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Julien Martinelli

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6 papers

2 author rows

ICLR Conference 2025 Conference Paper

PABBO: Preferential Amortized Black-Box Optimization

Xinyu Zhang
Daolang Huang
Samuel Kaski
Julien Martinelli

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 surrogate model for the latent function, usually a Gaussian process, and an acquisition strategy to select the next candidate pair to get user feedback on. Due to the non-conjugacy of the associated likelihood, every PBO step requires a significant amount of computations with various approximate inference techniques. This computational overhead is incompatible with the way humans interact with computers, hindering the use of PBO in real-world cases. Building on the recent advances of amortized BO, we propose to circumvent this issue by fully amortizing PBO, meta-learning both the surrogate and the acquisition function. Our method comprises a novel transformer neural process architecture, trained using reinforcement learning and tailored auxiliary losses. On a benchmark composed of synthetic and real-world datasets, our method is several orders of magnitude faster than the usual Gaussian process-based strategies and often outperforms them in accuracy.

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NeurIPS Conference 2025 Conference Paper

Position: Biology is the Challenge Physics-Informed ML Needs to Evolve

Julien Martinelli

Physics-Informed Machine Learning (PIML) has successfully integrated mechanistic understanding into machine learning, particularly in domains governed by well-known physical laws. This success has motivated efforts to apply PIML to biology, a field rich in dynamical systems but shaped by different constraints. Biological modeling, however, presents unique challenges: multi-faceted and uncertain prior knowledge, heterogeneous and noisy data, partial observability, and complex, high-dimensional networks. \textbf{In this position paper, we argue that these challenges should not be seen as obstacles to PIML, but as catalysts for its evolution. We propose Biology-Informed Machine Learning (BIML): a principled extension of PIML that retains its structural grounding while adapting to the practical realities of biology. }Rather than replacing PIML, BIML retools its methods to operate under softer, probabilistic forms of prior knowledge. We outline four foundational pillars as a roadmap for this transition: uncertainty quantification, contextualization, constrained latent structure inference, and scalability. Foundation Models and Large Language Models will be key enablers, bridging human expertise with computational modeling. We conclude with concrete recommendations to build the BIML ecosystem and channel PIML-inspired innovation toward challenges of high scientific and societal relevance.

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UAI Conference 2025 Conference Paper

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 sources. Transfer learning is a framework for specifying and refining this knowledge about sets of source (training) and target (prediction) data. A challenging open problem is addressing the empirical phenomenon of negative transfer, whereby the transfer learner performs worse on the target data after taking the source data into account than before. We first introduce a Bayesian perspective on negative transfer, and then a method to address it. The key insight from our formulation is that negative transfer can stem from misspecified prior information about non-transferable causes of the source data. Our proposed method, proxy-informed robust method for probabilistic transfer learning (PROMPT), does not require prior knowledge of the source data (the data sources may be "unknown"). PROMPT is thus applicable when differences between tasks are unobserved, such as in the presence of latent confounders. Moreover, the learner need not have access to observations in the target task (may not have the ability to "fine-tune"), and instead makes use of proxy (indirect) information. Our theoretical results show that the threat of negative transfer does not depend on the informativeness of the proxy information, highlighting the usefulness of PROMPT in cases where only noisy indirect information, such as human feedback, is available.

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NeurIPS Conference 2025 Conference Paper

Robust and Computation-Aware Gaussian Processes

Marshal 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. 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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UAI Conference 2024 Conference Paper

Bayesian Active Learning in the Presence of Nuisance Parameters

Sabina J. Sloman
Ayush Bharti
Julien Martinelli
Samuel Kaski

In many settings, such as scientific inference, optimization, and transfer learning, the learner has a well-defined objective, which can be treated as estimation of a target parameter, and no intrinsic interest in characterizing the entire data-generating process. Usually, the learner must also contend with additional sources of uncertainty or variables — with nuisance parameters. Bayesian active learning, or sequential optimal experimental design, can straightforwardly accommodate the presence of nuisance parameters, and so is a natural active learning framework for such problems. However, the introduction of nuisance parameters can lead to bias in the Bayesian learner’s estimate of the target parameters, a phenomenon we refer to as negative interference. We characterize the threat of negative interference and how it fundamentally changes the nature of the Bayesian active learner’s task. We show that the extent of negative interference can be extremely large, and that accurate estimation of the nuisance parameters is critical to reducing it. The Bayesian active learner is confronted with a dilemma: whether to spend a finite acquisition budget in pursuit of estimation of the target or of the nuisance parameters. Our setting encompasses Bayesian transfer learning as a special case, and our results shed light on the phenomenon of negative transfer between learning environments.

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UAI Conference 2024 Conference Paper

Learning relevant contextual variables within Bayesian optimization

Julien Martinelli
Ayush Bharti
Armi Tiihonen
S. T. John
Louis Filstroff
Sabina J. Sloman
Patrick Rinke
Samuel Kaski

Contextual Bayesian Optimization (CBO) efficiently optimizes black-box functions with respect to design variables, while simultaneously integrating _contextual_ information regarding the environment, such as experimental conditions. However, the relevance of contextual variables is not necessarily known beforehand. Moreover, contextual variables can sometimes be optimized themselves at additional cost, a setting overlooked by current CBO algorithms. Cost-sensitive CBO would simply include optimizable contextual variables as part of the design variables based on their cost. Instead, we adaptively select a subset of contextual variables to include in the optimization, based on the trade-off between their _relevance_ and the additional cost incurred by optimizing them compared to leaving them to be determined by the environment. We learn the relevance of contextual variables by sensitivity analysis of the posterior surrogate model while minimizing the cost of optimization by leveraging recent developments on early stopping for BO. We empirically evaluate our proposed Sensitivity-Analysis-Driven Contextual BO (_SADCBO_) method against alternatives on both synthetic and real-world experiments, together with extensive ablation studies, and demonstrate a consistent improvement across examples.

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