Gabriel Mahuas

Giovanni Marraffini, Gabriel Mahuas, Trinidad Borrell et al.

Brain foundation models (BFMs) are self-supervised Transformers pretrained on fMRI data. We posit that these models should capture each subject's cognitive performance from their fMRI signal. Yet across three state-of-the-art BFMs and every readout we test, they predict cognition worse than a linear regression from the $\sim$80K parameters of the functional connectivity matrix (FC). The gap widens with scale: BrainLM's 650M model predicts cognition worse than its 111M. We attribute this to a \textbf{variance allocation problem}: BFM pretraining captures the variance components that dominate fMRI but not the higher-order structure that predicts cognition. Our per-cumulant analysis of the reconstructed signal shows that the second-order covariance is partially preserved, while the third-order co-skewness tensor is largely destroyed. To recover what BFMs lose, we design a linear pipeline that projects the fMRI signal into the subspace that best preserves its co-skewness and computes FC there. This \textbf{exceeds raw FC and every pretrained BFM} on every dataset and parcellation we test, outperforming prior state-of-the-art under controlled evaluation \textbf{with no pretraining and no GPU}. We \textbf{recover the raw-FC ceiling on BrainLM's forward pass} by finetuning with a loss targeted at this same subspace. This shows that the bottleneck is the pretraining objective, not the architecture or the model size.

Yassir Bendou, Omar Ezzahir, Eduardo Fernandes Montesuma et al.

Prompt learning has emerged as an effective technique for fine-tuning large-scale foundation models for downstream tasks. However, conventional prompt tuning methods are prone to overfitting and can struggle with out-of-distribution generalization. To address these limitations, Bayesian prompt learning has been proposed, which frames prompt optimization as a Bayesian inference problem to enhance robustness. This paper introduces Repulsive Bayesian Prompt Learning (ReBaPL), a novel method for Bayesian prompt learning, designed to efficiently explore the complex and often multimodal posterior landscape of prompts. Our method integrates a cyclical step-size schedule with a stochastic gradient Hamiltonian Monte Carlo (SGHMC) algorithm, enabling alternating phases of exploration to discover new modes, and exploitation to refine existing modes. Furthermore, we introduce a repulsive force derived from a potential function over probability metrics (including Maximum Mean Discrepancy and Wasserstein distance) computed on the distributions of representations produced by different prompts. This representation-space repulsion diversifies exploration and prevents premature collapse to a single mode. Our approach allows for a more comprehensive characterization of the prompt posterior distribution, leading to improved generalization. In contrast to prior Bayesian prompt learning methods, our method provides a modular plug-and-play Bayesian extension of any existing prompt learning method based on maximum likelihood estimation. We demonstrate the efficacy of ReBaPL on several benchmark datasets, showing superior performance over state-of-the-art methods for prompt learning.

Gabriel Mahuas, Giulio Isacchini, Olivier Marre et al.

Generalized linear models are one of the most efficient paradigms for predicting the correlated stochastic activity of neuronal networks in response to external stimuli, with applications in many brain areas. However, when dealing with complex stimuli, the inferred coupling parameters often do not generalize across different stimulus statistics, leading to degraded performance and blowup instabilities. Here, we develop a two-step inference strategy that allows us to train robust generalized linear models of interacting neurons, by explicitly separating the effects of correlations in the stimulus from network interactions in each training step. Applying this approach to the responses of retinal ganglion cells to complex visual stimuli, we show that, compared to classical methods, the models trained in this way exhibit improved performance, are more stable, yield robust interaction networks, and generalize well across complex visual statistics. The method can be extended to deep convolutional neural networks, leading to models with high predictive accuracy for both the neuron firing rates and their correlations.