Understanding communication and information processing among brain regions of interest (ROIs) is highly dependent on long-range connectivity, which plays a crucial role in facilitating diverse functional neural integration across the entire brain. However, previous studies generally focused on the short-range dependencies within brain networks while neglecting the long-range dependencies, limiting an integrated understanding of brain-wide communication. To address this limitation, we propose Adaptive Long-range aware TransformER (ALTER), a brain graph transformer to capture long-range dependencies between brain ROIs utilizing biased random walk. Specifically, we present a novel long-range aware strategy to explicitly capture long-range dependencies between brain ROIs. By guiding the walker towards the next hop with higher correlation value, our strategy simulates the real-world brain-wide communication. Furthermore, by employing the transformer framework, ALERT adaptively integrates both short-and long-range dependencies between brain ROIs, enabling an integrated understanding of multi-level communication across the entire brain. Extensive experiments on ABIDE and ADNI datasets demonstrate that ALTER consistently outperforms generalized state-of-the-art graph learning methods (including SAN, Graphormer, GraphTrans, and LRGNN) and other graph learning based brain network analysis methods (including FBNETGEN, BrainNetGNN, BrainGNN, and BrainNETTF) in neurological disease diagnosis.

Graph neural networks (GNNs) are widely used for modelling graph-structured data in numerous applications. However, with their inherently finite aggregation layers, existing GNN models may not be able to effectively capture long-range dependencies in the underlying graphs. Motivated by this limitation, we propose a GNN model with infinite depth, which we call Efficient Infinite-Depth Graph Neural Networks (EIGNN), to efficiently capture very long-range dependencies. We theoretically derive a closed-form solution of EIGNN which makes training an infinite-depth GNN model tractable. We then further show that we can achieve more efficient computation for training EIGNN by using eigendecomposition. The empirical results of comprehensive experiments on synthetic and real-world datasets show that EIGNN has a better ability to capture long-range dependencies than recent baselines, and consistently achieves state-of-the-art performance. Furthermore, we show that our model is also more robust against both noise and adversarial perturbations on node features.

Graph Neural Networks (GNNs) are widely used deep learning models that learn meaningful representations from graph-structured data. Due to the finite nature of the underlying recurrent structure, current GNN methods may struggle to capture long-range dependencies in underlying graphs. To overcome this difficulty, we propose a graph learning framework, called Implicit Graph Neural Networks (IGNN), where predictions are based on the solution of a fixed-point equilibrium equation involving implicitly defined state vectors. We use the Perron-Frobenius theory to derive sufficient conditions that ensure well-posedness of the framework. Leveraging implicit differentiation, we derive a tractable projected gradient descent method to train the framework. Experiments on a comprehensive range of tasks show that IGNNs consistently capture long-range dependencies and outperform state-of-the-art GNN models.

Hypergraphs offer a generalized framework for capturing high-order relationships between entities and have been widely applied in various domains, including healthcare, social networks, and bioinformatics. Hypergraph neural networks, which rely on message-passing between nodes over hyperedges to learn latent representations, have emerged as the method of choice for predictive tasks in many of these domains. These approaches typically perform only a small number of message-passing rounds to learn the representations, which they then utilize for predictions. The small number of message-passing rounds comes at a cost, as the representations only capture local information and forego long-range high-order dependencies. However, as we demonstrate, blindly increasing the message-passing rounds to capture long-range dependency also degrades the performance of hyper-graph neural networks. Recent works have demonstrated that implicit graph neural networks capture long-range dependencies in standard graphs while maintaining performance. Despite their popularity, prior work has not studied long-range dependency issues on hypergraph neural networks. Here, we first demonstrate that existing hypergraph neural networks lose predictive power when aggregating more information to capture long-range dependency. We then propose Implicit Hypergraph Neural Network (IHNN), a novel framework that jointly learns fixed-point representations for both nodes and hyperedges in an end-to-end manner to alleviate this issue. Leveraging implicit differentiation, we introduce a tractable projected gradient descent approach to train the model efficiently. Extensive experiments on real-world hypergraphs for node classification demonstrate that IHNN outperforms the closest prior works in most settings, establishing a new state-of-the-art in hypergraph learning.

We conducted extensive experiments on the Waymo Open and nuScenes datasets.

In the field of multi-organ medical image segmentation, recent methods frequently employ Transformers to capture long-range dependencies from image features. However, these methods overlook the high computational cost of Transformers and their deficiencies in extracting local detailed information. To address high computational costs and inadequate local detail information, we reassess the design of feature extraction modules and propose a new deep-learning network called LamFormer for fine-grained segmentation tasks across multiple organs. LamFormer is a novel U-shaped network that employs Linear Attention Mamba (LAM) in an enhanced pyramid encoder to capture multi-scale long-range dependencies. We construct the Parallel Hierarchical Feature Aggregation (PHFA) module to aggregate features from different layers of the encoder, narrowing the semantic gap among features while filtering information. Finally, we design the Reduced Transformer (RT), which utilizes a distinct computational approach to globally model up-sampled features. RRT enhances the extraction of detailed local information and improves the network's capability to capture long-range dependencies. LamFormer outperforms existing segmentation methods on seven complex and diverse datasets, demonstrating exceptional performance. Moreover, the proposed network achieves a balance between model performance and model complexity.

To achieve this, most modern GNNs follow a "message passing" mechanism: at