Related papers: Motif-based Graph Self-Supervised Learning for Mol…

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…

Trapped by the label scarcity in molecular property prediction and drug design, graph contrastive learning (GCL) came forward. Leading contrastive learning works show two kinds of view generators, that is, random or learnable data…

Learning expressive molecular representations is crucial to facilitate the accurate prediction of molecular properties. Despite the significant advancement of graph neural networks (GNNs) in molecular representation learning, they generally…

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph…

Pretrained Graph Neural Networks have been widely adopted for various molecular property prediction tasks. Despite their ability to encode structural and relational features of molecules, traditional fine-tuning of such pretrained GNNs on…

Graph pre-training strategies have been attracting a surge of attention in the graph mining community, due to their flexibility in parameterizing graph neural networks (GNNs) without any label information. The key idea lies in encoding…

While graph neural networks have shown remarkable success in molecular property prediction, current approaches like the Equivariant Subgraph Aggregation Networks (ESAN) treat molecules as bags of independent substructures, overlooking…

Graph neural networks (GNNs) are able to achieve promising performance on multiple graph downstream tasks such as node classification and link prediction. Comparatively lesser work has been done to design GNNs which can operate directly for…

Graph Neural Networks (GNNs) have achieved promising performance in semi-supervised node classification in recent years. However, the problem of insufficient supervision, together with representation collapse, largely limits the performance…

Graph neural networks (GNNs) often struggle to learn discriminative node representations for heterophilic graphs, where connected nodes tend to have dissimilar labels and feature similarity provides weak structural cues. We propose…

Subgraph classification is an emerging field in graph representation learning where the task is to classify a group of nodes (i.e., a subgraph) within a graph. Subgraph classification has applications such as predicting the cellular…

Gaussian processes (GPs) are an attractive class of machine learning models because of their simplicity and flexibility as building blocks of more complex Bayesian models. Meanwhile, graph neural networks (GNNs) emerged recently as a…

Semi-supervised learning (SSL) over graph-structured data emerges in many network science applications. To efficiently manage learning over graphs, variants of graph neural networks (GNNs) have been developed recently. By succinctly…

Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual…

Graph Neural Networks (GNNs) have become a building block in graph data processing, with wide applications in critical domains. The growing needs to deploy GNNs in high-stakes applications necessitate explainability for users in the…

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures,…

Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…

We propose a mask pretraining method for Graph Neural Networks (GNNs) to improve their performance on fitting potential energy surfaces, particularly in water systems. GNNs are pretrained by recovering spatial information related to…

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…

Recent advances in molecular representation learning have produced highly effective encodings of molecules for numerous cheminformatics and bioinformatics tasks. However, extracting general chemical insight while balancing predictive…