Daily Papers

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Brain-Computer Interface (BCI) systems allow users to perform actions by translating their brain activity into commands. Such systems usually need a training phase, consisting in training a classification algorithm to discriminate between mental states using specific features from the recorded signals. This phase of feature selection and training is crucial for BCI performance and presents specific constraints to be met in a clinical context, such as post-stroke rehabilitation. In this paper, we present HappyFeat, a software making Motor Imagery (MI) based BCI experiments easier, by gathering all necessary manipulations and analysis in a single convenient GUI and via automation of experiment or analysis parameters. The resulting workflow allows for effortlessly selecting the best features, helping to achieve good BCI performance in time-constrained environments. Alternative features based on Functional Connectivity can be used and compared or combined with Power Spectral Density, allowing a network-oriented approach. We then give details of HappyFeat's main mechanisms, and a review of its performances in typical use cases. We also show that it can be used as an efficient tool for comparing different metrics extracted from the signals, to train the classification algorithm. To this end, we show a comparison between the commonly-used Power Spectral Density and network metrics based on Functional Connectivity. HappyFeat is available as an open-source project which can be freely downloaded on GitHub.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on functional connectivity (FC) profile, broadly falling into two main categories. The Fixed-FC approaches, utilizing the FC profile which represents the linear temporal relation within the brain network, are limited by failing to capture informative brain temporal dynamics. On the other hand, the Dynamic-FC approaches, modeling the evolving FC profile over time, often exhibit less satisfactory performance due to challenges in handling the inherent noisy nature of fMRI data. To address these challenges, we propose Brain Masked Auto-Encoder (BrainMAE) for learning representations directly from fMRI time-series data. Our approach incorporates two essential components: a region-aware graph attention mechanism designed to capture the relationships between different brain ROIs, and a novel self-supervised masked autoencoding framework for effective model pre-training. These components enable the model to capture rich temporal dynamics of brain activity while maintaining resilience to inherent noise in fMRI data. Our experiments demonstrate that BrainMAE consistently outperforms established baseline methods by significant margins in four distinct downstream tasks. Finally, leveraging the model's inherent interpretability, our analysis of model-generated representations reveals findings that resonate with ongoing research in the field of neuroscience.

The structure of biological neural circuits-modular, hierarchical, and sparsely interconnected-reflects an efficient trade-off between wiring cost, functional specialization, and robustness. These principles offer valuable insights for artificial neural network (ANN) design, especially as networks grow in depth and scale. Sparsity, in particular, has been widely explored for reducing memory and computation, improving speed, and enhancing generalization. Motivated by systems neuroscience findings, we explore how patterns of functional connectivity in the mouse visual cortex-specifically, ensemble-to-ensemble communication, can inform ANN design. We introduce G2GNet, a novel architecture that imposes sparse, modular connectivity across feedforward layers. Despite having significantly fewer parameters than fully connected models, G2GNet achieves superior accuracy on standard vision benchmarks. To our knowledge, this is the first architecture to incorporate biologically observed functional connectivity patterns as a structural bias in ANN design. We complement this static bias with a dynamic sparse training (DST) mechanism that prunes and regrows edges during training. We also propose a Hebbian-inspired rewiring rule based on activation correlations, drawing on principles of biological plasticity. G2GNet achieves up to 75% sparsity while improving accuracy by up to 4.3% on benchmarks, including Fashion-MNIST, CIFAR-10, and CIFAR-100, outperforming dense baselines with far fewer computations.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Most modern Text2SQL systems prompt large language models (LLMs) with entire schemas -- mostly column information -- alongside the user's question. While effective on small databases, this approach fails on real-world schemas that exceed LLM context limits, even for commercial models. The recent Spider 2.0 benchmark exemplifies this with hundreds of tables and tens of thousands of columns, where existing systems often break. Current mitigations either rely on costly multi-step prompting pipelines or filter columns by ranking them against user's question independently, ignoring inter-column structure. To scale existing systems, we introduce \toolname, an open-source, LLM-efficient schema filtering framework that compacts Text2SQL prompts by (i) ranking columns with a query-aware LLM encoder enriched with values and metadata, (ii) reranking inter-connected columns via a lightweight graph transformer over functional dependencies, and (iii) selecting a connectivity-preserving sub-schema with a Steiner-tree heuristic. Experiments on real datasets show that \toolname achieves near-perfect recall and higher precision than CodeS, SchemaExP, Qwen rerankers, and embedding retrievers, while maintaining sub-second median latency and scaling to schemas with 23,000+ columns. Our source code is available at https://github.com/thanhdath/grast-sql.

Early diagnosis of mild cognitive impairment (MCI) and subjective cognitive decline (SCD) utilizing multi-modal magnetic resonance imaging (MRI) is a pivotal area of research. While various regional and connectivity features from functional MRI (fMRI) and diffusion tensor imaging (DTI) have been employed to develop diagnosis models, most studies integrate these features without adequately addressing their alignment and interactions. This limits the potential to fully exploit the synergistic contributions of combined features and modalities. To solve this gap, our study introduces a novel Hierarchical Alignments and Hierarchical Interactions (HA-HI) method for MCI and SCD classification, leveraging the combined strengths of fMRI and DTI. HA-HI efficiently learns significant MCI- or SCD- related regional and connectivity features by aligning various feature types and hierarchically maximizing their interactions. Furthermore, to enhance the interpretability of our approach, we have developed the Synergistic Activation Map (SAM) technique, revealing the critical brain regions and connections that are indicative of MCI/SCD. Comprehensive evaluations on the ADNI dataset and our self-collected data demonstrate that HA-HI outperforms other existing methods in diagnosing MCI and SCD, making it a potentially vital and interpretable tool for early detection. The implementation of this method is publicly accessible at https://github.com/ICI-BCI/Dual-MRI-HA-HI.git.

The Wilson-Cowan model for metapopulation, a Neural Mass Network Model, treats different subcortical regions of the brain as connected nodes, with connections representing various types of structural, functional, or effective neuronal connectivity between these regions. Each region comprises interacting populations of excitatory and inhibitory cells, consistent with the standard Wilson-Cowan model. By incorporating stable attractors into such a metapopulation model's dynamics, we transform it into a learning algorithm capable of achieving high image and text classification accuracy. We test it on MNIST and Fashion MNIST, in combination with convolutional neural networks, on CIFAR-10 and TF-FLOWERS, and, in combination with a transformer architecture (BERT), on IMDB, always showing high classification accuracy. These numerical evaluations illustrate that minimal modifications to the Wilson-Cowan model for metapopulation can reveal unique and previously unobserved dynamics.