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Graph representation learning is a fundamental problem for modeling relational data and benefits a number of downstream applications. Traditional Bayesian-based graph models and recent deep learning based GNN either suffer from…

Generative models generate vast numbers of hypothetical materials, necessitating fast, accurate models for property prediction. Graph Neural Networks (GNNs) excel in this domain but face challenges like high training costs, domain…

Graph neural networks (GNNs) learn representations from network data with naturally distributed architectures, rendering them well-suited candidates for decentralized learning. Oftentimes, this decentralized graph support changes with time…

Partitioning is a known problem in computer science and is critical in chip design workflows, as advancements in this area can significantly influence design quality and efficiency. Deep Learning (DL) techniques, particularly those…

We introduce pyGSL, a Python library that provides efficient implementations of state-of-the-art graph structure learning models along with diverse datasets to evaluate them on. The implementations are written in GPU-friendly ways, allowing…

Graph Neural Networks (GNNs) aim to extend deep learning techniques to graph data and have achieved significant progress in graph analysis tasks (e.g., node classification) in recent years. However, similar to other deep neural networks…

Understanding disease-gene associations is essential for unravelling disease mechanisms and advancing diagnostics and therapeutics. Traditional approaches based on manual curation and literature review are labour-intensive and not scalable,…

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

Dynamic graph learning (DGL) aims to learn informative and temporally-evolving node embeddings to support downstream tasks such as link prediction. A fundamental challenge in DGL lies in effectively modeling both the temporal dynamics and…

Reinforcement learning is well known for its ability to model sequential tasks and learn latent data patterns adaptively. Deep learning models have been widely explored and adopted in regression and classification tasks. However, deep…

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…

Deep graph models have achieved great success in network representation learning. However, their focus on pairwise relationships restricts their ability to learn pervasive higher-order interactions in real-world systems, which can be…

Detecting the Maximum Common Subgraph (MCS) between two input graphs is fundamental for applications in drug synthesis, malware detection, cloud computing, etc. However, MCS computation is NP-hard, and state-of-the-art MCS solvers rely on…

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…

Predicting molecular properties is essential for drug discovery, and computational methods can greatly enhance this process. Molecular graphs have become a focus for representation learning, with Graph Neural Networks (GNNs) widely used.…

Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the…

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand…

Deep learning is emerging as an effective tool in drug discovery, with potential applications in both predictive and generative models. Generative Flow Networks (GFlowNets/GFNs) are a recently introduced method recognized for the ability to…

We present GNN-Suite, a robust modular framework for constructing and benchmarking Graph Neural Network (GNN) architectures in computational biology. GNN-Suite standardises experimentation and reproducibility using the Nextflow workflow to…

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and…