相关论文: Structure-Aware Compound-Protein Affinity Predicti…

Learning the structure--dynamics correlation in disordered systems is a long-standing problem. Here, we use unsupervised machine learning employing graph neural networks (GNN) to investigate the local structures in disordered systems. We…

The quest for accurate prediction of drug molecule properties poses a fundamental challenge in the realm of Artificial Intelligence Drug Discovery (AIDD). An effective representation of drug molecules emerges as a pivotal component in this…

Deep convolutional neural network (CNN) training via iterative optimization has had incredible success in finding optimal parameters. However, modern CNN architectures often contain millions of parameters. Thus, any given model for a single…

Molecular property calculations are the bedrock of chemical physics. High-fidelity \textit{ab initio} modeling techniques for computing the molecular properties can be prohibitively expensive, and motivate the development of…

While Graph Neural Networks (GNNs) have achieved remarkable results in a variety of applications, recent studies exposed important shortcomings in their ability to capture the structure of the underlying graph. It has been shown that the…

Graph neural networks (GNNs) are shown to be successful in modeling applications with graph structures. However, training an accurate GNN model requires a large collection of labeled data and expressive features, which might be inaccessible…

Graph convolutional neural networks (GCNNs) have become a machine learning workhorse for screening the chemical space of crystalline materials in fields such as catalysis and energy storage, by predicting properties from structures.…

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…

In this work, we provide a new formulation for Graph Convolutional Neural Networks (GCNNs) for link prediction on graph data that addresses common challenges for biomedical knowledge graphs (KGs). We introduce a regularized attention…

Graph Neural Network (GNN) is a popular architecture for the analysis of chemical molecules, and it has numerous applications in material and medicinal science. Current lines of GNNs developed for molecular analysis, however, do not fit…

In the field of chemistry, the objective is to create novel molecules with desired properties, facilitating accurate property predictions for applications such as material design and drug screening. However, existing graph deep learning…

Graph Neural Networks (GNNs) have demonstrated exceptional efficacy in relational learning tasks, including node classification and link prediction. However, their application raises significant fairness concerns, as GNNs can perpetuate and…

This paper focuses on learning representation on the whole graph level in an unsupervised manner. Learning graph-level representation plays an important role in a variety of real-world issues such as molecule property prediction, protein…

Large-scale {\it in vitro} drug sensitivity screens are an important tool in personalized oncology to predict the effectiveness of potential cancer drugs. The prediction of the sensitivity of cancer cell lines to a panel of drugs is a…

Rationalizing which parts of a molecule drive the predictions of a molecular graph convolutional neural network (GCNN) can be difficult. To help, we propose two simple regularization techniques to apply during the training of GCNNs: Batch…

Graph neural networks (GNNs) are widely applied in graph data modeling. However, existing GNNs are often trained in a task-driven manner that fails to fully capture the intrinsic nature of the graph structure, resulting in sub-optimal node…

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs…

Graphs are widely used to describe real-world objects and their interactions. Graph Neural Networks (GNNs) as a de facto model for analyzing graphstructured data, are highly sensitive to the quality of the given graph structures. Therefore,…

Graph Neural Networks (GNNs) are the currently most effective methods for predicting molecular properties but there remains a need for more accurate models. GNN accuracy can be improved by increasing the model complexity but this also…

Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…