Related papers: Few-shot link prediction via graph neural networks…
Knowledge graph (KG) is used to represent data in terms of entities and structural relations between the entities. This representation can be used to solve complex problems such as recommendation systems and question answering. In this…
Drug repurposing is more relevant than ever due to drug development's rising costs and the need to respond to emerging diseases quickly. Knowledge graph embedding enables drug repurposing using heterogeneous data sources combined with…
Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning…
Link prediction for knowledge graphs aims to predict missing connections between entities. Prevailing methods are limited to a transductive setting and hard to process unseen entities. The recent proposed subgraph-based models provided…
Many practical graph problems, such as knowledge graph construction and drug-drug interaction prediction, require to handle multi-relational graphs. However, handling real-world multi-relational graphs with Graph Neural Networks (GNNs) is…
In the last decades, people have been consuming and combining more drugs than before, increasing the number of Drug-Drug Interactions (DDIs). To predict unknown DDIs, recently, studies started incorporating Knowledge Graphs (KGs) since they…
Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…
Few-shot inductive link prediction on knowledge graphs (KGs) aims to predict missing links for unseen entities with few-shot links observed. Previous methods are limited to transductive scenarios, where entities exist in the knowledge…
Drug combinations are frequently used for the treatment of cancer patients in order to increase efficacy, decrease adverse side effects, or overcome drug resistance. Given the enormous number of drug combinations, it is cost- and…
Background: Computational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan…
Drug repurposing has historically been an economically infeasible process for identifying novel uses for abandoned drugs. Modern machine learning has enabled the identification of complex biochemical intricacies in candidate drugs; however,…
The embedding of Biomedical Knowledge Graphs (BKGs) generates robust representations, valuable for a variety of artificial intelligence applications, including predicting drug combinations and reasoning disease-drug relationships.…
Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing. While deep graph models have demonstrated success in modeling complex biological systems, existing…
Coronavirus Disease 2019 (COVID-19) has been creating a worldwide pandemic situation. Repurposing drugs, already shown to be free of harmful side effects, for the treatment of COVID-19 patients is an important option in launching novel…
Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease…
Knowledge graphs (KGs) are powerful tools that codify relational behaviour between entities in knowledge bases. KGs can simultaneously model many different types of subject-predicate-object and higher-order relations. As such, they offer a…
Knowledge graphs (KGs) on COVID-19 have been constructed to accelerate the research process of COVID-19. However, KGs are always incomplete, especially the new constructed COVID-19 KGs. Link prediction task aims to predict missing entities…
The paper utilizes the graph embeddings generated for entities of a large biomedical database to perform link prediction to capture various new relationships among different entities. A novel node similarity measure is proposed that…
Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug…
Graph neural networks (GNNs) can learn effective node representations that significantly improve link prediction accuracy. However, most GNN-based link prediction algorithms are incompetent to predict weak ties connecting different…