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Knowledge graph embedding (KGE) models achieved state-of-the-art results on many knowledge graph tasks including link prediction and information retrieval. Despite the superior performance of KGE models in practice, we discover a deficiency…

Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED,…

Background: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally…

Knowledge Graph Embedding (KGE) techniques play a pivotal role in transforming symbolic Knowledge Graphs (KGs) into numerical representations, thereby enhancing various deep learning models for knowledge-augmented applications. Unlike…

As an efficient model for knowledge organization, the knowledge graph has been widely adopted in several fields, e.g., biomedicine, sociology, and education. And there is a steady trend of learning embedding representations of knowledge…

Traditional knowledge graph embedding (KGE) methods typically require preserving the entire knowledge graph (KG) with significant training costs when new knowledge emerges. To address this issue, the continual knowledge graph embedding…

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without…

The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…

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.…

Knowledge hypergraphs generalize knowledge graphs using hyperedges to connect multiple entities and depict complicated relations. Existing methods either transform hyperedges into an easier-to-handle set of binary relations or view…

The ability of knowledge graphs to represent complex relationships at scale has led to their adoption for various needs including knowledge representation, question-answering, and recommendation systems. Knowledge graphs are often…

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…

Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug…

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…

Knowledge graph embedding~(KGE) aims to represent entities and relations into low-dimensional vectors for many real-world applications. The representations of entities and relations are learned via contrasting the positive and negative…

Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…

Medicinal synergy prediction is a powerful tool in drug discovery and development that harnesses the principles of combination therapy to enhance therapeutic outcomes by improving efficacy, reducing toxicity, and preventing drug resistance.…

Knowledge graph embedding (KGE), which maps entities and relations in a knowledge graph into continuous vector spaces, has achieved great success in predicting missing links in knowledge graphs. However, knowledge graphs often contain…

Knowledge Graph Embedding (KGE) has proven to be an effective approach to solving the Knowledge Graph Completion (KGC) task. Relational patterns which refer to relations with specific semantics exhibiting graph patterns are an important…