diff --git a/README.md b/README.md index 2d8d9646..63ef58d7 100644 --- a/README.md +++ b/README.md @@ -153,23 +153,38 @@ The following models, proposed in literature, have a module in [literature](kgcn to create a ``keras.models.Model``. The models can but must not be build completely from `kgcnn.layers` and can for example include original implementations (with proper licencing). -* **[GCN](kgcnn/literature/GCN)**: [Semi-Supervised Classification with Graph Convolutional Networks](https://arxiv.org/abs/1609.02907) by Kipf et al. (2016) -* **[Schnet](kgcnn/literature/Schnet)**: [SchNet – A deep learning architecture for molecules and materials ](https://aip.scitation.org/doi/10.1063/1.5019779) by Schütt et al. (2017) +* **[AttentiveFP](kgcnn/literature/AttentiveFP)**: [Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism](https://pubs.acs.org/doi/10.1021/acs.jmedchem.9b00959) by Xiong et al. (2019) +* **[CGCNN](kgcnn/literature/CGCNN)**: [Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.145301) by Xie et al. (2018) +* **[CMPNN](kgcnn/literature/CMPNN)**: [Communicative Representation Learning on Attributed Molecular Graphs](https://www.ijcai.org/proceedings/2020/0392.pdf) by Song et al. (2020) +* **[DGIN](kgcnn/literature/DGIN)**: [Improved Lipophilicity and Aqueous Solubility Prediction with Composite Graph Neural Networks ](https://pubmed.ncbi.nlm.nih.gov/34684766/) by Wieder et al. (2021) +* **[DimeNetPP](kgcnn/literature/DimeNetPP)**: [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://arxiv.org/abs/2011.14115) by Klicpera et al. (2020) +* **[DMPNN](kgcnn/literature/DMPNN)**: [Analyzing Learned Molecular Representations for Property Prediction](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00237) by Yang et al. (2019) +* **[EGNN](kgcnn/literature/EGNN)**: [E(n) Equivariant Graph Neural Networks](https://arxiv.org/abs/2102.09844) by Satorras et al. (2021) * **[GAT](kgcnn/literature/GAT)**: [Graph Attention Networks](https://arxiv.org/abs/1710.10903) by Veličković et al. (2018) -* **[GraphSAGE](kgcnn/literature/GraphSAGE)**: [Inductive Representation Learning on Large Graphs](http://arxiv.org/abs/1706.02216) by Hamilton et al. (2017) -* **[GIN](kgcnn/literature/GIN)**: [How Powerful are Graph Neural Networks?](https://arxiv.org/abs/1810.00826) by Xu et al. (2019) -* **[GNNExplainer](kgcnn/literature/GNNExplain)**: [GNNExplainer: Generating Explanations for Graph Neural Networks](https://arxiv.org/abs/1903.03894) by Ying et al. (2019)
... and many more (click to expand). - * **[GATv2](kgcnn/literature/GATv2)**: [How Attentive are Graph Attention Networks?](https://arxiv.org/abs/2105.14491) by Brody et al. (2021) -* **[DMPNN](kgcnn/literature/DMPNN)**: [Analyzing Learned Molecular Representations for Property Prediction](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00237) by Yang et al. (2019) -* **[AttentiveFP](kgcnn/literature/AttentiveFP)**: [Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism](https://pubs.acs.org/doi/10.1021/acs.jmedchem.9b00959) by Xiong et al. (2019) -* **[PAiNN](kgcnn/literature/PAiNN)**: [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://arxiv.org/pdf/2102.03150.pdf) by Schütt et al. (2020) +* **[GCN](kgcnn/literature/GCN)**: [Semi-Supervised Classification with Graph Convolutional Networks](https://arxiv.org/abs/1609.02907) by Kipf et al. (2016) +* **[GIN](kgcnn/literature/GIN)**: [How Powerful are Graph Neural Networks?](https://arxiv.org/abs/1810.00826) by Xu et al. (2019) +* **[GNNExplainer](kgcnn/literature/GNNExplain)**: [GNNExplainer: Generating Explanations for Graph Neural Networks](https://arxiv.org/abs/1903.03894) by Ying et al. (2019) +* **[GNNFilm](kgcnn/literature/GNNFilm)**: [GNN-FiLM: Graph Neural Networks with Feature-wise Linear Modulation](https://arxiv.org/abs/1906.12192) by Marc Brockschmidt (2020) +* **[GraphSAGE](kgcnn/literature/GraphSAGE)**: [Inductive Representation Learning on Large Graphs](http://arxiv.org/abs/1706.02216) by Hamilton et al. (2017) +* **[HamNet](kgcnn/literature/HamNet)**: [HamNet: Conformation-Guided Molecular Representation with Hamiltonian Neural Networks](https://arxiv.org/abs/2105.03688) by Li et al. (2021) +* **[HDNNP2nd](kgcnn/literature/HDNNP2nd)**: [Atom-centered symmetry functions for constructing high-dimensional neural network potentials](https://aip.scitation.org/doi/abs/10.1063/1.3553717) by Jörg Behler (2011) +* **[INorp](kgcnn/literature/INorp)**: [Interaction Networks for Learning about Objects,Relations and Physics](https://arxiv.org/abs/1612.00222) by Battaglia et al. (2016) +* **[MAT](kgcnn/literature/MAT)**: [Molecule Attention Transformer](https://arxiv.org/abs/2002.08264) by Maziarka et al. (2020) +* **[MEGAN](kgcnn/literature/MEGAN)**: [MEGAN: Multi-explanation Graph Attention Network](https://link.springer.com/chapter/10.1007/978-3-031-44067-0_18) by Teufel et al. (2023) +* **[Megnet](kgcnn/literature/Megnet)**: [Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals](https://doi.org/10.1021/acs.chemmater.9b01294) by Chen et al. (2019) +* **[MXMNet](kgcnn/literature/MXMNet)**: [Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures](https://arxiv.org/abs/2011.07457) by Zhang et al. (2020) * **[NMPN](kgcnn/literature/NMPN)**: [Neural Message Passing for Quantum Chemistry](http://arxiv.org/abs/1704.01212) by Gilmer et al. (2017) -* **[CGCNN](kgcnn/literature/CGCNN)**: [Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.145301) by Xie et al. (2018) +* **[Unet](kgcnn/literature/Unet)**: [Graph U-Nets](http://proceedings.mlr.press/v97/gao19a/gao19a.pdf) by H. Gao and S. Ji (2019) +* **[PAiNN](kgcnn/literature/PAiNN)**: [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://arxiv.org/pdf/2102.03150.pdf) by Schütt et al. (2020) +* **[RGCN](kgcnn/literature/RGCN)**: [Modeling Relational Data with Graph Convolutional Networks](https://arxiv.org/abs/1703.06103) by Schlichtkrull et al. (2017) +* **[rGIN](kgcnn/literature/rGIN)** [Random Features Strengthen Graph Neural Networks](https://arxiv.org/abs/2002.03155) by Sato et al. (2020) +* **[Schnet](kgcnn/literature/Schnet)**: [SchNet – A deep learning architecture for molecules and materials ](https://aip.scitation.org/doi/10.1063/1.5019779) by Schütt et al. (2017) + To be completed ...
diff --git a/kgcnn/literature/INorp/__init__.py b/kgcnn/literature/INorp/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/kgcnn/literature/MAT/__init__.py b/kgcnn/literature/MAT/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/kgcnn/literature/MEGAN/__init__.py b/kgcnn/literature/MEGAN/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/kgcnn/literature/MXMNet/__init__.py b/kgcnn/literature/MXMNet/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/kgcnn/literature/rGIN/__init__.py b/kgcnn/literature/rGIN/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/training/train_graph.py b/training/train_graph.py index 858b90a7..650d0679 100644 --- a/training/train_graph.py +++ b/training/train_graph.py @@ -24,7 +24,7 @@ parser = argparse.ArgumentParser(description='Train a GNN on a graph regression or classification task.') parser.add_argument("--hyper", required=False, help="Filepath to hyperparameter config file (.py or .json).", default="hyper/hyper_freesolv.py") -parser.add_argument("--category", required=False, help="Graph model to train.", default="CMPNN") +parser.add_argument("--category", required=False, help="Graph model to train.", default="GIN") parser.add_argument("--model", required=False, help="Graph model to train.", default=None) parser.add_argument("--dataset", required=False, help="Name of the dataset.", default=None) parser.add_argument("--make", required=False, help="Name of the class for model.", default=None)