34 citations · 47 across the 11 of their papers we have counts for
13 papers
PairIT: Autoregressive Transformers for Low-Data Molecule Optimization
Hannah Lawrence, Bodhi P. Vani, Ji Won Park +5
Generating novel molecules with desired properties is a central challenge in drug discovery. Although foundational work focused on de novo generation, practical use cases require a…
Conformal Policy Control
Drew Prinster, Clara Fannjiang, Ji Won Park +4
An agent must try new behaviors to explore and improve. In high-stakes environments, an agent that violates safety constraints may cause harm and must be taken offline, curtailing…
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 obtaini…
Supervised Contrastive Block Disentanglement
Taro Makino, Ji Won Park, Natasa Tagasovska +11
Real-world datasets often combine data collected under different experimental conditions. This yields larger datasets, but also introduces spurious correlations that make it diffic…
Semiparametric conformal prediction
Ji Won Park, Robert Tibshirani, Kyunghyun Cho
Many risk-sensitive applications require well-calibrated prediction sets over multiple, potentially correlated target variables, for which the prediction algorithm may report corre…
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design
Nataša Tagasovska, Ji Won Park, Matthieu Kirchmeyer +8
Machine learning (ML) has demonstrated significant promise in accelerating drug design. Active ML-guided optimization of therapeutic molecules typically relies on a surrogate model…
Integration of Graph Neural Network and Neural-ODEs for Tumor Dynamic Prediction
Omid Bazgir, Zichen Wang, Ji Won Park +2
In anti-cancer drug development, a major scientific challenge is disentangling the complex relationships between high-dimensional genomics data from patient tumor samples, the corr…
Blind Biological Sequence Denoising with Self-Supervised Set Learning
Nathan Ng, Ji Won Park, Jae Hyeon Lee +3
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 repeated…
BOtied: Multi-objective Bayesian optimization with tied multivariate ranks
Ji Won Park, Nataša Tagasovska, Michael Maser +2
Many scientific and industrial applications require the joint optimization of multiple, potentially competing objectives. Multi-objective Bayesian optimization (MOBO) is a sample-e…
Chain of Log-Concave Markov Chains
Saeed Saremi, Ji Won Park, Francis 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…
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers
Michael Maser, Ji Won Park, Joshua Yao-Yu Lin +3
We investigate Siamese networks for learning related embeddings for augmented samples of molecular conformers. We find that a non-contrastive (positive-pair only) auxiliary task ai…
GAUCHE: A Library for Gaussian Processes in Chemistry
Ryan-Rhys Griffiths, Leo Klarner, Henry B. Moss +24
We introduce GAUCHE, a library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantag…
PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design
Ji Won Park, Samuel Stanton, Saeed Saremi +6
Bayesian optimization offers a sample-efficient framework for navigating the exploration-exploitation trade-off in the vast design space of biological sequences. Whereas it is poss…