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Constructing transferable descriptors for conformation representation of molecular and biological systems finds numerous applications in drug discovery, learning-based molecular dynamics, and protein mechanism analysis. Geometric graph…

Subgraph matching plays an important role in electronic design automation (EDA) and circuit verification. Traditional rule-based methods have limitations in generalizing to arbitrary target circuits. Furthermore, node-to-node matching…

Structure-based Deep Fusion models were recently shown to outperform several physics- and machine learning-based protein-ligand binding affinity prediction methods. As part of a multi-institutional COVID-19 pandemic response, over 500…

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…

The exploration of Graph Neural Networks (GNNs) for processing graph-structured data has expanded, particularly their potential for causal analysis due to their universal approximation capabilities. Anticipated to significantly enhance…

Background: Virtual Screening (VS) has become an essential tool in drug discovery, enabling the rapid and cost-effective identification of potential bioactive molecules. Among recent advancements, Graph Neural Networks (GNNs) have gained…

We present distributed algorithms for training dynamic Graph Neural Networks (GNN) on large scale graphs spanning multi-node, multi-GPU systems. To the best of our knowledge, this is the first scaling study on dynamic GNN. We devise…

Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many…

Accurate prediction of drug-drug interactions (DDI) is crucial for medication safety and effective drug development. However, existing methods often struggle to capture structural information across different scales, from local functional…

Graph neural networks have received increased attention over the past years due to their promising ability to handle graph-structured data, which can be found in many real-world problems such as recommended systems and drug synthesis. Most…

Graph Neural Networks (GNNs) are recognized as potent tools for processing real-world data organized in graph structures. Especially inductive GNNs, which allow for the processing of graph-structured data without relying on predefined graph…

Graph Neural Networks (GNNs) have emerged as powerful tools for predicting outcomes in graph-structured data. However, a notable limitation of GNNs is their inability to provide robust uncertainty estimates, which undermines their…

Deep learning is an important method for molecular design and exhibits considerable ability to predict molecular properties, including physicochemical, bioactive, and ADME/T (absorption, distribution, metabolism, excretion, and toxicity)…

Networks are ubiquitous in the real world. Link prediction, as one of the key problems for network-structured data, aims to predict whether there exists a link between two nodes. The traditional approaches are based on the explicit…

Timely and rapid diagnoses are core to informing on optimum interventions that curb the spread of COVID-19. The use of medical images such as chest X-rays and CTs has been advocated to supplement the Reverse-Transcription Polymerase Chain…

Graph neural networks (GNNs) have drawn increasing attention in recent years and achieved remarkable performance in many graph-based tasks, especially in semi-supervised learning on graphs. However, most existing GNNs are based on the…

The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based…

Graph Neural Networks (GNNs) have received considerable attention since its introduction. It has been widely applied in various fields due to its ability to represent graph structured data. However, the application of GNNs is constrained by…

The COVID-19 epidemic has become a major safety and health threat worldwide. Imaging diagnosis is one of the most effective ways to screen COVID-19. This project utilizes several open-source or public datasets to present an open-source…

The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the…