--Recent advancements in Graph Contrastive Learning (GCL) have demonstrated remarkable effectiveness in improving graph representations. However, relying on predefined augmentations (e.g., node dropping, edge perturbation, attribute masking) may result in the loss of task-relevant information and a lack of adaptability to diverse input data. Furthermore, the selection of negative samples remains rarely explored. In this paper, we introduce HyperGCL, a novel multimodal GCL framework from a hypergraph perspective. HyperGCL constructs three distinct hypergraph views by jointly utilizing the input graph's structure and attributes, enabling a comprehensive integration of multiple modalities in contrastive learning. A learnable adaptive topology augmentation technique enhances these views by preserving important relations and filtering out noise. View-specific encoders capture essential characteristics from each view, while a network-aware contrastive loss leverages the underlying topology to define positive and negative samples effectively. Extensive experiments on benchmark datasets demonstrate that HyperGCL achieves state-of-the-art node classification performance. Building on the success of contrastive learning (CL) in computer vision and natural language processing [1], [2], CL approaches have been extended to graph data--known as Graph Contrastive Learning (GCL)--where Graph Neural Networks (GNNs) learn robust representations by maximizing agreement between augmented graph views [3]-[6]. First, they often depend on handcrafted augmentations such as node dropping, edge perturbation, and attribute masking.

Resting-state functional magnetic resonance imaging (rs-fMRI) offers valuable insights into the human brain's functional organization and is a powerful tool for investigating the relationship between brain function and cognitive processes, as it allows for the functional organization of the brain to be captured without relying on a specific task or stimuli. In this study, we introduce a novel attention mechanism for graphs with subnetworks, named Self-Clustering Graph Transformer (SCGT), designed to handle the issue of uniform node updates in graph transformers. By using static functional connectivity (FC) correlation features as input to the transformer model, SCGT effectively captures the sub-network structure of the brain by performing cluster-specific updates to the nodes, unlike uniform node updates in vanilla graph transformers, further allowing us to learn and interpret the subclusters. We validate our approach on the Adolescent Brain Cognitive Development (ABCD) dataset, comprising 7,957 participants, for the prediction of total cognitive score and gender classification. Our results demonstrate that SCGT outperforms the vanilla graph transformer method and other recent models, offering a promising tool for modeling brain functional connectivity and interpreting the underlying subnetwork structures.

Graph Neural Network (GNN) achieves great success for node-level and graph-level tasks via encoding meaningful topological structures of networks in various domains, ranging from social to biological networks. However, repeated aggregation operations lead to excessive mixing of node representations, particularly in dense regions with multiple GNN layers, resulting in nearly indistinguishable embeddings. This phenomenon leads to the oversmoothing problem that hampers downstream graph analytics tasks. To overcome this issue, we propose a novel and flexible truss-based graph sparsification model that prunes edges from dense regions of the graph. Pruning redundant edges in dense regions helps to prevent the aggregation of excessive neighborhood information during hierarchical message passing and pooling in GNN models. We then utilize our sparsification model in the state-of-the-art baseline GNNs and pooling models, such as GIN, SAGPool, GMT, DiffPool, MinCutPool, HGP-SL, DMonPool, and AdamGNN. Extensive experiments on different real-world datasets show that our model significantly improves the performance of the baseline GNN models in the graph classification task.

Resting-state functional magnetic resonance imaging (rs-fMRI) is a noninvasive technique pivotal for understanding human neural mechanisms of intricate cognitive processes. Most rs-fMRI studies compute a single static functional connectivity matrix across brain regions of interest, or dynamic functional connectivity matrices with a sliding window approach. These approaches are at risk of oversimplifying brain dynamics and lack proper consideration of the goal at hand. While deep learning has gained substantial popularity for modeling complex relational data, its application to uncovering the spatiotemporal dynamics of the brain is still limited. We propose a novel interpretable deep learning framework that learns goal-specific functional connectivity matrix directly from time series and employs a specialized graph neural network for the final classification. Our model, DSAM, leverages temporal causal convolutional networks to capture the temporal dynamics in both low- and high-level feature representations, a temporal attention unit to identify important time points, a self-attention unit to construct the goal-specific connectivity matrix, and a novel variant of graph neural network to capture the spatial dynamics for downstream classification. To validate our approach, we conducted experiments on the Human Connectome Project dataset with 1075 samples to build and interpret the model for the classification of sex group, and the Adolescent Brain Cognitive Development Dataset with 8520 samples for independent testing. Compared our proposed framework with other state-of-art models, results suggested this novel approach goes beyond the assumption of a fixed connectivity matrix and provides evidence of goal-specific brain connectivity patterns, which opens up the potential to gain deeper insights into how the human brain adapts its functional connectivity specific to the task at hand.

Modeling the interactions between drugs, targets, and diseases is paramount in drug discovery and has significant implications for precision medicine and personalized treatments. Current approaches frequently consider drug-target or drug-disease interactions individually, ignoring the interdependencies among all three entities. Within human metabolic systems, drugs interact with protein targets in cells, influencing target activities and subsequently impacting biological pathways to promote healthy functions and treat diseases. Moving beyond binary relationships and exploring tighter triple relationships is essential to understanding drugs' mechanism of action (MoAs). Moreover, identifying the heterogeneity of drugs, targets, and diseases, along with their distinct characteristics, is critical to model these complex interactions appropriately. To address these challenges, we effectively model the interconnectedness of all entities in a heterogeneous graph and develop a novel Heterogeneous Graph Triplet Attention Network (\texttt{HeTriNet}). \texttt{HeTriNet} introduces a novel triplet attention mechanism within this heterogeneous graph structure. Beyond pairwise attention as the importance of an entity for the other one, we define triplet attention to model the importance of pairs for entities in the drug-target-disease triplet prediction problem. Experimental results on real-world datasets show that \texttt{HeTriNet} outperforms several baselines, demonstrating its remarkable proficiency in uncovering novel drug-target-disease relationships.

Resting-state functional magnetic resonance imaging (rsfMRI) is a powerful tool for investigating the relationship between brain function and cognitive processes as it allows for the functional organization of the brain to be captured without relying on a specific task or stimuli. In this paper, we present a novel modeling architecture called BrainRGIN for predicting intelligence (fluid, crystallized, and total intelligence) using graph neural networks on rsfMRI derived static functional network connectivity matrices. Extending from the existing graph convolution networks, our approach incorporates a clustering-based embedding and graph isomorphism network in the graph convolutional layer to reflect the nature of the brain sub-network organization and efficient network expression, in combination with TopK pooling and attention-based readout functions. We evaluated our proposed architecture on a large dataset, specifically the Adolescent Brain Cognitive Development Dataset, and demonstrated its effectiveness in predicting individual differences in intelligence. Our model achieved lower mean squared errors and higher correlation scores than existing relevant graph architectures and other traditional machine learning models for all of the intelligence prediction tasks. The middle frontal gyrus exhibited a significant contribution to both fluid and crystallized intelligence, suggesting their pivotal role in these cognitive processes. Total composite scores identified a diverse set of brain regions to be relevant which underscores the complex nature of total intelligence.

Hypergraphs, with their capacity to depict high-order relationships, have emerged as a significant extension of traditional graphs. Although Graph Neural Networks (GNNs) have remarkable performance in graph representation learning, their extension to hypergraphs encounters challenges due to their intricate structures. Furthermore, current hypergraph transformers, a special variant of GNN, utilize semantic feature-based self-attention, ignoring topological attributes of nodes and hyperedges. To address these challenges, we propose a Topology-guided Hypergraph Transformer Network (THTN). In this model, we first formulate a hypergraph from a graph while retaining its structural essence to learn higher-order relations within the graph. Then, we design a simple yet effective structural and spatial encoding module to incorporate the topological and spatial information of the nodes into their representation. Further, we present a structure-aware self-attention mechanism that discovers the important nodes and hyperedges from both semantic and structural viewpoints. By leveraging these two modules, THTN crafts an improved node representation, capturing both local and global topological expressions. Extensive experiments conducted on node classification tasks demonstrate that the performance of the proposed model consistently exceeds that of the existing approaches.

Sequence classification has a wide range of real-world applications in different domains, such as genome classification in health and anomaly detection in business. However, the lack of explicit features in sequence data makes it difficult for machine learning models. While Neural Network (NN) models address this with learning features automatically, they are limited to capturing adjacent structural connections and ignore global, higher-order information between the sequences. To address these challenges in the sequence classification problems, we propose a novel Hypergraph Attention Network model, namely Seq-HyGAN. To capture the complex structural similarity between sequence data, we first create a hypergraph where the sequences are depicted as hyperedges and subsequences extracted from sequences are depicted as nodes. Additionally, we introduce an attention-based Hypergraph Neural Network model that utilizes a two-level attention mechanism. This model generates a sequence representation as a hyperedge while simultaneously learning the crucial subsequences for each sequence. We conduct extensive experiments on four data sets to assess and compare our model with several state-of-the-art methods. Experimental results demonstrate that our proposed Seq-HyGAN model can effectively classify sequence data and significantly outperform the baselines. We also conduct case studies to investigate the contribution of each module in Seq-HyGAN.

Drug-Drug Interactions (DDIs) may hamper the functionalities of drugs, and in the worst scenario, they may lead to adverse drug reactions (ADRs). Predicting all DDIs is a challenging and critical problem. Most existing computational models integrate drug-centric information from different sources and leverage them as features in machine learning classifiers to predict DDIs. However, these models have a high chance of failure, especially for the new drugs when all the information is not available. This paper proposes a novel Hypergraph Neural Network (HyGNN) model based on only the SMILES string of drugs, available for any drug, for the DDI prediction problem. To capture the drug similarities, we create a hypergraph from drugs' chemical substructures extracted from the SMILES strings. Then, we develop HyGNN consisting of a novel attention-based hypergraph edge encoder to get the representation of drugs as hyperedges and a decoder to predict the interactions between drug pairs. Furthermore, we conduct extensive experiments to evaluate our model and compare it with several state-of-the-art methods. Experimental results demonstrate that our proposed HyGNN model effectively predicts DDIs and impressively outperforms the baselines with a maximum ROC-AUC and PR-AUC of 97.9% and 98.1%, respectively.

Graph Neural networks (GNNs) have recently become a powerful technique for many graph-related tasks including graph classification. Current GNN models apply different graph pooling methods that reduce the number of nodes and edges to learn the higher-order structure of the graph in a hierarchical way. All these methods primarily rely on the one-hop neighborhood. However, they do not consider the higherorder structure of the graph. In this work, we propose a multi-channel Motif-based Graph Pooling method named (MPool) that captures the higher-order graph structure with motif and also local and global graph structure with a combination of selection and clustering-based pooling operation. As the first channel, we develop node selection-based graph pooling by designing a node ranking model considering the motif adjacency of nodes. As the second channel, we develop cluster-based graph pooling by designing a spectral clustering model using motif adjacency. As the final layer, the result of each channel is aggregated into the final graph representation. We perform extensive experiments on eight benchmark datasets and show that our proposed method shows better accuracy than the baseline methods for graph classification tasks.