Related papers: Layer-to-Layer Knowledge Mixing in Graph Neural Ne…

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…

The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide…

Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful…

Molecular property prediction (MPP) is a fundamental but challenging task in the computer-aided drug discovery process. More and more recent works employ different graph-based models for MPP, which have made considerable progress in…

Leveraging Large Language Models (LLMs) for Knowledge Graph Completion (KGC) is promising but hindered by a fundamental granularity mismatch. LLMs operate on fragmented token sequences, whereas entities are the fundamental units in…

Graph Neural Networks (GNNs) are promising surrogates for quantum mechanical calculations as they establish unprecedented low errors on collections of molecular dynamics (MD) trajectories. Thanks to their fast inference times they promise…

We explore a "best-of-both" approach to modelling molecular properties by combining learned molecular descriptors from a graph neural network (GNN) with general-purpose descriptors and a mixed ensemble of machine learning (ML) models. We…

Atomistic materials modeling is a critical task with wide-ranging applications, from drug discovery to materials science, where accurate predictions of the target material property can lead to significant advancements in scientific…

Multiplex graphs, with multiple edge types (graph views) among common nodes, provide richer structural semantics and better modeling capabilities. Multiplex Graph Neural Networks (MGNNs), typically comprising view-specific GNNs and a…

In this study, we present a framework aimed at enhancing molecular property prediction through the integration of local descriptors obtained from large-scale pretrained machine learning potentials into three-dimensional graph neural…

The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise…

While Language Models (LMs) are the workhorses of NLP, their interplay with structured knowledge graphs (KGs) is still actively researched. Current methods for encoding such graphs typically either (i) linearize them for embedding with LMs…

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new…

Code Language Models (codeLMs) and Graph Neural Networks (GNNs) are widely used in code vulnerability detection. However, GNNs often rely on aggregating information from adjacent nodes, limiting structural information propagation across…

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes…

Graphs are pervasive in the real-world, such as social network analysis, bioinformatics, and knowledge graphs. Graph neural networks (GNNs) have great ability in node classification, a fundamental task on graphs. Unfortunately, conventional…

Graph Neural Networks (GNNs) have shown remarkable performance in the healthcare domain. However, what remained challenging is quantifying the predictive uncertainty of GNNs, which is an important aspect of trustworthiness in clinical…

Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great…

The ability of knowledge graphs to represent complex relationships at scale has led to their adoption for various needs including knowledge representation, question-answering, and recommendation systems. Knowledge graphs are often…

This study presents a novel Machine Learning Algorithm, named Chemical Environment Graph Neural Network (ChemGNN), designed to accelerate materials property prediction and advance new materials discovery. Graphitic carbon nitride (g-C3N4)…