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Ji Won Park

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6 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

Efficient semantic uncertainty quantification in language models via diversity-steered sampling

Ji Won Park
Kyunghyun Cho

Accurately estimating semantic aleatoric and epistemic uncertainties in large language models (LLMs) is particularly challenging in free-form question answering (QA), where obtaining stable estimates often requires many expensive generations. We introduce a diversity-steered sampler that discourages semantically redundant outputs during decoding, covers both autoregressive and masked diffusion paradigms, and yields substantial sample-efficiency gains. The key idea is to inject a continuous semantic-similarity penalty into the model’s proposal distribution using a natural language inference (NLI) model lightly finetuned on partial prefixes or intermediate diffusion states. We debias downstream uncertainty estimates with importance reweighting and shrink their variance with control variates. Across four QA benchmarks, our method matches or surpasses baselines while covering more semantic clusters with the same number of samples. Being modular and requiring no gradient access to the base LLM, the framework promises to serve as a drop-in enhancement for uncertainty estimation in risk-sensitive model deployments.

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ICML Conference 2025 Conference Paper

Reliable Algorithm Selection for Machine Learning-Guided Design

Clara Wong-Fannjiang
Ji Won Park

Algorithms for machine learning-guided design, or design algorithms, use machine learning-based predictions to propose novel objects with desired property values. Given a new design task—for example, to design novel proteins with high binding affinity to a therapeutic target—one must choose a design algorithm and specify any hyperparameters and predictive and/or generative models involved. How can these decisions be made such that the resulting designs are successful? This paper proposes a method for design algorithm selection, which aims to select design algorithms that will produce a distribution of design labels satisfying a user-specified success criterion—for example, that at least ten percent of designs’ labels exceed a threshold. It does so by combining designs’ predicted property values with held-out labeled data to reliably forecast characteristics of the label distributions produced by different design algorithms, building upon techniques from prediction-powered inference (Angelopoulos et al. , 2023). The method is guaranteed with high probability to return design algorithms that yield successful label distributions (or the null set if none exist), if the density ratios between the design and labeled data distributions are known. We demonstrate the method’s effectiveness in simulated protein and RNA design tasks, in settings with either known or estimated density ratios.

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TMLR Journal 2024 Journal Article

Blind Biological Sequence Denoising with Self-Supervised Set Learning

Nathan Hoyen Ng
Ji Won Park
Jae Hyeon Lee
Ryan Lewis Kelly
Stephen Ra
Kyunghyun Cho

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate multiple subreads, or noisy obser- vations of the same sequence. Denoising these subreads with alignment-based approaches often fails when too few subreads are available or error rates are too high. In this paper, we propose a novel method for blindly denoising sets of sequences without directly observing clean source sequence labels. Our method, Self-Supervised Set Learning (SSSL), gathers subreads together in an embedding space and estimates a single set embedding as the mid- point of the subreads in both the latent and sequence spaces. This set embedding represents the “average” of the subreads and can be decoded into a prediction of the clean sequence. In experiments on simulated long-read DNA data, SSSL methods denoise small reads of ≤ 6 subreads with 17% fewer errors and large reads of > 6 subreads with 8% fewer errors compared to the best baseline. On a real dataset of antibody sequences, SSSL improves over baselines on two self-supervised metrics, with a significant improvement on difficult small reads that comprise over 60% of the test set. By accurately denoising these reads, SSSL promises to better realize the potential of high-throughput DNA sequencing data for downstream scientific applications.

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ICML Conference 2024 Conference Paper

BOtied: Multi-objective Bayesian optimization with tied multivariate ranks

Ji Won Park
Natasa Tagasovska
Michael Maser
Stephen Ra
Kyunghyun Cho

Many scientific and industrial applications require the joint optimization of multiple, potentially competing objectives. Multi-objective Bayesian optimization (MOBO) is a sample-efficient framework for identifying Pareto-optimal solutions. At the heart of MOBO is the acquisition function, which determines the next candidate to evaluate by navigating the best compromises among the objectives. Acquisition functions that rely on integrating over the objective space scale poorly to a large number of objectives. In this paper, we show a natural connection between the non-dominated solutions and the highest multivariate rank, which coincides with the extreme level line of the joint cumulative distribution function (CDF). Motivated by this link, we propose the CDF indicator, a Pareto-compliant metric for evaluating the quality of approximate Pareto sets, that can complement the popular hypervolume indicator. We then introduce an acquisition function based on the CDF indicator, called BOtied. BOtied can be implemented efficiently with copulas, a statistical tool for modeling complex, high-dimensional distributions. Our experiments on a variety of synthetic and real-world experiments demonstrate that BOtied outperforms state-of-the-art MOBO algorithms while being computationally efficient for many objectives.

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ICLR Conference 2024 Conference Paper

Chain of Log-Concave Markov Chains

Saeed Saremi
Ji Won Park
Francis R. Bach

We introduce a theoretical framework for sampling from unnormalized densities based on a smoothing scheme that uses an isotropic Gaussian kernel with a single fixed noise scale. We prove one can decompose sampling from a density (minimal assumptions made on the density) into a sequence of sampling from log-concave conditional densities via accumulation of noisy measurements with equal noise levels. Our construction is unique in that it keeps track of a history of samples, making it non-Markovian as a whole, but it is lightweight algorithmically as the history only shows up in the form of a running empirical mean of samples. Our sampling algorithm generalizes walk-jump sampling (Saremi & Hyvärinen, 2019). The "walk" phase becomes a (non-Markovian) chain of (log-concave) Markov chains. The "jump" from the accumulated measurements is obtained by empirical Bayes. We study our sampling algorithm quantitatively using the 2-Wasserstein metric and compare it with various Langevin MCMC algorithms. We also report a remarkable capacity of our algorithm to "tunnel" between modes of a distribution.

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NeurIPS Conference 2023 Conference Paper

GAUCHE: A Library for Gaussian Processes in Chemistry

Ryan-Rhys Griffiths
Leo Klarner
Henry Moss
Aditya Ravuri
Sang Truong
Yuanqi Du
Samuel Stanton
Gary Tom

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https: //github. com/leojklarner/gauche.

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