Graph Neural Networks (GNNs) have achieved great success in various graph mining tasks.However, drastic performance degradation is always observed when a GNN is stacked with many layers. As a result, most GNNs only have shallow architectures, which limits their expressive power and exploitation of deep neighborhoods.Most recent studies attribute the performance degradation of deep GNNs to the \textit{over-smoothing} issue. In this paper, we disentangle the conventional graph convolution operation into two independent operations: \textit{Propagation} (\textbf{P}) and \textit{Transformation} (\textbf{T}).Following this, the depth of a GNN can be split into the propagation depth ($D_p$) and the transformation depth ($D_t$). Through extensive experiments, we find that the major cause for the performance degradation of deep GNNs is the \textit{model degradation} issue caused by large $D_t$ rather than the \textit{over-smoothing} issue mainly caused by large $D_p$. Further, we present \textit{Adaptive Initial Residual} (AIR), a plug-and-play module compatible with all kinds of GNN architectures, to alleviate the \textit{model degradation} issue and the \textit{over-smoothing} issue simultaneously. Experimental results on six real-world datasets demonstrate that GNNs equipped with AIR outperform most GNNs with shallow architectures owing to the benefits of both large $D_p$ and $D_t$, while the time costs associated with AIR can be ignored.
Graph Neural Networks (GNNs) have shown tremendous strides in performance for graph-structured problems especially in the domains of natural language processing, computer vision and recommender systems. Inspired by the success of the transformer architecture, there has been an ever-growing body of work on attention variants of GNNs attempting to advance the state of the art in many of these problems. Incorporating "attention" into graph mining has been viewed as a way to overcome the noisiness, heterogenity and complexity associated with graph-structured data as well as to encode soft-inductive bias. It is hence crucial and advantageous to study these variants from a bird's-eye view to assess their strengths and weaknesses. We provide a systematic and focused tutorial centered around attention based GNNs in a hope to benefit researchers dealing with graph-structured problems. Our tutorial looks at GNN variants from the point of view of the attention function and iteratively builds the reader's understanding of different graph attention variants.
Transformers have achieved remarkable performance in widespread fields, including natural language processing, computer vision and graph mining. However, vanilla Transformer architectures have not yielded promising improvements in the Knowledge Graph (KG) representations, where the translational distance paradigm dominates this area. Note that vanilla Transformer architectures struggle to capture the intrinsically heterogeneous structural and semantic information of knowledge graphs. To this end, we propose a new variant of Transformer for knowledge graph representations dubbed Relphormer. Specifically, we introduce Triple2Seq which can dynamically sample contextualized sub-graph sequences as the input to alleviate the heterogeneity issue. We propose a novel structure-enhanced self-attention mechanism to encode the relational information and keep the semantic information within entities and relations. Moreover, we utilize masked knowledge modeling for general knowledge graph representation learning, which can be applied to various KG-based tasks including knowledge graph completion, question answering, and recommendation. Experimental results on six datasets show that Relphormer can obtain better performance compared with baselines. Code is available in https://github.com/zjunlp/Relphormer.
MRI-based modeling of brain networks has been widely used to understand functional and structural interactions and connections among brain regions, and factors that affect them, such as brain development and disease. Graph mining on brain networks may facilitate the discovery of novel biomarkers for clinical phenotypes and neurodegenerative diseases. Since brain networks derived from functional and structural MRI describe the brain topology from different perspectives, exploring a representation that combines these cross-modality brain networks is non-trivial. Most current studies aim to extract a fused representation of the two types of brain network by projecting the structural network to the functional counterpart. Since the functional network is dynamic and the structural network is static, mapping a static object to a dynamic object is suboptimal. However, mapping in the opposite direction is not feasible due to the non-negativity requirement of current graph learning techniques. Here, we propose a novel graph learning framework, known as Deep Signed Brain Networks (DSBN), with a signed graph encoder that, from an opposite perspective, learns the cross-modality representations by projecting the functional network to the structural counterpart. We validate our framework on clinical phenotype and neurodegenerative disease prediction tasks using two independent, publicly available datasets (HCP and OASIS). The experimental results clearly demonstrate the advantages of our model compared to several state-of-the-art methods.
Candidate retrieval is the first stage in recommendation systems, where a light-weight system is used to retrieve potentially relevant items for an input user. These candidate items are then ranked and pruned in later stages of recommender systems using a more complex ranking model. As the top of the recommendation funnel, it is important to retrieve a high-recall candidate set to feed into downstream ranking models. A common approach is to leverage approximate nearest neighbor (ANN) search from a single dense query embedding; however, this approach this can yield a low-diversity result set with many near duplicates. As users often have multiple interests, candidate retrieval should ideally return a diverse set of candidates reflective of the user's multiple interests. To this end, we introduce kNN-Embed, a general approach to improving diversity in dense ANN-based retrieval. kNN-Embed represents each user as a smoothed mixture over learned item clusters that represent distinct "interests" of the user. By querying each of a user's mixture component in proportion to their mixture weights, we retrieve a high-diversity set of candidates reflecting elements from each of a user's interests. We experimentally compare kNN-Embed to standard ANN candidate retrieval, and show significant improvements in overall recall and improved diversity across three datasets. Accompanying this work, we open source a large Twitter follow-graph dataset (https://huggingface.co/datasets/Twitter/TwitterFollowGraph), to spur further research in graph-mining and representation learning for recommender systems.
Nowadays, the analysis of complex phenomena modeled by graphs plays a crucial role in many real-world application domains where decisions can have a strong societal impact. However, numerous studies and papers have recently revealed that machine learning models could lead to potential disparate treatment between individuals and unfair outcomes. In that context, algorithmic contributions for graph mining are not spared by the problem of fairness and present some specific challenges related to the intrinsic nature of graphs: (1) graph data is non-IID, and this assumption may invalidate many existing studies in fair machine learning, (2) suited metric definitions to assess the different types of fairness with relational data and (3) algorithmic challenge on the difficulty of finding a good trade-off between model accuracy and fairness. This survey is the first one dedicated to fairness for relational data. It aims to present a comprehensive review of state-of-the-art techniques in fairness on graph mining and identify the open challenges and future trends. In particular, we start by presenting several sensible application domains and the associated graph mining tasks with a focus on edge prediction and node classification in the sequel. We also recall the different metrics proposed to evaluate potential bias at different levels of the graph mining process; then we provide a comprehensive overview of recent contributions in the domain of fair machine learning for graphs, that we classify into pre-processing, in-processing and post-processing models. We also propose to describe existing graph data, synthetic and real-world benchmarks. Finally, we present in detail five potential promising directions to advance research in studying algorithmic fairness on graphs.
Graph mining algorithms have been playing a significant role in myriad fields over the years. However, despite their promising performance on various graph analytical tasks, most of these algorithms lack fairness considerations. As a consequence, they could lead to discrimination towards certain populations when exploited in human-centered applications. Recently, algorithmic fairness has been extensively studied in graph-based applications. In contrast to algorithmic fairness on independent and identically distributed (i.i.d.) data, fairness in graph mining has exclusive backgrounds, taxonomies, and fulfilling techniques. In this survey, we provide a comprehensive and up-to-date introduction of existing literature under the context of fair graph mining. Specifically, we propose a novel taxonomy of fairness notions on graphs, which sheds light on their connections and differences. We further present an organized summary of existing techniques that promote fairness in graph mining. Finally, we summarize the widely used datasets in this emerging research field and provide insights on current research challenges and open questions, aiming at encouraging cross-breeding ideas and further advances.
Tigerlily is a TigerGraph based system designed to solve the drug interaction prediction task. In this machine learning task, we want to predict whether two drugs have an adverse interaction. Our framework allows us to solve this highly relevant real-world problem using graph mining techniques in these steps: (a) Using PyTigergraph we create a heterogeneous biological graph of drugs and proteins. (b) We calculate the personalized PageRank scores of drug nodes in the TigerGraph Cloud. (c) We embed the nodes using sparse non-negative matrix factorization of the personalized PageRank matrix. (d) Using the node embeddings we train a gradient boosting based drug interaction predictor.
Graph mining tasks arise from many different application domains, ranging from social networks, transportation to E-commerce, etc., which have been receiving great attention from the theoretical and algorithmic design communities in recent years, and there has been some pioneering work employing the research-rich Reinforcement Learning (RL) techniques to address graph data mining tasks. However, these graph mining methods and RL models are dispersed in different research areas, which makes it hard to compare them. In this survey, we provide a comprehensive overview of RL and graph mining methods and generalize these methods to Graph Reinforcement Learning (GRL) as a unified formulation. We further discuss the applications of GRL methods across various domains and summarize the method descriptions, open-source codes, and benchmark datasets of GRL methods. Furthermore, we propose important directions and challenges to be solved in the future. As far as we know, this is the latest work on a comprehensive survey of GRL, this work provides a global view and a learning resource for scholars. In addition, we create an online open-source for both interested scholars who want to enter this rapidly developing domain and experts who would like to compare GRL methods.
Graph representation learning has attracted tremendous attention due to its remarkable performance in many real-world applications. However, prevailing supervised graph representation learning models for specific tasks often suffer from label sparsity issue as data labeling is always time and resource consuming. In light of this, few-shot learning on graphs (FSLG), which combines the strengths of graph representation learning and few-shot learning together, has been proposed to tackle the performance degradation in face of limited annotated data challenge. There have been many studies working on FSLG recently. In this paper, we comprehensively survey these work in the form of a series of methods and applications. Specifically, we first introduce FSLG challenges and bases, then categorize and summarize existing work of FSLG in terms of three major graph mining tasks at different granularity levels, i.e., node, edge, and graph. Finally, we share our thoughts on some future research directions of FSLG. The authors of this survey have contributed significantly to the AI literature on FSLG over the last few years.
Graph neural networks (GNNs) have drawn significant research attention recently, mostly under the setting of semi-supervised learning. When task-agnostic representations are preferred or supervision is simply unavailable, the auto-encoder framework comes in handy with a natural graph reconstruction objective for unsupervised GNN training. However, existing graph auto-encoders are designed to reconstruct the direct links, so GNNs trained in this way are only optimized towards proximity-oriented graph mining tasks, and will fall short when the topological structures matter. In this work, we revisit the graph encoding process of GNNs which essentially learns to encode the neighborhood information of each node into an embedding vector, and propose a novel graph decoder to reconstruct the entire neighborhood information regarding both proximity and structure via Neighborhood Wasserstein Reconstruction (NWR). Specifically, from the GNN embedding of each node, NWR jointly predicts its node degree and neighbor feature distribution, where the distribution prediction adopts an optimal-transport loss based on the Wasserstein distance. Extensive experiments on both synthetic and real-world network datasets show that the unsupervised node representations learned with NWR have much more advantageous in structure-oriented graph mining tasks, while also achieving competitive performance in proximity-oriented ones.
To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. Among three knowledge graph completion models, TransE outperformed the other two (MR = 13.45, Hits@1 = 0.306). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.
Accurate real-time traffic forecast is critical for intelligent transportation systems (ITS) and it serves as the cornerstone of various smart mobility applications. Though this research area is dominated by deep learning, recent studies indicate that the accuracy improvement by developing new model structures is becoming marginal. Instead, we envision that the improvement can be achieved by transferring the "forecasting-related knowledge" across cities with different data distributions and network topologies. To this end, this paper aims to propose a novel transferable traffic forecasting framework: Domain Adversarial Spatial-Temporal Network (DASTNet). DASTNet is pre-trained on multiple source networks and fine-tuned with the target network's traffic data. Specifically, we leverage the graph representation learning and adversarial domain adaptation techniques to learn the domain-invariant node embeddings, which are further incorporated to model the temporal traffic data. To the best of our knowledge, we are the first to employ adversarial multi-domain adaptation for network-wide traffic forecasting problems. DASTNet consistently outperforms all state-of-the-art baseline methods on three benchmark datasets. The trained DASTNet is applied to Hong Kong's new traffic detectors, and accurate traffic predictions can be delivered immediately (within one day) when the detector is available. Overall, this study suggests an alternative to enhance the traffic forecasting methods and provides practical implications for cities lacking historical traffic data.
Background and Objective High medicine diversity has always been a significant challenge for prescription, causing confusion or doubt in physicians' decision-making process. This paper aims to develop a medicine recommender system called RecoMed to aid the physician in the prescription process of hypertension by providing information about what medications have been prescribed by other doctors and figuring out what other medicines can be recommended in addition to the one in question. Methods There are two steps to the developed method: First, association rule mining algorithms are employed to find medicine association rules. The second step entails graph mining and clustering to present an enriched recommendation via ATC code, which itself comprises several steps. First, the initial graph is constructed from historical prescription data. Then, data pruning is performed in the second step, after which the medicines with a high repetition rate are removed at the discretion of a general medical practitioner. Next, the medicines are matched to a well-known medicine classification system called the ATC code to provide an enriched recommendation. And finally, the DBSCAN and Louvain algorithms cluster medicines in the final step. Results A list of recommended medicines is provided as the system's output, and physicians can choose one or more of the medicines based on the patient's clinical symptoms. Only the medicines of class 2, related to high blood pressure medications, are used to assess the system's performance. The results obtained from this system have been reviewed and confirmed by an expert in this field.
Transformers have achieved remarkable performance in a myriad of fields including natural language processing and computer vision. However, when it comes to the graph mining area, where graph neural network (GNN) has been the dominant paradigm, transformers haven't achieved competitive performance, especially on the node classification task. Existing graph transformer models typically adopt fully-connected attention mechanism on the whole input graph and thus suffer from severe scalability issues and are intractable to train in data insufficient cases. To alleviate these issues, we propose a novel Gophormer model which applies transformers on ego-graphs instead of full-graphs. Specifically, Node2Seq module is proposed to sample ego-graphs as the input of transformers, which alleviates the challenge of scalability and serves as an effective data augmentation technique to boost model performance. Moreover, different from the feature-based attention strategy in vanilla transformers, we propose a proximity-enhanced attention mechanism to capture the fine-grained structural bias. In order to handle the uncertainty introduced by the ego-graph sampling, we further propose a consistency regularization and a multi-sample inference strategy for stabilized training and testing, respectively. Extensive experiments on six benchmark datasets are conducted to demonstrate the superiority of Gophormer over existing graph transformers and popular GNNs, revealing the promising future of graph transformers.
Network representation learning (NRL) advances the conventional graph mining of social networks, knowledge graphs, and complex biomedical and physics information networks. Over dozens of network representation learning algorithms have been reported in the literature. Most of them focus on learning node embeddings for homogeneous networks, but they differ in the specific encoding schemes and specific types of node semantics captured and used for learning node embedding. This survey paper reviews the design principles and the different node embedding techniques for network representation learning over homogeneous networks. To facilitate the comparison of different node embedding algorithms, we introduce a unified reference framework to divide and generalize the node embedding learning process on a given network into preprocessing steps, node feature extraction steps and node embedding model training for a NRL task such as link prediction and node clustering. With this unifying reference framework, we highlight the representative methods, models, and techniques used at different stages of the node embedding model learning process. This survey not only helps researchers and practitioners to gain an in-depth understanding of different network representation learning techniques but also provides practical guidelines for designing and developing the next generation of network representation learning algorithms and systems.
Given a node-attributed graph, how can we efficiently represent it with few numerical features that expressively reflect its topology and attribute information? We propose A-DOGE, for Attributed DOS-based Graph Embedding, based on density of states (DOS, a.k.a. spectral density) to tackle this problem. A-DOGE is designed to fulfill a long desiderata of desirable characteristics. Most notably, it capitalizes on efficient approximation algorithms for DOS, that we extend to blend in node labels and attributes for the first time, making it fast and scalable for large attributed graphs and graph databases. Being based on the entire eigenspectrum of a graph, A-DOGE can capture structural and attribute properties at multiple ("glocal") scales. Moreover, it is unsupervised (i.e. agnostic to any specific objective) and lends itself to various interpretations, which makes it is suitable for exploratory graph mining tasks. Finally, it processes each graph independent of others, making it amenable for streaming settings as well as parallelization. Through extensive experiments, we show the efficacy and efficiency of A-DOGE on exploratory graph analysis and graph classification tasks, where it significantly outperforms unsupervised baselines and achieves competitive performance with modern supervised GNNs, while achieving the best trade-off between accuracy and runtime.
Understanding linguistic modality is widely seen as important for downstream tasks such as Question Answering and Knowledge Graph Population. Entailment Graph learning might also be expected to benefit from attention to modality. We build Entailment Graphs using a news corpus filtered with a modality parser, and show that stripping modal modifiers from predicates in fact increases performance. This suggests that for some tasks, the pragmatics of modal modification of predicates allows them to contribute as evidence of entailment.
We present a novel method for injecting temporality into entailment graphs to address the problem of spurious entailments, which may arise from similar but temporally distinct events involving the same pair of entities. We focus on the sports domain in which the same pairs of teams play on different occasions, with different outcomes. We present an unsupervised model that aims to learn entailments such as win/lose $\rightarrow$ play, while avoiding the pitfall of learning non-entailments such as win $\not\rightarrow$ lose. We evaluate our model on a manually constructed dataset, showing that incorporating time intervals and applying a temporal window around them, are effective strategies.
Community detection, aiming to group the graph nodes into clusters with dense inner-connection, is a fundamental graph mining task. Recently, it has been studied on the heterogeneous graph, which contains multiple types of nodes and edges, posing great challenges for modeling the high-order relationship between nodes. With the surge of graph embedding mechanism, it has also been adopted to community detection. A remarkable group of works use the meta-path to capture the high-order relationship between nodes and embed them into nodes' embedding to facilitate community detection. However, defining meaningful meta-paths requires much domain knowledge, which largely limits their applications, especially on schema-rich heterogeneous graphs like knowledge graphs. To alleviate this issue, in this paper, we propose to exploit the context path to capture the high-order relationship between nodes, and build a Context Path-based Graph Neural Network (CP-GNN) model. It recursively embeds the high-order relationship between nodes into the node embedding with attention mechanisms to discriminate the importance of different relationships. By maximizing the expectation of the co-occurrence of nodes connected by context paths, the model can learn the nodes' embeddings that both well preserve the high-order relationship between nodes and are helpful for community detection. Extensive experimental results on four real-world datasets show that CP-GNN outperforms the state-of-the-art community detection methods.