Graph neural networks and their current applications in bioinformatics

XM Zhang, L Liang, L Liu, MJ Tang - Frontiers in genetics, 2021 - frontiersin.org
Graph neural networks (GNNs), as a branch of deep learning in non-Euclidean space,
perform particularly well in various tasks that process graph structure data. With the rapid …

Multimodal learning with graphs

Y Ektefaie, G Dasoulas, A Noori, M Farhat… - Nature Machine …, 2023 - nature.com
Artificial intelligence for graphs has achieved remarkable success in modelling complex
systems, ranging from dynamic networks in biology to interacting particle systems in physics …

Ab initio solution of the many-electron Schrödinger equation with deep neural networks

D Pfau, JS Spencer, AGDG Matthews… - Physical review research, 2020 - APS
Given access to accurate solutions of the many-electron Schrödinger equation, nearly all
chemistry could be derived from first principles. Exact wave functions of interesting chemical …

Structure-based de novo drug design using 3D deep generative models

Y Li, J Pei, L Lai - Chemical science, 2021 - pubs.rsc.org
Deep generative models are attracting much attention in the field of de novo molecule
design. Compared to traditional methods, deep generative models can be trained in a fully …

Molecular sets (MOSES): a benchmarking platform for molecular generation models

D Polykovskiy, A Zhebrak… - Frontiers in …, 2020 - frontiersin.org
Generative models are becoming a tool of choice for exploring the molecular space. These
models learn on a large training dataset and produce novel molecular structures with similar …

Learning data-driven discretizations for partial differential equations

Y Bar-Sinai, S Hoyer, J Hickey… - Proceedings of the …, 2019 - National Acad Sciences
The numerical solution of partial differential equations (PDEs) is challenging because of the
need to resolve spatiotemporal features over wide length-and timescales. Often, it is …

Graph convolutional networks for computational drug development and discovery

M Sun, S Zhao, C Gilvary, O Elemento… - Briefings in …, 2020 - academic.oup.com
Despite the fact that deep learning has achieved remarkable success in various domains
over the past decade, its application in molecular informatics and drug discovery is still …

Kohn-Sham equations as regularizer: Building prior knowledge into machine-learned physics

L Li, S Hoyer, R Pederson, R Sun, ED Cubuk, P Riley… - Physical review …, 2021 - APS
Including prior knowledge is important for effective machine learning models in physics and
is usually achieved by explicitly adding loss terms or constraints on model architectures …

A graph representation of molecular ensembles for polymer property prediction

M Aldeghi, CW Coley - Chemical Science, 2022 - pubs.rsc.org
Synthetic polymers are versatile and widely used materials. Similar to small organic
molecules, a large chemical space of such materials is hypothetically accessible …

Developing an improved crystal graph convolutional neural network framework for accelerated materials discovery

CW Park, C Wolverton - Physical Review Materials, 2020 - APS
The recently proposed crystal graph convolutional neural network (CGCNN) offers a highly
versatile and accurate machine learning (ML) framework by learning material properties …