Link prediction (LP) is a fundamental task in graph representation learning, with numerous applications in diverse domains. However, the generalizability of LP models is often compromised due to the presence of noisy or spurious information in graphs and the inherent incompleteness of graph data. To address these challenges, we draw inspiration from the Information Bottleneck principle and propose a novel data augmentation method, COmplete and REduce (CORE) to learn compact and predictive augmentations for LP models. In particular, CORE aims to recover missing edges in graphs while simultaneously removing noise from the graph structures, thereby enhancing the model's robustness and performance. Extensive experiments on multiple benchmark datasets demonstrate the applicability and superiority of CORE over state-of-the-art methods, showcasing its potential as a leading approach for robust LP in graph representation learning.
The discovery of drug-target interactions (DTIs) plays a crucial role in pharmaceutical development. The deep learning model achieves more accurate results in DTI prediction due to its ability to extract robust and expressive features from drug and target chemical structures. However, existing deep learning methods typically generate drug features via aggregating molecular atom representations, ignoring the chemical properties carried by motifs, i.e., substructures of the molecular graph. The atom-drug double-level molecular representation learning can not fully exploit structure information and fails to interpret the DTI mechanism from the motif perspective. In addition, sequential model-based target feature extraction either fuses limited contextual information or requires expensive computational resources. To tackle the above issues, we propose a hierarchical graph representation learning-based DTI prediction method (HiGraphDTI). Specifically, HiGraphDTI learns hierarchical drug representations from triple-level molecular graphs to thoroughly exploit chemical information embedded in atoms, motifs, and molecules. Then, an attentional feature fusion module incorporates information from different receptive fields to extract expressive target features.Last, the hierarchical attention mechanism identifies crucial molecular segments, which offers complementary views for interpreting interaction mechanisms. The experiment results not only demonstrate the superiority of HiGraphDTI to the state-of-the-art methods, but also confirm the practical ability of our model in interaction interpretation and new DTI discovery.
We propose a graph-based representation learning framework for video summarization. First, we convert an input video to a graph where nodes correspond to each of the video frames. Then, we impose sparsity on the graph by connecting only those pairs of nodes that are within a specified temporal distance. We then formulate the video summarization task as a binary node classification problem, precisely classifying video frames whether they should belong to the output summary video. A graph constructed this way aims to capture long-range interactions among video frames, and the sparsity ensures the model trains without hitting the memory and compute bottleneck. Experiments on two datasets(SumMe and TVSum) demonstrate the effectiveness of the proposed nimble model compared to existing state-of-the-art summarization approaches while being one order of magnitude more efficient in compute time and memory
Message passing has become the dominant framework in graph representation learning. The essential idea of the message-passing framework is to update node embeddings based on the information aggregated from local neighbours. However, most existing aggregation methods have not encoded neighbour-level message interactions into the aggregated message, resulting in an information lost in embedding generation. And this information lost could be accumulated and become more serious as more layers are added to the graph network model. To address this issue, we propose a neighbour-level message interaction information encoding method for improving graph representation learning. For messages that are aggregated at a node, we explicitly generate an encoding between each message and the rest messages using an encoding function. Then we aggregate these learned encodings and take the sum of the aggregated encoding and the aggregated message to update the embedding for the node. By this way, neighbour-level message interaction information is integrated into the generated node embeddings. The proposed encoding method is a generic method which can be integrated into message-passing graph convolutional networks. Extensive experiments are conducted on six popular benchmark datasets across four highly-demanded tasks. The results show that integrating neighbour-level message interactions achieves improved performance of the base models, advancing the state of the art results for representation learning over graphs.
Studies continually find that message-passing graph convolutional networks suffer from the over-smoothing issue. Basically, the issue of over-smoothing refers to the phenomenon that the learned embeddings for all nodes can become very similar to one another and therefore are uninformative after repeatedly applying message passing iterations. Intuitively, we can expect the generated embeddings become smooth asymptotically layerwisely, that is each layer of graph convolution generates a smoothed version of embeddings as compared to that generated by the previous layer. Based on this intuition, we propose RandAlign, a stochastic regularization method for graph convolutional networks. The idea of RandAlign is to randomly align the learned embedding for each node with that of the previous layer using randomly interpolation in each graph convolution layer. Through alignment, the smoothness of the generated embeddings is explicitly reduced. To better maintain the benefit yielded by the graph convolution, in the alignment step we introduce to first scale the embedding of the previous layer to the same norm as the generated embedding and then perform random interpolation for aligning the generated embedding. RandAlign is a parameter-free method and can be directly applied without introducing additional trainable weights or hyper-parameters. We experimentally evaluate RandAlign on different graph domain tasks on seven benchmark datasets. The experimental results show that RandAlign is a general method that improves the generalization performance of various graph convolutional network models and also improves the numerical stability of optimization, advancing the state of the art performance for graph representation learning.
In the domain of dynamic graph representation learning (DGRL), the efficient and comprehensive capture of temporal evolution within real-world networks is crucial. Spiking Neural Networks (SNNs), known as their temporal dynamics and low-power characteristic, offer an efficient solution for temporal processing in DGRL task. However, owing to the spike-based information encoding mechanism of SNNs, existing DGRL methods employed SNNs face limitations in their representational capacity. Given this issue, we propose a novel framework named Spike-induced Graph Neural Network (SiGNN) for learning enhanced spatialtemporal representations on dynamic graphs. In detail, a harmonious integration of SNNs and GNNs is achieved through an innovative Temporal Activation (TA) mechanism. Benefiting from the TA mechanism, SiGNN not only effectively exploits the temporal dynamics of SNNs but also adeptly circumvents the representational constraints imposed by the binary nature of spikes. Furthermore, leveraging the inherent adaptability of SNNs, we explore an in-depth analysis of the evolutionary patterns within dynamic graphs across multiple time granularities. This approach facilitates the acquisition of a multiscale temporal node representation.Extensive experiments on various real-world dynamic graph datasets demonstrate the superior performance of SiGNN in the node classification task.
This paper investigates a link between Graph Neural Networks (GNNs) and Binary Programming (BP) problems, laying the groundwork for GNNs to approximate solutions for these computationally challenging problems. By analyzing the sensitivity of BP problems, we are able to frame the solution of BP problems as a heterophilic node classification task. We then propose Binary-Programming GNN (BPGNN), an architecture that integrates graph representation learning techniques with BP-aware features to approximate BP solutions efficiently. Additionally, we introduce a self-supervised data generation mechanism, to enable efficient and tractable training data acquisition even for large-scale BP problems. Experimental evaluations of BPGNN across diverse BP problem sizes showcase its superior performance compared to exhaustive search and heuristic approaches. Finally, we discuss open challenges in the under-explored field of BP problems with GNNs.
We explore the adoption of graph representation learning (GRL) algorithms to investigate similarities across services offered by Decentralized Finance (DeFi) protocols. Following existing literature, we use Ethereum transaction data to identify the DeFi building blocks. These are sets of protocol-specific smart contracts that are utilized in combination within single transactions and encapsulate the logic to conduct specific financial services such as swapping or lending cryptoassets. We propose a method to categorize these blocks into clusters based on their smart contract attributes and the graph structure of their smart contract calls. We employ GRL to create embedding vectors from building blocks and agglomerative models for clustering them. To evaluate whether they are effectively grouped in clusters of similar functionalities, we associate them with eight financial functionality categories and use this information as the target label. We find that in the best-case scenario purity reaches .888. We use additional information to associate the building blocks with protocol-specific target labels, obtaining comparable purity (.864) but higher V-Measure (.571); we discuss plausible explanations for this difference. In summary, this method helps categorize existing financial products offered by DeFi protocols, and can effectively automatize the detection of similar DeFi services, especially within protocols.
Heterogeneous graphs are ubiquitous in real-world applications because they can represent various relationships between different types of entities. Therefore, learning embeddings in such graphs is a critical problem in graph machine learning. However, existing solutions for this problem fail to scale to large heterogeneous graphs due to their high computational complexity. To address this issue, we propose a Multi-Level Embedding framework of nodes on a heterogeneous graph (HeteroMILE) - a generic methodology that allows contemporary graph embedding methods to scale to large graphs. HeteroMILE repeatedly coarsens the large sized graph into a smaller size while preserving the backbone structure of the graph before embedding it, effectively reducing the computational cost by avoiding time-consuming processing operations. It then refines the coarsened embedding to the original graph using a heterogeneous graph convolution neural network. We evaluate our approach using several popular heterogeneous graph datasets. The experimental results show that HeteroMILE can substantially reduce computational time (approximately 20x speedup) and generate an embedding of better quality for link prediction and node classification.
Multimodal recommender systems work by augmenting the representation of the products in the catalogue through multimodal features extracted from images, textual descriptions, or audio tracks characterising such products. Nevertheless, in real-world applications, only a limited percentage of products come with multimodal content to extract meaningful features from, making it hard to provide accurate recommendations. To the best of our knowledge, very few attention has been put into the problem of missing modalities in multimodal recommendation so far. To this end, our paper comes as a preliminary attempt to formalise and address such an issue. Inspired by the recent advances in graph representation learning, we propose to re-sketch the missing modalities problem as a problem of missing graph node features to apply the state-of-the-art feature propagation algorithm eventually. Technically, we first project the user-item graph into an item-item one based on co-interactions. Then, leveraging the multimodal similarities among co-interacted items, we apply a modified version of the feature propagation technique to impute the missing multimodal features. Adopted as a pre-processing stage for two recent multimodal recommender systems, our simple approach performs better than other shallower solutions on three popular datasets.
Graph representation learning has rapidly emerged as a pivotal field of study. Despite its growing popularity, the majority of research has been confined to embedding single-layer graphs, which fall short in representing complex systems with multifaceted relationships. To bridge this gap, we introduce MPXGAT, an innovative attention-based deep learning model tailored to multiplex graph embedding. Leveraging the robustness of Graph Attention Networks (GATs), MPXGAT captures the structure of multiplex networks by harnessing both intra-layer and inter-layer connections. This exploitation facilitates accurate link prediction within and across the network's multiple layers. Our comprehensive experimental evaluation, conducted on various benchmark datasets, confirms that MPXGAT consistently outperforms state-of-the-art competing algorithms.
Graph representation learning is a fundamental research issue in various domains of applications, of which the inductive learning problem is particularly challenging as it requires models to generalize to unseen graph structures during inference. In recent years, graph neural networks (GNNs) have emerged as powerful graph models for inductive learning tasks such as node classification, whereas they typically heavily rely on the annotated nodes under a fully supervised training setting. Compared with the GNN-based methods, variational graph auto-encoders (VGAEs) are known to be more generalizable to capture the internal structural information of graphs independent of node labels and have achieved prominent performance on multiple unsupervised learning tasks. However, so far there is still a lack of work focusing on leveraging the VGAE framework for inductive learning, due to the difficulties in training the model in a supervised manner and avoiding over-fitting the proximity information of graphs. To solve these problems and improve the model performance of VGAEs for inductive graph representation learning, in this work, we propose the Self-Label Augmented VGAE model. To leverage the label information for training, our model takes node labels as one-hot encoded inputs and then performs label reconstruction in model training. To overcome the scarcity problem of node labels for semi-supervised settings, we further propose the Self-Label Augmentation Method (SLAM), which uses pseudo labels generated by our model with a node-wise masking approach to enhance the label information. Experiments on benchmark inductive learning graph datasets verify that our proposed model archives promising results on node classification with particular superiority under semi-supervised learning settings.
Graph representation learning has become a crucial task in machine learning and data mining due to its potential for modeling complex structures such as social networks, chemical compounds, and biological systems. Spiking neural networks (SNNs) have recently emerged as a promising alternative to traditional neural networks for graph learning tasks, benefiting from their ability to efficiently encode and process temporal and spatial information. In this paper, we propose a novel approach that integrates attention mechanisms with SNNs to improve graph representation learning. Specifically, we introduce an attention mechanism for SNN that can selectively focus on important nodes and corresponding features in a graph during the learning process. We evaluate our proposed method on several benchmark datasets and show that it achieves comparable performance compared to existing graph learning techniques.
Graph Neural Networks (GNNs) have emerged as the most powerful weapon for various graph tasks due to the message-passing mechanism's great local information aggregation ability. However, over-smoothing has always hindered GNNs from going deeper and capturing multi-hop neighbors. Unlike GNNs, Transformers can model global information and multi-hop interactions via multi-head self-attention and a proper Transformer structure can show more immunity to the over-smoothing problem. So, can we propose a novel framework to combine GNN and Transformer, integrating both GNN's local information aggregation and Transformer's global information modeling ability to eliminate the over-smoothing problem? To realize this, this paper proposes a collaborative learning scheme for GNN-Transformer and constructs GTC architecture. GTC leverages the GNN and Transformer branch to encode node information from different views respectively, and establishes contrastive learning tasks based on the encoded cross-view information to realize self-supervised heterogeneous graph representation. For the Transformer branch, we propose Metapath-aware Hop2Token and CG-Hetphormer, which can cooperate with GNN to attentively encode neighborhood information from different levels. As far as we know, this is the first attempt in the field of graph representation learning to utilize both GNN and Transformer to collaboratively capture different view information and conduct cross-view contrastive learning. The experiments on real datasets show that GTC exhibits superior performance compared with state-of-the-art methods. Codes can be available at https://github.com/PHD-lanyu/GTC.
Graph neural networks have achieved remarkable success in learning graph representations, especially graph Transformer, which has recently shown superior performance on various graph mining tasks. However, graph Transformer generally treats nodes as tokens, which results in quadratic complexity regarding the number of nodes during self-attention computation. The graph MLP Mixer addresses this challenge by using the efficient MLP Mixer technique from computer vision. However, the time-consuming process of extracting graph tokens limits its performance. In this paper, we present a novel architecture named ChebMixer, a newly graph MLP Mixer that uses fast Chebyshev polynomials-based spectral filtering to extract a sequence of tokens. Firstly, we produce multiscale representations of graph nodes via fast Chebyshev polynomial-based spectral filtering. Next, we consider each node's multiscale representations as a sequence of tokens and refine the node representation with an effective MLP Mixer. Finally, we aggregate the multiscale representations of nodes through Chebyshev interpolation. Owing to the powerful representation capabilities and fast computational properties of MLP Mixer, we can quickly extract more informative node representations to improve the performance of downstream tasks. The experimental results prove our significant improvements in a variety of scenarios ranging from graph node classification to medical image segmentation.
Resource allocation in tactical ad-hoc networks presents unique challenges due to their dynamic and multi-hop nature. Accurate prediction of future network connectivity is essential for effective resource allocation in such environments. In this paper, we introduce the Spatial-Temporal Graph Encoder-Decoder (STGED) framework for Tactical Communication Networks that leverages both spatial and temporal features of network states to learn latent tactical behaviors effectively. STGED hierarchically utilizes graph-based attention mechanism to spatially encode a series of communication network states, leverages a recurrent neural network to temporally encode the evolution of states, and a fully-connected feed-forward network to decode the connectivity in the future state. Through extensive experiments, we demonstrate that STGED consistently outperforms baseline models by large margins across different time-steps input, achieving an accuracy of up to 99.2\% for the future state prediction task of tactical communication networks.
Graphs are ubiquitous in real-world scenarios and encompass a diverse range of tasks, from node-, edge-, and graph-level tasks to transfer learning. However, designing specific tasks for each type of graph data is often costly and lacks generalizability. Recent endeavors under the "Pre-training + Fine-tuning" or "Pre-training + Prompt" paradigms aim to design a unified framework capable of generalizing across multiple graph tasks. Among these, graph autoencoders (GAEs), generative self-supervised models, have demonstrated their potential in effectively addressing various graph tasks. Nevertheless, these methods typically employ multi-stage training and require adaptive designs, which on one hand make it difficult to be seamlessly applied to diverse graph tasks and on the other hand overlook the negative impact caused by discrepancies in task objectives between the different stages. To address these challenges, we propose GA^2E, a unified adversarially masked autoencoder capable of addressing the above challenges seamlessly. Specifically, GA^2E proposes to use the subgraph as the meta-structure, which remains consistent across all graph tasks (ranging from node-, edge-, and graph-level to transfer learning) and all stages (both during training and inference). Further, GA^2E operates in a \textbf{"Generate then Discriminate"} manner. It leverages the masked GAE to reconstruct the input subgraph whilst treating it as a generator to compel the reconstructed graphs resemble the input subgraph. Furthermore, GA^2E introduces an auxiliary discriminator to discern the authenticity between the reconstructed (generated) subgraph and the input subgraph, thus ensuring the robustness of the graph representation through adversarial training mechanisms. We validate GA^2E's capabilities through extensive experiments on 21 datasets across four types of graph tasks.
Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).
Graph Neural Networks (GNNs) have garnered widespread attention for their potential to address the challenges posed by graph representation learning, which face complex graph-structured data across various domains. However, due to the inherent complexity and interconnectedness of graphs, accurately annotating graph data for training GNNs is extremely challenging. To address this issue, we have introduced Partial Label Learning (PLL) into graph representation learning. PLL is a critical weakly supervised learning problem where each training instance is associated with a set of candidate labels, including the ground-truth label and the additional interfering labels. PLL allows annotators to make errors, which reduces the difficulty of data labeling. Subsequently, we propose a novel graph representation learning method that enables GNN models to effectively learn discriminative information within the context of PLL. Our approach utilizes potential cause extraction to obtain graph data that holds causal relationships with the labels. By conducting auxiliary training based on the extracted graph data, our model can effectively eliminate the interfering information in the PLL scenario. We support the rationale behind our method with a series of theoretical analyses. Moreover, we conduct extensive evaluations and ablation studies on multiple datasets, demonstrating the superiority of our proposed method.
Over the last few years, various multi-view graph clustering methods have shown promising performances. However, we argue that these methods can have limitations. In particular, they are often unnecessarily complex, leading to scalability problems that make them prohibitive for most real-world graph applications. Furthermore, many of them can handle only specific types of multi-view graphs. Another limitation is that the process of learning graph representations is separated from the clustering process, and in some cases these methods do not even learn a graph representation, which severely restricts their flexibility and usefulness. In this paper we propose a simple yet effective linear model that addresses the dual tasks of multi-view attributed graph representation learning and clustering in a unified framework. The model starts by performing a first-order neighborhood smoothing step for the different individual views, then gives each one a weight corresponding to its importance. Finally, an iterative process of simultaneous clustering and representation learning is performed w.r.t. the importance of each view, yielding a consensus embedding and partition of the graph. Our model is generic and can deal with any type of multi-view graph. Finally, we show through extensive experimentation that this simple model consistently achieves competitive performances w.r.t. state-of-the-art multi-view attributed graph clustering models, while at the same time having training times that are shorter, in some cases by orders of magnitude.