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Biomedical knowledge graphs underwrite drug repurposing and clinical decision support, yet the upstream ontologies they depend on update on independent cycles that add millions of edges and deprecate hundreds of thousands more between…
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…
The advent of large language models (LLMs) has revolutionized the integration of knowledge graphs (KGs) in biomedical and cognitive sciences, overcoming limitations in traditional machine learning methods for capturing intricate semantic…
Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and…
Knowledge Graph Embedding (KGE) methods have gained enormous attention from a wide range of AI communities including Natural Language Processing (NLP) for text generation, classification and context induction. Embedding a huge number of…
Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes. Predicting missing links in these graphs can boost many important applications, such as drug design and repurposing. Recent work has…
Large Language Models (LLMs) often suffer from hallucinations, which Retrieval-Augmented Generation (RAG) and GraphRAG mitigate by incorporating external knowledge and knowledge graphs (KGs). However, GraphRAG remains text-centric due to…
Benefiting from the powerful expressive capability of graphs, graph-based approaches have been popularly applied to handle multi-modal medical data and achieved impressive performance in various biomedical applications. For disease…
This paper introduces MatKG, a novel graph database of key concepts in material science spanning the traditional material-structure-property-processing paradigm. MatKG is autonomously generated through transformer-based, large language…
Multimodal knowledge graph completion (MMKGC) aims to predict missing links in multimodal knowledge graphs (MMKGs) by leveraging information from various modalities alongside structural data. Existing MMKGC approaches primarily extend…
Biomedical knowledge graphs (KG) are heterogenous networks consisting of biological entities as nodes and relations between them as edges. These entities and relations are extracted from millions of research papers and unified in a single…
Molecular representation learning is pivotal in predicting molecular properties and advancing drug design. Traditional methodologies, which predominantly rely on homogeneous graph encoding, are limited by their inability to integrate…
Electronic Health Records (EHRs) and routine documentation practices play a vital role in patients' daily care, providing a holistic record of health, diagnoses, and treatment. However, complex and verbose EHR narratives overload healthcare…
Multimodal reasoning with large language models (LLMs) often suffers from hallucinations and the presence of deficient or outdated knowledge within LLMs. Some approaches have sought to mitigate these issues by employing textual knowledge…
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…
Combining different modalities of data from human tissues has been critical in advancing biomedical research and personalised medical care. In this study, we leverage a graph embedding model (i.e VGAE) to perform link prediction on…
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…
Currently, there is a rapidly increasing need for high-quality biomedical knowledge graphs (BioKG) that provide direct and precise biomedical knowledge. In the context of COVID-19, this issue is even more necessary to be highlighted.…
Knowledge graph (KG) embedding encodes the entities and relations from a KG into low-dimensional vector spaces to support various applications such as KG completion, question answering, and recommender systems. In real world, knowledge…
Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes…