Deep learning in drug discovery: an integrative review and future challenges

H Askr, E Elgeldawi, H Aboul Ella… - Artificial Intelligence …, 2023 - Springer
Recently, using artificial intelligence (AI) in drug discovery has received much attention
since it significantly shortens the time and cost of develo** new drugs. Deep learning (DL) …

Graph neural networks in recommender systems: a survey

S Wu, F Sun, W Zhang, X **e, B Cui - ACM Computing Surveys, 2022 - dl.acm.org
With the explosive growth of online information, recommender systems play a key role to
alleviate such information overload. Due to the important application value of recommender …

Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking

Z Wu, J Wang, H Du, D Jiang, Y Kang, D Li… - Nature …, 2023 - nature.com
Graph neural networks (GNNs) have been widely used in molecular property prediction, but
explaining their black-box predictions is still a challenge. Most existing explanation methods …

The shapley value in machine learning

B Rozemberczki, L Watson, P Bayer… - … Joint Conference on …, 2022 - research.ed.ac.uk
Over the last few years, the Shapley value, a solution concept from cooperative game theory,
has found numerous applications in machine learning. In this paper, we first discuss …

Interpretable and generalizable graph learning via stochastic attention mechanism

S Miao, M Liu, P Li - International Conference on Machine …, 2022 - proceedings.mlr.press
Interpretable graph learning is in need as many scientific applications depend on learning
models to collect insights from graph-structured data. Previous works mostly focused on …

Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y **e… - arxiv preprint arxiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Evaluating explainability for graph neural networks

C Agarwal, O Queen, H Lakkaraju, M Zitnik - Scientific Data, 2023 - nature.com
As explanations are increasingly used to understand the behavior of graph neural networks
(GNNs), evaluating the quality and reliability of GNN explanations is crucial. However …

Explainability in graph neural networks: A taxonomic survey

H Yuan, H Yu, S Gui, S Ji - IEEE transactions on pattern …, 2022 - ieeexplore.ieee.org
Deep learning methods are achieving ever-increasing performance on many artificial
intelligence tasks. A major limitation of deep models is that they are not amenable to …

Discovering invariant rationales for graph neural networks

YX Wu, X Wang, A Zhang, X He, TS Chua - arxiv preprint arxiv …, 2022 - arxiv.org
Intrinsic interpretability of graph neural networks (GNNs) is to find a small subset of the input
graph's features--rationale--which guides the model prediction. Unfortunately, the leading …

A knowledge-guided pre-training framework for improving molecular representation learning

H Li, R Zhang, Y Min, D Ma, D Zhao, J Zeng - Nature Communications, 2023 - nature.com
Learning effective molecular feature representation to facilitate molecular property prediction
is of great significance for drug discovery. Recently, there has been a surge of interest in pre …