Related papers: Do we need equivariant models for molecule generat…
Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…
Equivariant diffusion models have achieved impressive performance in 3D molecule generation. These models incorporate Euclidean symmetries of 3D molecules by utilizing an SE(3)-equivariant denoising network. However, specialized equivariant…
This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does…
Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules.…
In this paper, we introduce group convolutional neural networks (GCNNs) equivariant to color variation. GCNNs have been designed for a variety of geometric transformations from 2D and 3D rotation groups, to semi-groups such as scale.…
Incorporating inductive biases into ML models is an active area of ML research, especially when ML models are applied to data about the physical world. Equivariant Graph Neural Networks (GNNs) have recently become a popular method for…
Using machine learning, we explore the utility of various deep neural networks (NN) when applied to high harmonic generation (HHG) scenarios. First, we train the NNs to predict the time-dependent dipole and spectra of HHG emission from…
Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to…
This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly…
Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making…
Graph neural networks (GNNs) have emerged as powerful tools to accurately predict materials and molecular properties in computational discovery pipelines. In this article, we exploit the invertible nature of these neural networks to…
Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…
Deep learning has revolutionized the computer vision and image classification domains. In this context Convolutional Neural Networks (CNNs) based architectures are the most widely applied models. In this article, we introduced two…
Graph neural networks (GNNs) have shown promise in learning unstructured mesh-based simulations of physical systems, including fluid dynamics. In tandem, geometric deep learning principles have informed the development of equivariant…
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…
Equivariance w.r.t. geometric transformations in neural networks improves data efficiency, parameter efficiency and robustness to out-of-domain perspective shifts. When equivariance is not designed into a neural network, the network can…
The difficult problem of relating the static structure of glassy liquids and their dynamics is a good target for Machine Learning, an approach which excels at finding complex patterns hidden in data. Indeed, this approach is currently a hot…
Equivariant neural networks (ENNs) are graph neural networks embedded in $\mathbb{R}^3$ and are well suited for predicting molecular properties. The ENN library e3nn has customizable convolutions, which can be designed to depend only on…
We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the…
Graph generation poses a significant challenge as it involves predicting a complete graph with multiple nodes and edges based on simply a given label. This task also carries fundamental importance to numerous real-world applications,…