Indigo ML knowledge base

Graph Neural Networks (GNN)

Existing comparisons

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00479-8

Graph Convolutional Networks (GCN)

https://towardsdatascience.com/graph-convolutional-networks-deep-99d7fee5706f https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00435-6

Graph Attention Networks (GAT)

https://petar-v.com/GAT/

Message Passing Neural Networks (MPNN)

https://arxiv.org/pdf/1704.01212v2.pdf

AttentiveFP

https://www.researchgate.net/profile/Zhaoping-Xiong/publication/335156258_Pushing_the_boundaries_of_molecular_representation_for_drug_discovery_with_graph_attention_mechanism/links/5e0aac65a6fdcc28374addc0/Pushing-the-boundaries-of-molecular-representation-for-drug-discovery-with-graph-attention-mechanism.pdf

Quantum deep field for molecule

This repo contains links to explanatory paper and framework "Quantum deep field for molecule". It is interesting and just for a review, the authors suggest a different approach for modeling molecules (probably only works for certain predictions related to electron density).

https://github.com/masashitsubaki/molecularGNN_smiles