Biology subjects

Thirion, B.

Publications and source records attributed to Thirion, B..

13 recordsLinked to original sources

bioRxiv2026

Functional Templates in fMRI: Building Accurate and Interpretable Group-Level Decoders

Inter-individual variability poses a significant challenge in decoding brain activity across subjects. While standard anatomical registration procedures reduce morphological differences, they fail to capture functional variability between subjects. Functional alignment methods address this issue by establishing voxel-to-voxel correspondences between pairs of individuals, thereby constructing a shared functional space. This shared space can be extended at the group level by generating a functional template. However, despite the availability of toolboxes, functional templates remain underused in fMRI analysis. Adopting this approach is currently difficult due to the diversity of existing methods and the lack of clear guidelines. Comprehensive evaluations of functional templates are limited to movie-watching paradigms. Here, we extensively compare functional alignment methods (Optimal Transport, Procrustes, Ridge regression, and Shared Response Model) and template construction strategies (in-sample, out-of-sample, pairwise) within the more general framework of task decoding. In this framework, decoding accuracy measures how well individual activation patterns align. Across multiple tasks and datasets, we demonstrate that population templates built using Optimal Transport (a) yield the highest decoding accuracy, (b) are not significantly biased by individual subjects, which facilitates generalization to new subjects, and (c) preserve the cortical signal topography.

neuroscience↗

bioRxiv2025

Languages of the brain: fMRI dissection of the amodal networks for language, mathematics, and social knowledge

The ability to compose complex mental representations by recombining simpler primitives is a characteristic of the human brain that manifests itself in a variety of domains such as spoken or written language, mathematics, or social reasoning. While it is known that these domains rest on partially distinct brain networks, they are rarely investigated together in the same paradigm. Here, we present a systematic functional MRI study of written and spoken word and sentence processing in each of these domains. In a true-false judgment task, adult participants were presented with a hierarchy of meaningless and meaningful stimuli bearing on various domains of general semantic knowledge and mathematics. The results show that distinct brain regions are activated by (1) syntax and semantics; (2) math versus non-math knowledge; (3) different domains of mathematics, such as geometry versus arithmetic; (4) social knowledge versus other knowledge. All of these regions are activated essentially identically in the written and spoken modalities. The results were replicated in a group of adolescents. Our experiments show that the human brain comprises distinct amodal networks for various domains of linguistic and semantic knowledge, and provide a simple paradigm to dissect them within a short fMRI session.

neuroscience↗

bioRxiv2025

An Interactive Brain Atlas of Knowledge

Biomedical knowledge about the brain increases every day, with a rapidly growing number of scientific publications, datasets, and software tools. While this informational plethora is not merely comprehensible by human beings, recent developments in information science and computational linguistics aim to make this knowledge programmatically accessible by literature mining. However, integrating these semantic methods into neuroimaging standards remains insufficient, hindering researchers from unraveling their full potential. Therefore, we developed the semantic meta-analysis platform The Virtual Brain adapter of semantics (TVBase) that projects biomedical knowledge preserved in over 36 million scientific articles onto a 3D standardized brain. The literature-mining platform SCAIView was used to extract ontologically defined biomedical entities and their associations with brain anatomy from the PubMed database. By querying a specific concept, the association strength with each anatomical term was calculated using entropy. To project the data onto a standardized brain, we created a unique transformation matrix that links over 800 anatomical terms to voxel coordinates of a parcellated standard brain. This novel method of knowledge projection extracts region-specific information about biomedical concepts from the literature to support translational multi-scale approaches to computational neuroscience. The multi-purpose software framework TVBase is openly available as a Python library. It aims for hypothesis-free neuroimaging pattern interpretation, hypothesis generation, and applications in personalized medicine.

neuroscience↗

bioRxiv2025

NeuroConText: Contrastive Learning for Neuroscience Meta-Analysis with Rich Text Representation

Brain meta-analysis is the common way to gather information about human brain function across the existing literature in order to formulate hypotheses and contextualize new findings. However, automated meta-analysis tools face challenges such as inconsistent terminology and difficulties in analyzing long texts and capturing semantic meaning because they still rely on bag-of-words approaches; furthermore, sparse coordinate reporting in articles distorts the activation distribution due to incomplete data. This paper introduces NeuroConText, a predictive text-to-brain modeling framework designed to support brain meta-analysis by bridging neuroscience text, brain location coordinates, and brain images within a shared latent space. This framework follows the predictive brain meta-analysis paradigm: it learns a regression from text descriptions to whole-brain activation maps and also enables the retrieval of relevant studies through contrastive learning, optimizing a multi-objective loss that combines retrieval and reconstruction objectives. Furthermore, NeuroConText supports second-level statistical synthesis by providing activation associated with top-K retrieved studies that can serve as input to coordinate-based meta-analysis (CBMA) methods. NeuroConText also leverages large language models (LLMs) to capture neuroscientific information from full-text articles, plus an LLM-based text augmentation strategy to handle short-text inputs. Quantitative and qualitative analyses demonstrate NeuroConTexts ability to enhance text-to-brain retrieval performance and reconstruct brain maps from neuroscience texts. We also show that predictive brain meta-analysis tools can infer brain activations in regions discussed in articles but absent in reported coordinates, potentially addressing the challenge of sparse coordinate reporting.

neuroscience↗

bioRxiv2024

Benchmarking Stroke Outcome Prediction through Comprehensive Data Analysis - NeuralCup 2023

Stroke remains a leading cause of mortality and long-term disability worldwide, with variable recovery trajectories posing substantial challenges in anticipating post-event care and rehabilitation planning. To address these challenges, we established the NeuralCup consortium to benchmark predictive models of stroke outcome through a collaborative, data-driven approach. This study presents findings from 15 international teams who used a comprehensive dataset including clinical and imaging data, to identify and compare predictors of motor, cognitive, and emotional outcomes one year post-stroke. Our analyses integrated traditional statistical approaches and novel machine learning algorithms to uncover optimal recipes for predicting each domain. The differences in these optimal recipes reflect distinct brain mechanisms in response to different tasks. Key predictors across all domains included infarct characteristics, T1-weighted MRI sequences, and demographic factors. Additionally, integrating FLAIR imaging and white matter tract analysis significantly improved the prediction of cognitive and motor outcomes, respectively. These findings support a multifaceted approach to stroke outcome prediction, underscoring the potential of collaborative data science to develop personalized care strategies that enhance recovery and quality of life for stroke survivors. To encourage further model development and validation, we provide access to the training dataset at http://neuralcup.bcblab.com

neuroscience↗

bioRxiv2024

Trained deep neural network models of the ventral visual pathway encode numerosity with robustness to object and scene identity

"Number sense", the ability to rapidly estimate object quantities in a visual scene without precise counting, is a crucial cognitive capacity found in humans and many other animals. Recent studies have identified artificial neurons tuned to numbers of items in biologically inspired vision models, even before training, and proposed these artificial neural networks as candidate models for the emergence of number sense in the brain. But real-world numerosity perception requires abstraction from the properties of individual objects and their contexts, unlike the simplified dot patterns used in previous studies. Using novel synthetically generated photorealistic stimuli, we show that deep convolutional neural networks optimized for object recognition encode information on approximate numerosity across diverse objects and scene types, which could be linearly read out from distributed activity patterns of later convolutional layers of different network architectures tested. In contrast, untrained networks with random weights failed to represent numerosity with abstractness to other visual properties, and instead captured mainly low-level visual features. Our findings emphasize the importance of using complex, naturalistic stimuli to investigate mechanisms of number sense in both biological and artificial systems, and suggest that the capacity of untrained networks to account for early life numerical abilities should be reassessed. They further point to a possible, so far underappreciated, contribution of the brains ventral visual pathway to representing numerosity with abstractness to other high-level visual properties.

neuroscience↗

bioRxiv2024

A nonlinear code for event probability in the human brain

Assessing probabilities and predicting future events are fundamental for perception and adaptive behavior, yet the neural representations of probability remain elusive. While previous studies have shown that neural activity in several brain regions correlates with probability-related factors such as surprise and uncertainty, similar correlations have not been found for probability. Here, using 7 Tesla functional magnetic resonance imaging, we uncover a representation of the probability of the next event in a sequence within the human dorsolateral prefrontal and intraparietal cortices. Crucially, univariate and multivariate analyses revealed that this representation employs a highly nonlinear code. Tuning curves for probability exhibit selectivity to various probability ranges, while the code for confidence accompanying these estimates is predominantly linear. The diversity of tuning curves we found recommends that future studies move from assuming linear correlates or simple canonical forms of tuning curves to considering richer representations whose benefits remain to be discovered.

neuroscience↗

bioRxiv2023

A reproducible benchmark of resting-state fMRI denoising strategies using fMRIPrep and Nilearn

Reducing contributions from non-neuronal sources is a crucial step in functional magnetic resonance imaging (fMRI) connectivity analyses. Many viable strategies for denoising fMRI are used in the literature, and practitioners rely on denoising benchmarks for guidance in the selection of an appropriate choice for their study. However, fMRI denoising software is an ever-evolving field, and the benchmarks can quickly become obsolete as the techniques or implementations change. In this work, we present a denoising benchmark featuring a range of denoising strategies, datasets and evaluation metrics for connectivity analyses, based on the popular fMRIprep software. The benchmark is implemented in a fully reproducible framework, where the provided research objects enable readers to reproduce or modify core computations, as well as the figures of the article using the Jupyter Book project and the Neurolibre reproducible preprint server (https://neurolibre.org/). We demonstrate how such a reproducible benchmark can be used for continuous evaluation of research software, by comparing two versions of the fMRIprep software package. The majority of benchmark results were consistent with prior literature. Scrubbing, a technique which excludes time points with excessive motion, combined with global signal regression, is generally effective at noise removal. Scrubbing however disrupts the continuous sampling of brain images and is incompatible with some statistical analyses, e.g. auto-regressive modeling. In this case, a simple strategy using motion parameters, average activity in select brain compartments, and global signal regression should be preferred. Importantly, we found that certain denoising strategies behave inconsistently across datasets and/or versions of fMRIPrep, or had a different behavior than in previously published benchmarks. This work will hopefully provide useful guidelines for the fMRIprep users community, and highlight the importance of continuous evaluation of research methods. Our reproducible benchmark infrastructure will facilitate such continuous evaluation in the future, and may also be applied broadly to different tools or even research fields.

neuroscience↗

bioRxiv2020

An empirical evaluation of functional alignment using inter-subject decoding

Inter-individual variability in the functional organization of the brain presents a major obstacle to identifying generalizable neural coding principles. Functional alignment--a class of methods that matches subjects neural signals based on their functional similarity--is a promising strategy for addressing this variability. To date, however, a range of functional alignment methods have been proposed and their relative performance is still unclear. In this work, we benchmark five functional alignment methods for inter-subject decoding on four publicly available datasets. Specifically, we consider three existing methods: piecewise Procrustes, searchlight Procrustes, and piecewise Optimal Transport. We also introduce and benchmark two new extensions of functional alignment methods: piecewise Shared Response Modelling (SRM), and intra-subject alignment. We find that functional alignment generally improves inter-subject decoding accuracy though the best performing method depends on the research context. Specifically, SRM and Optimal Transport perform well at both the region-of-interest level of analysis as well as at the whole-brain scale when aggregated through a piecewise scheme. We also benchmark the computational efficiency of each of the surveyed methods, providing insight into their usability and scalability. Taking inter-subject decoding accuracy as a quantification of inter-subject similarity, our results support the use of functional alignment to improve inter-subject comparisons in the face of variable structure-function organization. We provide open implementations of all methods used.

neuroscience↗

bioRxiv2020

Beyond brain age: Empirically-derived proxy measures of mental health

BackgroundBiological aging is revealed by physical measures, e.g., DNA probes or brain scans. Instead, individual differences in mental function are explained by psychological constructs, e.g., intelligence or neuroticism. These constructs are typically assessed by tailored neuropsychological tests that build on expert judgement and require careful interpretation. Could machine learning on large samples from the general population be used to build proxy measures of these constructs that do not require human intervention? ResultsHere, we built proxy measures by applying machine learning on multimodal MR images and rich sociodemographic information from the largest biomedical cohort to date: the UK Biobank. Objective model comparisons revealed that all proxies captured the target constructs and were as useful, and sometimes more useful than the original measures for characterizing real-world health behavior (sleep, exercise, tobacco, alcohol consumption). We observed this complementarity of proxy measures and original measures when modeling from brain signals or sociodemographic data, capturing multiple health-related constructs. ConclusionsPopulation modeling with machine learning can derive measures of mental health from brain signals and questionnaire data, which may complement or even substitute for psychometric assessments in clinical populations. Key PointsO_LIWe applied machine learning on more than 10.000 individuals from the general population to define empirical approximations of health-related psychological measures that do not require human judgment. C_LIO_LIWe found that machine-learning enriched the given psychological measures via approximation from brain and sociodemographic data: Resulting proxy measures related as well or better to real-world health behavior than the original measures. C_LIO_LIModel comparisons showed that sociodemographic information contributed most to characterizing psychological traits beyond aging. C_LI

neuroscience↗

bioRxiv2020

Functional Annotation of Human Cognitive States using Deep Graph Convolution

A key goal in neuroscience is to understand brain mechanisms of cognitive functions. An emerging approach is "brain decoding", which consists of inferring a set of experimental conditions performed by a participant, using pattern classification of brain activity. Few works so far have attempted to train a brain decoding model that would generalize across many different cognitive tasks drawn from multiple cognitive domains. To tackle this problem, we proposed a multidomain brain decoder that automatically learns the spatiotemporal dynamics of brain response within a short time window using a deep learning approach. We evaluated the decoding model on a large population of 1200 participants, under 21 different experimental conditions spanning six different cognitive domains, acquired from the Human Connectome Project task-fMRI database. Using a 10s window of fMRI response, the 21 cognitive states were identified with a test accuracy of 90% (chance level 4.8%). Performance remained good when using a 6s window (82%). It was even feasible to decode cognitive states from a single fMRI volume (720ms), with the performance following the shape of the hemodynamic response. Moreover, a saliency map analysis demonstrated that the high decoding performance was driven by the response of biologically meaningful brain regions. Together, we provide an automated tool to annotate human brain activity with fine temporal resolution and fine cognitive granularity. Our model shows potential applications as a reference model for domain adaptation, possibly making contributions in a variety of domains, including neurological and psychiatric disorders.

neuroscience↗

bioRxiv2018

Brain-based ranking of cognitive domains to predict schizophrenia

Schizophrenia is a devastating brain disorder that disturbs sensory perception, motor action, and abstract thought. Its clinical phenotype implies dysfunction of various mental domains, which has motivated a series of theories regarding the underlying pathophysiology. Aiming at a predictive benchmark of a catalogue of cognitive functions, we developed a bottom-up machine-learning strategy and provide a proof of principle in a multi-site clinical dataset (n=324). Existing neuroscientific knowledge on diverse cognitive domains was first condensed into neuro-topographical maps. We then examined how the ensuing meta-analytic cognitive priors can distinguish patients and controls using brain morphology and intrinsic functional connectivity. Some affected cognitive domains supported well-studied directions of research on auditory evaluation and social cognition. However, rarely suspected cognitive domains also emerged as disease-relevant, including self-oriented processing of bodily sensations in gustation and pain. Such algorithmic charting of the cognitive landscape can be used to make targeted recommendations for future mental health research.

neuroscience↗

bioRxiv2018

Prediction and inference diverge in biomedicine:Simulations and real-world data

In the 20th century many advances in biological knowledge and evidence-based medicine were supported by p-values and accompanying methods. In the beginning 21st century, ambitions towards precision medicine put a premium on detailed predictions for single individuals. The shift causes tension between traditional methods used to infer statistically significant group differences and burgeoning machine-learning tools suited to forecast an individuals future. This comparison applies the linear model for identifying significant contributing variables and for finding the most predictive variable sets. In systematic data simulations and common medical datasets, we explored how statistical inference and pattern recognition can agree and diverge. Across analysis scenarios, even small predictive performances typically coincided with finding underlying significant statistical relationships. However, even statistically strong findings with very low p-values shed little light on their value for achieving accurate prediction in the same dataset. More complete understanding of different ways to define important associations is a prerequisite for reproducible research findings that can serve to personalize clinical care.

bioinformatics↗