Neighborhood and PageRank methods for pairwise link prediction

Introduction Network representation can give a holistic view of relationships for biomedical entities through network topology. Link prediction estimates the probability of link formation between the pair of unconnected nodes. In the drug discovery process, the link prediction method not only enables the detection of connectivity patterns but also predicts the effects of one biomedical entity to multiple entities simultaneously and vice versa, which is useful for many applications. Areas covered The authors provide a comprehensive overview of network link prediction in drug discovery. Link prediction methodologies such as similarity-based approaches, embedding-based approaches, probabilistic model-based approaches, and preprocessing methods are summarized with examples. In addition to describing their properties and limitations, the authors discuss the applications of link prediction in drug discovery based on the relationship between biomedical concepts. Expert opinion Link prediction is a powerful method to infer the existence of novel relationships in drug discovery. However, link prediction has been hampered by the sparsity of data and the lack of negative links in biomedical networks. With preprocessing to balance positive and negative samples and the collection of more data, the authors believe it is possible to develop more reliable link prediction methods that can become invaluable tools for successful drug discovery.

Link prediction based on bipartite networks can not only mine hidden relationships between different types of nodes, but also reveal the inherent law of network evolution. Existing bipartite network link prediction is mainly based on the global structure that cannot analyze the role of the local structure in link prediction. To tackle this problem, this paper proposes a deep link-prediction (DLP) method by leveraging the local structure of bipartite networks. The method first extracts the local structure between target nodes and observes structural information between nodes from a local perspective. Then, representation learning of the local structure is performed on the basis of the graph neural network to extract latent features between target nodes. Lastly, a deep-link prediction model is trained on the basis of latent features between target nodes to achieve link prediction. Experimental results on five datasets showed that DLP achieved significant improvement over existing state-of-the-art link prediction methods. In addition, this paper analyzes the relationship between local structure and link prediction, confirming the effectiveness of a local structure in link prediction.

Improving local clustering based top-L link prediction methods via asymmetric link clustering information

Many link prediction methods have been developed in past few decades in network science, and most of them are tailored for specific fields that lose generalities. Luckily, a recent work named Structural Perturbation Method (SPM) proposed a consistency index of network organization without priori knowledge, and it did not need to test those predicting methods first. Since demonstrating whether there is a link between two nodes is usually costly, we want to replace link confirmation with link prediction. In this paper, we use the SPM method to study the structure of US political blog network and analyze the link predictability at different network scales. The experimental results show that we can obtain basic intrinsic features of the network structure and can get ideal prediction results as long as 20% of the network structures.

Link prediction is widely used in network analysis to identify future links between nodes. Link prediction has an important place in terms of being applicable to many real-world networks with dynamic structure. Networks with dynamic structure, such as social networks, scientific collaboration networks and metabolic networks, are networks in which link prediction studies are performed. In addition, it is seen that there are few studies showing the feasibility of link prediction by creating networks from different areas. In this study, in order to show the applicability of link prediction processes in different fields link prediction was made by applying traditional link prediction methods in the networks formed from the data of football competitions played after the groups between the years 2004–2017 in the UEFA European League. The AUC metric was used to measure the success of forecasting. The results show that link prediction methods can be used in sports networks.

Link prediction aims to find the missing link in current networks or estimate the likelihood the link will appear in the future. In many real-world scenarios, networks can be massive and drastically evolving. Many recent works concentrated on how to solve the procession of massive data, which cares less about the effects of the temporal information. In some dynamic networks, the edge that appears a long time ago will have fewer effects on the appearance of edges in the future. The accuracy of link prediction in dynamic networks can be further improved by adding temporal information in prediction measures. In this paper, we mainly explore the effects of the link temporal information in the graph stream link prediction. We design a graph stream-based framework to solve link prediction problems in dynamic networks which can provide a convenient platform to implement different link prediction methods for dynamic networks, and evaluate these methods on a fair basis. Then, we proposed the Time Decay-based Link Prediction (TDLP) method to improve the efficient of link prediction problem in the dynamic networks. TDLP extends the neighborhood-based measure with time decay functions in graph stream scenarios which can handle temporal information and massive data. Experiment results demonstrate that the accuracy of link prediction for dynamic networks can be efficiently improved in our TDLP method.

An evidential link prediction method and link predictability based on Shannon entropy

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.

Many link prediction methods have been developed to infer unobserved links or predict missing links based on the observed network structure that is always incomplete and subject to interfering noise. Thus, the performance of existing methods is usually limited in that their computation depends only on input graph structures, and they do not consider external information. The effects of social influence and homophily suggest that both network structure and node attribute information should help to resolve the task of link prediction. This work proposes SASNMF, a link prediction unified framework based on non-negative matrix factorization that considers not only graph structure but also the internal and external auxiliary information, which refers to both the node attributes and the structural latent feature information extracted from the network. Furthermore, three different combinations of internal and external information are proposed and input into the framework to solve the link prediction problem. Extensive experimental results on thirteen real networks, five node attribute networks and eight non-attribute networks show that the proposed framework has competitive performance compared with benchmark methods and state-of-the-art methods, indicating the superiority of the presented algorithm.

Improving embedding-based link prediction performance using clustering

A heterogeneous information network, which is composed of various types of nodes and edges, has a complex structure and rich information content, and is widely used in social networks, academic networks, e-commerce, and other fields. Link prediction, as a key task to reveal the unobserved relationships in the network, is of great significance in heterogeneous information networks. This paper reviews the application of presentation-based learning methods in link prediction of heterogeneous information networks. This paper introduces the basic concepts of heterogeneous information networks, and the theoretical basis of representation learning, and discusses the specific application of the deep learning model in node embedding learning and link prediction in detail. The effectiveness and superiority of these methods on multiple real data sets are demonstrated by experimental verification.

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

In the link prediction problem, formulated as a binary classification problem, we want to classify each pair of disconnected nodes in the network whether they will be connected by a link in the future. We study link formation in social networks with two types of links over several time periods. To solve the link prediction problem, we follow the approach of counting 3-node graphlets and suggest three extensions to the original method. By performing experiments on two real-world social networks we show that the new methods have a predictive power, however, network evolution cannot be explained by one specific feature at all time points. We also observe that some network properties can point at features which are more effective for temporal link prediction.

Bounded link prediction in very large networks

Proximity measures for link prediction based on temporal events