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.
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 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.
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.
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.
Graph Neural Networks (GNNs) have already been widely applied in various graph mining tasks. However, they suffer from the shallow architecture issue, which is the key impediment that hinders the model performance improvement. Although several relevant approaches have been proposed, none of the existing studies provides an in-depth understanding of the root causes of performance degradation in deep GNNs. In this paper, we conduct the first systematic experimental evaluation to present the fundamental limitations of shallow architectures. Based on the experimental results, we answer the following two essential questions: (1) what actually leads to the compromised performance of deep GNNs; (2) when we need and how to build deep GNNs. The answers to the above questions provide empirical insights and guidelines for researchers to design deep and well-performed GNNs. To show the effectiveness of our proposed guidelines, we present Deep Graph Multi-Layer Perceptron (DGMLP), a powerful approach (a paradigm in its own right) that helps guide deep GNN designs. Experimental results demonstrate three advantages of DGMLP: 1) high accuracy -- it achieves state-of-the-art node classification performance on various datasets; 2) high flexibility -- it can flexibly choose different propagation and transformation depths according to graph size and sparsity; 3) high scalability and efficiency -- it supports fast training on large-scale graphs. Our code is available in https://github.com/zwt233/DGMLP.
Recently, Network Embedding (NE) has become one of the most attractive research topics in machine learning and data mining. NE approaches have achieved promising performance in various of graph mining tasks including link prediction and node clustering and classification. A wide variety of NE methods focus on the proximity of networks. They learn community-oriented embedding for each node, where the corresponding representations are similar if two nodes are closer to each other in the network. Meanwhile, there is another type of structural similarity, i.e., role-based similarity, which is usually complementary and completely different from the proximity. In order to preserve the role-based structural similarity, the problem of role-oriented NE is raised. However, compared to community-oriented NE problem, there are only a few role-oriented embedding approaches proposed recently. Although less explored, considering the importance of roles in analyzing networks and many applications that role-oriented NE can shed light on, it is necessary and timely to provide a comprehensive overview of existing role-oriented NE methods. In this review, we first clarify the differences between community-oriented and role-oriented network embedding. Afterwards, we propose a general framework for understanding role-oriented NE and a two-level categorization to better classify existing methods. Then, we select some representative methods according to the proposed categorization and briefly introduce them by discussing their motivation, development and differences. Moreover, we conduct comprehensive experiments to empirically evaluate these methods on a variety of role-related tasks including node classification and clustering (role discovery), top-k similarity search and visualization using some widely used synthetic and real-world datasets...
Relation prediction among entities in images is an important step in scene graph generation (SGG), which further impacts various visual understanding and reasoning tasks. Existing SGG frameworks, however, require heavy training yet are incapable of modeling unseen (i.e.,zero-shot) triplets. In this work, we stress that such incapability is due to the lack of commonsense reasoning,i.e., the ability to associate similar entities and infer similar relations based on general understanding of the world. To fill this gap, we propose CommOnsense-integrAted sCenegrapHrElation pRediction (COACHER), a framework to integrate commonsense knowledge for SGG, especially for zero-shot relation prediction. Specifically, we develop novel graph mining pipelines to model the neighborhoods and paths around entities in an external commonsense knowledge graph, and integrate them on top of state-of-the-art SGG frameworks. Extensive quantitative evaluations and qualitative case studies on both original and manipulated datasets from Visual Genome demonstrate the effectiveness of our proposed approach.
Graphs have been widely used in data mining and machine learning due to their unique representation of real-world objects and their interactions. As graphs are getting bigger and bigger nowadays, it is common to see their subgraphs separately collected and stored in multiple local systems. Therefore, it is natural to consider the subgraph federated learning setting, where each local system holds a small subgraph that may be biased from the distribution of the whole graph. Hence, the subgraph federated learning aims to collaboratively train a powerful and generalizable graph mining model without directly sharing their graph data. In this work, towards the novel yet realistic setting of subgraph federated learning, we propose two major techniques: (1) FedSage, which trains a GraphSage model based on FedAvg to integrate node features, link structures, and task labels on multiple local subgraphs; (2) FedSage+, which trains a missing neighbor generator along FedSage to deal with missing links across local subgraphs. Empirical results on four real-world graph datasets with synthesized subgraph federated learning settings demonstrate the effectiveness and efficiency of our proposed techniques. At the same time, consistent theoretical implications are made towards their generalization ability on the global graphs.
Federated learning has emerged as an important paradigm for training machine learning models in different domains. For graph-level tasks such as graph classification, graphs can also be regarded as a special type of data samples, which can be collected and stored in separate local systems. Similar to other domains, multiple local systems, each holding a small set of graphs, may benefit from collaboratively training a powerful graph mining model, such as the popular graph neural networks (GNNs). To provide more motivation towards such endeavors, we analyze real-world graphs from different domains to confirm that they indeed share certain graph properties that are statistically significant compared with random graphs. However, we also find that different sets of graphs, even from the same domain or same dataset, are non-IID regarding both graph structures and node features. To handle this, we propose a graph clustered federated learning (GCFL) framework that dynamically finds clusters of local systems based on the gradients of GNNs, and theoretically justify that such clusters can reduce the structure and feature heterogeneity among graphs owned by the local systems. Moreover, we observe the gradients of GNNs to be rather fluctuating in GCFL which impedes high-quality clustering, and design a gradient sequence-based clustering mechanism based on dynamic time warping (GCFL+). Extensive experimental results and in-depth analysis demonstrate the effectiveness of our proposed frameworks.
Data scientists across disciplines are increasingly in need of exploratory analysis tools for data sets with a high volume of features of mixed data type (quantitative continuous and discrete categorical). We introduce Sirius, a novel visualization package for researchers to explore feature relationships among mixed data types using mutual information. The visualization of feature relationships aids data scientists in finding meaningful dependence among features prior to the development of predictive modeling pipelines, which can inform downstream analysis such as feature selection, feature extraction, and early detection of potential proxy variables. Using an information theoretic approach, Sirius supports network visualization of heterogeneous data sets (consisting of continuous and discrete data types), and provides a user interface for exploring feature pairs with locally significant mutual information scores. Mutual information algorithm and bivariate chart types are assigned on a data type pairing basis (continuous-continuous, discrete-discrete, and discrete-continuous). We show how this tool can be used for tasks such as hypothesis confirmation, identification of predictive features, suggestions for feature extraction, or early warning of data abnormalities. The accompanying website for this paper can be accessed at https://sirius.universalities.com/. All code and supplemental materials can be accessed at https://osf.io/pdm9r/.
Finding dense subgraphs of a large graph is a standard problem in graph mining that has been studied extensively both for its theoretical richness and its many practical applications. In this paper we introduce a new family of dense subgraph objectives, parameterized by a single parameter $p$, based on computing generalized means of degree sequences of a subgraph. Our objective captures both the standard densest subgraph problem and the maximum $k$-core as special cases, and provides a way to interpolate between and extrapolate beyond these two objectives when searching for other notions of dense subgraphs. In terms of algorithmic contributions, we first show that our objective can be minimized in polynomial time for all $p \geq 1$ using repeated submodular minimization. A major contribution of our work is analyzing the performance of different types of peeling algorithms for dense subgraphs both in theory and practice. We prove that the standard peeling algorithm can perform arbitrarily poorly on our generalized objective, but we then design a more sophisticated peeling method which for $p \geq 1$ has an approximation guarantee that is always at least $1/2$ and converges to 1 as $p \rightarrow \infty$. In practice, we show that this algorithm obtains extremely good approximations to the optimal solution, scales to large graphs, and highlights a range of different meaningful notions of density on graphs coming from numerous domains. Furthermore, it is typically able to approximate the densest subgraph problem better than the standard peeling algorithm, by better accounting for how the removal of one node affects other nodes in its neighborhood.
Graph embedding is essential for graph mining tasks. With the prevalence of graph data in real-world applications, many methods have been proposed in recent years to learn high-quality graph embedding vectors various types of graphs. However, most existing methods usually randomly select the negative samples from the original graph to enhance the training data without considering the noise. In addition, most of these methods only focus on the explicit graph structures and cannot fully capture complex semantics of edges such as various relationships or asymmetry. In order to address these issues, we propose a robust and generalized framework for adversarial graph embedding based on generative adversarial networks. Inspired by generative adversarial network, we propose a robust and generalized framework for adversarial graph embedding, named AGE. AGE generates the fake neighbor nodes as the enhanced negative samples from the implicit distribution, and enables the discriminator and generator to jointly learn each node's robust and generalized representation. Based on this framework, we propose three models to handle three types of graph data and derive the corresponding optimization algorithms, i.e., UG-AGE and DG-AGE for undirected and directed homogeneous graphs, respectively, and HIN-AGE for heterogeneous information networks. Extensive experiments show that our methods consistently and significantly outperform existing state-of-the-art methods across multiple graph mining tasks, including link prediction, node classification, and graph reconstruction.
The anonymity of blockchain has accelerated the growth of illegal activities and criminal behaviors on cryptocurrency platforms. Although decentralization is one of the typical characteristics of blockchain, we urgently call for effective regulation to detect these illegal behaviors to ensure the safety and stability of user transactions. Identity inference, which aims to make a preliminary inference about account identity, plays a significant role in blockchain security. As a common tool, graph mining technique can effectively represent the interactive information between accounts and be used for identity inference. However, existing methods cannot balance scalability and end-to-end architecture, resulting high computational consumption and weak feature representation. In this paper, we present a novel approach to analyze user's behavior from the perspective of the transaction subgraph, which naturally transforms the identity inference task into a graph classification pattern and effectively avoids computation in large-scale graph. Furthermore, we propose a generic end-to-end graph neural network model, named $\text{I}^2 \text{BGNN}$, which can accept subgraph as input and learn a function mapping the transaction subgraph pattern to account identity, achieving de-anonymization. Extensive experiments on EOSG and ETHG datasets demonstrate that the proposed method achieve the state-of-the-art performance in identity inference.