12 papers
In-Context Batch Black-box Optimization via Flow Matching
Quoc-Anh Hoang Nguyen, Xinyu Zhang, Daolang Huang +2
Batch black-box optimization is important for expensive systems where many candidates can be evaluated in parallel, yet only a few rounds of evaluation are affordable. In this regi…
In-Context Learning for Latent Space Bayesian Optimization
Tuan A. Vu, Harri Lähdesmäki, Julien Martinelli
Bayesian optimization (BO) is a central tool for sample-efficient design, and latent-space Bayesian optimization (LSBO) extends it to structured objects such as molecules and prote…
Bayesian Nonparametric Mixed-Effect ODEs with Gaussian Processes
Julien Martinelli, Maksim Sinelnikov, Harri Lähdesmäki +2
Dynamical modelling in pharmacometrics, systems biology, and epidemiology often involves subjects with related but distinct dynamics, observed through temporally sparse and irregul…
Online Sharp-Calibrated Bayesian Optimization
Marshal Arijona Sinaga, Julien Martinelli, Teemu Turpeinen +1
Bayesian optimization (BO) is a widely used framework for optimizing expensive black-box functions, commonly based on Gaussian process (GP) surrogate models. Its effectiveness reli…
In-Context Black-Box Optimization with Unreliable Feedback
Nicolas Samuel Blumer, Julien Martinelli, Samuel Kaski
Black-box optimization in science and engineering often comes with side information: experts, simulators, pretrained predictors, or heuristics can suggest which candidates look pro…
Joint Bayesian Inference of Genetic Effect Sizes and PK Parameters in Nonlinear Mixed-Effects Models
Julien Martinelli, Ibtissem Rebai, David W. Haas +1
High-dimensional genetic covariate selection in population pharmacokinetic (PK) models is challenging due to the cohort's restricted size and high correlation among single-nucleoti…
In-Context Multi-Objective Optimization
Xinyu Zhang, Conor Hassan, Julien Martinelli +2
Balancing competing objectives is omnipresent across disciplines, from drug design to autonomous systems. Multi-objective Bayesian optimization is a promising solution for such exp…
Robust and Computation-Aware Gaussian Processes
Marshal Arijona Sinaga, Julien Martinelli, Samuel Kaski
Gaussian processes (GPs) are widely used for regression and optimization tasks such as Bayesian optimization (BO) due to their expressiveness and principled uncertainty estimates.…
Challenges in interpretability of additive models
Xinyu Zhang, Julien Martinelli, ST John
We review generalized additive models as a type of ``transparent'' model that has recently seen renewed interest in the deep learning community as neural additive models. We highli…
PABBO: Preferential Amortized Black-Box Optimization
Xinyu Zhang, Daolang Huang, Samuel Kaski +1
Preferential Bayesian Optimization (PBO) is a sample-efficient method to learn latent user utilities from preferential feedback over a pair of designs. It relies on a statistical s…
Proxy-informed Bayesian transfer learning with unknown sources
Sabina J. Sloman, Julien Martinelli, Samuel Kaski
Generalization outside the scope of one's training data requires leveraging prior knowledge about the effects that transfer, and the effects that don't, between different data sour…
Anchor-Based Heteroscedastic Noise for Preferential Bayesian Optimization
Marshal Arijona Sinaga, Julien Martinelli, Samuel Kaski
Preferential Bayesian optimization (PBO) learns latent utilities from pairwise comparisons, but most existing methods assume homoscedastic comparison noise. This is inadequate in h…