage of our methods over various baseline methods

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NeurIPS Conference 2023 Conference Paper

On the Convergence of Black-Box Variational Inference

Kyurae Kim
Jisu Oh
Kaiwen Wu
Yian Ma
Jacob Gardner

We provide the first convergence guarantee for black-box variational inference (BBVI) with the reparameterization gradient. While preliminary investigations worked on simplified versions of BBVI (e. g. , bounded domain, bounded support, only optimizing for the scale, and such), our setup does not need any such algorithmic modifications. Our results hold for log-smooth posterior densities with and without strong log-concavity and the location-scale variational family. Notably, our analysis reveals that certain algorithm design choices commonly employed in practice, such as nonlinear parameterizations of the scale matrix, can result in suboptimal convergence rates. Fortunately, running BBVI with proximal stochastic gradient descent fixes these limitations and thus achieves the strongest known convergence guarantees. We evaluate this theoretical insight by comparing proximal SGD against other standard implementations of BBVI on large-scale Bayesian inference problems.

NeurIPS Conference 2023 Conference Paper

The Behavior and Convergence of Local Bayesian Optimization

Kaiwen Wu
Kyurae Kim
Roman Garnett
Jacob Gardner

A recent development in Bayesian optimization is the use of local optimization strategies, which can deliver strong empirical performance on high-dimensional problems compared to traditional global strategies. The "folk wisdom" in the literature is that the focus on local optimization sidesteps the curse of dimensionality; however, little is known concretely about the expected behavior or convergence of Bayesian local optimization routines. We first study the behavior of the local approach, and find that the statistics of individual local solutions of Gaussian process sample paths are surprisingly good compared to what we would expect to recover from global methods. We then present the first rigorous analysis of such a Bayesian local optimization algorithm recently proposed by Müller et al. (2021), and derive convergence rates in both the noisy and noiseless settings.

NeurIPS Conference 2023 Conference Paper

Variational Gaussian Processes with Decoupled Conditionals

Xinran Zhu
Kaiwen Wu
Natalie Maus
Jacob Gardner
David Bindel

Variational Gaussian processes (GPs) approximate exact GP inference by using a small set of inducing points to form a sparse approximation of the true posterior, with the fidelity of the model increasing with additional inducing points. Although the approximation error in principle can be reduced through the use of more inducing points, this leads to scaling optimization challenges and computational complexity. To achieve scalability, inducing point methods typically introduce conditional independencies and then approximations to the training and test conditional distributions. In this paper, we consider an alternative approach to modifying the training and test conditionals, in which we make them more flexible. In particular, we investigate decoupling the parametric form of the predictive mean and covariance in the conditionals, and learn independent parameters for predictive mean and covariance. We derive new evidence lower bounds (ELBO) under these more flexible conditionals, and provide two concrete examples of applying the decoupled conditionals. Empirically, we find this additional flexibility leads to improved model performance on a variety of regression tasks and Bayesian optimization (BO) applications.

NeurIPS Conference 2022 Conference Paper

Local Bayesian optimization via maximizing probability of descent

Quan Nguyen
Kaiwen Wu
Jacob Gardner
Roman Garnett

Local optimization presents a promising approach to expensive, high-dimensional black-box optimization by sidestepping the need to globally explore the search space. For objective functions whose gradient cannot be evaluated directly, Bayesian optimization offers one solution -- we construct a probabilistic model of the objective, design a policy to learn about the gradient at the current location, and use the resulting information to navigate the objective landscape. Previous work has realized this scheme by minimizing the variance in the estimate of the gradient, then moving in the direction of the expected gradient. In this paper, we re-examine and refine this approach. We demonstrate that, surprisingly, the expected value of the gradient is not always the direction maximizing the probability of descent, and in fact, these directions may be nearly orthogonal. This observation then inspires an elegant optimization scheme seeking to maximize the probability of descent while moving in the direction of most-probable descent. Experiments on both synthetic and real-world objectives show that our method outperforms previous realizations of this optimization scheme and is competitive against other, significantly more complicated baselines.

NeurIPS Conference 2022 Conference Paper

Local Latent Space Bayesian Optimization over Structured Inputs

Natalie Maus
Haydn Jones
Juston Moore
Matt J. Kusner
John Bradshaw
Jacob Gardner

Bayesian optimization over the latent spaces of deep autoencoder models (DAEs) has recently emerged as a promising new approach for optimizing challenging black-box functions over structured, discrete, hard-to-enumerate search spaces (e. g. , molecules). Here the DAE dramatically simplifies the search space by mapping inputs into a continuous latent space where familiar Bayesian optimization tools can be more readily applied. Despite this simplification, the latent space typically remains high-dimensional. Thus, even with a well-suited latent space, these approaches do not necessarily provide a complete solution, but may rather shift the structured optimization problem to a high-dimensional one. In this paper, we propose LOL-BO, which adapts the notion of trust regions explored in recent work on high-dimensional Bayesian optimization to the structured setting. By reformulating the encoder to function as both an encoder for the DAE globally and as a deep kernel for the surrogate model within a trust region, we better align the notion of local optimization in the latent space with local optimization in the input space. LOL-BO achieves as much as 20 times improvement over state-of-the-art latent space Bayesian optimization methods across six real-world benchmarks, demonstrating that improvement in optimization strategies is as important as developing better DAE models.

NeurIPS Conference 2022 Conference Paper

Markov Chain Score Ascent: A Unifying Framework of Variational Inference with Markovian Gradients

Kyurae Kim
Jisu Oh
Jacob Gardner
Adji Bousso Dieng
Hongseok Kim

Minimizing the inclusive Kullback-Leibler (KL) divergence with stochastic gradient descent (SGD) is challenging since its gradient is defined as an integral over the posterior. Recently, multiple methods have been proposed to run SGD with biased gradient estimates obtained from a Markov chain. This paper provides the first non-asymptotic convergence analysis of these methods by establishing their mixing rate and gradient variance. To do this, we demonstrate that these methods—which we collectively refer to as Markov chain score ascent (MCSA) methods—can be cast as special cases of the Markov chain gradient descent framework. Furthermore, by leveraging this new understanding, we develop a novel MCSA scheme, parallel MCSA (pMCSA), that achieves a tighter bound on the gradient variance. We demonstrate that this improved theoretical result translates to superior empirical performance.

NeurIPS Conference 2021 Conference Paper

Scaling Gaussian Processes with Derivative Information Using Variational Inference

Misha Padidar
Xinran Zhu
Leo Huang
Jacob Gardner
David Bindel

Gaussian processes with derivative information are useful in many settings where derivative information is available, including numerous Bayesian optimization and regression tasks that arise in the natural sciences. Incorporating derivative observations, however, comes with a dominating $O(N^3D^3)$ computational cost when training on $N$ points in $D$ input dimensions. This is intractable for even moderately sized problems. While recent work has addressed this intractability in the low-$D$ setting, the high-$N$, high-$D$ setting is still unexplored and of great value, particularly as machine learning problems increasingly become high dimensional. In this paper, we introduce methods to achieve fully scalable Gaussian process regression with derivatives using variational inference. Analogous to the use of inducing values to sparsify the labels of a training set, we introduce the concept of inducing directional derivatives to sparsify the partial derivative information of the training set. This enables us to construct a variational posterior that incorporates derivative information but whose size depends neither on the full dataset size $N$ nor the full dimensionality $D$. We demonstrate the full scalability of our approach on a variety of tasks, ranging from a high dimensional Stellarator fusion regression task to training graph convolutional neural networks on PubMed using Bayesian optimization. Surprisingly, we additionally find that our approach can improve regression performance even in settings where only label data is available.

NeurIPS Conference 2020 Conference Paper

Efficient Nonmyopic Bayesian Optimization via One-Shot Multi-Step Trees

Shali Jiang
Daniel Jiang
Maximilian Balandat
Brian Karrer
Jacob Gardner
Roman Garnett

Bayesian optimization is a sequential decision making framework for optimizing expensive-to-evaluate black-box functions. Computing a full lookahead policy amounts to solving a highly intractable stochastic dynamic program. Myopic approaches, such as expected improvement, are often adopted in practice, but they ignore the long-term impact of the immediate decision. Existing nonmyopic approaches are mostly heuristic and/or computationally expensive. In this paper, we provide the first efficient implementation of general multi-step lookahead Bayesian optimization, formulated as a sequence of nested optimization problems within a multi-step scenario tree. Instead of solving these problems in a nested way, we equivalently optimize all decision variables in the full tree jointly, in a "one-shot" fashion. Combining this with an efficient method for implementing multi-step Gaussian process "fantasization, " we demonstrate that multi-step expected improvement is computationally tractable and exhibits performance superior to existing methods on a wide range of benchmarks.

NeurIPS Conference 2020 Conference Paper

Fast Matrix Square Roots with Applications to Gaussian Processes and Bayesian Optimization

Geoff Pleiss
Martin Jankowiak
David Eriksson
Anil Damle
Jacob Gardner

Matrix square roots and their inverses arise frequently in machine learning, e. g. , when sampling from high-dimensional Gaussians N(0, K) or “whitening” a vector b against covariance matrix K. While existing methods typically require O(N^3) computation, we introduce a highly-efficient quadratic-time algorithm for computing K^{1/2}b, K^{-1/2}b, and their derivatives through matrix-vector multiplication (MVMs). Our method combines Krylov subspace methods with a rational approximation and typically achieves 4 decimal places of accuracy with fewer than 100 MVMs. Moreover, the backward pass requires little additional computation. We demonstrate our method's applicability on matrices as large as 50, 000 by 50, 000 - well beyond traditional methods - with little approximation error. Applying this increased scalability to variational Gaussian processes, Bayesian optimization, and Gibbs sampling results in more powerful models with higher accuracy. In particular, we perform variational GP inference with up to 10, 000 inducing points and perform Gibbs sampling on a 25, 000-dimensional problem.

NeurIPS Conference 2019 Conference Paper

Exact Gaussian Processes on a Million Data Points

Ke Wang
Geoff Pleiss
Jacob Gardner
Stephen Tyree
Kilian Weinberger
Andrew Gordon Wilson

Gaussian processes (GPs) are flexible non-parametric models, with a capacity that grows with the available data. However, computational constraints with standard inference procedures have limited exact GPs to problems with fewer than about ten thousand training points, necessitating approximations for larger datasets. In this paper, we develop a scalable approach for exact GPs that leverages multi-GPU parallelization and methods like linear conjugate gradients, accessing the kernel matrix only through matrix multiplication. By partitioning and distributing kernel matrix multiplies, we demonstrate that an exact GP can be trained on over a million points, a task previously thought to be impossible with current computing hardware. Moreover, our approach is generally applicable, without constraints to grid data or specific kernel classes. Enabled by this scalability, we perform the first-ever comparison of exact GPs against scalable GP approximations on datasets with $10^4 \! -\! 10^6$ data points, showing dramatic performance improvements.

NeurIPS Conference 2019 Conference Paper

Scalable Global Optimization via Local Bayesian Optimization

David Eriksson
Michael Pearce
Jacob Gardner
Ryan Turner
Matthias Poloczek

Bayesian optimization has recently emerged as a popular method for the sample-efficient optimization of expensive black-box functions. However, the application to high-dimensional problems with several thousand observations remains challenging, and on difficult problems Bayesian optimization is often not competitive with other paradigms. In this paper we take the view that this is due to the implicit homogeneity of the global probabilistic models and an overemphasized exploration that results from global acquisition. This motivates the design of a local probabilistic approach for global optimization of large-scale high-dimensional problems. We propose the TuRBO algorithm that fits a collection of local models and performs a principled global allocation of samples across these models via an implicit bandit approach. A comprehensive evaluation demonstrates that TuRBO outperforms state-of-the-art methods from machine learning and operations research on problems spanning reinforcement learning, robotics, and the natural sciences.

NeurIPS Conference 2018 Conference Paper

GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration

Jacob Gardner
Geoff Pleiss
Kilian Weinberger
David Bindel
Andrew Wilson

Despite advances in scalable models, the inference tools used for Gaussian processes (GPs) have yet to fully capitalize on developments in computing hardware. We present an efficient and general approach to GP inference based on Blackbox Matrix-Matrix multiplication (BBMM). BBMM inference uses a modified batched version of the conjugate gradients algorithm to derive all terms for training and inference in a single call. BBMM reduces the asymptotic complexity of exact GP inference from O(n^3) to O(n^2). Adapting this algorithm to scalable approximations and complex GP models simply requires a routine for efficient matrix-matrix multiplication with the kernel and its derivative. In addition, BBMM uses a specialized preconditioner to substantially speed up convergence. In experiments we show that BBMM effectively uses GPU hardware to dramatically accelerate both exact GP inference and scalable approximations. Additionally, we provide GPyTorch, a software platform for scalable GP inference via BBMM, built on PyTorch.

AAAI Conference 2015 Conference Paper

A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

Quan Zhou
Wenlin Chen
Shiji Song
Jacob Gardner
Kilian Weinberger
Yixin Chen

Algorithmic reductions are one of the corner stones of theoretical computer science. Surprisingly, to-date, they have only played a limited role in machine learning. In this paper we introduce a formal and practical reduction between two of the most widely used machine learning algorithms: from the Elastic Net (and the Lasso as a special case) to the Support Vector Machine. First, we derive the reduction and summarize it in only 11 lines of MATLABTM. Then, we demonstrate its high impact potential by translating recent advances in parallelizing SVM solvers directly to the Elastic Net. The resulting algorithm is a parallel solver for the Elastic Net (and Lasso) that naturally utilizes GPU and multi-core CPUs. We evaluate it on twelve real world data sets, and show that it yields identical results as the popular (and highly optimized) glmnet implementation but is up-to two orders of magnitude faster.

NeurIPS Conference 2015 Conference Paper

Bayesian Active Model Selection with an Application to Automated Audiometry

Jacob Gardner
Gustavo Malkomes
Roman Garnett
Kilian Weinberger
Dennis Barbour
John Cunningham

We introduce a novel information-theoretic approach for active model selection and demonstrate its effectiveness in a real-world application. Although our method can work with arbitrary models, we focus on actively learning the appropriate structure for Gaussian process (GP) models with arbitrary observation likelihoods. We then apply this framework to rapid screening for noise-induced hearing loss (NIHL), a widespread and preventible disability, if diagnosed early. We construct a GP model for pure-tone audiometric responses of patients with NIHL. Using this and a previously published model for healthy responses, the proposed method is shown to be capable of diagnosing the presence or absence of NIHL with drastically fewer samples than existing approaches. Further, the method is extremely fast and enables the diagnosis to be performed in real time.