Heterogeneous Network Embedding Research Articles

TemporalHAN: Hierarchical attention-based heterogeneous temporal network embedding

Heterogeneous temporal network embedding aims to learn each node of different types of a heterogeneous temporal network in each snapshot into a low-dimensional vector representation, which can be used for various network analysis tasks such as node classification and relationship prediction. Our work proposes a novel heterogeneous temporal graph neural network embedding framework (TemporalHAN) based on hierarchical attention using a temporal convolutional network (TCN). In particular, we introduce node-level and semantic-level attention into heterogeneous graph neural networks to identify the importance of different levels between nodes. For each snapshot, we first utilise a new random walk algorithm (NRWA) to collect strongly connected heterogeneous neighbours for each node of different types and group them by node types. In addition, the algorithm utilises a damping factor to ensure that the more recent snapshots allocate more random walk steps. We then utilise node-level and semantic-level attention to learn the importance between a node and its random walk neighbour for a specific node type and learn the importance of different node-type for this node, respectively. Finally, we adopt TCN to capture the evolution information between snapshots. Experimental results on relationship prediction and node classification reveal that the TemporalHAN is competitive against diverse state-of-the-art approaches. Our code is available at https://github.com/Legendary-L/THAN.

Interpretable answer retrieval based on heterogeneous network embedding

Community question answering is a rising technology based on users' autonomous interactive behaviors, such as posting their issues, answering questions based on their experience, and commenting on existing questions. As a result of its use of natural language for communication and stimulation of user interest in information sharing, it has increasingly taken the place of other channels as the main way that people learn new things. Multi-type entity characteristics fusion and poor answer interpretability are the two major concerns that currently plague community answer prediction research. The Interpretable Answer Retrieval Method Based on Heterogeneous Network Embedding (IARHNE) is what we present in this work. It combines complex entity features and generates interpretable predicted answers. In order to incorporate the interactions of several kinds of individuals in answer social retrieval, we first build a heterogeneity graph. In order to acquire entity embeddings, we secondly use the heterogeneous graph neural network. We then adopt the vector distance to convert the entity matching problem in the heterogeneous information network into a homogeneous node similarity job. Finally, using entity correlation to predict answers, we provide a list of answers to the new query and interpret them using meta-paths. Comparative studies using three authentic datasets demonstrate the benefits of IARHNE for interpretative question-answering research.

MHGCN+: Multiplex Heterogeneous Graph Convolutional Network

Heterogeneous graph convolutional networks have gained great popularity in tackling various network analytical tasks on heterogeneous graph data, ranging from link prediction to node classification. However, most existing works ignore the relation heterogeneity with multiplex networks between multi-typed nodes and the different importance of relations in meta-paths for node embedding, which can hardly capture the heterogeneous structure signals across different relations. To tackle this challenge, this work proposes a M ultiplex H eterogeneous G raph C onvolutional N etwork (MHGCN+) for multiplex heterogeneous network embedding. Our MHGCN+ can automatically learn the useful heterogeneous meta-path interactions of different lengths with different importance in multiplex heterogeneous networks through multi-layer convolution aggregation. Additionally, we effectively integrate both multi-relation structural signals and attribute semantics into the learned node embeddings with both unsupervised and semi-supervised learning paradigms. Extensive experiments on seven real-world datasets with various network analytical tasks demonstrate the significant superiority of MHGCN+ against state-of-the-art embedding baselines in terms of all evaluation metrics. The source code of our method is available at: https://github.com/FuChF/MHGCN-plus.

An Adaptive Semantic Mining Framework for Heterogeneous Information Network Embedding

Heterogeneous information network (HIN) embedding aims to map heterogeneous nodes to the low-dimensional vector space. The existing embedding models cannot determine the optimal length of semantics automatically and reveal full semantic information adaptively for different heterogeneous networks. To address this challenge, an HIN embedding model with adaptive semantic mining is proposed. First, we project heterogeneous nodes into the same space and aggregate the features of target types in the first-degree range. Then, the semantics of different node types is combined through the attention mechanism, and latent meta-paths are mined using the attention coefficients. Finally, multiple feature aggregation layers are stacked with residual blocks. The residual weights control the proportion of semantics transferred between layers to aggregate more distal features selectively. In addition, we designed the Selected DropLink unit to remove links which transfer negative information, which can further improve the resistance of model to over-smoothing. Experiments show that our model can obtain more accurate embedding results and can automatically mine complex semantic connections between heterogeneous nodes without prior definition of meta-path and semantic depth.

NAGNE: Node-to-Attribute Generation Network Embedding for Heterogeneous Network

Heterogeneous network embedding aims to project multiple types of nodes into a low-dimensional space, and has become increasingly ubiquitous. However, several challenges have not been addressed so far. First, existing heterogeneous network embedding techniques typically rely on meta-paths to deal with the complex heterogeneous network. Using these meta-paths requires prior knowledge from domain experts for optimal meta-path selection. Second, few existing models can effectively consider both heterogeneous structural information and heterogeneous node attribute information. Third, existing models preserve the structure information by considering the first- and/or the second-order proximities, which cannot capture long-range structural information. To address these limitations, we propose a novel attributed heterogeneous network embedding model referred to as Node-to-Attribute Generation Network Embedding (NAGNE). NAGNE comprises two major components, the attributed random walk which samples node sequences in attributed heterogeneous network, and the node-to-attribute generation which learns the mapping that translates each node sequence itself from the node sequence to the node attribute sequence. Extensive experiments on three heterogeneous network datasets demonstrate that NAGNE outperforms state-of-the-art baselines in various data mining tasks.

MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules

According to the expression of miRNA in pathological processes, miRNAs can be divided into oncogenes or tumor suppressors. Prediction of the regulation relations between miRNAs and small molecules (SMs) becomes a vital goal for miRNA-target therapy. But traditional biological approaches are laborious and expensive. Thus, there is an urgent need to develop a computational model. In this study, we proposed a computational model to predict whether the regulatory relationship between miRNAs and SMs is up-regulated or down-regulated. Specifically, we first use the Large-scale Information Network Embedding (LINE) algorithm to construct the node features from the self-similarity networks, then use the General Attributed Multiplex Heterogeneous Network Embedding (GATNE) algorithm to extract the topological information from the attribute network, and finally utilize the Light Gradient Boosting Machine (LightGBM) algorithm to predict the regulatory relationship between miRNAs and SMs. In the fivefold cross-validation experiment, the average accuracies of the proposed model on the SM2miR dataset reached 79.59% and 80.37% for up-regulation pairs and down-regulation pairs, respectively. In addition, we compared our model with another published model. Moreover, in the case study for 5-FU, 7 of 10 candidate miRNAs are confirmed by related literature. Therefore, we believe that our model can promote the research of miRNA-targeted therapy.

A data fusion framework based on heterogeneous information network embedding for trigger-action programming in IoT

A data fusion framework based on heterogeneous information network embedding for trigger-action programming in IoT

Temporal Heterogeneous Information Network Embedding via Semantic Evolution

Real-world networks are often heterogeneous and constantly changing over time. Evolution reveals the trend of network development, which is vital for predicting its future state, and network embedding can effectively learn the information from it. Nevertheless, previous works only consider the impact of meta-path instances or node neighbors on the network dynamics but ignore the relationship between them, and hence the hidden semantic information is missed, which will result in performance deterioration. Therefore, we propose a novel temporal heterogeneous information network embedding method (SemE), which abstracts the instance of the meta-path as semantic units and then considers the interaction between them to discover deeper semantic information. Specifically, we first construct semantic networks by the Ethernet topology and the interaction between semantic units. The semantic units are sampled based on a pre-designed meta-path-guided random walk. To further capture the semantic evolution of the semantic network, we learn the embedding of nodes by the attention-Hawkes process. Finally, we generate the final embedding by aggregating the structure, semantic and temporal information with the attention mechanism. Experiments on three real-world temporal heterogeneous information networks show that our model performs better than competitive counterparts.

PMPTCE-HNEA: Predicting Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network Embedding Algorithm

Background: Metabolic chemical reaction is one of the main types of fundamental processes to maintain life. Generally, each reaction needs an enzyme. The metabolic pathway collects a series of chemical reactions at the system level. As compounds and enzymes are two important components in each metabolic pathway, identification of metabolic pathways that a given compound or enzyme can participate is the first important step for understanding the mechanism of metabolic pathways. Objective: The purpose of this study was to build efficient computational methods to predict the metabolic pathways of compounds and enzymes. Methods: Novel multi-label classifiers were proposed to identify metabolic pathway types, reported in KEGG, of compounds and enzymes. Three heterogeneous networks defining compounds and enzymes as nodes were constructed. To extract more informative features of compounds and enzymes, we generalized the powerful network embedding algorithm, Mashup, to its heterogeneous network version, named MashupH. RAndom k-labELsets (RAKEL) was employed to build the classifiers and support vector machine or random forest was selected as the base classification algorithm. Results: The 10-fold cross-validation results indicated the good performance of the proposed classifiers and such performance was superior to the previous classifier that adopted features yielded by Mashup. Furthermore, some key parameters of MashupH that might contribute to or influence the classifiers were analyzed. Conclusion: The features yielded by MashupH were more informative than those produced by Mashup on heterogeneous networks. This was the main reason the new classifiers were superior to those using features yielded by Mashup.

Multiplex heterogeneous network representation learning with unipath based global awareness neural network

Network embedding has gained great popularity in tackling various network analytical tasks, such as link prediction and node classification. However, most existing works from heterogeneous networks ignore the relation heterogeneity with multiplex networks between multi-typed nodes. To tackle this challenge, this work proposes a Unipath based global Awareness neural Network (UAN) for attributed multiplex heterogeneous network embedding. Our UAN can automatically learn useful interactions of unipath networks and the base network. Additionally, we effectively integrate both multi-relation structural signals and attribute semantics into the learned node embeddings with both unsupervised and semi-supervised learning paradigms. Extensive experiments were conducted on real-world datasets in three different domains and various network analysis tasks were performed. Experimental results demonstrate the significant superiority of UAN against state-of-the-art embedding baselines in terms of all evaluation metrics.

Protein Complex Identification Based on Heterogeneous Protein Information Network.

Protein complexes are the foundation of all cellular activities, and accurately identifying them is crucial for studying cellular systems. The efficient discovery of protein complexes is a focus of research in the field of bioinformatics. Most existing methods for protein complex identification are based on the structure of the protein-protein interaction (PPI) network, whereas some methods attempt to integrate biological information to enhance the features of the protein network for complex identification. Existing protein complex identification methods are unable to fully integrate network topology information and biological attribute information. Most of these methods are based on homogeneous networks and cannot distinguish the importance of different attributes and protein nodes. To address these issues, a GO attribute Heterogeneous Attention network Embedding (GHAE) method based on heterogeneous protein information networks is proposed. First, GHAE incorporates Gene Ontology (GO) information into the PPI network, constructing a heterogeneous protein information network. Then, GHAE uses a dual attention mechanism and heterogeneous graph convolutional representation learning method to learn protein features and to identify protein complexes. The experimental results show that building heterogeneous protein information networks can fully integrate valuable biological information. The heterogeneous graph embedding learning method can simultaneously mine the features of protein and GO attributes, thereby improving the performance of protein complex identification.

How to select crowdsourcing teams with limited information? A heterogeneous information network embedding approach

How to select crowdsourcing teams with limited information? A heterogeneous information network embedding approach

Source-Aware Embedding Training on Heterogeneous Information Networks

ABSTRACT Heterogeneous information networks (HINs) have been extensively applied to real-world tasks, such as recommendation systems, social networks, and citation networks. While existing HIN representation learning methods can effectively learn the semantic and structural features in the network, little awareness was given to the distribution discrepancy of subgraphs within a single HIN. However, we find that ignoring such distribution discrepancy among subgraphs from multiple sources would hinder the effectiveness of graph embedding learning algorithms. This motivates us to propose SUMSHINE (Scalable Unsupervised Multi-Source Heterogeneous Information Network Embedding)—a scalable unsupervised framework to align the embedding distributions among multiple sources of an HIN. Experimental results on real-world datasets in a variety of downstream tasks validate the performance of our method over the state-of-the-art heterogeneous information network embedding algorithms.

NRWalk2Vec-HIN: spammer group detection based on heterogeneous information network embedding over social media

NRWalk2Vec-HIN: spammer group detection based on heterogeneous information network embedding over social media

Multi-view computable online learner modeling by heterogeneous network: An AI-enabled perspective

To support accurate personalized online intelligent education applications in the big data environment, computable online learner modeling is very important. It can accurately capture the unique needs and characteristics of learners in a computable way and provides customized learning experiences. We propose a structured semantic embedding-based approach for online learner modeling, which considers both the multidimensional learners' characteristics and heterogeneous information on the learning context to develop a comprehensive learner model. Specifically, an AI-enabled heterogeneous information network embedding technique is employed to encode complications of different learners' characteristics and rich relationships between them, which integrate different explicit characteristic information and implicit association information about inherent multidimensional interactions for computable learners modeling. Extensive experimental results and evaluations demonstrate that the proposed model achieves the optimal performance on the Precision@N and Recall@N metrics in course recommendation tasks, and the Accuracy and F−score metrics in learner clustering tasks are also better than other baseline models, which prove the ability to boost the performance of downstream tasks by incorporating and capturing the underlying semantic and structural information among different types of nodes to fuse the embedding for learner modeling.

HeteEdgeWalk: A Heterogeneous Edge Memory Random Walk for Heterogeneous Information Network Embedding.

Most Heterogeneous Information Network (HIN) embedding methods use meta-paths to guide random walks to sample from HIN and perform representation learning in order to overcome the bias of traditional random walks that are more biased towards high-order nodes. Their performance depends on the suitability of the generated meta-paths for the current HIN. The definition of meta-paths requires domain expertise, which makes the results overly dependent on the meta-paths. Moreover, it is difficult to represent the structure of complex HIN with a single meta-path. In a meta-path guided random walk, some of the heterogeneous structures (e.g., node type(s)) are not among the node types specified by the meta-path, making this heterogeneous information ignored. In this paper, HeteEdgeWalk, a solution method that does not involve meta-paths, is proposed. We design a dynamically adjusted bidirectional edge-sampling walk strategy. Specifically, edge sampling and the storage of recently selected edge types are used to better sample the network structure in a more balanced and comprehensive way. Finally, node classification and clustering experiments are performed on four real HINs with in-depth analysis. The results show a maximum performance improvement of 2% in node classification and at least 0.6% in clustering compared to baselines. This demonstrates the superiority of the method to effectively capture semantic information from HINs.

Higher-order memory guided temporal random walk for dynamic heterogeneous network embedding

Network embedding (NE) aims at learning node embeddings via structure-based sampling. However, there are complex patterns in network structure (heterogeneity, higher-order dependence, dynamics) in the real world. The existing methods suffer from high dependence and constraints on manually designed higher-order structures and loss of fine-grained temporal information. To solve the above challenges, we propose a novel higher-order memory guided temporal random walk for dynamic heterogeneous network embedding (HoMo-DyHNE). The proposed model is a two-stage architecture consisting of a meta-structure-independent random walk algorithm namely HoMo-TRW with transition vectors and higher-order memory, and a Hawkes-based featured Skip-gram (HFSG) incorporating a multivariate Hawkes point process to measure the history-current association intensity. Extensive experiments demonstrate the superior effectiveness of our proposed method.

HeMGNN: Heterogeneous Network Embedding Based on a Mixed Graph Neural Network

Network embedding is an effective way to realize the quantitative analysis of large-scale networks. However, mainstream network embedding models are limited by the manually pre-set metapaths, which leads to the unstable performance of the model. At the same time, the information from homogeneous neighbors is mostly focused in encoding the target node, while ignoring the role of heterogeneous neighbors in the node embedding. This paper proposes a new embedding model, HeMGNN, for heterogeneous networks. The framework of the HeMGNN model is divided into two modules: the metapath subgraph extraction module and the node embedding mixing module. In the metapath subgraph extraction module, HeMGNN automatically generates and filters out the metapaths related to domain mining tasks, so as to effectively avoid the excessive dependence of network embedding on artificial prior knowledge. In the node embedding mixing module, HeMGNN integrates the information of homogeneous and heterogeneous neighbors when learning the embedding of the target nodes. This makes the node vectors generated according to the HeMGNN model contain more abundant topological and semantic information provided by the heterogeneous networks. The Rich semantic information makes the node vectors achieve good performance in downstream domain mining tasks. The experimental results show that, compared to the baseline models, the average classification and clustering performance of HeMGNN has improved by up to 0.3141 and 0.2235, respectively.

A multi-view contrastive learning for heterogeneous network embedding

Graph contrastive learning has been developed to learn discriminative node representations on homogeneous graphs. However, it is not clear how to augment the heterogeneous graphs without substantially altering the underlying semantics or how to design appropriate pretext tasks to fully capture the rich semantics preserved in heterogeneous information networks (HINs). Moreover, early investigations demonstrate that contrastive learning suffer from sampling bias, whereas conventional debiasing techniques (e.g., hard negative mining) are empirically shown to be inadequate for graph contrastive learning. How to mitigate the sampling bias on heterogeneous graphs is another important yet neglected problem. To address the aforementioned challenges, we propose a novel multi-view heterogeneous graph contrastive learning framework in this paper. We use metapaths, each of which depicts a complementary element of HINs, as the augmentation to generate multiple subgraphs (i.e., multi-views), and propose a novel pretext task to maximize the coherence between each pair of metapath-induced views. Furthermore, we employ a positive sampling strategy to explicitly select hard positives by jointly considering semantics and structures preserved on each metapath view to alleviate the sampling bias. Extensive experiments demonstrate MCL consistently outperforms state-of-the-art baselines on five real-world benchmark datasets and even its supervised counterparts in some settings.

DeHIN: A Decentralized Framework for Embedding Large-Scale Heterogeneous Information Networks

Modeling heterogeneity by extraction and exploitation of high-order information from heterogeneous information networks (HINs) has been attracting immense research attention in recent times. Such heterogeneous network embedding (HNE) methods effectively harness the heterogeneity of small-scale HINs. However, in the real world, the size of HINs grow exponentially with the continuous introduction of new nodes and different types of links, making it a billion-scale network. Learning node embeddings on such HINs creates a performance bottleneck for existing HNE methods that are commonly centralized, i.e., complete data and the model are both on a single machine. To address large-scale HNE tasks with strong efficiency and effectiveness guarantee, we present <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Decentralized Embedding Framework for Heterogeneous Information Network</i> (DeHIN) in this paper. In DeHIN, we generate a distributed parallel pipeline that utilizes hypergraphs in order to infuse parallelization into the HNE task. DeHIN presents a context preserving partition mechanism that innovatively formulates a large HIN as a hypergraph, whose hyperedges connect semantically similar nodes. Our framework then adopts a decentralized strategy to efficiently partition HINs by adopting a tree-like pipeline. Then, each resulting subnetwork is assigned to a distributed worker, which employs the deep information maximization theorem to locally learn node embeddings from the partition it receives. We further devise a novel embedding alignment scheme to precisely project independently learned node embeddings from all subnetworks onto a common vector space, thus allowing for downstream tasks like link prediction and node classification. As shown from our experimental results, DeHIN significantly improves the efficiency and accuracy of existing HNE models as well as outperforms the large-scale graph embedding frameworks by efficiently scaling up to large-scale HINs.