Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the pre-training framework have achieved impressive results. However, these methods heavily rely on biochemical experts, and retrieving and summarizing vast amounts of domain knowledge literature is both time-consuming and expensive. Large Language Models (LLMs) have demonstrated remarkable performance in understanding and efficiently providing general knowledge. Nevertheless, they occasionally exhibit hallucinations and lack precision in generating domain-specific knowledge. Conversely, Domain-specific Small Models (DSMs) possess rich domain knowledge and can accurately calculate molecular domain-related metrics. However, due to their limited model size and singular functionality, they lack the breadth of knowledge necessary for comprehensive representation learning. To leverage the advantages of both approaches in molecular property prediction, we propose a novel Molecular Graph representation learning framework that integrates Large language models and Domain-specific small models (MolGraph-LarDo). Technically, we design a two-stage prompt strategy where DSMs are introduced to calibrate the knowledge provided by LLMs, enhancing the accuracy of domain-specific information and thus enabling LLMs to generate more precise textual descriptions for molecular samples. Subsequently, we employ a multi-modal alignment method to coordinate various modalities, including molecular graphs and their corresponding descriptive texts, to guide the pre-training of molecular representations. Extensive experiments demonstrate the effectiveness of the proposed method.
Temporal knowledge graph reasoning (TKGR) is increasingly gaining attention for its ability to extrapolate new events from historical data, thereby enriching the inherently incomplete temporal knowledge graphs. Existing graph-based representation learning frameworks have made significant strides in developing evolving representations for both entities and relational embeddings. Despite these achievements, there's a notable tendency in these models to inadvertently learn biased data representations and mine spurious correlations, consequently failing to discern the causal relationships between events. This often leads to incorrect predictions based on these false correlations. To address this, we propose an innovative Causal Enhanced Graph Representation Learning framework for TKGR (named CEGRL-TKGR). This framework introduces causal structures in graph-based representation learning to unveil the essential causal relationships between events, ultimately enhancing the performance of the TKGR task. Specifically, we first disentangle the evolutionary representations of entities and relations in a temporal knowledge graph sequence into two distinct components, namely causal representations and confounding representations. Then, drawing on causal intervention theory, we advocate the utilization of causal representations for predictions, aiming to mitigate the effects of erroneous correlations caused by confounding features, thus achieving more robust and accurate predictions. Finally, extensive experimental results on six benchmark datasets demonstrate the superior performance of our model in the link prediction task.
Textual graphs are ubiquitous in real-world applications, featuring rich text information with complex relationships, which enables advanced research across various fields. Textual graph representation learning aims to generate low-dimensional feature embeddings from textual graphs that can improve the performance of downstream tasks. A high-quality feature embedding should effectively capture both the structural and the textual information in a textual graph. However, most textual graph dataset benchmarks rely on word2vec techniques to generate feature embeddings, which inherently limits their capabilities. Recent works on textual graph representation learning can be categorized into two folds: supervised and unsupervised methods. Supervised methods finetune a language model on labeled nodes, which have limited capabilities when labeled data is scarce. Unsupervised methods, on the other hand, extract feature embeddings by developing complex training pipelines. To address these limitations, we propose a novel unified unsupervised learning autoencoder framework, named Node Level Graph AutoEncoder (NodeGAE). We employ language models as the backbone of the autoencoder, with pretraining on text reconstruction. Additionally, we add an auxiliary loss term to make the feature embeddings aware of the local graph structure. Our method maintains simplicity in the training process and demonstrates generalizability across diverse textual graphs and downstream tasks. We evaluate our method on two core graph representation learning downstream tasks: node classification and link prediction. Comprehensive experiments demonstrate that our approach substantially enhances the performance of diverse graph neural networks (GNNs) across multiple textual graph datasets.
Unified graph representation learning aims to produce node embeddings, which can be applied to multiple downstream applications. However, existing studies based on graph neural networks and language models either suffer from the limitations of numerous training needed toward specific downstream predictions or have shallow semantic features. In this work, we propose a novel Path-LLM model to learn unified graph representation, which leverages a powerful large language model (LLM) to incorporate our proposed path features. Our Path-LLM framework consists of several well-designed techniques. First, we develop a new mechanism of long-to-short shortest path (L2SP) selection, which covers essential connections between different dense groups. An in-depth comparison of different path selection plans is offered to illustrate the strength of our designed L2SP. Then, we design path textualization to obtain L2SP-based training texts. Next, we feed the texts into a self-supervised LLM training process to learn embeddings. Extensive experiments on benchmarks validate the superiority of Path-LLM against the state-of-the-art WalkLM method on two classical graph learning tasks (node classification and link prediction) and one NP-hard graph query processing task (keyword search), meanwhile saving more than 90% of training paths.
Graph learning methods have been extensively applied in diverse application areas. However, what kind of inherent graph properties e.g. graph proximity, graph structural information has been encoded into graph representation learning for downstream tasks is still under-explored. In this paper, we propose a novel graph probing framework (GraphProbe) to investigate and interpret whether the family of graph learning methods has encoded different levels of knowledge in graph representation learning. Based on the intrinsic properties of graphs, we design three probes to systematically investigate the graph representation learning process from different perspectives, respectively the node-wise level, the path-wise level, and the structural level. We construct a thorough evaluation benchmark with nine representative graph learning methods from random walk based approaches, basic graph neural networks and self-supervised graph methods, and probe them on six benchmark datasets for node classification, link prediction and graph classification. The experimental evaluation verify that GraphProbe can estimate the capability of graph representation learning. Remaking results have been concluded: GCN and WeightedGCN methods are relatively versatile methods achieving better results with respect to different tasks.
The advent of the "pre-train, prompt" paradigm has recently extended its generalization ability and data efficiency to graph representation learning, following its achievements in Natural Language Processing (NLP). Initial graph prompt tuning approaches tailored specialized prompting functions for Graph Neural Network (GNN) models pre-trained with specific strategies, such as edge prediction, thus limiting their applicability. In contrast, another pioneering line of research has explored universal prompting via adding prompts to the input graph's feature space, thereby removing the reliance on specific pre-training strategies. However, the necessity to add feature prompts to all nodes remains an open question. Motivated by findings from prompt tuning research in the NLP domain, which suggest that highly capable pre-trained models need less conditioning signal to achieve desired behaviors, we advocate for strategically incorporating necessary and lightweight feature prompts to certain graph nodes to enhance downstream task performance. This introduces a combinatorial optimization problem, requiring a policy to decide 1) which nodes to prompt and 2) what specific feature prompts to attach. We then address the problem by framing the prompt incorporation process as a sequential decision-making problem and propose our method, RELIEF, which employs Reinforcement Learning (RL) to optimize it. At each step, the RL agent selects a node (discrete action) and determines the prompt content (continuous action), aiming to maximize cumulative performance gain. Extensive experiments on graph and node-level tasks with various pre-training strategies in few-shot scenarios demonstrate that our RELIEF outperforms fine-tuning and other prompt-based approaches in classification performance and data efficiency. The code is available at https://github.com/JasonZhujp/RELIEF.
Dynamic graphs (DG) are often used to describe evolving interactions between nodes in real-world applications. Temporal patterns are a natural feature of DGs and are also key to representation learning. However, existing dynamic GCN models are mostly composed of static GCNs and sequence modules, which results in the separation of spatiotemporal information and cannot effectively capture complex temporal patterns in DGs. To address this problem, this study proposes a spatial-temporal graph convolutional networks with diversified transformation (STGCNDT), which includes three aspects: a) constructing a unified graph tensor convolutional network (GTCN) using tensor M-products without the need to represent spatiotemporal information separately; b) introducing three transformation schemes in GTCN to model complex temporal patterns to aggregate temporal information; and c) constructing an ensemble of diversified transformation schemes to obtain higher representation capabilities. Empirical studies on four DGs that appear in communication networks show that the proposed STGCNDT significantly outperforms state-of-the-art models in solving link weight estimation tasks due to the diversified transformations.
Graph Neural Networks (GNNs)-based recommendation algorithms typically assume that training and testing data are drawn from independent and identically distributed (IID) spaces. However, this assumption often fails in the presence of out-of-distribution (OOD) data, resulting in significant performance degradation. In this study, we construct a Structural Causal Model (SCM) to analyze interaction data, revealing that environmental confounders (e.g., the COVID-19 pandemic) lead to unstable correlations in GNN-based models, thus impairing their generalization to OOD data. To address this issue, we propose a novel approach, graph representation learning via causal diffusion (CausalDiffRec) for OOD recommendation. This method enhances the model's generalization on OOD data by eliminating environmental confounding factors and learning invariant graph representations. Specifically, we use backdoor adjustment and variational inference to infer the real environmental distribution, thereby eliminating the impact of environmental confounders. This inferred distribution is then used as prior knowledge to guide the representation learning in the reverse phase of the diffusion process to learn the invariant representation. In addition, we provide a theoretical derivation that proves optimizing the objective function of CausalDiffRec can encourage the model to learn environment-invariant graph representations, thereby achieving excellent generalization performance in recommendations under distribution shifts. Our extensive experiments validate the effectiveness of CausalDiffRec in improving the generalization of OOD data, and the average improvement is up to 10.69% on Food, 18.83% on KuaiRec, 22.41% on Yelp2018, and 11.65% on Douban datasets.
Graph Neural Networks (GNNs) have received extensive research attention due to their powerful information aggregation capabilities. Despite the success of GNNs, most of them suffer from the popularity bias issue in a graph caused by a small number of popular categories. Additionally, real graph datasets always contain incorrect node labels, which hinders GNNs from learning effective node representations. Graph contrastive learning (GCL) has been shown to be effective in solving the above problems for node classification tasks. Most existing GCL methods are implemented by randomly removing edges and nodes to create multiple contrasting views, and then maximizing the mutual information (MI) between these contrasting views to improve the node feature representation. However, maximizing the mutual information between multiple contrasting views may lead the model to learn some redundant information irrelevant to the node classification task. To tackle this issue, we propose an effective Contrastive Graph Representation Learning with Adversarial Cross-view Reconstruction and Information Bottleneck (CGRL) for node classification, which can adaptively learn to mask the nodes and edges in the graph to obtain the optimal graph structure representation. Furthermore, we innovatively introduce the information bottleneck theory into GCLs to remove redundant information in multiple contrasting views while retaining as much information as possible about node classification. Moreover, we add noise perturbations to the original views and reconstruct the augmented views by constructing adversarial views to improve the robustness of node feature representation. Extensive experiments on real-world public datasets demonstrate that our method significantly outperforms existing state-of-the-art algorithms.
HAL (\textit{Hyper Articles en Ligne}) is the French national publication repository, used by most higher education and research organizations for their open science policy. Although it is a rich repository of academic documents, its potential for advanced research has not been fully explored. We present HALvest, a unique dataset that bridges the gap between citation networks and the full text of HAL-submitted articles to help with authorship attribution and verification. This first iteration consists of approximately 700,000 documents, spanning 56 languages across 13 identified domains. We transform articles' metadata into a citation network, producing a heterogeneous graph. This graph includes uniquely identified authors on HAL, as well as all open-access documents and their references. Finally, we mine 14.5 million high-quality sequence pairs from HALvest for contrastive learning purposes. By providing different views of HAL, suited for modern machine learning, we aim to assist practitioners in better analyzing and interpreting research dynamics.
In recent years, spiking neural networks (SNNs) have attracted substantial interest due to their potential to replicate the energy-efficient and event-driven processing of biological neurons. Despite this, the application of SNNs in graph representation learning, particularly for non-Euclidean data, remains underexplored, and the influence of spiking dynamics on graph learning is not yet fully understood. This work seeks to address these gaps by examining the unique properties and benefits of spiking dynamics in enhancing graph representation learning. We propose a spike-based graph neural network model that incorporates spiking dynamics, enhanced by a novel spatial-temporal feature normalization (STFN) technique, to improve training efficiency and model stability. Our detailed analysis explores the impact of rate coding and temporal coding on SNN performance, offering new insights into their advantages for deep graph networks and addressing challenges such as the oversmoothing problem. Experimental results demonstrate that our SNN models can achieve competitive performance with state-of-the-art graph neural networks (GNNs) while considerably reducing computational costs, highlighting the potential of SNNs for efficient neuromorphic computing applications in complex graph-based scenarios.
Recent advancements in graph neural networks (GNNs) and heterogeneous GNNs (HGNNs) have advanced node embeddings and relationship learning for various tasks. However, existing methods often rely on domain-specific predefined meta-paths, which are coarse-grained and focus solely on aspects like node type, limiting their ability to capture complex interactions. We introduce MF2Vec, a model that uses multi-faceted (fine-grained) paths instead of predefined meta-paths. MF2Vec extracts paths via random walks and generates multi-faceted vectors, ignoring predefined schemas. This method learns diverse aspects of nodes and their relationships, constructs a homogeneous network, and creates node embeddings for classification, link prediction, and clustering. Extensive experiments show that MF2Vec outperforms existing methods, offering a more flexible and comprehensive framework for analyzing complex networks. The code is available at https://anonymous.4open.science/r/MF2Vec-6ABC.
This paper investigates the advantages of representing and processing semantic knowledge extracted into graphs within the emerging paradigm of semantic communications. The proposed approach leverages semantic and pragmatic aspects, incorporating recent advances on large language models (LLMs) to achieve compact representations of knowledge to be processed and exchanged between intelligent agents. This is accomplished by using the cascade of LLMs and graph neural networks (GNNs) as semantic encoders, where information to be shared is selected to be meaningful at the receiver. The embedding vectors produced by the proposed semantic encoder represent information in the form of triplets: nodes (semantic concepts entities), edges(relations between concepts), nodes. Thus, semantic information is associated with the representation of relationships among elements in the space of semantic concept abstractions. In this paper, we investigate the potential of achieving high compression rates in communication by incorporating relations that link elements within graph embeddings. We propose sending semantic symbols solely equivalent to node embeddings through the wireless channel and inferring the complete knowledge graph at the receiver. Numerical simulations illustrate the effectiveness of leveraging knowledge graphs to semantically compress and transmit information.
Unsupervised graph representation learning (UGRL) based on graph neural networks (GNNs), has received increasing attention owing to its efficacy in handling graph-structured data. However, existing UGRL methods ideally assume that the node features are noise-free, which makes them fail to distinguish between useful information and noise when applied to real data with noisy features, thus affecting the quality of learned representations. This urges us to take node noisy features into account in real-world UGRL. With empirical analysis, we reveal that feature propagation, the essential operation in GNNs, acts as a "double-edged sword" in handling noisy features - it can both denoise and diffuse noise, leading to varying feature quality across nodes, even within the same node at different hops. Building on this insight, we propose a novel UGRL method based on Multi-hop feature Quality Estimation (MQE for short). Unlike most UGRL models that directly utilize propagation-based GNNs to generate representations, our approach aims to learn representations through estimating the quality of propagated features at different hops. Specifically, we introduce a Gaussian model that utilizes a learnable "meta-representation" as a condition to estimate the expectation and variance of multi-hop propagated features via neural networks. In this way, the "meta representation" captures the semantic and structural information underlying multiple propagated features but is naturally less susceptible to interference by noise, thereby serving as high-quality node representations beneficial for downstream tasks. Extensive experiments on multiple real-world datasets demonstrate that MQE in learning reliable node representations in scenarios with diverse types of feature noise.
Discrete-Time Dynamic Graphs (DTDGs), which are prevalent in real-world implementations and notable for their ease of data acquisition, have garnered considerable attention from both academic researchers and industry practitioners. The representation learning of DTDGs has been extensively applied to model the dynamics of temporally changing entities and their evolving connections. Currently, DTDG representation learning predominantly relies on GNN+RNN architectures, which manifest the inherent limitations of both Graph Neural Networks (GNNs) and Recurrent Neural Networks (RNNs). GNNs suffer from the over-smoothing issue as the models architecture goes deeper, while RNNs struggle to capture long-term dependencies effectively. GNN+RNN architectures also grapple with scaling to large graph sizes and long sequences. Additionally, these methods often compute node representations separately and focus solely on individual node characteristics, thereby overlooking the behavior intersections between the two nodes whose link is being predicted, such as instances where the two nodes appear together in the same context or share common neighbors. This paper introduces a novel representation learning method DTFormer for DTDGs, pivoting from the traditional GNN+RNN framework to a Transformer-based architecture. Our approach exploits the attention mechanism to concurrently process topological information within the graph at each timestamp and temporal dynamics of graphs along the timestamps, circumventing the aforementioned fundamental weakness of both GNNs and RNNs. Moreover, we enhance the model's expressive capability by incorporating the intersection relationships among nodes and integrating a multi-patching module. Extensive experiments conducted on six public dynamic graph benchmark datasets confirm our model's efficacy, achieving the SOTA performance.
Designing effective graph neural networks (GNNs) with message passing has two fundamental challenges, i.e., determining optimal message-passing pathways and designing local aggregators. Previous methods of designing optimal pathways are limited with information loss on the input features. On the other hand, existing local aggregators generally fail to extract multi-scale features and approximate diverse operators under limited parameter scales. In contrast to these methods, Euclidean convolution has been proven as an expressive aggregator, making it a perfect candidate for GNN construction. However, the challenges of generalizing Euclidean convolution to graphs arise from the irregular structure of graphs. To bridge the gap between Euclidean space and graph topology, we propose a differentiable method that applies permutations to calibrate input graphs for Euclidean convolution. The permutations constrain all nodes in a row regardless of their input order and therefore enable the flexible generalization of Euclidean convolution to graphs. Based on the graph calibration, we propose the Compressed Convolution Network (CoCN) for hierarchical graph representation learning. CoCN follows local feature-learning and global parameter-sharing mechanisms of convolution neural networks. The whole model can be trained end-to-end, with compressed convolution applied to learn individual node features and their corresponding structure features. CoCN can further borrow successful practices from Euclidean convolution, including residual connection and inception mechanism. We validate CoCN on both node-level and graph-level benchmarks. CoCN achieves superior performance over competitive GNN baselines. Codes are available at https://github.com/sunjss/CoCN.
Graph recommender (GR) is a type of graph neural network (GNNs) encoder that is customized for extracting information from the user-item interaction graph. Due to its strong performance on the recommendation task, GR has gained significant attention recently. Graph contrastive learning (GCL) is also a popular research direction that aims to learn, often unsupervised, GNNs with certain contrastive objectives. As a general graph representation learning method, GCLs have been widely adopted with the supervised recommendation loss for joint training of GRs. Despite the intersection of GR and GCL research, theoretical understanding of the relationship between the two fields is surprisingly sparse. This vacancy inevitably leads to inefficient scientific research. In this paper, we aim to bridge the gap between the field of GR and GCL from the perspective of encoders and loss functions. With mild assumptions, we theoretically show an astonishing fact that graph recommender is equivalent to a commonly-used single-view graph contrastive model. Specifically, we find that (1) the classic encoder in GR is essentially a linear graph convolutional network with one-hot inputs, and (2) the loss function in GR is well bounded by a single-view GCL loss with certain hyperparameters. The first observation enables us to explain crucial designs of GR models, e.g., the removal of self-loop and nonlinearity. And the second finding can easily prompt many cross-field research directions. We empirically show a remarkable result that the recommendation loss and the GCL loss can be used interchangeably. The fact that we can train GR models solely with the GCL loss is particularly insightful, since before this work, GCLs were typically viewed as unsupervised methods that need fine-tuning. We also discuss some potential future works inspired by our theory.
Recent years have witnessed a thriving growth of computing facilities connected at the network edge, cultivating edge networks as a fundamental infrastructure for supporting miscellaneous intelligent services.Meanwhile, Artificial Intelligence (AI) frontiers have extrapolated to the graph domain and promoted Graph Intelligence (GI). Given the inherent relation between graphs and networks, the interdiscipline of graph learning and edge networks, i.e., Edge GI or EGI, has revealed a novel interplay between them -- GI aids in optimizing edge networks, while edge networks facilitate GI model deployment. Driven by this delicate closed-loop, EGI is recognized as a promising solution to fully unleash the potential of edge computing power and is garnering growing attention. Nevertheless, research on EGI remains nascent, and there is a soaring demand within both the communications and AI communities for a dedicated venue to share recent advancements. To this end, this paper promotes the concept of EGI, explores its scope and core principles, and conducts a comprehensive survey concerning recent research efforts on this emerging field. Specifically, this paper introduces and discusses: 1) fundamentals of edge computing and graph learning,2) emerging techniques centering on the closed loop between graph intelligence and edge networks, and 3) open challenges and research opportunities of future EGI. By bridging the gap across communication, networking, and graph learning areas, we believe that this survey can garner increased attention, foster meaningful discussions, and inspire further research ideas in EGI.
Spectral Graph Neural Networks have demonstrated superior performance in graph representation learning. However, many current methods focus on employing shared polynomial coefficients for all nodes, i.e., learning node-unified filters, which limits the filters' flexibility for node-level tasks. The recent DSF attempts to overcome this limitation by learning node-wise coefficients based on positional encoding. However, the initialization and updating process of the positional encoding are burdensome, hindering scalability on large-scale graphs. In this work, we propose a scalable node-wise filter, PolyAttn. Leveraging the attention mechanism, PolyAttn can directly learn node-wise filters in an efficient manner, offering powerful representation capabilities. Building on PolyAttn, we introduce the whole model, named PolyFormer. In the lens of Graph Transformer models, PolyFormer, which calculates attention scores within nodes, shows great scalability. Moreover, the model captures spectral information, enhancing expressiveness while maintaining efficiency. With these advantages, PolyFormer offers a desirable balance between scalability and expressiveness for node-level tasks. Extensive experiments demonstrate that our proposed methods excel at learning arbitrary node-wise filters, showing superior performance on both homophilic and heterophilic graphs, and handling graphs containing up to 100 million nodes. The code is available at https://github.com/air029/PolyFormer.
Despite the success of Heterogeneous Graph Neural Networks (HGNNs) in modeling real-world Heterogeneous Information Networks (HINs), challenges such as expressiveness limitations and over-smoothing have prompted researchers to explore Graph Transformers (GTs) for enhanced HIN representation learning. However, research on GT in HINs remains limited, with two key shortcomings in existing work: (1) A node's neighbors at different distances in HINs convey diverse semantics. Unfortunately, existing methods ignore such differences and uniformly treat neighbors within a given distance in a coarse manner, which results in semantic confusion. (2) Nodes in HINs have various types, each with unique semantics. Nevertheless, existing methods mix nodes of different types during neighbor aggregation, hindering the capture of proper correlations between nodes of diverse types. To bridge these gaps, we design an innovative structure named (k,t)-ring neighborhood, where nodes are initially organized by their distance, forming different non-overlapping k-ring neighborhoods for each distance. Within each k-ring structure, nodes are further categorized into different groups according to their types, thus emphasizing the heterogeneity of both distances and types in HINs naturally. Based on this structure, we propose a novel Hierarchical Heterogeneous Graph Transformer (HHGT) model, which seamlessly integrates a Type-level Transformer for aggregating nodes of different types within each k-ring neighborhood, followed by a Ring-level Transformer for aggregating different k-ring neighborhoods in a hierarchical manner. Extensive experiments are conducted on downstream tasks to verify HHGT's superiority over 14 baselines, with a notable improvement of up to 24.75% in NMI and 29.25% in ARI for node clustering task on the ACM dataset compared to the best baseline.