Functional Magnetic Resonance Imaging (fMRI) provides useful insights into the brain function both during task or rest. Representing fMRI data using correlation matrices is found to be a reliable method of analyzing the inherent connectivity of the brain in the resting and active states. Graph Neural Networks (GNNs) have been widely used for brain network analysis due to their inherent explainability capability. In this work, we introduce a novel framework using contrastive self-supervised learning graph transformers, incorporating a brain network transformer encoder with random graph alterations. The proposed network leverages both contrastive learning and graph alterations to effectively train the graph transformer for autism detection. Our approach, tested on Autism Brain Imaging Data Exchange (ABIDE) data, demonstrates superior autism detection, achieving an AUROC of 82.6 and an accuracy of 74%, surpassing current state-of-the-art methods.

Graph Neural Networks (GNNs) are popular deep learning models designed to process graph-structured data through recursive neighborhood aggregations in the message passing process. When applied to semi-supervised node classification, the message-passing enables GNNs to understand short-range spatial interactions, but also causes them to suffer from over-smoothing and over-squashing. These challenges hinder model expressiveness and prevent the use of deeper models to capture long-range node interactions (LRIs) within the graph. Popular solutions for LRIs detection are either too expensive to process large graphs due to high time complexity or fail to generalize across diverse graph structures. To address these limitations, we propose a mechanism called \emph{information flow control}, which leverages a novel connectivity measure, called \emph{information flow score}, to address over-smoothing and over-squashing with linear computational overhead, supported by theoretical evidence. Finally, to prove the efficacy of our methodology we design DeltaGNN, the first scalable and generalizable approach for detecting long-range and short-range interactions. We benchmark our model across 10 real-world datasets, including graphs with varying sizes, topologies, densities, and homophilic ratios, showing superior performance with limited computational complexity. The implementation of the proposed methods are publicly available at https://github.com/basiralab/DeltaGNN.

Brain graph super-resolution (SR) is an under-explored yet highly relevant task in network neuroscience. It circumvents the need for costly and time-consuming medical imaging data collection, preparation, and processing. Current SR methods leverage graph neural networks (GNNs) thanks to their ability to natively handle graph-structured datasets. However, most GNNs perform node feature learning, which presents two significant limitations: (1) they require computationally expensive methods to learn complex node features capable of inferring connectivity strength or edge features, which do not scale to larger graphs; and (2) computations in the node space fail to adequately capture higher-order brain topologies such as cliques and hubs. However, numerous studies have shown that brain graph topology is crucial in identifying the onset and presence of various neurodegenerative disorders like Alzheimer and Parkinson. Motivated by these challenges and applications, we propose our STP-GSR framework. It is the first graph SR architecture to perform representation learning in higher-order topological space. Specifically, using the primal-dual graph formulation from graph theory, we develop an efficient mapping from the edge space of our low-resolution (LR) brain graphs to the node space of a high-resolution (HR) dual graph. This approach ensures that node-level computations on this dual graph correspond naturally to edge-level learning on our HR brain graphs, thereby enforcing strong topological consistency within our framework. Additionally, our framework is GNN layer agnostic and can easily learn from smaller, scalable GNNs, reducing computational requirements. We comprehensively benchmark our framework across seven key topological measures and observe that it significantly outperforms the previous state-of-the-art methods and baselines.

The understanding of the convoluted evolution of infant brain networks during the first postnatal year is pivotal for identifying the dynamics of early brain connectivity development. Existing deep learning solutions suffer from three major limitations. First, they cannot generalize to multi-trajectory prediction tasks, where each graph trajectory corresponds to a particular imaging modality or connectivity type (e.g., T1-w MRI). Second, existing models require extensive training datasets to achieve satisfactory performance which are often challenging to obtain. Third, they do not efficiently utilize incomplete time series data. To address these limitations, we introduce FedGmTE-Net++, a federated graph-based multi-trajectory evolution network. Using the power of federation, we aggregate local learnings among diverse hospitals with limited datasets. As a result, we enhance the performance of each hospital's local generative model, while preserving data privacy. The three key innovations of FedGmTE-Net++ are: (i) presenting the first federated learning framework specifically designed for brain multi-trajectory evolution prediction in a data-scarce environment, (ii) incorporating an auxiliary regularizer in the local objective function to exploit all the longitudinal brain connectivity within the evolution trajectory and maximize data utilization, (iii) introducing a two-step imputation process, comprising a preliminary KNN-based precompletion followed by an imputation refinement step that employs regressors to improve similarity scores and refine imputations. Our comprehensive experimental results showed the outperformance of FedGmTE-Net++ in brain multi-trajectory prediction from a single baseline graph in comparison with benchmark methods.

Learning from limited data has been extensively studied in machine learning, considering that deep neural networks achieve optimal performance when trained using a large amount of samples. Although various strategies have been proposed for centralized training, the topic of federated learning with small datasets remains largely unexplored. Moreover, in realistic scenarios, such as settings where medical institutions are involved, the number of participating clients is also constrained. In this work, we propose a novel federated learning framework, named RepTreeFL. At the core of the solution is the concept of a replica, where we replicate each participating client by copying its model architecture and perturbing its local data distribution. Our approach enables learning from limited data and a small number of clients by aggregating a larger number of models with diverse data distributions. Furthermore, we leverage the hierarchical structure of the client network (both original and virtual), alongside the model diversity across replicas, and introduce a diversity-based tree aggregation, where replicas are combined in a tree-like manner and the aggregation weights are dynamically updated based on the model discrepancy. We evaluated our method on two tasks and two types of data, graph generation and image classification (binary and multi-class), with both homogeneous and heterogeneous model architectures. Experimental results demonstrate the effectiveness and outperformance of RepTreeFL in settings where both data and clients are limited. Our code is available at https://github.com/basiralab/RepTreeFL.

Graph Neural Network (GNN) ushered in a new era of machine learning with interconnected datasets. While traditional neural networks can only be trained on independent samples, GNN allows for the inclusion of inter-sample interactions in the training process. This gain, however, incurs additional memory cost, rendering most GNNs unscalable for real-world applications involving vast and complicated networks with tens of millions of nodes (e.g., social circles, web graphs, and brain graphs). This means that storing the graph in the main memory can be difficult, let alone training the GNN model with significantly less GPU memory. While much of the recent literature has focused on either mini-batching GNN methods or quantization, graph reduction methods remain largely scarce. Furthermore, present graph reduction approaches have several drawbacks. First, most graph reduction focuses only on the inference stage (e.g., condensation and distillation) and requires full graph GNN training, which does not reduce training memory footprint. Second, many methods focus solely on the graph's structural aspect, ignoring the initial population feature-label distribution, resulting in a skewed post-reduction label distribution. Here, we propose a Feature-Label COnstrained graph Net collapse, FALCON, to address these limitations. Our three core contributions lie in (i) designing FALCON, a topology-aware graph reduction technique that preserves feature-label distribution; (ii) implementation of FALCON with other memory reduction methods (i.e., mini-batched GNN and quantization) for further memory reduction; (iii) extensive benchmarking and ablation studies against SOTA methods to evaluate FALCON memory reduction. Our extensive results show that FALCON can significantly collapse various public datasets while achieving equal prediction quality across GNN models. Code: https://github.com/basiralab/FALCON

Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI.

The challenges of collecting medical data on neurological disorder diagnosis problems paved the way for learning methods with scarce number of samples. Due to this reason, one-shot learning still remains one of the most challenging and trending concepts of deep learning as it proposes to simulate the human-like learning approach in classification problems. Previous studies have focused on generating more accurate fingerprints of the population using graph neural networks (GNNs) with connectomic brain graph data. Thereby, generated population fingerprints named connectional brain template (CBTs) enabled detecting discriminative bio-markers of the population on classification tasks. However, the reverse problem of data augmentation from single graph data representing brain connectivity has never been tackled before. In this paper, we propose an augmentation pipeline in order to provide improved metrics on our binary classification problem. Divergently from the previous studies, we examine augmentation from a single population template by utilizing graph-based generative adversarial network (gGAN) architecture for a classification problem. We benchmarked our proposed solution on AD/LMCI dataset consisting of brain connectomes with Alzheimer's Disease (AD) and Late Mild Cognitive Impairment (LMCI). In order to evaluate our model's generalizability, we used cross-validation strategy and randomly sampled the folds multiple times. Our results on classification not only provided better accuracy when augmented data generated from one sample is introduced, but yields more balanced results on other metrics as well.

Predicting the evolution of the brain network, also called connectome, by foreseeing changes in the connectivity weights linking pairs of anatomical regions makes it possible to spot connectivity-related neurological disorders in earlier stages and detect the development of potential connectomic anomalies. Remarkably, such a challenging prediction problem remains least explored in the predictive connectomics literature. It is a known fact that machine learning (ML) methods have proven their predictive abilities in a wide variety of computer vision problems. However, ML techniques specifically tailored for the prediction of brain connectivity evolution trajectory from a single timepoint are almost absent. To fill this gap, we organized a Kaggle competition where 20 competing teams designed advanced machine learning pipelines for predicting the brain connectivity evolution from a single timepoint. The competing teams developed their ML pipelines with a combination of data pre-processing, dimensionality reduction, and learning methods. Utilizing an inclusive evaluation approach, we ranked the methods based on two complementary evaluation metrics (mean absolute error (MAE) and Pearson Correlation Coefficient (PCC)) and their performances using different training and testing data perturbation strategies (single random split and cross-validation). The final rank was calculated using the rank product for each competing team across all evaluation measures and validation strategies. In support of open science, the developed 20 ML pipelines along with the connectomic dataset are made available on GitHub. The outcomes of this competition are anticipated to lead to the further development of predictive models that can foresee the evolution of brain connectivity over time, as well as other types of networks (e.g., genetic networks).

Estimating a representative and discriminative brain network atlas (BNA) is a nascent research field in mapping a population of brain networks in health and disease. Although limited, existing BNA estimation methods have several limitations. First, they primarily rely on a similarity network diffusion and fusion technique, which only considers node degree as a topological measure in the cross-network diffusion process, thereby overlooking rich topological measures of the brain network (e.g., centrality). Second, both diffusion and fusion techniques are implemented in fully unsupervised manner, which might decrease the discriminative power of the estimated BNAs. To fill these gaps, we propose a supervised multi-topology network cross-diffusion (SM-netFusion) framework for estimating a BNA satisfying : (i) well-representativeness (captures shared traits across subjects), (ii) well-centeredness (optimally close to all subjects), and (iii) high discriminativeness (can easily and efficiently identify discriminative brain connections that distinguish between two populations). For a specific class, given the cluster labels of the training data, we learn a weighted combination of the topological diffusion kernels derived from degree, closeness and eigenvector centrality measures in a supervised manner. Specifically, we learn the cross-diffusion process by normalizing the training brain networks using the learned diffusion kernels. Our SM-netFusion produces the most centered and representative template in comparison with its variants and state-of-the-art methods and further boosted the classification of autistic subjects by 5-15%. SM-netFusion presents the first work for supervised network cross-diffusion based on graph topological measures, which can be further leveraged to design an efficient graph feature selection method for training predictive learners in network neuroscience.