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Julien Martinelli

Julien Martinelli contributes to research discovery and scholarly infrastructure.

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Machine Learning Artificial Intelligence

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preprint2026arXiv

Bayesian Nonparametric Mixed-Effect ODEs with Gaussian Processes

Dynamical modelling is central to many scientific domains, including pharmacometrics, systems biology, physiology, and epidemiology. In these settings, heterogeneity is often intrinsic: different subjects or units follow related but distinct continuous-time dynamics. Classical nonlinear mixed-effects Ordinary Differential Equation (ODE) models address this by combining population-level structure with subject-specific effects, but they rely on a parametric vector field and are therefore vulnerable to structural misspecification and unmodelled mechanisms. This motivates nonparametric approaches that can retain principled uncertainty quantification, yet existing nonparametric ODE methods typically assume a single shared dynamical system rather than an explicit mixed-effect hierarchy over subject-specific dynamics. We propose MEGPODE, a Bayesian nonparametric mixed-effect ODE model in which each subject's vector field is decomposed into a shared population component and a subject-specific deviation, both endowed with Gaussian process (GP) priors. To avoid repeated ODE solves per subject during training, we combine state-space GP trajectory priors with virtual collocation observations, yielding Kalman-smoothing trajectory updates and closed-form regressions for the vector fields. Across controlled heterogeneous ODE benchmarks spanning oscillatory, biomedical systems, MEGPODE improves population-field recovery and subject-level trajectory prediction relative to strong baselines.

preprint2026arXiv

In-Context Black-Box Optimization with Unreliable Feedback

Black-box optimization in science and engineering often comes with side information: experts, simulators, pretrained predictors, or heuristics can suggest which candidates look promising. This information can accelerate search, but it can also be biased, input-dependent, or misleading. Feedback-aware BO methods typically handle one task at a time, limiting their ability to generalize over multiple sources of feedback. In-context optimizers address cross-task adaptation, but usually assume that optimization history is the only available signal at test time. We study feedback-informed in-context black-box optimization (FICBO), where a pretrained optimizer conditions on both the observed history and cheap auxiliary feedback for the current candidate set. We introduce a structured feedback prior that models how feedback sources vary in their access, relevance, and distortion relative to the true objective, and use it to pretrain a feedback-aware transformer. At test time, the model estimates source reliability in context by comparing observed objective values with auxiliary signals, improving query selection. On synthetic and real-world tasks, FICBO effectively exploits informative feedback while remaining robust to weak or misleading sources, improving over other baselines. Empirical investigations further illustrate how the model perceives test-time sources, offering insights into its interpretability and decision-making process.

preprint2026arXiv

Online Sharp-Calibrated Bayesian Optimization

Bayesian optimization (BO) is a widely used framework for optimizing expensive black-box functions, commonly based on Gaussian process (GP) surrogate models. Its effectiveness relies on uncertainty quantification that is both sharp (informative) and well-calibrated along the BO trajectory. In practice, GP kernel hyperparameters are unknown and are refit online from sequentially collected (non-i.i.d.) data, which can yield miscalibrated or overly conservative uncertainty and lies outside the fixed-kernel assumptions of standard BO regret theory. We propose Online Sharp-Calibrated Bayesian Optimization (OSCBO), a BO algorithm that adaptively balances GP sharpness and calibration by casting hyperparameter selection as a constrained online-learning problem. We also show that OSCBO preserves sublinear regret bounds by leveraging the theoretical guarantees of the underlying online learning algorithm. Empirically, OSCBO performs competitively across synthetic and real-world benchmarks, ranking among the strongest methods in final simple regret while maintaining robust cumulative-regret behavior.

preprint2025arXiv

Robust and Computation-Aware Gaussian Processes

Gaussian processes (GPs) are widely used for regression and optimization tasks such as Bayesian optimization (BO) due to their expressiveness and principled uncertainty estimates. However, in settings with large datasets corrupted by outliers, standard GPs and their sparse approximations struggle with computational tractability and robustness. We introduce Robust Computation-aware Gaussian Process (RCaGP), a novel GP model that jointly addresses these challenges by combining a principled treatment of approximation-induced uncertainty with robust generalized Bayesian updating. The key insight is that robustness and approximation-awareness are not orthogonal but intertwined: approximations can exacerbate the impact of outliers, and mitigating one without the other is insufficient. Unlike previous work that focuses narrowly on either robustness or approximation quality, RCaGP combines both in a principled and scalable framework, thus effectively managing both outliers and computational uncertainties introduced by approximations such as low-rank matrix multiplications. Our model ensures more conservative and reliable uncertainty estimates, a property we rigorously demonstrate. Additionally, we establish a robustness property and show that the mean function is key to preserving it, motivating a tailored model selection scheme for robust mean functions. Empirical results confirm that solving these challenges jointly leads to superior performance across both clean and outlier-contaminated settings, both on regression and high-throughput Bayesian optimization benchmarks.

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