A comprehensive survey on deep graph representation learning

W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin… - Neural Networks, 2024 - Elsevier
Graph representation learning aims to effectively encode high-dimensional sparse graph-
structured data into low-dimensional dense vectors, which is a fundamental task that has …

Concepts of artificial intelligence for computer-assisted drug discovery

X Yang, Y Wang, R Byrne, G Schneider… - Chemical …, 2019 - ACS Publications
Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides
opportunities for the discovery and development of innovative drugs. Various machine …

Uni-mol: A universal 3d molecular representation learning framework

G Zhou, Z Gao, Q Ding, H Zheng, H Xu, Z Wei, L Zhang… - 2023 - chemrxiv.org
Molecular representation learning (MRL) has gained tremendous attention due to its critical
role in learning from limited supervised data for applications like drug design. In most MRL …

Molecular contrastive learning of representations via graph neural networks

Y Wang, J Wang, Z Cao… - Nature Machine …, 2022 - nature.com
Molecular machine learning bears promise for efficient molecular property prediction and
drug discovery. However, labelled molecule data can be expensive and time consuming to …

Self-supervised graph transformer on large-scale molecular data

Y Rong, Y Bian, T Xu, W Xie, Y Wei… - Advances in neural …, 2020 - proceedings.neurips.cc
How to obtain informative representations of molecules is a crucial prerequisite in AI-driven
drug design and discovery. Recent researches abstract molecules as graphs and employ …

ChemBERTa: large-scale self-supervised pretraining for molecular property prediction

S Chithrananda, G Grand, B Ramsundar - arXiv preprint arXiv:2010.09885, 2020 - arxiv.org
GNNs and chemical fingerprints are the predominant approaches to representing molecules
for property prediction. However, in NLP, transformers have become the de-facto standard …

[HTML][HTML] Cryptocurrency trading: a comprehensive survey

F Fang, C Ventre, M Basios, L Kanthan… - Financial Innovation, 2022 - Springer
In recent years, the tendency of the number of financial institutions to include
cryptocurrencies in their portfolios has accelerated. Cryptocurrencies are the first pure digital …

Smiles-bert: large scale unsupervised pre-training for molecular property prediction

S Wang, Y Guo, Y Wang, H Sun, J Huang - Proceedings of the 10th ACM …, 2019 - dl.acm.org
With the rapid progress of AI in both academia and industry, Deep Learning has been widely
introduced into various areas in drug discovery to accelerate its pace and cut R&D costs …

[HTML][HTML] Learning continuous and data-driven molecular descriptors by translating equivalent chemical representations

R Winter, F Montanari, F Noé, DA Clevert - Chemical science, 2019 - pubs.rsc.org
There has been a recent surge of interest in using machine learning across chemical space
in order to predict properties of molecules or design molecules and materials with the …

DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks

M Karimi, D Wu, Z Wang, Y Shen - Bioinformatics, 2019 - academic.oup.com
Motivation Drug discovery demands rapid quantification of compound–protein interaction
(CPI). However, there is a lack of methods that can predict compound–protein affinity from …