Link prediction (inferring missing or future connections between nodes in a graph) is a fundamental problem in network science with widespread applications in, e.g., biological systems, recommender systems, finance and cybersecurity. The ability to accurately predict links has significant real-world applications, such as detecting fraudulent financial transactions or identifying drug-target interactions in biomedicine. Despite a rich literature, link prediction is still challenging, especially for graphs enriched with information on edges (direction) and nodes (attributes). In fact, research on link prediction, especially the one based on Graph Deep Learning (GDL), has mostly focused on undirected graphs, without fully leveraging node attributes. Here, we fill this gap by proposing Gravity-GraphSAGE (GG-SAGE), a modified version of GraphSAGE, a GDL model for node embeddings, composed of a gravity-inspired decoder. This implementation is the first example in the literature of a GraphSAGE backbone adopted for directed link prediction. Using the benchmark datasets Cora, Citeseer, PubMed and 16 real-world graphs from the online Netzschleuder repository, we show that our proposed model outperforms state-of-the-art GDL link prediction techniques. Using further experimental evidence, we relate the quality of the output of our model with various characteristics of the graph, suggesting that our framework scales well when applied to data of increasing complexity.

Pseudo labeling (PL) is a wide-applied strategy to enlarge the labeled dataset by self-annotating the potential samples during the training process. Several works have shown that it can improve the graph learning model performance in general. However, we notice that the incorrect labels can be fatal to the graph training process. Inappropriate PL may result in the performance degrading, especially on graph data where the noise can propagate. Surprisingly, the corresponding error is seldom theoretically analyzed in the literature.

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization-based baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings which highlights that the negative edges used in the current evaluation are easy. To sample more challenging negative edges, we introduce two novel negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

Network embedding plays a significant role in a variety of applications. To capture the topology of the network, most of the existing network embedding algorithms follow a sampling training procedure, which maximizes the similarity (e.g., embedding vectors' dot product) between positively sampled node pairs and minimizes the similarity between negatively sampled node pairs in the embedding space. Typically, close node pairs function as positive samples while distant node pairs are usually considered as negative samples. However, under different or even competing sampling strategies, some methods champion sampling distant node pairs as positive samples to encapsulate longer distance information in link prediction, whereas others advocate adding close nodes into the negative sample set to boost the performance of node recommendation. In this paper, we seek to understand the intrinsic relationships between these competing strategies. To this end, we identify two properties (discrimination and monotonicity) that given any node pair proximity distribution, node embeddings should embrace. Moreover, we quantify the empirical error of the trained similarity score w.r.t. the sampling strategy, which leads to an important finding that the discrimination property and the monotonicity property for all node pairs can not be satisfied simultaneously in real-world applications. Guided by such analysis, a simple yet novel model (SENSEI) is proposed, which seamlessly fulfills the discrimination property and the partial monotonicity within the top-K ranking list. Extensive experiments show that SENSEI outperforms the state-of-the-arts in plain network embedding.

Link prediction attempts to predict whether an unseen edge exists based on only a portion of edges of a graph. A flurry of methods have been introduced in recent years that attempt to make use of graph neural networks (GNNs) for this task. Furthermore, new and diverse datasets have also been created to better evaluate the effectiveness of these new models. However, multiple pitfalls currently exist that hinder our ability to properly evaluate these new methods. These pitfalls mainly include: (1) Lower than actual performance on multiple baselines, (2) A lack of a unified data split and evaluation metric on some datasets, and (3) An unrealistic evaluation setting that uses easy negative samples. To overcome these challenges, we first conduct a fair comparison across prominent methods and datasets, utilizing the same dataset and hyperparameter search settings. We then create a more practical evaluation setting based on a Heuristic Related Sampling Technique (HeaRT), which samples hard negative samples via multiple heuristics. The new evaluation setting helps promote new challenges and opportunities in link prediction by aligning the evaluation with real-world situations.