MGLGAN：a generative adversarial model based on multi-layer graph convolution net and recurrent neural networks for link prediction

Network representation learning algorithms, which aim at automatically encoding graphs into low-dimensional vector representations with a variety of node similarity definitions, have a wide range of downstream applications. Most existing methods either have low accuracies in downstream tasks or a very limited application field, such as article classification in citation networks. In this paper, we propose a novel network representation method, named Link Prediction based Network Representation (LPNR), which generalizes the latest graph neural network and optimizes a carefully designed objective function that preserves linkage structures. LPNR can not only learn meaningful node representations that achieve competitive accuracy in node centrality measurement and community detection but also achieve high accuracy in the link prediction task. Experiments prove the effectiveness of LPNR on three real-world networks. With the mini-batch and fixed sampling strategy, LPNR can learn the embedding of large graphs in a few hours.

In recent years, network embedding has attracted much attention from researchers and achieved excellent performance. But few works investigate the adaptability of network embedding, especially for performance in different network structures. Heterogeneity, as a universal topological characteristic, plays a prominent role in network behaviors. In this study, we investigate the effect of heterogeneity on the effectiveness of existing network embedding approaches. We conduct experiments in scale-free networks with varying power exponents from both macro and micro perspectives to address link prediction and node similarity tasks, respectively. The results indicate that network embedding approaches can be divided into two classes according to their performance in the link prediction task. As the network heterogeneity decreases, the performance of approaches in the first class declines, while the performance of approaches in the second class initially improves and then declines. Moreover, our simulation discovers that, based on the node similarity metric, nodes are partitioned into two clusters by approaches, corresponding to large-degree nodes and small-degree nodes, respectively. Furthermore, approaches in the same class present similar characteristics between large-degree nodes and small-degree nodes, and the embedding is interpreted to some extent. Performance variations in the link prediction task can be explained by the characteristics of approaches, and similar characteristics are confirmed in experiments on real networks. Based on the findings for link prediction, we offer a brief guide for choosing an appropriate method based on the extent of heterogeneity. The investigation provides insight into network embedding and offers some interpretation of embedding.

Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer’s, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet’s interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.

Cross-subject emotion recognition in brain-computer interface based on frequency band attention graph convolutional adversarial neural networks

Knowledge graph embedding models are used to learn low‐dimensional representations of entities and relations in knowledge graphs. In this paper, we propose Multi‐RAttE, an attention‐based learning method for multiple relational knowledge graph embedding representation, which divides the information transfer in the knowledge graph into cross‐relational information transfer and relation‐specific information transfer, and divides the embedding of knowledge graph entities into structural embedding and multi‐relational embedding for joint learning. To objectively analyse the performance of the Multi‐RAttE model, we select two typical datasets and different representative baseline models for experimental evaluation on several tasks such as link prediction, multi‐relation prediction and node classification. The experimental results show that the Multi‐RAttE model improves 8% over the state‐of‐the‐art model Composition‐based Multi‐Relational Graph Convolutional Networks (CompGCN) in terms of Hits@1 metric on the link prediction task on FB15k‐237 dataset; on the multi‐relation prediction task, the accuracy improves by 1.8% and 3.7% in the auc metric and F1 metric, respectively. The experimental results have proved that the Multi‐RAttE model can effectively perform the representation of multiple relations.

With regards to network structured data nowadays, link prediction stands out as a key problem. It has been observed that interactions between the entities act as the basic foundations of many applications in various fields such as chemistry, biology, or social networks. In the previous studies on this subject, most of the approaches used heuristics methods with an evaluation function to find the similarity index between entities, thereby predicting the possibility of links between them. However, heuristics methods are based on assumptions about the existence of associations between entities; thus its shortcoming is that when these assumptions are not accurate, the results of the algorithm would be reduced significantly. Taking those into considerations, in this paper, we propose a method to solve this problem based on deep graph convolutional neural network. Experimental results on paper citation network dataset have shown that particular and this method is promising.KeywordsGraph neural networksDeep graph convolutional neural networkLink predictionPaper citation network

Video-based human action recognition is one of the most important and challenging areas of research in the field of computer vision. Human action recognition has found many pragmatic applications in video surveillance, human-computer interaction, entertainment, autonomous driving, etc. Owing to the recent development of deep learning methods for human action recognition, the performance of action recognition has significantly enhanced for challenging datasets. Deep learning techniques are mainly used for recognizing actions in images and videos comprising of Euclidean data. A recent development in deep learning methods is the extension of these techniques to non-Euclidean data or graph data with many nodes and edges. Human body skeleton resembles a graph, therefore, the graph convolutional network (GCN) is applicable to the non-Euclidean body skeleton. In the past few years, GCN has emerged as an important tool for skeleton-based action recognition. Therefore, we conduct a survey using GCN methods for action recognition. Herein, we present a comprehensive overview of recent GCN techniques for action recognition, propose a taxonomy for the categorization of GCN techniques for action recognition, carry out a detailed study of the benchmark datasets, enlist relevant resources and open-source codes, and finally provide an outline for future research directions and trends. To the best of authors' knowledge, this is the first survey for action recognition using GCN techniques.

The link prediction problem is a time-evolving model in network science that has simultaneously abetted myriad applications and experienced extensive methodological improvement. Inferring the possibility of emerging links in dynamic social networks, also known as the dynamic link prediction task, is complex and challenging. In contrast to the link prediction in cross-sectional networks, dynamic link prediction methods need to cater to the actor-level temporal changes and associated evolutionary information regarding their micro- (i.e., link formation/deletion) and mesoscale (i.e., community formation) network structure. With the advent of abundant community detection algorithms, the research community has examined community-aware link prediction strategies in static networks. However, the same task in dynamic networks where, apart from the actors and links among them, their community pattern is also dynamic, is yet to be explored. Evolutionary community-aware information, including the associated link structure and temporal neighborhood changes, can effectively be mined to build dynamic similarity metrics for dynamic link prediction. This study aims to develop and integrate such dynamic features with machine learning algorithms for link prediction tasks in dynamic social networks. It also compares the performances of these features against well-known similarity metrics (i.e., ResourceAllocation) for static networks and a time series-based link prediction strategy in dynamic networks. These proposed features achieved high-performance scores, representing them as prospective candidates for both dynamic link prediction tasks and modeling the network growth.

Real-world graphs are dynamic, constantly evolving with new interactions, such as financial transactions in financial networks. Temporal Graph Neural Networks (TGNNs) have been developed to effectively capture the evolving patterns in dynamic graphs. While these models have demonstrated their superiority, being widely adopted in various important fields, their vulnerabilities against adversarial attacks remain largely unexplored. In this paper, we propose T-SPEAR, a simple and effective adversarial attack method for link prediction on continuous-time dynamic graphs, focusing on investigating the vulnerabilities of TGNNs. Specifically, before the training procedure of a victim model, which is a TGNN for link prediction, we inject edge perturbations to the data that are unnoticeable in terms of the four constraints we propose, and yet effective enough to cause malfunction of the victim model. Moreover, we propose a robust training approach T-SHIELD to mitigate the impact of adversarial attacks. By using edge filtering and enforcing temporal smoothness to node embeddings, we enhance the robustness of the victim model. Our experimental study shows that T-SPEAR significantly degrades the victim model's performance on link prediction tasks, and even more, our attacks are transferable to other TGNNs, which differ from the victim model assumed by the attacker. Moreover, we demonstrate that T-SHIELD effectively filters out adversarial edges and exhibits robustness against adversarial attacks, surpassing the link prediction performance of the naive TGNN by up to 11.2% under T-SPEAR. The code and datasets are available at https://github.com/wooner49/T-spear-shield

With the large amount of complex network data that is increasingly available on the Web, link prediction has become a popular data-mining research field. The focus of this paper is on a link-prediction task that can be formulated as a binary classification problem in complex networks. To solve this link-prediction problem, a sparse-classification algorithm called “Truncated Kernel Projection Machine” that is based on empirical-feature selection is proposed. The proposed algorithm is a novel way to achieve a realization of sparse empirical-feature-based learning that is different from those of the regularized kernel-projection machines. The algorithm is more appealing than those of the previous outstanding learning machines since it can be computed efficiently, and it is also implemented easily and stably during the link-prediction task. The algorithm is applied here for link-prediction tasks in different complex networks, and an investigation of several classification algorithms was performed for comparison. The experimental results show that the proposed algorithm outperformed the compared algorithms in several key indices with a smaller number of test errors and greater stability.

Deep models can be made scale-invariant when trained with multi-scale information. Images can be easily made multi-scale, given their grid-like structures. Extending this to generic graphs poses major challenges. For example, in link prediction tasks, inputs are represented as graphs consisting of nodes and edges. Currently, the state-of-the-art model for link prediction uses supervised heuristic learning, which learns graph structure features centered on two target nodes. It then learns graph neural networks to predict the existence of links based on graph structure features. Thus, the performance of link prediction models highly depends on graph structure features. In this work, we propose a novel node aggregation method that can transform the enclosing subgraph into different scales and preserve the relationship between two target nodes for link prediction. A theory for analyzing the information loss during the re-scaling procedure is also provided. Graphs in different scales can provide scale-invariant information, which enables graph neural networks to learn invariant features and improve link prediction performance. Our experimental results on 14 datasets from different areas demonstrate that our proposed method outperforms the state-of-the-art methods by employing multi-scale graphs without additional parameters.

Graph representation learning is a fundamental technique for machine learning (ML) on complex networks. Given an input network, these methods represent the vertices by low-dimensional real-valued vectors. These vectors can be used for a multitude of downstream ML tasks. We study one of the most important such task, link prediction. Much of the recent literature on graph representation learning has shown remarkable success in link prediction. On closer investigation, we observe that the performance is measured by the AUC (area under the curve), which suffers biases. Since the ground truth in link prediction is sparse, we design a vertex-centric measure of performance, called the VCMPR@k plots. Under this measure, we show that link predictors using graph representations show poor scores. Despite having extremely high AUC scores, the predictors miss much of the ground truth. We identify a mathematical connection between this performance, the sparsity of the ground truth, and the low-dimensional geometry of the node embeddings. Under a formal theoretical framework, we prove that low-dimensional vectors cannot capture sparse ground truth using dot product similarities (the standard practice in the literature). Our results call into question existing results on link prediction and pose a significant scientific challenge for graph representation learning. The VCMPR plots identify specific scientific challenges for link prediction using low-dimensional node embeddings.

Network embedding models aim to learn low-dimensional representations for nodes and/or edges in graphs. For social networks, learning edge representations is especially beneficial as we need to describe or explain the relationships, activities, and interactions between users. Existing approaches that learn stand-alone node embeddings, and represent edges as pairs of node embeddings, are limited in their applicability because nodes participate in multiple relationships, which should be considered. In addition, social networks often contain multiple types of edges, which yields multi-view contexts that need to be considered in the representation. In this paper, we propose a new methodology, MERL, that (1) captures asymmetry in multiple views by learning well-defined edge representations that are responsive to the difference between the source and destination node roles, and (2) incorporates textual communications to identify multiple source of social signals (e.g. strength and affinity) that moderate the impact of different views between users. Our experiments show that MERL outperforms alternative state-of-the-art embedding models on link prediction and multilabel classification tasks across multiple views in social network datasets. We further analyze the learned embeddings of MERL and demonstrate they are more correlated with the existence of view-based edges compared to previous methods.

We propose to use segment graph convolutional and recurrent neural networks (Seg-GCRNs), which use only word embedding and sentence syntactic dependencies, to classify relations from clinical notes without manual feature engineering. In this study, the relations between 2 medical concepts are classified by simultaneously learning representations of text segments in the context of sentence syntactic dependency: preceding, concept1, middle, concept2, and succeeding segments. Seg-GCRN was systematically evaluated on the i2b2/VA relation classification challenge datasets. Experiments show that Seg-GCRN attains state-of-the-art micro-averaged F-measure for all 3 relation categories: 0.692 for classifying medical treatment-problem relations, 0.827 for medical test-problem relations, and 0.741 for medical problem-medical problem relations. Comparison with the previous state-of-the-art segment convolutional neural network (Seg-CNN) suggests that adding syntactic dependency information helps refine medical word embedding and improves concept relation classification without manual feature engineering. Seg-GCRN can be trained efficiently for the i2b2/VA dataset on a GPU platform.

Users of online social networks voluntarily participate in different user groups or communities. Researches suggest the presence of strong local community structure in these social networks, i.e., users tend to meet other people via mutual friendship. Recently, different approaches have considered communities structure information for increasing the link prediction accuracy. Nevertheless, these approaches consider that users belong to just one community. In this paper, we propose three measures for the link prediction task which take into account all different communities that users belong to. We perform experiments for both unsupervised and supervised link prediction strategies. The evaluation method considers the links imbalance problem. Results show that our proposals outperform state-of-the-art unsupervised link prediction measures and help to improve the link prediction task approached as a supervised strategy.KeywordsLink predictionsocial networkscommunitiessocial network analysisgraph mining