Related papers: Multiscale Gaussian network model (mGNM) and multi…

Network theory has proven invaluable in unraveling complex protein interactions. Previous studies have employed statistical methods rooted in network theory, including the Gaussian graphical model, to infer networks among proteins,…

Gaussian processes regression models are an appealing machine learning method as they learn expressive non-linear models from exemplar data with minimal parameter tuning and estimate both the mean and covariance of unseen points. However,…

Modern microelectronic devices are composed of interfaces between a large number of materials, many of which are in amorphous or polycrystalline phases. Modeling such non-crystalline materials using first-principles methods such as density…

Two of the most popular modelling paradigms in computer vision are feed-forward neural networks (FFNs) and probabilistic graphical models (GMs). Various connections between the two have been studied in recent works, such as e.g. expressing…

We derive an asymptotic expansion for the log likelihood of Gaussian mixture models (GMMs) with equal covariance matrices in the low signal-to-noise regime. The expansion reveals an intimate connection between two types of algorithms for…

Mesh-based Graph Neural Networks (GNNs) have recently shown capabilities to simulate complex multiphysics problems with accelerated performance times. However, mesh-based GNNs require a large number of message-passing (MP) steps and suffer…

Traditional Graph Neural Networks (GNNs) rely on message passing, which amounts to permutation-invariant local aggregation of neighbour features. Such a process is isotropic and there is no notion of `direction' on the graph. We present a…

Graph Neural Networks (GNNs) have become powerful tools for learning from graph-structured data, finding applications across diverse domains. However, as graph sizes and connectivity increase, standard GNN training methods face significant…

Volunteer computing grids offer super-computing levels of computing power at the relatively low cost of operating a server. In previous work, the authors have shown that it is possible to take traditionally iterative evolutionary algorithms…

Graph neural network (GNN) architectures have emerged as promising force field models, exhibiting high accuracy in predicting complex energies and forces based on atomic identities and Cartesian coordinates. To expand the applicability of…

Traditional simulation of complex mechanical systems relies on numerical solvers of Partial Differential Equations (PDEs), e.g., using the Finite Element Method (FEM). The FEM solvers frequently suffer from intensive computation cost and…

Recently, graph neural networks (GNNs) have been successfully applied to recommender systems. In recommender systems, the user's feedback behavior on an item is usually the result of multiple factors acting at the same time. However, a…

The interpretation of observations of atomic and molecular tracers in the galactic and extragalactic interstellar medium (ISM) requires comparisons with state-of-the-art astrophysical models to infer some physical conditions. Usually, ISM…

Neural Networks (GNNs) have revolutionized the molecular discovery to understand patterns and identify unknown features that can aid in predicting biophysical properties and protein-ligand interactions. However, current models typically…

Predicting protein-ligand binding affinity is an essential part of computer-aided drug design. However, generalisable and performant global binding affinity models remain elusive, particularly in low data regimes. Despite the evolution of…

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…

Recently, fine-tuning large-scale pre-trained GNNs has yielded remarkable attention in adapting pre-trained GNN models for downstream graph learning tasks. One representative fine-tuning method is to exploit adapter (termed AdapterGNN)…

Generative Adversarial Network (GAN)-based synthesis of fat suppressed (FS) MRIs from non-FS proton density sequences has the potential to accelerate acquisition of knee MRIs. However, GANs trained on single-site data have poor…

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…