Related papers: Grappa -- A Machine Learned Molecular Mechanics Fo…

Designing a network to learn a molecule structure given its physical/chemical properties is a hard problem, but is useful for drug discovery tasks. In this paper, we incorporate higher-order relational learning of Factor Graphs with strong…

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can…

Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…

Recent works have shown the promise of learning pre-trained models for 3D molecular representation. However, existing pre-training models focus predominantly on equilibrium data and largely overlook off-equilibrium conformations. It is…

Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with…

Machine-learning force fields (MLFF) should be accurate, computationally and data efficient, and applicable to molecules, materials, and interfaces thereof. Currently, MLFFs often introduce tradeoffs that restrict their practical…

Machine-learned force fields (MLFFs), especially pre-trained foundation models, are transforming computational materials science by enabling ab initio-level accuracy at molecular dynamics scales. Yet their rapid rise raises a key question:…

Machine learning force fields (MLFFs) promise to accurately describe the potential energy surface of molecules at the ab initio level of theory with improved computational efficiency. Within MLFFs, equivariant graph neural networks (EQNNs)…

Data-driven modeling approaches can produce fast surrogates to study large-scale physics problems. Among them, graph neural networks (GNNs) that operate on mesh-based data are desirable because they possess inductive biases that promote…

Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…

We develop a combined machine learning (ML) and quantum mechanics approach that enables data-efficient reconstruction of flexible molecular force fields from high-level ab initio calculations, through the consideration of fundamental…

Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising…

We present an approach to generate machine-learned force fields (MLFF) with beyond density functional theory (DFT) accuracy. Our approach combines on-the-fly active learning and $\Delta$-machine learning in order to generate an MLFF for…

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…

Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit…

Cross-partition edges dominate the cost of distributed GNN training: fetching remote features and activations per iteration overwhelms the network as graphs deepen and partition counts grow. Grappa is a distributed GNN training framework…

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods,…

Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…

Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…