arXiv subjects

Vincent Fortuin

Publications and source records attributed to Vincent Fortuin.

At least 19 recordsLinked to original sources

arXiv2026

Constraining the lives and times of exoplanets through evolutionary Bayesian retrievals

Static retrieval frameworks are leading tools for interpreting exoplanet observations, yet time-independent modelling leaves them prone to degeneracy and unable to resolve exoplanets' histories. The compositions and structures of surveyed super-Earth and sub-Neptune sub-populations remain unclear, but are shaped by physics acting across Gyr timescales. Interpreting these planets as static non-evolving snapshots allows multiple degenerate scenarios to explain their observed properties. We develop a generalised parameter retrieval framework, built on asynchronous Bayesian optimisation to efficiently dispatch a multi-physics forward-model, resolving exoplanets' evolving properties from their initial magma ocean conditions to the present day. By building Bayesian retrievals into the PROTEUS framework, sensitive coupled interior-atmosphere interactions are naturally resolved and interpretations are constrained to physically permissible scenarios. We test evolutionary retrievals with three exoplanet prototypes: a young sub-Neptune, an older super-Earth, and a warm terrestrial planet - representative of the surveyed exoplanet population. Evolutionary retrieval jointly infers their mantle redox conditions, metallic core fractions, and early volatile inventories from spectroscopically accessible observables. Some scenarios remain subject to well-established degeneracies between core fractions and volatile budgets. Terrestrial-mass exoplanets benefit from strong observable-parameter correlations that lift these degeneracies; we recover post-formation volatile inventories with <20 percent error. Exoplanet science is primed for incoming JWST, PLATO, Roman, and ELT data - observations which necessitate careful interpretation. Adoption of time-evolved models lifts interpretive degeneracies, providing the means to understand the deep interiors and lifetime histories of worlds throughout our galaxy.

astro-ph.EP↗

arXiv2026

Decision-Aligned Evaluation of Uncertainty Quantification

Uncertainty estimates in machine learning are typically evaluated using generic metrics such as the negative log-likelihood and expected calibration error, yet good performance on such metrics does not necessarily imply high utility in downstream decisions. We introduce decision-alignment, a criterion that reveals which evaluation metrics meaningfully align with downstream utilities. Applying this framework, we show that many widely used uncertainty metrics are either misaligned with common decision problems or encode pathological prior beliefs about the downstream task. We then propose prior-weighted utility metrics, a special class of proper scoring rules that provides decision-aligned uncertainty evaluation. Across benchmark experiments and real-world case studies, our metrics consistently align with realized decision utility, while conventional metrics do not. Our results surface flaws in the current UQ evaluation protocol and offer a principled extension of existing metrics toward decision-relevant UQ evaluation.

cs.LG↗

arXiv2026

Gaussian Mean Field Variational Inference can Overestimate Predictive Variance

Mean Field Variational Inference (MFVI) is widely understood to underestimate posterior variance. By analysing conjugate Bayesian Linear Regression (BLR), we show that this characterization is incomplete: while MFVI underestimates the variance in parameter space, it can overestimate the predictive variance compared to the exact posterior. We show that if the MFVI posterior underestimates predictive variances in some directions, it necessarily overestimates them in others. Crucially, this overestimation occurs in directions where the training data concentrates. This leads to the surprising result that, for a test point drawn from the training distribution, MFVI's expected predictive variance exceeds that of the exact posterior. We demonstrate a pathological case of this effect, where the MFVI posterior fails to reduce predictive variance compared to the prior on in distribution data. We connect these results to the Cold Posterior Effect, arguing that varying the temperature can correct this overestimation, yielding predictions closer to those of the exact posterior. We validate our theory on synthetic and real-world regression tasks.

stat.ML↗

arXiv2026

Position: agentic AI orchestration should be Bayes-consistent

LLMs excel at predictive tasks and complex reasoning tasks, but many high-value deployments rely on decisions under uncertainty, for example, which tool to call, which expert to consult, or how many resources to invest. While the usefulness and feasibility of Bayesian approaches remain unclear for LLM inference, this position paper argues that the control layer of an agentic AI system (that orchestrates LLMs and tools) is a clear case where Bayesian principles should shine. Bayesian decision theory provides a framework for agentic systems that can help to maintain beliefs over task-relevant latent quantities, to update these beliefs from observed agentic and human-AI interactions, and to choose actions. Making LLMs themselves explicitly Bayesian belief-updating engines remains computationally intensive and conceptually nontrivial as a general modeling target. In contrast, this paper argues that coherent decision-making requires Bayesian principles at the orchestration level of the agentic system, not necessarily the LLM agent parameters. This paper articulates practical properties for Bayesian control that fit modern agentic AI systems and human-AI collaboration, and provides concrete examples and design patterns to illustrate how calibrated beliefs and utility-aware policies can improve agentic AI orchestration.

cs.AI↗

arXiv2026

Standard Acquisition Is Sufficient for Asynchronous Bayesian Optimization

Asynchronous Bayesian optimization is widely used for gradient-free optimization in domains with independent parallel experiments and varying evaluation times. Existing methods posit that standard acquisitions lead to redundant and repeated queries, proposing complex solutions to enforce diversity in queries. Challenging this fundamental premise, we show that methods, like the Upper Confidence Bound, can in fact achieve theoretical guarantees essentially equivalent to those of sequential Thompson sampling. A conceptual analysis of asynchronous Bayesian optimization reveals that existing works neglect intermediate posterior updates, which we find to be generally sufficient to avoid redundant queries. Further investigation shows that by penalizing busy locations, diversity-enforcing methods can over-explore in asynchronous settings, reducing their performance. Our extensive experiments demonstrate that simple standard acquisition functions match or outperform purpose-built asynchronous methods across synthetic and real-world tasks.

stat.ML↗

arXiv2026

In-Context Function Learning in Large Language Models

Large language models (LLMs) can learn from a few demonstrations provided at inference time. We study this in-context learning phenomenon through the lens of Gaussian Processes (GPs). We build controlled experiments where models observe sequences of multivariate scalar-valued function samples drawn from known GP priors. We evaluate prediction error in relation to the number of demonstrations and compare against two principled references: (i) an empirical GP-regression learner that gives a lower bound on achievable error, and (ii) the expected error of a 1-nearest-neighbor (1-NN) rule, which gives a data-driven upper bound. Across model sizes, we find that LLM learning curves are strongly influenced by the function-generating kernels and approach the GP lower bound as the number of demonstrations increases. We then study the inductive biases of these models using a likelihood-based analysis. We find that LLM predictions are most likely under less smooth GP kernels. Finally, we explore whether post-training can shift these inductive biases and improve sample-efficiency on functions sampled from GPs with smoother kernels. We find that both reinforcement learning and supervised fine-tuning can effectively shift inductive biases in the direction of the training data. Together, our framework quantifies the extent to which LLMs behave like GP learners and provides tools for steering their inductive biases for continuous function learning tasks.

cs.LG↗

arXiv2026

Amortising Inference and Meta-Learning Priors in Neural Networks

One of the core facets of Bayesianism is in the updating of prior beliefs in light of new evidence$\text{ -- }$so how can we maintain a Bayesian approach if we have no prior beliefs in the first place? This is one of the central challenges in the field of Bayesian deep learning, where it is not clear how to represent beliefs about a prediction task by prior distributions over model parameters. Bridging the fields of Bayesian deep learning and probabilistic meta-learning, we introduce a way to $\textit{learn}$ a weights prior from a collection of datasets by introducing a way to perform per-dataset amortised variational inference. The model we develop can be viewed as a neural process whose latent variable is the set of weights of a BNN and whose decoder is the neural network parameterised by a sample of the latent variable itself. This unique model allows us to study the behaviour of Bayesian neural networks under well-specified priors, use Bayesian neural networks as flexible generative models, and perform desirable but previously elusive feats in neural processes such as within-task minibatching or meta-learning under extreme data-starvation.

stat.ML↗

arXiv2025

On the Effect of Regularization on Nonparametric Mean-Variance Regression

Uncertainty quantification is vital for decision-making and risk assessment in machine learning. Mean-variance regression models, which predict both a mean and residual noise for each data point, provide a simple approach to uncertainty quantification. However, overparameterized mean-variance models struggle with signal-to-noise ambiguity, deciding whether prediction targets should be attributed to signal (mean) or noise (variance). At one extreme, models fit all training targets perfectly with zero residual noise, while at the other, they provide constant, uninformative predictions and explain the targets as noise. We observe a sharp phase transition between these extremes, driven by model regularization. Empirical studies with varying regularization levels illustrate this transition, revealing substantial variability across repeated runs. To explain this behavior, we develop a statistical field theory framework, which captures the observed phase transition in alignment with experimental results. This analysis reduces the regularization hyperparameter search space from two dimensions to one, significantly lowering computational costs. Experiments on UCI datasets and the large-scale ClimSim dataset demonstrate robust calibration performance, effectively quantifying predictive uncertainty.

stat.ML↗

arXiv2025

Data-Driven Discovery of Feature Groups in Clinical Time Series

Clinical time series data are critical for patient monitoring and predictive modeling. These time series are typically multivariate and often comprise hundreds of heterogeneous features from different data sources. The grouping of features based on similarity and relevance to the prediction task has been shown to enhance the performance of deep learning architectures. However, defining these groups a priori using only semantic knowledge is challenging, even for domain experts. To address this, we propose a novel method that learns feature groups by clustering weights of feature-wise embedding layers. This approach seamlessly integrates into standard supervised training and discovers the groups that directly improve downstream performance on clinically relevant tasks. We demonstrate that our method outperforms static clustering approaches on synthetic data and achieves performance comparable to expert-defined groups on real-world medical data. Moreover, the learned feature groups are clinically interpretable, enabling data-driven discovery of task-relevant relationships between variables.

cs.LG↗

arXiv2025

Beyond Quantification: Navigating Uncertainty in Professional AI Systems

The growing integration of large language models across professional domains transforms how experts make critical decisions in healthcare, education, and law. While significant research effort focuses on getting these systems to communicate their outputs with probabilistic measures of reliability, many consequential forms of uncertainty in professional contexts resist such quantification. A physician pondering the appropriateness of documenting possible domestic abuse, a teacher assessing cultural sensitivity, or a mathematician distinguishing procedural from conceptual understanding face forms of uncertainty that cannot be reduced to percentages. This paper argues for moving beyond simple quantification toward richer expressions of uncertainty essential for beneficial AI integration. We propose participatory refinement processes through which professional communities collectively shape how different forms of uncertainty are communicated. Our approach acknowledges that uncertainty expression is a form of professional sense-making that requires collective development rather than algorithmic optimization.

cs.HC↗

arXiv2025

ProSpero: Active Learning for Robust Protein Design Beyond Wild-Type Neighborhoods

Designing protein sequences of both high fitness and novelty is a challenging task in data-efficient protein engineering. Exploration beyond wild-type neighborhoods often leads to biologically implausible sequences or relies on surrogate models that lose fidelity in novel regions. Here, we propose ProSpero, an active learning framework in which a frozen pre-trained generative model is guided by a surrogate updated from oracle feedback. By integrating fitness-relevant residue selection with biologically-constrained Sequential Monte Carlo sampling, our approach enables exploration beyond wild-type neighborhoods while preserving biological plausibility. We show that our framework remains effective even when the surrogate is misspecified. ProSpero consistently outperforms or matches existing methods across diverse protein engineering tasks, retrieving sequences of both high fitness and novelty.

cs.LG↗

arXiv2025

Sparse Gaussian Neural Processes

Despite significant recent advances in probabilistic meta-learning, it is common for practitioners to avoid using deep learning models due to a comparative lack of interpretability. Instead, many practitioners simply use non-meta-models such as Gaussian processes with interpretable priors, and conduct the tedious procedure of training their model from scratch for each task they encounter. While this is justifiable for tasks with a limited number of data points, the cubic computational cost of exact Gaussian process inference renders this prohibitive when each task has many observations. To remedy this, we introduce a family of models that meta-learn sparse Gaussian process inference. Not only does this enable rapid prediction on new tasks with sparse Gaussian processes, but since our models have clear interpretations as members of the neural process family, it also allows manual elicitation of priors in a neural process for the first time. In meta-learning regimes for which the number of observed tasks is small or for which expert domain knowledge is available, this offers a crucial advantage.

stat.ML↗

arXiv2025

Can Transformers Learn Full Bayesian Inference in Context?

Transformers have emerged as the dominant architecture in the field of deep learning, with a broad range of applications and remarkable in-context learning (ICL) capabilities. While not yet fully understood, ICL has already proved to be an intriguing phenomenon, allowing transformers to learn in context -- without requiring further training. In this paper, we further advance the understanding of ICL by demonstrating that transformers can perform full Bayesian inference for commonly used statistical models in context. More specifically, we introduce a general framework that builds on ideas from prior fitted networks and continuous normalizing flows and enables us to infer complex posterior distributions for models such as generalized linear models and latent factor models. Extensive experiments on real-world datasets demonstrate that our ICL approach yields posterior samples that are similar in quality to state-of-the-art MCMC or variational inference methods that do not operate in context. The source code for this paper is available at https://github.com/ArikReuter/ICL_for_Full_Bayesian_Inference.

cs.LG↗

arXiv2024

OneProt: Towards Multi-Modal Protein Foundation Models

Recent advances in Artificial Intelligence have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, text, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of protein modality encoders in a lightweight fine-tuning scheme that focuses on pairwise alignment with sequence data rather than requiring full matches. This novel approach comprises a mix of Graph Neural Networks and transformer architectures. It demonstrates strong performance in retrieval tasks and showcases the efficacy of multi-modal systems in Protein Machine Learning through a broad spectrum of downstream baselines, including enzyme function prediction and binding site analysis. Furthermore, OneProt enables the transfer of representational information from specialized encoders to the sequence encoder, enhancing capabilities for distinguishing evolutionarily related and unrelated sequences and exhibiting representational properties where evolutionarily related proteins align in similar directions within the latent space. In addition, we extensively investigate modality ablations to identify the encoders that contribute most to predictive performance, highlighting the significance of the binding site encoder, which has not been used in similar models previously. This work expands the horizons of multi-modal protein models, paving the way for transformative applications in drug discovery, biocatalytic reaction planning, and protein engineering.

cs.LG↗

arXiv2024

Stein Variational Newton Neural Network Ensembles

Deep neural network ensembles are powerful tools for uncertainty quantification, which have recently been re-interpreted from a Bayesian perspective. However, current methods inadequately leverage second-order information of the loss landscape, despite the recent availability of efficient Hessian approximations. We propose a novel approximate Bayesian inference method that modifies deep ensembles to incorporate Stein Variational Newton updates. Our approach uniquely integrates scalable modern Hessian approximations, achieving faster convergence and more accurate posterior distribution approximations. We validate the effectiveness of our method on diverse regression and classification tasks, demonstrating superior performance with a significantly reduced number of training epochs compared to existing ensemble-based methods, while enhancing uncertainty quantification and robustness against overfitting.

stat.ML↗

arXiv2024

Parameter-efficient Bayesian Neural Networks for Uncertainty-aware Depth Estimation

State-of-the-art computer vision tasks, like monocular depth estimation (MDE), rely heavily on large, modern Transformer-based architectures. However, their application in safety-critical domains demands reliable predictive performance and uncertainty quantification. While Bayesian neural networks provide a conceptually simple approach to serve those requirements, they suffer from the high dimensionality of the parameter space. Parameter-efficient fine-tuning (PEFT) methods, in particular low-rank adaptations (LoRA), have emerged as a popular strategy for adapting large-scale models to down-stream tasks by performing parameter inference on lower-dimensional subspaces. In this work, we investigate the suitability of PEFT methods for subspace Bayesian inference in large-scale Transformer-based vision models. We show that, indeed, combining BitFit, DiffFit, LoRA, and CoLoRA, a novel LoRA-inspired PEFT method, with Bayesian inference enables more robust and reliable predictive performance in MDE.

cs.CV↗

arXiv2024

Towards Dynamic Feature Acquisition on Medical Time Series by Maximizing Conditional Mutual Information

Knowing which features of a multivariate time series to measure and when is a key task in medicine, wearables, and robotics. Better acquisition policies can reduce costs while maintaining or even improving the performance of downstream predictors. Inspired by the maximization of conditional mutual information, we propose an approach to train acquirers end-to-end using only the downstream loss. We show that our method outperforms random acquisition policy, matches a model with an unrestrained budget, but does not yet overtake a static acquisition strategy. We highlight the assumptions and outline avenues for future work.

cs.LG↗

arXiv2024

FSP-Laplace: Function-Space Priors for the Laplace Approximation in Bayesian Deep Learning

Laplace approximations are popular techniques for endowing deep networks with epistemic uncertainty estimates as they can be applied without altering the predictions of the trained network, and they scale to large models and datasets. While the choice of prior strongly affects the resulting posterior distribution, computational tractability and lack of interpretability of the weight space typically limit the Laplace approximation to isotropic Gaussian priors, which are known to cause pathological behavior as depth increases. As a remedy, we directly place a prior on function space. More precisely, since Lebesgue densities do not exist on infinite-dimensional function spaces, we recast training as finding the so-called weak mode of the posterior measure under a Gaussian process (GP) prior restricted to the space of functions representable by the neural network. Through the GP prior, one can express structured and interpretable inductive biases, such as regularity or periodicity, directly in function space, while still exploiting the implicit inductive biases that allow deep networks to generalize. After model linearization, the training objective induces a negative log-posterior density to which we apply a Laplace approximation, leveraging highly scalable methods from matrix-free linear algebra. Our method provides improved results where prior knowledge is abundant (as is the case in many scientific inference tasks). At the same time, it stays competitive for black-box supervised learning problems, where neural networks typically excel.

cs.LG↗