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Register a new userBrain Multigraph Prediction using Topology-Aware Adversarial Graph Neural Network
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Islem Rekik
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Brain graphs (i.e, connectomes) constructed from medical scans such as magnetic resonance imaging (MRI) have become increasingly important tools to characterize the abnormal changes in the human brain. Due to the high acquisition cost and processing time of multimodal MRI, existing deep learning frameworks based on Generative Adversarial Network (GAN) focused on predicting the missing multimodal medical images from a few existing modalities. While brain graphs help better understand how a particular disorder can change the connectional facets of the brain, synthesizing a target brain multigraph (i.e, multiple brain graphs) from a single source brain graph is strikingly lacking. Additionally, existing graph generation works mainly learn one model for each target domain which limits their scalability in jointly predicting multiple target domains. Besides, while they consider the global topological scale of a graph (i.e., graph connectivity structure), they overlook the local topology at the node scale (e.g., how central a node is in the graph). To address these limitations, we introduce topology-aware graph GAN architecture (topoGAN), which jointly predicts multiple brain graphs from a single brain graph while preserving the topological structure of each target graph. Its three key innovations are: (i) designing a novel graph adversarial auto-encoder for predicting multiple brain graphs from a single one, (ii) clustering the encoded source graphs in order to handle the mode collapse issue of GAN and proposing a cluster-specific decoder, (iii) introducing a topological loss to force the prediction of topologically sound target brain graphs. The experimental results using five target domains demonstrated the outperformance of our method in brain multigraph prediction from a single graph in comparison with baseline approaches.
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Several works based on Generative Adversarial Networks (GAN) have been recently proposed to predict a set of medical images from a single modality (e.g, FLAIR MRI from T1 MRI). However, such frameworks are primarily designed to operate on images, limiting their generalizability to non-Euclidean geometric data such as brain graphs. While a growing number of connectomic studies has demonstrated the promise of including brain graphs for diagnosing neurological disorders, no geometric deep learning work was designed for multiple target brain graphs prediction from a source brain graph. Despite the momentum the field of graph generation has gained in the last two years, existing works have two critical drawbacks. First, the bulk of such works aims to learn one model for each target domain to generate from a source domain. Thus, they have a limited scalability in jointly predicting multiple target domains. Second, they merely consider the global topological scale of a graph (i.e., graph connectivity structure) and overlook the local topology at the node scale of a graph (e.g., how central a node is in the graph). To meet these challenges, we introduce MultiGraphGAN architecture, which not only predicts multiple brain graphs from a single brain graph but also preserves the topological structure of each target graph to predict. Its three core contributions lie in: (i) designing a graph adversarial auto-encoder for jointly predicting brain graphs from a single one, (ii) handling the mode collapse problem of GAN by clustering the encoded source graphs and proposing a cluster-specific decoder, (iii) introducing a topological loss to force the reconstruction of topologically sound target brain graphs. Our MultiGraphGAN significantly outperformed its variants thereby showing its great potential in multi-view brain graph generation from a single graph.
Graph neural networks (GNNs) have witnessed an unprecedented proliferation in tackling several problems in computer vision, computer-aided diagnosis, and related fields. While prior studies have focused on boosting the model accuracy, quantifying the reproducibility of the most discriminative features identified by GNNs is still an intact problem that yields concerns about their reliability in clinical applications in particular. Specifically, the reproducibility of biological markers across clinical datasets and distribution shifts across classes (e.g., healthy and disordered brains) is of paramount importance in revealing the underpinning mechanisms of diseases as well as propelling the development of personalized treatment. Motivated by these issues, we propose, for the first time, reproducibility-based GNN selection (RG-Select), a framework for GNN reproducibility assessment via the quantification of the most discriminative features (i.e., biomarkers) shared between different models. To ascertain the soundness of our framework, the reproducibility assessment embraces variations of different factors such as training strategies and data perturbations. Despite these challenges, our framework successfully yielded replicable conclusions across different training strategies and various clinical datasets. Our findings could thus pave the way for the development of biomarker trustworthiness and reliability assessment methods for computer-aided diagnosis and prognosis tasks. RG-Select code is available on GitHub at https://github.com/basiralab/RG-Select.
With the increasing popularity of graph-based learning, graph neural networks (GNNs) emerge as the essential tool for gaining insights from graphs. However, unlike the conventional CNNs that have been extensively explored and exhaustively tested, people are still worrying about the GNNs robustness under the critical settings, such as financial services. The main reason is that existing GNNs usually serve as a black-box in predicting and do not provide the uncertainty on the predictions. On the other side, the recent advancement of Bayesian deep learning on CNNs has demonstrated its success of quantifying and explaining such uncertainties to fortify CNN models. Motivated by these observations, we propose UAG, the first systematic solution to defend adversarial attacks on GNNs through identifying and exploiting hierarchical uncertainties in GNNs. UAG develops a Bayesian Uncertainty Technique (BUT) to explicitly capture uncertainties in GNNs and further employs an Uncertainty-aware Attention Technique (UAT) to defend adversarial attacks on GNNs. Intensive experiments show that our proposed defense approach outperforms the state-of-the-art solutions by a significant margin.
Brain image analysis has advanced substantially in recent years with the proliferation of neuroimaging datasets acquired at different resolutions. While research on brain image super-resolution has undergone a rapid development in the recent years, brain graph super-resolution is still poorly investigated because of the complex nature of non-Euclidean graph data. In this paper, we propose the first-ever deep graph super-resolution (GSR) framework that attempts to automatically generate high-resolution (HR) brain graphs with N nodes (i.e., anatomical regions of interest (ROIs)) from low-resolution (LR) graphs with N nodes where N < N. First, we formalize our GSR problem as a node feature embedding learning task. Once the HR nodes embeddings are learned, the pairwise connectivity strength between brain ROIs can be derived through an aggregation rule based on a novel Graph U-Net architecture. While typically the Graph U-Net is a node-focused architecture where graph embedding depends mainly on node attributes, we propose a graph-focused architecture where the node feature embedding is based on the graph topology. Second, inspired by graph spectral theory, we break the symmetry of the U-Net architecture by super-resolving the low-resolution brain graph structure and node content with a GSR layer and two graph convolutional network layers to further learn the node embeddings in the HR graph. Third, to handle the domain shift between the ground-truth and the predicted HR brain graphs, we incorporate adversarial regularization to align their respective distributions. Our proposed AGSR-Net framework outperformed its variants for predicting high-resolution functional brain graphs from low-resolution ones. Our AGSR-Net code is available on GitHub at https://github.com/basiralab/AGSR-Net.
Graph neural network (GNN) explanations have largely been facilitated through post-hoc introspection. While this has been deemed successful, many post-hoc explanation methods have been shown to fail in capturing a models learned representation. Due to this problem, it is worthwhile to consider how one might train a model so that it is more amenable to post-hoc analysis. Given the success of adversarial training in the computer vision domain to train models with more reliable representations, we propose a similar training paradigm for GNNs and analyze the respective impact on a models explanations. In instances without ground truth labels, we also determine how well an explanation method is utilizing a models learned representation through a new metric and demonstrate adversarial training can help better extract domain-relevant insights in chemistry.
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