arXiv subjects

Kyurae Kim

Publications and source records attributed to Kyurae Kim.

At least 19 recordsLinked to original sources

arXiv2026

Large-scale empirical tuning and comparison of default optimizers for variational inference

Black-box variational inference (BBVI) is a methodology for posterior approximation that relies on stochastic optimization. In practice, the stochastic optimizers underpinning BBVI generally require extensive problem-specific tuning, which undermines its promise as a truly "black box" inference algorithm. However, over the past decade, many new adaptive stochastic optimization algorithms have been developed that reduce or remove entirely the need for tuning. In this work, we investigate this new collection of adaptive methods in the context of BBVI, with the goal of establishing the current state of the art in tuning-free optimization-based inference. In particular, we present a large-scale empirical evaluation of 56 stochastic gradient-based optimization algorithms applied to 1092 Bayesian inference optimization problems, involving over 550,000 individual optimization runs and 15 core-years of compute. The optimization algorithms we evaluate are chosen to represent a wide spectrum of recent approaches and the benchmark problems are chosen to span a range of difficulty, with posterior target dimension 1-10^4, condition number 1-10^8, and a range of variational families. Our results show that no single method dominates, but running a selection of 5 algorithms suffices to reliably get close to the best-possible observed performance. We thus provide a strong baseline for applications where expert tuning is not possible and for comparison when developing new stochastic optimization algorithms.

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arXiv2026

A Theoretical Comparison of No-U-Turn Sampler Variants: Necessary and Sufficient Convergence Conditions and Mixing Time Analysis under Gaussian Targets

The No-U-Turn Sampler (NUTS) is the computational workhorse of modern Bayesian software libraries, yet its qualitative and quantitative convergence guarantees were established only recently. A significant gap remains in the theoretical comparison of its two main variants: NUTS-mul and NUTS-BPS, which use multinomial sampling and biased progressive sampling, respectively, for index selection. In this paper, we address this gap in three contributions. First, we derive the first necessary conditions for geometric ergodicity for both variants. Second, we establish the first sufficient conditions for geometric ergodicity and ergodicity for NUTS-mul. Third, we obtain the first mixing time result for NUTS-BPS on a standard Gaussian distribution. Our results show that NUTS-mul and NUTS-BPS exhibit nearly identical qualitative behavior, with geometric ergodicity depending on the tail properties of the target distribution. However, they differ quantitatively in their convergence rates. More precisely, when initialized in the typical set of the canonical Gaussian measure, the mixing times of both NUTS-mul and NUTS-BPS scale as $O(d^{1/4})$ up to logarithmic factors, where $d$ denotes the dimension. Nevertheless, the associated constants are strictly smaller for NUTS-BPS.

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arXiv2026

Stochastic Gradient Variational Inference with Price's Gradient Estimator from Bures-Wasserstein to Parameter Space

For approximating a target distribution given only its unnormalized log-density, stochastic gradient-based variational inference (VI) algorithms are a popular approach. For example, Wasserstein VI (WVI) and black-box VI (BBVI) perform gradient descent in measure space (Bures-Wasserstein space) and parameter space, respectively. Previously, for the Gaussian variational family, convergence guarantees for WVI have shown superiority over existing results for black-box VI with the reparametrization gradient, suggesting the measure space approach might provide some unique benefits. In this work, however, we close this gap by obtaining identical state-of-the-art iteration complexity guarantees for both. In particular, we identify that WVI's superiority stems from the specific gradient estimator it uses, which BBVI can also leverage with minor modifications. The estimator in question is usually associated with Price's theorem and utilizes second-order information (Hessians) of the target log-density. We will refer to this as Price's gradient. On the flip side, WVI can be made more widely applicable by using the reparametrization gradient, which requires only gradients of the log-density. We empirically demonstrate that the use of Price's gradient is the major source of performance improvement.

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arXiv2026

Purely Agent-Driven Black-Box Optimization for Biological Design

Many key challenges in biological design -- such as small-molecule drug discovery, antimicrobial peptide development, and protein engineering -- can be framed as black-box optimization over vast, complex structured spaces. Existing methods rely mainly on raw structural data and struggle to exploit the rich scientific literature. While large language models (LLMs) have been added to these pipelines, they have been confined to narrow roles within structure-centered optimizers. We instead cast biological black-box optimization as an agent-driven, language-based reasoning process. We introduce Purely Agent-driven BLack-box Optimization (PABLO), a hierarchical agentic system that uses scientific LLMs pretrained on chemistry and biology literature to generate and iteratively refine biological candidates. On both the standard GuacaMol molecular design and antimicrobial peptide optimization tasks, PABLO achieves state-of-the-art performance, substantially improving sample efficiency and final objective values over established baselines. Compared to prior optimization methods that incorporate LLMs, PABLO achieves competitive token usage per run despite relying on LLMs throughout the optimization loop. Beyond raw performance, the agentic formulation offers key advantages for realistic design: it naturally incorporates semantic task descriptions, retrieval-augmented domain knowledge, and complex constraints. In follow-up in vitro validation, PABLO-optimized peptides showed strong activity against drug-resistant pathogens, underscoring the practical potential of PABLO for therapeutic discovery.

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arXiv2025

Analysis of kinetic Langevin Monte Carlo under the stochastic exponential Euler discretization from underdamped all the way to overdamped

Simulating the kinetic Langevin dynamics is a popular approach for sampling from distributions, where only their unnormalized densities are available. Various discretizations of the kinetic Langevin dynamics have been considered, where the resulting algorithm is collectively referred to as the kinetic Langevin Monte Carlo (KLMC) or underdamped Langevin Monte Carlo. Specifically, the stochastic exponential Euler discretization, or exponential integrator for short, has previously been studied under strongly log-concave and log-Lipschitz smooth potentials via the synchronous Wasserstein coupling strategy. Existing analyses, however, impose restrictions on the parameters that do not explain the behavior of KLMC under various choices of parameters. In particular, all known results fail to hold in the overdamped regime, suggesting that the exponential integrator degenerates in the overdamped limit. In this work, we revisit the synchronous Wasserstein coupling analysis of KLMC with the exponential integrator. Our refined analysis results in Wasserstein contractions and bounds on the asymptotic bias that hold under weaker restrictions on the parameters, which assert that the exponential integrator is capable of stably simulating the kinetic Langevin dynamics in the overdamped regime, as long as proper time acceleration is applied.

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arXiv2025

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

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.

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arXiv2025

Tuning Sequential Monte Carlo Samplers via Greedy Incremental Divergence Minimization

The performance of sequential Monte Carlo (SMC) samplers heavily depends on the tuning of the Markov kernels used in the path proposal. For SMC samplers with unadjusted Markov kernels, standard tuning objectives, such as the Metropolis-Hastings acceptance rate or the expected-squared jump distance, are no longer applicable. While stochastic gradient-based end-to-end optimization has been explored for tuning SMC samplers, they often incur excessive training costs, even for tuning just the kernel step sizes. In this work, we propose a general adaptation framework for tuning the Markov kernels in SMC samplers by minimizing the incremental Kullback-Leibler (KL) divergence between the proposal and target paths. For step size tuning, we provide a gradient- and tuning-free algorithm that is generally applicable for kernels such as Langevin Monte Carlo (LMC). We further demonstrate the utility of our approach by providing a tailored scheme for tuning kinetic LMC used in SMC samplers. Our implementations are able to obtain a full schedule of tuned parameters at the cost of a few vanilla SMC runs, which is a fraction of gradient-based approaches.

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arXiv2025

Personalized Convolutional Dictionary Learning of Physiological Time Series

Human physiological signals tend to exhibit both global and local structures: the former are shared across a population, while the latter reflect inter-individual variability. For instance, kinetic measurements of the gait cycle during locomotion present common characteristics, although idiosyncrasies may be observed due to biomechanical disposition or pathology. To better represent datasets with local-global structure, this work extends Convolutional Dictionary Learning (CDL), a popular method for learning interpretable representations, or dictionaries, of time-series data. In particular, we propose Personalized CDL (PerCDL), in which a local dictionary models local information as a personalized spatiotemporal transformation of a global dictionary. The transformation is learnable and can combine operations such as time warping and rotation. Formal computational and statistical guarantees for PerCDL are provided and its effectiveness on synthetic and real human locomotion data is demonstrated.

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arXiv2025

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

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.

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arXiv2024

Bayesian Wideband Signal Detection via Source Signal Marginalization and RJMCMC

Consider an array receiving unknown wideband signals from an unknown number of sources $k$. Wideband signals can occupy arbitrarily wide bandwidths, rendering demodulation-based approaches inapplicable, a common situation in settings involving acoustic signals. Here, we aim to determine $k$ given $N$ noisy array-valued measurements, a task known as the "detection problem," for which Bayesian model comparison is a common approach. To render Bayesian inference tractable, it is typically necessary to marginalize the source signals. Unfortunately, for wideband signals, naive marginalization has an unaffordable time complexity of $\mathcal{O}(N^3 k^3)$. As a result, fully Bayesian signal detection has yet to be demonstrated in wideband settings. In this work, we propose a wideband signal model that allows for computationally tractable marginalization of the source signals. We begin from the canonical model of linear time-invariant (LTI) signal propagation, which is then augmented into a circular convolution, all without loss of generality. This allows for efficient computation in the frequency domain, where the resulting linear system admits a decomposition into a sparse matrix we refer to as a \textit{stripe matrix decomposition}. Exploiting this sparsity pattern reduces the time complexity of computing the marginal likelihood to $\mathcal{O}(N k^3)$. These computational improvements enable efficient posterior inference via reversible-jump Markov chain Monte Carlo (RJMCMC). In this work, we use the non-reversible extension of RJMCMC (NRJMCMC), which often achieves lower autocorrelation and faster convergence than RJMCMC. Detection of the latent source signals can then be performed in a fully Bayesian manner using samples drawn by NRJMCMC. We evaluate our procedure by comparing it against generalized likelihood ratio testing (GLRT) and information criteria.

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arXiv2024

Approximation-Aware Bayesian Optimization

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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arXiv2024

Demystifying SGD with Doubly Stochastic Gradients

Optimization objectives in the form of a sum of intractable expectations are rising in importance (e.g., diffusion models, variational autoencoders, and many more), a setting also known as "finite sum with infinite data." For these problems, a popular strategy is to employ SGD with doubly stochastic gradients (doubly SGD): the expectations are estimated using the gradient estimator of each component, while the sum is estimated by subsampling over these estimators. Despite its popularity, little is known about the convergence properties of doubly SGD, except under strong assumptions such as bounded variance. In this work, we establish the convergence of doubly SGD with independent minibatching and random reshuffling under general conditions, which encompasses dependent component gradient estimators. In particular, for dependent estimators, our analysis allows fined-grained analysis of the effect correlations. As a result, under a per-iteration computational budget of $b \times m$, where $b$ is the minibatch size and $m$ is the number of Monte Carlo samples, our analysis suggests where one should invest most of the budget in general. Furthermore, we prove that random reshuffling (RR) improves the complexity dependence on the subsampling noise.

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arXiv2024

The Behavior and Convergence of Local Bayesian Optimization

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.

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arXiv2024

Stochastic Approximation with Biased MCMC for Expectation Maximization

The expectation maximization (EM) algorithm is a widespread method for empirical Bayesian inference, but its expectation step (E-step) is often intractable. Employing a stochastic approximation scheme with Markov chain Monte Carlo (MCMC) can circumvent this issue, resulting in an algorithm known as MCMC-SAEM. While theoretical guarantees for MCMC-SAEM have previously been established, these results are restricted to the case where asymptotically unbiased MCMC algorithms are used. In practice, MCMC-SAEM is often run with asymptotically biased MCMC, for which the consequences are theoretically less understood. In this work, we fill this gap by analyzing the asymptotics and non-asymptotics of SAEM with biased MCMC steps, particularly the effect of bias. We also provide numerical experiments comparing the Metropolis-adjusted Langevin algorithm (MALA), which is asymptotically unbiased, and the unadjusted Langevin algorithm (ULA), which is asymptotically biased, on synthetic and real datasets. Experimental results show that ULA is more stable with respect to the choice of Langevin stepsize and can sometimes result in faster convergence.

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arXiv2024

Provably Scalable Black-Box Variational Inference with Structured Variational Families

Variational families with full-rank covariance approximations are known not to work well in black-box variational inference (BBVI), both empirically and theoretically. In fact, recent computational complexity results for BBVI have established that full-rank variational families scale poorly with the dimensionality of the problem compared to e.g. mean-field families. This is particularly critical to hierarchical Bayesian models with local variables; their dimensionality increases with the size of the datasets. Consequently, one gets an iteration complexity with an explicit $\mathcal{O}(N^2)$ dependence on the dataset size $N$. In this paper, we explore a theoretical middle ground between mean-field variational families and full-rank families: structured variational families. We rigorously prove that certain scale matrix structures can achieve a better iteration complexity of $\mathcal{O}\left(N\right)$, implying better scaling with respect to $N$. We empirically verify our theoretical results on large-scale hierarchical models.

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arXiv2024

On the Convergence of Black-Box Variational Inference

We provide the first convergence guarantee for full black-box variational inference (BBVI), also known as Monte Carlo variational inference. 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. Also, our analysis reveals that certain algorithm design choices commonly employed in practice, particularly, nonlinear parameterizations of the scale of the variational approximation, can result in suboptimal convergence rates. Fortunately, running BBVI with proximal stochastic gradient descent fixes these limitations, and thus achieves the strongest known convergence rate guarantees. We evaluate this theoretical insight by comparing proximal SGD against other standard implementations of BBVI on large-scale Bayesian inference problems.

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arXiv2023

Linear Convergence of Black-Box Variational Inference: Should We Stick the Landing?

We prove that black-box variational inference (BBVI) with control variates, particularly the sticking-the-landing (STL) estimator, converges at a geometric (traditionally called "linear") rate under perfect variational family specification. In particular, we prove a quadratic bound on the gradient variance of the STL estimator, one which encompasses misspecified variational families. Combined with previous works on the quadratic variance condition, this directly implies convergence of BBVI with the use of projected stochastic gradient descent. For the projection operator, we consider a domain with triangular scale matrices, which the projection onto is computable in $\Theta(d)$ time, where $d$ is the dimensionality of the target posterior. We also improve existing analysis on the regular closed-form entropy gradient estimators, which enables comparison against the STL estimator, providing explicit non-asymptotic complexity guarantees for both.

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arXiv2023

Practical and Matching Gradient Variance Bounds for Black-Box Variational Bayesian Inference

Understanding the gradient variance of black-box variational inference (BBVI) is a crucial step for establishing its convergence and developing algorithmic improvements. However, existing studies have yet to show that the gradient variance of BBVI satisfies the conditions used to study the convergence of stochastic gradient descent (SGD), the workhorse of BBVI. In this work, we show that BBVI satisfies a matching bound corresponding to the $ABC$ condition used in the SGD literature when applied to smooth and quadratically-growing log-likelihoods. Our results generalize to nonlinear covariance parameterizations widely used in the practice of BBVI. Furthermore, we show that the variance of the mean-field parameterization has provably superior dimensional dependence.

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