arXiv subjects

Alexandre Gramfort

Publications and source records attributed to Alexandre Gramfort.

At least 19 recordsLinked to original sources

arXiv2026

Learning Regularization Structure for Biosignal Template Estimation

Estimating event-locked templates from bio-signal recordings via regularized least-squares requires choosing both the regularization structure and its magnitude, choices that are typically made heuristically. We develop a data-driven framework based on Stein's Unbiased Risk Estimate (SURE) that jointly optimizes both. By parameterizing the regularization operator as a convolution kernel, our method learns the penalty structure directly from the data, combining smoothness enforcement with ridge-like shrinkage in a way that cannot be achieved by scaling a fixed difference operator. While standard SURE assumes white noise, biosignal noise exhibits temporal autocorrelation. We therefore extend SURE to colored noise by replacing its scalar trace term with a structured correction based on the noise covariance matrix. For AR(1) noise, this correction requires only two parameters, the noise variance and the lag-1 autocorrelation, both estimable from pre-event baselines. Cross-modality validation on auditory event-related potentials, P300 brain--computer interface data, and ECG morphology demonstrates consistent gains compared to alternative methods, all at $K=5$ events per class - the regime most relevant for rapid calibration and personalization.

eess.SP↗

arXiv2025

EEG Foundation Challenge: From Cross-Task to Cross-Subject EEG Decoding

Current electroencephalogram (EEG) decoding models are typically trained on small numbers of subjects performing a single task. Here, we introduce a large-scale, code-submission-based competition comprising two challenges. First, the Transfer Challenge asks participants to build and test a model that can zero-shot decode new tasks and new subjects from their EEG data. Second, the Psychopathology factor prediction Challenge asks participants to infer subject measures of mental health from EEG data. For this, we use an unprecedented, multi-terabyte dataset of high-density EEG signals (128 channels) recorded from over 3,000 child to young adult subjects engaged in multiple active and passive tasks. We provide several tunable neural network baselines for each of these two challenges, including a simple network and demographic-based regression models. Developing models that generalise across tasks and individuals will pave the way for ML network architectures capable of adapting to EEG data collected from diverse tasks and individuals. Similarly, predicting mental health-relevant personality trait values from EEG might identify objective biomarkers useful for clinical diagnosis and design of personalised treatment for psychological conditions. Ultimately, the advances spurred by this challenge could contribute to the development of computational psychiatry and useful neurotechnology, and contribute to breakthroughs in both fundamental neuroscience and applied clinical research.

eess.SP↗

arXiv2025

PSDNorm: Test-Time Temporal Normalization for Deep Learning in Sleep Staging

Distribution shift poses a significant challenge in machine learning, particularly in biomedical applications using data collected across different subjects, institutions, and recording devices, such as sleep data. While existing normalization layers, BatchNorm, LayerNorm and InstanceNorm, help mitigate distribution shifts, when applied over the time dimension they ignore the dependencies and auto-correlation inherent to the vector coefficients they normalize. In this paper, we propose PSDNorm that leverages Monge mapping and temporal context to normalize feature maps in deep learning models for signals. Evaluations with architectures based on U-Net or transformer backbones trained on 10K subjects across 10 datasets, show that PSDNorm achieves state-of-the-art performance on unseen left-out datasets while being more robust to data scarcity.

cs.LG↗

arXiv2025

Multi-View Causal Discovery without Non-Gaussianity: Identifiability and Algorithms

Causal discovery is a difficult problem that typically relies on strong assumptions on the data-generating model, such as non-Gaussianity. In practice, many modern applications provide multiple related views of the same system, which has rarely been considered for causal discovery. Here, we leverage this multi-view structure to achieve causal discovery with weak assumptions. We propose a multi-view linear Structural Equation Model (SEM) that extends the well-known framework of non-Gaussian disturbances by alternatively leveraging correlation over views. We prove the identifiability of the model for acyclic SEMs. Subsequently, we propose several multi-view causal discovery algorithms, inspired by single-view algorithms (DirectLiNGAM, PairwiseLiNGAM, and ICA-LiNGAM). The new methods are validated through simulations and applications on neuroimaging data, where they enable the estimation of causal graphs between brain regions.

cs.LG↗

arXiv2025

MVICAD2: Multi-View Independent Component Analysis with Delays and Dilations

Machine learning techniques in multi-view settings face significant challenges, particularly when integrating heterogeneous data, aligning feature spaces, and managing view-specific biases. These issues are prominent in neuroscience, where data from multiple subjects exposed to the same stimuli are analyzed to uncover brain activity dynamics. In magnetoencephalography (MEG), where signals are captured at the scalp level, estimating the brain's underlying sources is crucial, especially in group studies where sources are assumed to be similar for all subjects. Common methods, such as Multi-View Independent Component Analysis (MVICA), assume identical sources across subjects, but this assumption is often too restrictive due to individual variability and age-related changes. Multi-View Independent Component Analysis with Delays (MVICAD) addresses this by allowing sources to differ up to a temporal delay. However, temporal dilation effects, particularly in auditory stimuli, are common in brain dynamics, making the estimation of time delays alone insufficient. To address this, we propose Multi-View Independent Component Analysis with Delays and Dilations (MVICAD2), which allows sources to differ across subjects in both temporal delays and dilations. We present a model with identifiable sources, derive an approximation of its likelihood in closed form, and use regularization and optimization techniques to enhance performance. Through simulations, we demonstrate that MVICAD2 outperforms existing multi-view ICA methods. We further validate its effectiveness using the Cam-CAN dataset, and showing how delays and dilations are related to aging.

cs.LG↗

arXiv2024

emg2qwerty: A Large Dataset with Baselines for Touch Typing using Surface Electromyography

Surface electromyography (sEMG) non-invasively measures signals generated by muscle activity with sufficient sensitivity to detect individual spinal neurons and richness to identify dozens of gestures and their nuances. Wearable wrist-based sEMG sensors have the potential to offer low friction, subtle, information rich, always available human-computer inputs. To this end, we introduce emg2qwerty, a large-scale dataset of non-invasive electromyographic signals recorded at the wrists while touch typing on a QWERTY keyboard, together with ground-truth annotations and reproducible baselines. With 1,135 sessions spanning 108 users and 346 hours of recording, this is the largest such public dataset to date. These data demonstrate non-trivial, but well defined hierarchical relationships both in terms of the generative process, from neurons to muscles and muscle combinations, as well as in terms of domain shift across users and user sessions. Applying standard modeling techniques from the closely related field of Automatic Speech Recognition (ASR), we show strong baseline performance on predicting key-presses using sEMG signals alone. We believe the richness of this task and dataset will facilitate progress in several problems of interest to both the machine learning and neuroscientific communities. Dataset and code can be accessed at https://github.com/facebookresearch/emg2qwerty.

cs.LG↗

arXiv2024

Multi-Source and Test-Time Domain Adaptation on Multivariate Signals using Spatio-Temporal Monge Alignment

Machine learning applications on signals such as computer vision or biomedical data often face significant challenges due to the variability that exists across hardware devices or session recordings. This variability poses a Domain Adaptation (DA) problem, as training and testing data distributions often differ. In this work, we propose Spatio-Temporal Monge Alignment (STMA) to mitigate these variabilities. This Optimal Transport (OT) based method adapts the cross-power spectrum density (cross-PSD) of multivariate signals by mapping them to the Wasserstein barycenter of source domains (multi-source DA). Predictions for new domains can be done with a filtering without the need for retraining a model with source data (test-time DA). We also study and discuss two special cases of the method, Temporal Monge Alignment (TMA) and Spatial Monge Alignment (SMA). Non-asymptotic concentration bounds are derived for the mappings estimation, which reveals a bias-plus-variance error structure with a variance decay rate of $\mathcal{O}(n_\ell^{-1/2})$ with $n_\ell$ the signal length. This theoretical guarantee demonstrates the efficiency of the proposed computational schema. Numerical experiments on multivariate biosignals and image data show that STMA leads to significant and consistent performance gains between datasets acquired with very different settings. Notably, STMA is a pre-processing step complementary to state-of-the-art deep learning methods.

cs.LG↗

arXiv2024

SKADA-Bench: Benchmarking Unsupervised Domain Adaptation Methods with Realistic Validation On Diverse Modalities

Unsupervised Domain Adaptation (DA) consists of adapting a model trained on a labeled source domain to perform well on an unlabeled target domain with some data distribution shift. While many methods have been proposed in the literature, fair and realistic evaluation remains an open question, particularly due to methodological difficulties in selecting hyperparameters in the unsupervised setting. With SKADA-bench, we propose a framework to evaluate DA methods on diverse modalities, beyond computer vision task that have been largely explored in the literature. We present a complete and fair evaluation of existing shallow algorithms, including reweighting, mapping, and subspace alignment. Realistic hyperparameter selection is performed with nested cross-validation and various unsupervised model selection scores, on both simulated datasets with controlled shifts and real-world datasets across diverse modalities, such as images, text, biomedical, and tabular data. Our benchmark highlights the importance of realistic validation and provides practical guidance for real-life applications, with key insights into the choice and impact of model selection approaches. SKADA-bench is open-source, reproducible, and can be easily extended with novel DA methods, datasets, and model selection criteria without requiring re-evaluating competitors. SKADA-bench is available on Github at https://github.com/scikit-adaptation/skada-bench.

cs.LG↗

arXiv2024

Geodesic Optimization for Predictive Shift Adaptation on EEG data

Electroencephalography (EEG) data is often collected from diverse contexts involving different populations and EEG devices. This variability can induce distribution shifts in the data $X$ and in the biomedical variables of interest $y$, thus limiting the application of supervised machine learning (ML) algorithms. While domain adaptation (DA) methods have been developed to mitigate the impact of these shifts, such methods struggle when distribution shifts occur simultaneously in $X$ and $y$. As state-of-the-art ML models for EEG represent the data by spatial covariance matrices, which lie on the Riemannian manifold of Symmetric Positive Definite (SPD) matrices, it is appealing to study DA techniques operating on the SPD manifold. This paper proposes a novel method termed Geodesic Optimization for Predictive Shift Adaptation (GOPSA) to address test-time multi-source DA for situations in which source domains have distinct $y$ distributions. GOPSA exploits the geodesic structure of the Riemannian manifold to jointly learn a domain-specific re-centering operator representing site-specific intercepts and the regression model. We performed empirical benchmarks on the cross-site generalization of age-prediction models with resting-state EEG data from a large multi-national dataset (HarMNqEEG), which included $14$ recording sites and more than $1500$ human participants. Compared to state-of-the-art methods, our results showed that GOPSA achieved significantly higher performance on three regression metrics ($R^2$, MAE, and Spearman's $\rho$) for several source-target site combinations, highlighting its effectiveness in tackling multi-source DA with predictive shifts in EEG data analysis. Our method has the potential to combine the advantages of mixed-effects modeling with machine learning for biomedical applications of EEG, such as multicenter clinical trials.

stat.ML↗

arXiv2024

Diffusion posterior sampling for simulation-based inference in tall data settings

Identifying the parameters of a non-linear model that best explain observed data is a core task across scientific fields. When such models rely on complex simulators, evaluating the likelihood is typically intractable, making traditional inference methods such as MCMC inapplicable. Simulation-based inference (SBI) addresses this by training deep generative models to approximate the posterior distribution over parameters using simulated data. In this work, we consider the tall data setting, where multiple independent observations provide additional information, allowing sharper posteriors and improved parameter identifiability. Building on the flourishing score-based diffusion literature, F-NPSE (Geffner et al., 2023) estimates the tall data posterior by composing individual scores from a neural network trained only for a single context observation. This enables more flexible and simulation-efficient inference than alternative approaches for tall datasets in SBI. However, it relies on costly Langevin dynamics during sampling. We propose a new algorithm that eliminates the need for Langevin steps by explicitly approximating the diffusion process of the tall data posterior. Our method retains the advantages of compositional score-based inference while being significantly faster and more stable than F-NPSE. We demonstrate its improved performance on toy problems and standard SBI benchmarks, and showcase its scalability by applying it to a complex real-world model from computational neuroscience.

stat.ML↗

arXiv2024

Cycling on the Freeway: The Perilous State of Open Source Neuroscience Software

Most scientists need software to perform their research (Barker et al., 2020; Carver et al., 2022; Hettrick, 2014; Hettrick et al., 2014; Switters and Osimo, 2019), and neuroscientists are no exception. Whether we work with reaction times, electrophysiological signals, or magnetic resonance imaging data, we rely on software to acquire, analyze, and statistically evaluate the raw data we obtain - or to generate such data if we work with simulations. In recent years there has been a shift toward relying on free, open-source scientific software (FOSSS) for neuroscience data analysis (Poldrack et al., 2019), in line with the broader open science movement in academia (McKiernan et al., 2016) and wider industry trends (Eghbal, 2016). Importantly, FOSSS is typically developed by working scientists (not professional software developers) which sets up a precarious situation given the nature of the typical academic workplace (wherein academics, especially in their early careers, are on short and fixed term contracts). In this paper, we will argue that the existing ecosystem of neuroscientific open source software is brittle, and discuss why and how the neuroscience community needs to come together to ensure a healthy growth of our software landscape to the benefit of all.

cs.CY↗

arXiv2024

Physics-informed and Unsupervised Riemannian Domain Adaptation for Machine Learning on Heterogeneous EEG Datasets

Combining electroencephalogram (EEG) datasets for supervised machine learning (ML) is challenging due to session, subject, and device variability. ML algorithms typically require identical features at train and test time, complicating analysis due to varying sensor numbers and positions across datasets. Simple channel selection discards valuable data, leading to poorer performance, especially with datasets sharing few channels. To address this, we propose an unsupervised approach leveraging EEG signal physics. We map EEG channels to fixed positions using field interpolation, facilitating source-free domain adaptation. Leveraging Riemannian geometry classification pipelines and transfer learning steps, our method demonstrates robust performance in brain-computer interface (BCI) tasks and potential biomarker applications. Comparative analysis against a statistical-based approach known as Dimensionality Transcending, a signal-based imputation called ComImp, source-dependent methods, as well as common channel selection and spherical spline interpolation, was conducted with leave-one-dataset-out validation on six public BCI datasets for a right-hand/left-hand classification task. Numerical experiments show that in the presence of few shared channels in train and test, the field interpolation consistently outperforms other methods, demonstrating enhanced classification performance across all datasets. When more channels are shared, field interpolation was found to be competitive with other methods and faster to compute than source-dependent methods.

eess.SP↗

arXiv2024

Weakly supervised covariance matrices alignment through Stiefel matrices estimation for MEG applications

This paper introduces a novel domain adaptation technique for time series data, called Mixing model Stiefel Adaptation (MSA), specifically addressing the challenge of limited labeled signals in the target dataset. Leveraging a domain-dependent mixing model and the optimal transport domain adaptation assumption, we exploit abundant unlabeled data in the target domain to ensure effective prediction by establishing pairwise correspondence with equivalent signal variances between domains. Theoretical foundations are laid for identifying crucial Stiefel matrices, essential for recovering underlying signal variances from a Riemannian representation of observed signal covariances. We propose an integrated cost function that simultaneously learns these matrices, pairwise domain relationships, and a predictor, classifier, or regressor, depending on the task. Applied to neuroscience problems, MSA outperforms recent methods in brain-age regression with task variations using magnetoencephalography (MEG) signals from the Cam-CAN dataset.

eess.SP↗

arXiv2023

MultiView Independent Component Analysis with Delays

Linear Independent Component Analysis (ICA) is a blind source separation technique that has been used in various domains to identify independent latent sources from observed signals. In order to obtain a higher signal-to-noise ratio, the presence of multiple views of the same sources can be used. In this work, we present MultiView Independent Component Analysis with Delays (MVICAD). This algorithm builds on the MultiView ICA model by allowing sources to be delayed versions of some shared sources: sources are shared across views up to some unknown latencies that are view- and source-specific. Using simulations, we demonstrate that MVICAD leads to better unmixing of the sources. Moreover, as ICA is often used in neuroscience, we show that latencies are age-related when applied to Cam-CAN, a large-scale magnetoencephalography (MEG) dataset. These results demonstrate that the MVICAD model can reveal rich effects on neural signals without human supervision.

cs.LG↗

arXiv2023

The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

q-bio.OT↗

arXiv2023

Evaluating the structure of cognitive tasks with transfer learning

Electroencephalography (EEG) decoding is a challenging task due to the limited availability of labelled data. While transfer learning is a promising technique to address this challenge, it assumes that transferable data domains and task are known, which is not the case in this setting. This study investigates the transferability of deep learning representations between different EEG decoding tasks. We conduct extensive experiments using state-of-the-art decoding models on two recently released EEG datasets, ERP CORE and M$^3$CV, containing over 140 subjects and 11 distinct cognitive tasks. We measure the transferability of learned representations by pre-training deep neural networks on one task and assessing their ability to decode subsequent tasks. Our experiments demonstrate that, even with linear probing transfer, significant improvements in decoding performance can be obtained, with gains of up to 28% compare with the pure supervised approach. Additionally, we discover evidence that certain decoding paradigms elicit specific and narrow brain activities, while others benefit from pre-training on a broad range of representations. By revealing which tasks transfer well and demonstrating the benefits of transfer learning for EEG decoding, our findings have practical implications for mitigating data scarcity in this setting. The transfer maps generated also provide insights into the hierarchical relations between cognitive tasks, hence enhancing our understanding of how these tasks are connected from a neuroscientific standpoint.

eess.SP↗

arXiv2023

L-C2ST: Local Diagnostics for Posterior Approximations in Simulation-Based Inference

Many recent works in simulation-based inference (SBI) rely on deep generative models to approximate complex, high-dimensional posterior distributions. However, evaluating whether or not these approximations can be trusted remains a challenge. Most approaches evaluate the posterior estimator only in expectation over the observation space. This limits their interpretability and is not sufficient to identify for which observations the approximation can be trusted or should be improved. Building upon the well-known classifier two-sample test (C2ST), we introduce L-C2ST, a new method that allows for a local evaluation of the posterior estimator at any given observation. It offers theoretically grounded and easy to interpret -- e.g. graphical -- diagnostics, and unlike C2ST, does not require access to samples from the true posterior. In the case of normalizing flow-based posterior estimators, L-C2ST can be specialized to offer better statistical power, while being computationally more efficient. On standard SBI benchmarks, L-C2ST provides comparable results to C2ST and outperforms alternative local approaches such as coverage tests based on highest predictive density (HPD). We further highlight the importance of local evaluation and the benefit of interpretability of L-C2ST on a challenging application from computational neuroscience.

stat.ML↗

arXiv2023

Convolutional Monge Mapping Normalization for learning on sleep data

In many machine learning applications on signals and biomedical data, especially electroencephalogram (EEG), one major challenge is the variability of the data across subjects, sessions, and hardware devices. In this work, we propose a new method called Convolutional Monge Mapping Normalization (CMMN), which consists in filtering the signals in order to adapt their power spectrum density (PSD) to a Wasserstein barycenter estimated on training data. CMMN relies on novel closed-form solutions for optimal transport mappings and barycenters and provides individual test time adaptation to new data without needing to retrain a prediction model. Numerical experiments on sleep EEG data show that CMMN leads to significant and consistent performance gains independent from the neural network architecture when adapting between subjects, sessions, and even datasets collected with different hardware. Notably our performance gain is on par with much more numerically intensive Domain Adaptation (DA) methods and can be used in conjunction with those for even better performances.

eess.SP↗