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The recent developments and growing interest in neural-symbolic models has shown that hybrid approaches can offer richer models for Artificial Intelligence. The integration of effective relational learning and reasoning methods is one of…

Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico…

Drug recommendation is an essential task in machine learning-based clinical decision support systems. However, the risk of drug-drug interactions (DDI) between co-prescribed medications remains a significant challenge. Previous studies have…

Personalized drug response has received public awareness in recent years. How to combine gene test result and drug sensitivity records is regarded as essential in the real-world implementation. Research articles are good sources to train…

Significant differences in protein structures hinder the generalization of existing drug-target interaction (DTI) models, which often rely heavily on pre-learned binding principles or detailed annotations. In contrast, BioBridge designs an…

Learning effective representations for Continuous-Time Dynamic Graphs (CTDGs) has garnered significant research interest, largely due to its powerful capabilities in modeling complex interactions between nodes. A fundamental and crucial…

Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models…

Recent methods for generating novel molecules use graph representations of molecules and employ various forms of graph convolutional neural networks for inference. However, training requires solving an expensive graph isomorphism problem,…

Diabetes is a worldwide health issue affecting millions of people. Machine learning methods have shown promising results in improving diabetes prediction, particularly through the analysis of diverse data types, namely gene expression data.…

Sampling is an established technique to scale graph neural networks to large graphs. Current approaches however assume the graphs to be homogeneous in terms of relations and ignore relation types, critically important in biomedical graphs.…

Drug target interaction (DTI) prediction is a foundational task for in silico drug discovery, which is costly and time-consuming due to the need of experimental search over large drug compound space. Recent years have witnessed promising…

The identification of drug-target interactions (DTI) is critical for drug discovery and repositioning, as it reveals potential therapeutic uses of existing drugs, accelerating development and reducing costs. However, most existing models…

We propose the molecular omics network (MOOMIN) a multimodal graph neural network used by AstraZeneca oncologists to predict the synergy of drug combinations for cancer treatment. Our model learns drug representations at multiple scales…

This paper studies learning the representations of whole graphs in both unsupervised and semi-supervised scenarios. Graph-level representations are critical in a variety of real-world applications such as predicting the properties of…

The prediction modeling of drug-target interactions is crucial to drug discovery and design, which has seen rapid advancements owing to deep learning technologies. Recently developed methods, such as those based on graph neural networks…

Recent years have witnessed rapid advances in graph representation learning, with the continuous embedding approach emerging as the dominant paradigm. However, such methods encounter issues regarding parameter efficiency, interpretability,…

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 genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…

Accurate prediction of drug target interactions is critical for accelerating drug discovery and elucidating complex biological mechanisms. In this work, we frame drug target prediction as a link prediction task on heterogeneous biomedical…

Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent…