Related papers: Benchmarking Graphormer on Large-Scale Molecular M…

To alleviate the local receptive issue of GCN, Transformers have been exploited to capture the long range dependences of nodes for graph data representation and learning. However, existing graph Transformers generally employ regular…

Graph transformers have gained popularity in various graph-based tasks by addressing challenges faced by traditional Graph Neural Networks. However, the quadratic complexity of self-attention operations and the extensive layering in graph…

As the emerging trend of graph-based deep learning, Graph Neural Networks (GNNs) excel for their capability to generate high-quality node feature vectors (embeddings). However, the existing one-size-fits-all GNN implementations are…

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different…

While Graph Neural Networks (GNNs) are popular in the deep learning community, they suffer from several challenges including over-smoothing, over-squashing, and gradient vanishing. Recently, a series of models have attempted to relieve…

Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…

Recent advances in graph neural networks (GNNs) have enabled more comprehensive modeling of molecules and molecular systems, thereby enhancing the precision of molecular property prediction and molecular simulations. Nonetheless, as the…

Molecular property prediction is a critical task in computational drug discovery. While recent advances in Graph Neural Networks (GNNs) and Transformers have shown to be effective and promising, they face the following limitations:…

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…

Many interesting datasets ubiquitous in machine learning and deep learning can be described via graphs. As the scale and complexity of graph-structured datasets increase, such as in expansive social networks, protein folding, chemical…

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…

The graph Transformer emerges as a new architecture and has shown superior performance on various graph mining tasks. In this work, we observe that existing graph Transformers treat nodes as independent tokens and construct a single long…

Graph Transformer (GT), as a special type of Graph Neural Networks (GNNs), utilizes multi-head attention to facilitate high-order message passing. However, this also imposes several limitations in node classification applications: 1) nodes…

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing,…

As powerful tools for representation learning on graphs, graph neural networks (GNNs) have facilitated various applications from drug discovery to recommender systems. Nevertheless, the effectiveness of GNNs is immensely challenged by…

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are…

Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…

Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…

Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from…