Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add DimeNet++ to README #4699

Merged
merged 2 commits into from
May 24, 2022
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).

## [2.0.5] - 2022-MM-DD
### Added
- Added the `DimeNet++` model ([#4432](https://github.com/pyg-team/pytorch_geometric/pull/4432))
- Added the `DimeNet++` model ([#4432](https://github.com/pyg-team/pytorch_geometric/pull/4432), [#4699](https://github.com/pyg-team/pytorch_geometric/pull/4699))
- Added an example of using PyG with PyTorch Ignite ([#4487](https://github.com/pyg-team/pytorch_geometric/pull/4487))
- Added `GroupAddRev` module with support for reducing training GPU memory ([#4671](https://github.com/pyg-team/pytorch_geometric/pull/4671))
- Added benchmarks via [`wandb`](https://wandb.ai/site) ([#4656](https://github.com/pyg-team/pytorch_geometric/pull/4656), [#4672](https://github.com/pyg-team/pytorch_geometric/pull/4672), [#4676](https://github.com/pyg-team/pytorch_geometric/pull/4676))
Expand Down
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ Our supported GNN models incorporate multiple message passing layers, and users
Unlike simple stacking of GNN layers, these models could involve pre-processing, additional learnable parameters, skip connections, graph coarsening, etc.

* **[SchNet](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.SchNet)** from Schütt *et al.*: [SchNet: A Continuous-filter Convolutional Neural Network for Modeling Quantum Interactions](https://arxiv.org/abs/1706.08566) (NIPS 2017) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/qm9_pretrained_schnet.py)]
* **[DimeNet](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.DimeNet)** from Klicpera *et al.*: [Directional Message Passing for Molecular Graphs](https://arxiv.org/abs/2003.03123) (ICLR 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/qm9_pretrained_dimenet.py)]
* **[DimeNet](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.DimeNet)** and **[DimeNetPlusPlus](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.DimeNetPlusPlus)** from Klicpera *et al.*: [Directional Message Passing for Molecular Graphs](https://arxiv.org/abs/2003.03123) (ICLR 2020) and [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://arxiv.org/abs/2011.14115) (NeurIPS-W 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/qm9_pretrained_dimenet.py)]
* **[Node2Vec](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.Node2Vec)** from Grover and Leskovec: [node2vec: Scalable Feature Learning for Networks](https://arxiv.org/abs/1607.00653) (KDD 2016) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/node2vec.py)]
* **[Deep Graph Infomax](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.DeepGraphInfomax)** from Veličković *et al.*: [Deep Graph Infomax](https://arxiv.org/abs/1809.10341) (ICLR 2019) [[**Example1**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/infomax_transductive.py), [**Example2**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/infomax_inductive.py)]
* **Deep Multiplex Graph Infomax** from Park *et al.*: [Unsupervised Attributed Multiplex Network Embedding](https://arxiv.org/abs/1911.06750) (AAAI 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/hetero/dmgi_unsup.py)]
Expand Down
4 changes: 0 additions & 4 deletions torch_geometric/nn/models/dimenet.py
Original file line number Diff line number Diff line change
Expand Up @@ -220,10 +220,6 @@ def forward(self, x, rbf, sbf, idx_kj, idx_ji):


class InteractionPPBlock(torch.nn.Module):
"""
The interaction block transforms each message embedding using
multiple residual blocks.
"""
def __init__(self, hidden_channels, int_emb_size, basis_emb_size,
num_spherical, num_radial, num_before_skip, num_after_skip,
act=swish):
Expand Down