Related papers: A Literature Review of Recent Graph Embedding Tech…

Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks…

Much of biomedical and healthcare data is encoded in discrete, symbolic form such as text and medical codes. There is a wealth of expert-curated biomedical domain knowledge stored in knowledge bases and ontologies, but the lack of reliable…

Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates…

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse…

Research on graph representation learning has received a lot of attention in recent years since many data in real-world applications come in form of graphs. High-dimensional graph data are often in irregular form, which makes them more…

Knowledge Graph Completion has been increasingly adopted as a useful method for helping address several tasks in biomedical research, such as drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge…

Graph is an important data representation which appears in a wide diversity of real-world scenarios. Effective graph analytics provides users a deeper understanding of what is behind the data, and thus can benefit a lot of useful…

Graph analytics can lead to better quantitative understanding and control of complex networks, but traditional methods suffer from high computational cost and excessive memory requirements associated with the high-dimensionality and…

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 embedding methods aim at finding useful graph representations by mapping nodes to a low-dimensional vector space. It is a task with important downstream applications, such as link prediction, graph reconstruction, data visualization,…

Graph embeddings have become a key and widely used technique within the field of graph mining, proving to be successful across a broad range of domains including social, citation, transportation and biological. Graph embedding techniques…

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…

Embedding static graphs in low-dimensional vector spaces plays a key role in network analytics and inference, supporting applications like node classification, link prediction, and graph visualization. However, many real-world networks…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

The way we analyse clinical texts has undergone major changes over the last years. The introduction of language models such as BERT led to adaptations for the (bio)medical domain like PubMedBERT and ClinicalBERT. These models rely on large…

The ubiquity of machine learning, particularly deep learning, applied to graphs is evident in applications ranging from cheminformatics (drug discovery) and bioinformatics (protein interaction prediction) to knowledge graph-based query…

Learning low-dimensional embeddings of knowledge graphs is a powerful approach used to predict unobserved or missing edges between entities. However, an open challenge in this area is developing techniques that can go beyond simple edge…

Graphs have a superior ability to represent relational data, like chemical compounds, proteins, and social networks. Hence, graph-level learning, which takes a set of graphs as input, has been applied to many tasks including comparison,…

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine…