arXiv subjects

Alexandre Gramfort

Publications and source records attributed to Alexandre Gramfort.

At least 37 records · Page 2Linked to original sources

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.

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arXiv2023

Toward a realistic model of speech processing in the brain with self-supervised learning

Several deep neural networks have recently been shown to generate activations similar to those of the brain in response to the same input. These algorithms, however, remain largely implausible: they require (1) extraordinarily large amounts of data, (2) unobtainable supervised labels, (3) textual rather than raw sensory input, and / or (4) implausibly large memory (e.g. thousands of contextual words). These elements highlight the need to identify algorithms that, under these limitations, would suffice to account for both behavioral and brain responses. Focusing on the issue of speech processing, we here hypothesize that self-supervised algorithms trained on the raw waveform constitute a promising candidate. Specifically, we compare a recent self-supervised architecture, Wav2Vec 2.0, to the brain activity of 412 English, French, and Mandarin individuals recorded with functional Magnetic Resonance Imaging (fMRI), while they listened to ~1h of audio books. Our results are four-fold. First, we show that this algorithm learns brain-like representations with as little as 600 hours of unlabelled speech -- a quantity comparable to what infants can be exposed to during language acquisition. Second, its functional hierarchy aligns with the cortical hierarchy of speech processing. Third, different training regimes reveal a functional specialization akin to the cortex: Wav2Vec 2.0 learns sound-generic, speech-specific and language-specific representations similar to those of the prefrontal and temporal cortices. Fourth, we confirm the similarity of this specialization with the behavior of 386 additional participants. These elements, resulting from the largest neuroimaging benchmark to date, show how self-supervised learning can account for a rich organization of speech processing in the brain, and thus delineate a path to identify the laws of language acquisition which shape the human brain.

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arXiv2023

Optimizing the Noise in Self-Supervised Learning: from Importance Sampling to Noise-Contrastive Estimation

Self-supervised learning is an increasingly popular approach to unsupervised learning, achieving state-of-the-art results. A prevalent approach consists in contrasting data points and noise points within a classification task: this requires a good noise distribution which is notoriously hard to specify. While a comprehensive theory is missing, it is widely assumed that the optimal noise distribution should in practice be made equal to the data distribution, as in Generative Adversarial Networks (GANs). We here empirically and theoretically challenge this assumption. We turn to Noise-Contrastive Estimation (NCE) which grounds this self-supervised task as an estimation problem of an energy-based model of the data. This ties the optimality of the noise distribution to the sample efficiency of the estimator, which is rigorously defined as its asymptotic variance, or mean-squared error. In the special case where the normalization constant only is unknown, we show that NCE recovers a family of Importance Sampling estimators for which the optimal noise is indeed equal to the data distribution. However, in the general case where the energy is also unknown, we prove that the optimal noise density is the data density multiplied by a correction term based on the Fisher score. In particular, the optimal noise distribution is different from the data distribution, and is even from a different family. Nevertheless, we soberly conclude that the optimal noise may be hard to sample from, and the gain in efficiency can be modest compared to choosing the noise distribution equal to the data's.

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arXiv2022

Validation Diagnostics for SBI algorithms based on Normalizing Flows

Building on the recent trend of new deep generative models known as Normalizing Flows (NF), simulation-based inference (SBI) algorithms can now efficiently accommodate arbitrary complex and high-dimensional data distributions. The development of appropriate validation methods however has fallen behind. Indeed, most of the existing metrics either require access to the true posterior distribution, or fail to provide theoretical guarantees on the consistency of the inferred approximation beyond the one-dimensional setting. This work proposes easy to interpret validation diagnostics for multi-dimensional conditional (posterior) density estimators based on NF. It also offers theoretical guarantees based on results of local consistency. The proposed workflow can be used to check, analyse and guarantee consistent behavior of the estimator. The method is illustrated with a challenging example that involves tightly coupled parameters in the context of computational neuroscience. This work should help the design of better specified models or drive the development of novel SBI-algorithms, hence allowing to build up trust on their ability to address important questions in experimental science.

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arXiv2022

Data augmentation for learning predictive models on EEG: a systematic comparison

Objective: The use of deep learning for electroencephalography (EEG) classification tasks has been rapidly growing in the last years, yet its application has been limited by the relatively small size of EEG datasets. Data augmentation, which consists in artificially increasing the size of the dataset during training, can be employed to alleviate this problem. While a few augmentation transformations for EEG data have been proposed in the literature, their positive impact on performance is often evaluated on a single dataset and compared to one or two competing augmentation methods. This work proposes to better validate the existing data augmentation approaches through a unified and exhaustive analysis. Approach: We compare quantitatively 13 different augmentations with two different predictive tasks, datasets and models, using three different types of experiments. Main results: We demonstrate that employing the adequate data augmentations can bring up to 45% accuracy improvements in low data regimes compared to the same model trained without any augmentation. Our experiments also show that there is no single best augmentation strategy, as the good augmentations differ on each task. Significance: Our results highlight the best data augmentations to consider for sleep stage classification and motor imagery brain-computer interfaces. More broadly, it demonstrates that EEG classification tasks benefit from adequate data augmentation

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arXiv2022

Benchopt: Reproducible, efficient and collaborative optimization benchmarks

Numerical validation is at the core of machine learning research as it allows to assess the actual impact of new methods, and to confirm the agreement between theory and practice. Yet, the rapid development of the field poses several challenges: researchers are confronted with a profusion of methods to compare, limited transparency and consensus on best practices, as well as tedious re-implementation work. As a result, validation is often very partial, which can lead to wrong conclusions that slow down the progress of research. We propose Benchopt, a collaborative framework to automate, reproduce and publish optimization benchmarks in machine learning across programming languages and hardware architectures. Benchopt simplifies benchmarking for the community by providing an off-the-shelf tool for running, sharing and extending experiments. To demonstrate its broad usability, we showcase benchmarks on three standard learning tasks: $\ell_2$-regularized logistic regression, Lasso, and ResNet18 training for image classification. These benchmarks highlight key practical findings that give a more nuanced view of the state-of-the-art for these problems, showing that for practical evaluation, the devil is in the details. We hope that Benchopt will foster collaborative work in the community hence improving the reproducibility of research findings.

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arXiv2022

Deep invariant networks with differentiable augmentation layers

Designing learning systems which are invariant to certain data transformations is critical in machine learning. Practitioners can typically enforce a desired invariance on the trained model through the choice of a network architecture, e.g. using convolutions for translations, or using data augmentation. Yet, enforcing true invariance in the network can be difficult, and data invariances are not always known a piori. State-of-the-art methods for learning data augmentation policies require held-out data and are based on bilevel optimization problems, which are complex to solve and often computationally demanding. In this work we investigate new ways of learning invariances only from the training data. Using learnable augmentation layers built directly in the network, we demonstrate that our method is very versatile. It can incorporate any type of differentiable augmentation and be applied to a broad class of learning problems beyond computer vision. We provide empirical evidence showing that our approach is easier and faster to train than modern automatic data augmentation techniques based on bilevel optimization, while achieving comparable results. Experiments show that while the invariances transferred to a model through automatic data augmentation are limited by the model expressivity, the invariance yielded by our approach is insensitive to it by design.

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arXiv2022

Deep Recurrent Encoder: A scalable end-to-end network to model brain signals

Understanding how the brain responds to sensory inputs is challenging: brain recordings are partial, noisy, and high dimensional; they vary across sessions and subjects and they capture highly nonlinear dynamics. These challenges have led the community to develop a variety of preprocessing and analytical (almost exclusively linear) methods, each designed to tackle one of these issues. Instead, we propose to address these challenges through a specific end-to-end deep learning architecture, trained to predict the brain responses of multiple subjects at once. We successfully test this approach on a large cohort of magnetoencephalography (MEG) recordings acquired during a one-hour reading task. Our Deep Recurrent Encoding (DRE) architecture reliably predicts MEG responses to words with a three-fold improvement over classic linear methods. To overcome the notorious issue of interpretability of deep learning, we describe a simple variable importance analysis. When applied to DRE, this method recovers the expected evoked responses to word length and word frequency. The quantitative improvement of the present deep learning approach paves the way to better understand the nonlinear dynamics of brain activity from large datasets.

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arXiv2022

Dual Extrapolation for Sparse Generalized Linear Models

Generalized Linear Models (GLM) form a wide class of regression and classification models, where prediction is a function of a linear combination of the input variables. For statistical inference in high dimension, sparsity inducing regularizations have proven to be useful while offering statistical guarantees. However, solving the resulting optimization problems can be challenging: even for popular iterative algorithms such as coordinate descent, one needs to loop over a large number of variables. To mitigate this, techniques known as screening rules and working sets diminish the size of the optimization problem at hand, either by progressively removing variables, or by solving a growing sequence of smaller problems. For both techniques, significant variables are identified thanks to convex duality arguments. In this paper, we show that the dual iterates of a GLM exhibit a Vector AutoRegressive (VAR) behavior after sign identification, when the primal problem is solved with proximal gradient descent or cyclic coordinate descent. Exploiting this regularity, one can construct dual points that offer tighter certificates of optimality, enhancing the performance of screening rules and helping to design competitive working set algorithms.

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arXiv2022

Implicit differentiation for fast hyperparameter selection in non-smooth convex learning

Finding the optimal hyperparameters of a model can be cast as a bilevel optimization problem, typically solved using zero-order techniques. In this work we study first-order methods when the inner optimization problem is convex but non-smooth. We show that the forward-mode differentiation of proximal gradient descent and proximal coordinate descent yield sequences of Jacobians converging toward the exact Jacobian. Using implicit differentiation, we show it is possible to leverage the non-smoothness of the inner problem to speed up the computation. Finally, we provide a bound on the error made on the hypergradient when the inner optimization problem is solved approximately. Results on regression and classification problems reveal computational benefits for hyperparameter optimization, especially when multiple hyperparameters are required.

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arXiv2022

The Optimal Noise in Noise-Contrastive Learning Is Not What You Think

Learning a parametric model of a data distribution is a well-known statistical problem that has seen renewed interest as it is brought to scale in deep learning. Framing the problem as a self-supervised task, where data samples are discriminated from noise samples, is at the core of state-of-the-art methods, beginning with Noise-Contrastive Estimation (NCE). Yet, such contrastive learning requires a good noise distribution, which is hard to specify; domain-specific heuristics are therefore widely used. While a comprehensive theory is missing, it is widely assumed that the optimal noise should in practice be made equal to the data, both in distribution and proportion. This setting underlies Generative Adversarial Networks (GANs) in particular. Here, we empirically and theoretically challenge this assumption on the optimal noise. We show that deviating from this assumption can actually lead to better statistical estimators, in terms of asymptotic variance. In particular, the optimal noise distribution is different from the data's and even from a different family.

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arXiv2022

DriPP: Driven Point Processes to Model Stimuli Induced Patterns in M/EEG Signals

The quantitative analysis of non-invasive electrophysiology signals from electroencephalography (EEG) and magnetoencephalography (MEG) boils down to the identification of temporal patterns such as evoked responses, transient bursts of neural oscillations but also blinks or heartbeats for data cleaning. Several works have shown that these patterns can be extracted efficiently in an unsupervised way, e.g., using Convolutional Dictionary Learning. This leads to an event-based description of the data. Given these events, a natural question is to estimate how their occurrences are modulated by certain cognitive tasks and experimental manipulations. To address it, we propose a point process approach. While point processes have been used in neuroscience in the past, in particular for single cell recordings (spike trains), techniques such as Convolutional Dictionary Learning make them amenable to human studies based on EEG/MEG signals. We develop a novel statistical point process model-called driven temporal point processes (DriPP)-where the intensity function of the point process model is linked to a set of point processes corresponding to stimulation events. We derive a fast and principled expectation-maximization (EM) algorithm to estimate the parameters of this model. Simulations reveal that model parameters can be identified from long enough signals. Results on standard MEG datasets demonstrate that our methodology reveals event-related neural responses-both evoked and induced-and isolates non-task specific temporal patterns.

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arXiv2022

LassoBench: A High-Dimensional Hyperparameter Optimization Benchmark Suite for Lasso

While Weighted Lasso sparse regression has appealing statistical guarantees that would entail a major real-world impact in finance, genomics, and brain imaging applications, it is typically scarcely adopted due to its complex high-dimensional space composed by thousands of hyperparameters. On the other hand, the latest progress with high-dimensional hyperparameter optimization (HD-HPO) methods for black-box functions demonstrates that high-dimensional applications can indeed be efficiently optimized. Despite this initial success, HD-HPO approaches are mostly applied to synthetic problems with a moderate number of dimensions, which limits its impact in scientific and engineering applications. We propose LassoBench, the first benchmark suite tailored for Weighted Lasso regression. LassoBench consists of benchmarks for both well-controlled synthetic setups (number of samples, noise level, ambient and effective dimensionalities, and multiple fidelities) and real-world datasets, which enables the use of many flavors of HPO algorithms to be studied and extended to the high-dimensional Lasso setting. We evaluate 6 state-of-the-art HPO methods and 3 Lasso baselines, and demonstrate that Bayesian optimization and evolutionary strategies can improve over the methods commonly used for sparse regression while highlighting limitations of these frameworks in very high-dimensional and noisy settings.

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arXiv2022

Inverting brain grey matter models with likelihood-free inference: a tool for trustable cytoarchitecture measurements

Effective characterisation of the brain grey matter cytoarchitecture with quantitative sensitivity to soma density and volume remains an unsolved challenge in diffusion MRI (dMRI). Solving the problem of relating the dMRI signal with cytoarchitectural characteristics calls for the definition of a mathematical model that describes brain tissue via a handful of physiologically-relevant parameters and an algorithm for inverting the model. To address this issue, we propose a new forward model, specifically a new system of equations, requiring a few relatively sparse b-shells. We then apply modern tools from Bayesian analysis known as likelihood-free inference (LFI) to invert our proposed model. As opposed to other approaches from the literature, our algorithm yields not only an estimation of the parameter vector $θ$ that best describes a given observed data point $x_0$, but also a full posterior distribution $p(θ|x_0)$ over the parameter space. This enables a richer description of the model inversion, providing indicators such as credible intervals for the estimated parameters and a complete characterization of the parameter regions where the model may present indeterminacies. We approximate the posterior distribution using deep neural density estimators, known as normalizing flows, and fit them using a set of repeated simulations from the forward model. We validate our approach on simulations using dmipy and then apply the whole pipeline on two publicly available datasets.

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arXiv2022

Averaging Spatio-temporal Signals using Optimal Transport and Soft Alignments

Several fields in science, from genomics to neuroimaging, require monitoring populations (measures) that evolve with time. These complex datasets, describing dynamics with both time and spatial components, pose new challenges for data analysis. We propose in this work a new framework to carry out averaging of these datasets, with the goal of synthesizing a representative template trajectory from multiple trajectories. We show that this requires addressing three sources of invariance: shifts in time, space, and total population size (or mass/amplitude). Here we draw inspiration from dynamic time warping (DTW), optimal transport (OT) theory and its unbalanced extension (UOT) to propose a criterion that can address all three issues. This proposal leverages a smooth formulation of DTW (Soft-DTW) that is shown to capture temporal shifts, and UOT to handle both variations in space and size. Our proposed loss can be used to define spatio-temporal barycenters as Fréchet means. Using Fenchel duality, we show how these barycenters can be computed efficiently, in parallel, via a novel variant of entropy-regularized debiased UOT. Experiments on handwritten letters and brain imaging data confirm our theoretical findings and illustrate the effectiveness of the proposed loss for spatio-temporal data.

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arXiv2022

2021 BEETL Competition: Advancing Transfer Learning for Subject Independence & Heterogenous EEG Data Sets

Transfer learning and meta-learning offer some of the most promising avenues to unlock the scalability of healthcare and consumer technologies driven by biosignal data. This is because current methods cannot generalise well across human subjects' data and handle learning from different heterogeneously collected data sets, thus limiting the scale of training data. On the other side, developments in transfer learning would benefit significantly from a real-world benchmark with immediate practical application. Therefore, we pick electroencephalography (EEG) as an exemplar for what makes biosignal machine learning hard. We design two transfer learning challenges around diagnostics and Brain-Computer-Interfacing (BCI), that have to be solved in the face of low signal-to-noise ratios, major variability among subjects, differences in the data recording sessions and techniques, and even between the specific BCI tasks recorded in the dataset. Task 1 is centred on the field of medical diagnostics, addressing automatic sleep stage annotation across subjects. Task 2 is centred on Brain-Computer Interfacing (BCI), addressing motor imagery decoding across both subjects and data sets. The BEETL competition with its over 30 competing teams and its 3 winning entries brought attention to the potential of deep transfer learning and combinations of set theory and conventional machine learning techniques to overcome the challenges. The results set a new state-of-the-art for the real-world BEETL benchmark.

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arXiv2022

CADDA: Class-wise Automatic Differentiable Data Augmentation for EEG Signals

Data augmentation is a key element of deep learning pipelines, as it informs the network during training about transformations of the input data that keep the label unchanged. Manually finding adequate augmentation methods and parameters for a given pipeline is however rapidly cumbersome. In particular, while intuition can guide this decision for images, the design and choice of augmentation policies remains unclear for more complex types of data, such as neuroscience signals. Besides, class-dependent augmentation strategies have been surprisingly unexplored in the literature, although it is quite intuitive: changing the color of a car image does not change the object class to be predicted, but doing the same to the picture of an orange does. This paper investigates gradient-based automatic data augmentation algorithms amenable to class-wise policies with exponentially larger search spaces. Motivated by supervised learning applications using EEG signals for which good augmentation policies are mostly unknown, we propose a new differentiable relaxation of the problem. In the class-agnostic setting, results show that our new relaxation leads to optimal performance with faster training than competing gradient-based methods, while also outperforming gradient-free methods in the class-wise setting. This work proposes also novel differentiable augmentation operations relevant for sleep stage classification.

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arXiv2021

Long-range and hierarchical language predictions in brains and algorithms

Deep learning has recently made remarkable progress in natural language processing. Yet, the resulting algorithms remain far from competing with the language abilities of the human brain. Predictive coding theory offers a potential explanation to this discrepancy: while deep language algorithms are optimized to predict adjacent words, the human brain would be tuned to make long-range and hierarchical predictions. To test this hypothesis, we analyze the fMRI brain signals of 304 subjects each listening to 70min of short stories. After confirming that the activations of deep language algorithms linearly map onto those of the brain, we show that enhancing these models with long-range forecast representations improves their brain-mapping. The results further reveal a hierarchy of predictions in the brain, whereby the fronto-parietal cortices forecast more abstract and more distant representations than the temporal cortices. Overall, this study strengthens predictive coding theory and suggests a critical role of long-range and hierarchical predictions in natural language processing.

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