Message Passing Neural Networks (MPNNs) have emerged as the {\em de facto} standard in graph representation learning. However, when it comes to link prediction, they often struggle, surpassed by simple heuristics such as Common Neighbor (CN). This discrepancy stems from a fundamental limitation: while MPNNs excel in node-level representation, they stumble with encoding the joint structural features essential to link prediction, like CN. To bridge this gap, we posit that, by harnessing the orthogonality of input vectors, pure message-passing can indeed capture joint structural features. Specifically, we study the proficiency of MPNNs in approximating CN heuristics. Based on our findings, we introduce the Message Passing Link Predictor (MPLP), a novel link prediction model. MPLP taps into quasi-orthogonal vectors to estimate link-level structural features, all while preserving the node-level complexities. Moreover, our approach demonstrates that leveraging message-passing to capture structural features could offset MPNNs' expressiveness limitations at the expense of estimation variance. We conduct experiments on benchmark datasets from various domains, where our method consistently outperforms the baseline methods.
Accurate acquisition of crowd flow at Points of Interest (POIs) is pivotal for effective traffic management, public service, and urban planning. Despite this importance, due to the limitations of urban sensing techniques, the data quality from most sources is inadequate for monitoring crowd flow at each POI. This renders the inference of accurate crowd flow from low-quality data a critical and challenging task. The complexity is heightened by three key factors: 1) The scarcity and rarity of labeled data, 2) The intricate spatio-temporal dependencies among POIs, and 3) The myriad correlations between precise crowd flow and GPS reports. To address these challenges, we recast the crowd flow inference problem as a self-supervised attributed graph representation learning task and introduce a novel Contrastive Self-learning framework for Spatio-Temporal data (CSST). Our approach initiates with the construction of a spatial adjacency graph founded on the POIs and their respective distances. We then employ a contrastive learning technique to exploit large volumes of unlabeled spatio-temporal data. We adopt a swapped prediction approach to anticipate the representation of the target subgraph from similar instances. Following the pre-training phase, the model is fine-tuned with accurate crowd flow data. Our experiments, conducted on two real-world datasets, demonstrate that the CSST pre-trained on extensive noisy data consistently outperforms models trained from scratch.
Real-world graphs naturally exhibit hierarchical or cyclical structures that are unfit for the typical Euclidean space. While there exist graph neural networks that leverage hyperbolic or spherical spaces to learn representations that embed such structures more accurately, these methods are confined under the message-passing paradigm, making the models vulnerable against side-effects such as oversmoothing and oversquashing. More recent work have proposed global attention-based graph Transformers that can easily model long-range interactions, but their extensions towards non-Euclidean geometry are yet unexplored. To bridge this gap, we propose Fully Product-Stereographic Transformer, a generalization of Transformers towards operating entirely on the product of constant curvature spaces. When combined with tokenized graph Transformers, our model can learn the curvature appropriate for the input graph in an end-to-end fashion, without the need of additional tuning on different curvature initializations. We also provide a kernelized approach to non-Euclidean attention, which enables our model to run in time and memory cost linear to the number of nodes and edges while respecting the underlying geometry. Experiments on graph reconstruction and node classification demonstrate the benefits of generalizing Transformers to the non-Euclidean domain.
Graph contrastive learning (GCL) has recently emerged as a promising approach for graph representation learning. Some existing methods adopt the 1-vs-K scheme to construct one positive and K negative samples for each graph, but it is difficult to set K. For those methods that do not use negative samples, it is often necessary to add additional strategies to avoid model collapse, which could only alleviate the problem to some extent. All these drawbacks will undoubtedly have an adverse impact on the generalizability and efficiency of the model. In this paper, to address these issues, we propose a novel graph self-contrast framework GraphSC, which only uses one positive and one negative sample, and chooses triplet loss as the objective. Specifically, self-contrast has two implications. First, GraphSC generates both positive and negative views of a graph sample from the graph itself via graph augmentation functions of various intensities, and use them for self-contrast. Second, GraphSC uses Hilbert-Schmidt Independence Criterion (HSIC) to factorize the representations into multiple factors and proposes a masked self-contrast mechanism to better separate positive and negative samples. Further, Since the triplet loss only optimizes the relative distance between the anchor and its positive/negative samples, it is difficult to ensure the absolute distance between the anchor and positive sample. Therefore, we explicitly reduced the absolute distance between the anchor and positive sample to accelerate convergence. Finally, we conduct extensive experiments to evaluate the performance of GraphSC against 19 other state-of-the-art methods in both unsupervised and transfer learning settings.
As the basic element of graph-structured data, node has been recognized as the main object of study in graph representation learning. A single node intuitively has multiple node-centered subgraphs from the whole graph (e.g., one person in a social network has multiple social circles based on his different relationships). We study this intuition under the framework of graph contrastive learning, and propose a multiple node-centered subgraphs contrastive representation learning method to learn node representation on graphs in a self-supervised way. Specifically, we carefully design a series of node-centered regional subgraphs of the central node. Then, the mutual information between different subgraphs of the same node is maximized by contrastive loss. Experiments on various real-world datasets and different downstream tasks demonstrate that our model has achieved state-of-the-art results.
Graph representation learning (GRL) has become a prominent tool for furthering the understanding of complex networks providing tools for network embedding, link prediction, and node classification. In this paper, we propose the Hybrid Membership-Latent Distance Model (HM-LDM) by exploring how a Latent Distance Model (LDM) can be constrained to a latent simplex. By controlling the edge lengths of the corners of the simplex, the volume of the latent space can be systematically controlled. Thereby communities are revealed as the space becomes more constrained, with hard memberships being recovered as the simplex volume goes to zero. We further explore a recent likelihood formulation for signed networks utilizing the Skellam distribution to account for signed weighted networks and extend the HM-LDM to the signed Hybrid Membership-Latent Distance Model (sHM-LDM). Importantly, the induced likelihood function explicitly attracts nodes with positive links and deters nodes from having negative interactions. We demonstrate the utility of HM-LDM and sHM-LDM on several real networks. We find that the procedures successfully identify prominent distinct structures, as well as how nodes relate to the extracted aspects providing favorable performances in terms of link prediction when compared to prominent baselines. Furthermore, the learned soft memberships enable easily interpretable network visualizations highlighting distinct patterns.
Graph Neural Networks (GNNs) have emerged as promising solutions for collaborative filtering (CF) through the modeling of user-item interaction graphs. The nucleus of existing GNN-based recommender systems involves recursive message passing along user-item interaction edges to refine encoded embeddings. Despite their demonstrated effectiveness, current GNN-based methods encounter challenges of limited receptive fields and the presence of noisy "interest-irrelevant" connections. In contrast, Transformer-based methods excel in aggregating information adaptively and globally. Nevertheless, their application to large-scale interaction graphs is hindered by inherent complexities and challenges in capturing intricate, entangled structural information. In this paper, we propose TransGNN, a novel model that integrates Transformer and GNN layers in an alternating fashion to mutually enhance their capabilities. Specifically, TransGNN leverages Transformer layers to broaden the receptive field and disentangle information aggregation from edges, which aggregates information from more relevant nodes, thereby enhancing the message passing of GNNs. Additionally, to capture graph structure information effectively, positional encoding is meticulously designed and integrated into GNN layers to encode such structural knowledge into node attributes, thus enhancing the Transformer's performance on graphs. Efficiency considerations are also alleviated by proposing the sampling of the most relevant nodes for the Transformer, along with two efficient sample update strategies to reduce complexity. Furthermore, theoretical analysis demonstrates that TransGNN offers increased expressiveness compared to GNNs, with only a marginal increase in linear complexity. Extensive experiments on five public datasets validate the effectiveness and efficiency of TransGNN.
Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.
Model Checking is widely applied in verifying the correctness of complex and concurrent systems against a specification. Pure symbolic approaches while popular, suffer from the state space explosion problem due to cross product operations required that make them prohibitively expensive for large-scale systems and/or specifications. In this paper, we propose to use graph representation learning (GRL) for solving linear temporal logic (LTL) model checking, where the system and the specification are expressed by a B{\"u}chi automaton and an LTL formula, respectively. A novel GRL-based framework \model, is designed to learn the representation of the graph-structured system and specification, which reduces the model checking problem to binary classification. Empirical experiments on two model checking scenarios show that \model achieves promising accuracy, with up to $11\times$ overall speedup against canonical SOTA model checkers and $31\times$ for satisfiability checking alone.
Sound events in daily life carry rich information about the objective world. The composition of these sounds affects the mood of people in a soundscape. Most previous approaches only focus on classifying and detecting audio events and scenes, but may ignore their perceptual quality that may impact humans' listening mood for the environment, e.g. annoyance. To this end, this paper proposes a novel hierarchical graph representation learning (HGRL) approach which links objective audio events (AE) with subjective annoyance ratings (AR) of the soundscape perceived by humans. The hierarchical graph consists of fine-grained event (fAE) embeddings with single-class event semantics, coarse-grained event (cAE) embeddings with multi-class event semantics, and AR embeddings. Experiments show the proposed HGRL successfully integrates AE with AR for AEC and ARP tasks, while coordinating the relations between cAE and fAE and further aligning the two different grains of AE information with the AR.
Accurate prediction of what types of patents that companies will apply for in the next period of time can figure out their development strategies and help them discover potential partners or competitors in advance. Although important, this problem has been rarely studied in previous research due to the challenges in modelling companies' continuously evolving preferences and capturing the semantic correlations of classification codes. To fill in this gap, we propose an event-based dynamic graph learning framework for patent application trend prediction. In particular, our method is founded on the memorable representations of both companies and patent classification codes. When a new patent is observed, the representations of the related companies and classification codes are updated according to the historical memories and the currently encoded messages. Moreover, a hierarchical message passing mechanism is provided to capture the semantic proximities of patent classification codes by updating their representations along the hierarchical taxonomy. Finally, the patent application trend is predicted by aggregating the representations of the target company and classification codes from static, dynamic, and hierarchical perspectives. Experiments on real-world data demonstrate the effectiveness of our approach under various experimental conditions, and also reveal the abilities of our method in learning semantics of classification codes and tracking technology developing trajectories of companies.
Handwritten mathematical expression recognition (HMER) has attracted extensive attention recently. However, current methods cannot explicitly study the interactions between different symbols, which may fail when faced similar symbols. To alleviate this issue, we propose a simple but efficient method to enhance semantic interaction learning (SIL). Specifically, we firstly construct a semantic graph based on the statistical symbol co-occurrence probabilities. Then we design a semantic aware module (SAM), which projects the visual and classification feature into semantic space. The cosine distance between different projected vectors indicates the correlation between symbols. And jointly optimizing HMER and SIL can explicitly enhances the model's understanding of symbol relationships. In addition, SAM can be easily plugged into existing attention-based models for HMER and consistently bring improvement. Extensive experiments on public benchmark datasets demonstrate that our proposed module can effectively enhance the recognition performance. Our method achieves better recognition performance than prior arts on both CROHME and HME100K datasets.
Despite Graph Neural Networks demonstrating considerable promise in graph representation learning tasks, GNNs predominantly face significant issues with over-fitting and over-smoothing as they go deeper as models of computer vision realm. In this work, we conduct a systematic study of deeper GNN research trajectories. Our findings indicate that the current success of deep GNNs primarily stems from (I) the adoption of innovations from CNNs, such as residual/skip connections, or (II) the tailor-made aggregation algorithms like DropEdge. However, these algorithms often lack intrinsic interpretability and indiscriminately treat all nodes within a given layer in a similar manner, thereby failing to capture the nuanced differences among various nodes. To this end, we introduce the Snowflake Hypothesis -- a novel paradigm underpinning the concept of ``one node, one receptive field''. The hypothesis draws inspiration from the unique and individualistic patterns of each snowflake, proposing a corresponding uniqueness in the receptive fields of nodes in the GNNs. We employ the simplest gradient and node-level cosine distance as guiding principles to regulate the aggregation depth for each node, and conduct comprehensive experiments including: (1) different training schemes; (2) various shallow and deep GNN backbones, and (3) various numbers of layers (8, 16, 32, 64) on multiple benchmarks (six graphs including dense graphs with millions of nodes); (4) compare with different aggregation strategies. The observational results demonstrate that our hypothesis can serve as a universal operator for a range of tasks, and it displays tremendous potential on deep GNNs. It can be applied to various GNN frameworks, enhancing its effectiveness when operating in-depth, and guiding the selection of the optimal network depth in an explainable and generalizable way.
Graph representation learning (GRL) methods, such as graph neural networks and graph transformer models, have been successfully used to analyze graph-structured data, mainly focusing on node classification and link prediction tasks. However, the existing studies mostly only consider local connectivity while ignoring long-range connectivity and the roles of nodes. In this paper, we propose Unified Graph Transformer Networks (UGT) that effectively integrate local and global structural information into fixed-length vector representations. First, UGT learns local structure by identifying the local substructures and aggregating features of the $k$-hop neighborhoods of each node. Second, we construct virtual edges, bridging distant nodes with structural similarity to capture the long-range dependencies. Third, UGT learns unified representations through self-attention, encoding structural distance and $p$-step transition probability between node pairs. Furthermore, we propose a self-supervised learning task that effectively learns transition probability to fuse local and global structural features, which could then be transferred to other downstream tasks. Experimental results on real-world benchmark datasets over various downstream tasks showed that UGT significantly outperformed baselines that consist of state-of-the-art models. In addition, UGT reaches the expressive power of the third-order Weisfeiler-Lehman isomorphism test (3d-WL) in distinguishing non-isomorphic graph pairs. The source code is available at https://github.com/NSLab-CUK/Unified-Graph-Transformer.
This study aims to validate whether the research performance of scholars correlates with how the scholars work together. Although the most straightforward approaches are centrality measurements or community detection, scholars mostly participate in multiple research groups and have different roles in each group. Thus, we concentrate on the subgraphs of co-authorship networks rooted in each scholar that cover (i) overlapping of the research groups on the scholar and (ii) roles of the scholar in the groups. This study calls the subgraphs “collaboration patterns” and applies subgraph embedding methods to discover and represent the collaboration patterns. Based on embedding the collaboration patterns, we have clustered scholars according to their collaboration styles. Then, we have examined whether scholars in each cluster have similar research performance, using the quantitative indicators. The coherence of the indicators cannot be solid proofs for validating the correlation between collaboration and performance. Nevertheless, the examination for clusters has exhibited that the collaboration patterns can reflect research styles of scholars. This information will enable us to predict the research performance more accurately since the research styles are more consistent and sustainable features of scholars than a few high-impact publications.
Representation learning methods have revolutionized machine learning on networks by converting discrete network structures into continuous domains. However, dynamic networks that evolve over time pose new challenges. To address this, dynamic representation learning methods have gained attention, offering benefits like reduced learning time and improved accuracy by utilizing temporal information. T-batching is a valuable technique for training dynamic network models that reduces training time while preserving vital conditions for accurate modeling. However, we have identified a limitation in the training loss function used with t-batching. Through mathematical analysis, we propose two alternative loss functions that overcome these issues, resulting in enhanced training performance. We extensively evaluate the proposed loss functions on synthetic and real-world dynamic networks. The results consistently demonstrate superior performance compared to the original loss function. Notably, in a real-world network characterized by diverse user interaction histories, the proposed loss functions achieved more than 26.9% enhancement in Mean Reciprocal Rank (MRR) and more than 11.8% improvement in Recall@10. These findings underscore the efficacy of the proposed loss functions in dynamic network modeling.
Textual graphs (TGs) are graphs whose nodes correspond to text (sentences or documents), which are widely prevalent. The representation learning of TGs involves two stages: (i) unsupervised feature extraction and (ii) supervised graph representation learning. In recent years, extensive efforts have been devoted to the latter stage, where Graph Neural Networks (GNNs) have dominated. However, the former stage for most existing graph benchmarks still relies on traditional feature engineering techniques. More recently, with the rapid development of language models (LMs), researchers have focused on leveraging LMs to facilitate the learning of TGs, either by jointly training them in a computationally intensive framework (merging the two stages), or designing complex self-supervised training tasks for feature extraction (enhancing the first stage). In this work, we present SimTeG, a frustratingly Simple approach for Textual Graph learning that does not innovate in frameworks, models, and tasks. Instead, we first perform supervised parameter-efficient fine-tuning (PEFT) on a pre-trained LM on the downstream task, such as node classification. We then generate node embeddings using the last hidden states of finetuned LM. These derived features can be further utilized by any GNN for training on the same task. We evaluate our approach on two fundamental graph representation learning tasks: node classification and link prediction. Through extensive experiments, we show that our approach significantly improves the performance of various GNNs on multiple graph benchmarks.
Traditional Graph Neural Network (GNN), as a graph representation learning method, is constrained by label information. However, Graph Contrastive Learning (GCL) methods, which tackle the label problem effectively, mainly focus on the feature information of the global graph or small subgraph structure (e.g., the first-order neighborhood). In the paper, we propose a Local Structure-aware Graph Contrastive representation Learning method (LS-GCL) to model the structural information of nodes from multiple views. Specifically, we construct the semantic subgraphs that are not limited to the first-order neighbors. For the local view, the semantic subgraph of each target node is input into a shared GNN encoder to obtain the target node embeddings at the subgraph-level. Then, we use a pooling function to generate the subgraph-level graph embeddings. For the global view, considering the original graph preserves indispensable semantic information of nodes, we leverage the shared GNN encoder to learn the target node embeddings at the global graph-level. The proposed LS-GCL model is optimized to maximize the common information among similar instances at three various perspectives through a multi-level contrastive loss function. Experimental results on five datasets illustrate that our method outperforms state-of-the-art graph representation learning approaches for both node classification and link prediction tasks.
A knowledge graph is a powerful representation of real-world entities and their relations. The vast majority of these relations are defined as positive statements, but the importance of negative statements is increasingly recognized, especially under an Open World Assumption. Explicitly considering negative statements has been shown to improve performance on tasks such as entity summarization and question answering or domain-specific tasks such as protein function prediction. However, no attention has been given to the exploration of negative statements by knowledge graph embedding approaches despite the potential of negative statements to produce more accurate representations of entities in a knowledge graph. We propose a novel approach, TrueWalks, to incorporate negative statements into the knowledge graph representation learning process. In particular, we present a novel walk-generation method that is able to not only differentiate between positive and negative statements but also take into account the semantic implications of negation in ontology-rich knowledge graphs. This is of particular importance for applications in the biomedical domain, where the inadequacy of embedding approaches regarding negative statements at the ontology level has been identified as a crucial limitation. We evaluate TrueWalks in ontology-rich biomedical knowledge graphs in two different predictive tasks based on KG embeddings: protein-protein interaction prediction and gene-disease association prediction. We conduct an extensive analysis over established benchmarks and demonstrate that our method is able to improve the performance of knowledge graph embeddings on all tasks.
Graph Neural Networks (GNNs) have demonstrated promising results on exploiting node representations for many downstream tasks through supervised end-to-end training. To deal with the widespread label scarcity issue in real-world applications, Graph Contrastive Learning (GCL) is leveraged to train GNNs with limited or even no labels by maximizing the mutual information between nodes in its augmented views generated from the original graph. However, the distribution of graphs remains unconsidered in view generation, resulting in the ignorance of unseen edges in most existing literature, which is empirically shown to be able to improve GCL's performance in our experiments. To this end, we propose to incorporate graph generative adversarial networks (GANs) to learn the distribution of views for GCL, in order to i) automatically capture the characteristic of graphs for augmentations, and ii) jointly train the graph GAN model and the GCL model. Specifically, we present GACN, a novel Generative Adversarial Contrastive learning Network for graph representation learning. GACN develops a view generator and a view discriminator to generate augmented views automatically in an adversarial style. Then, GACN leverages these views to train a GNN encoder with two carefully designed self-supervised learning losses, including the graph contrastive loss and the Bayesian personalized ranking Loss. Furthermore, we design an optimization framework to train all GACN modules jointly. Extensive experiments on seven real-world datasets show that GACN is able to generate high-quality augmented views for GCL and is superior to twelve state-of-the-art baseline methods. Noticeably, our proposed GACN surprisingly discovers that the generated views in data augmentation finally conform to the well-known preferential attachment rule in online networks.