Metadata-Version: 2.4
Name: chebai-graph
Version: 1.1.0
Summary: GNNs for ChEB-AI
Author-email: Martin Glauer <martin.glauer@ovgu.de>
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: chebai
Requires-Dist: descriptastorus
Requires-Dist: tox ; extra == "dev"
Requires-Dist: isort ; extra == "linters"
Requires-Dist: pre-commit ; extra == "linters"
Requires-Dist: black ; extra == "linters"
Provides-Extra: dev
Provides-Extra: linters


# ChEB-AI Graph

Graph-based models for molecular property prediction and ontology classification, built on top of the [`python-chebai`](https://github.com/ChEB-AI/python-chebai) codebase.



## Installation

To install this repository, download it and run

```bash
pip install .
```

or install it directly with
```bash
pip install git+https://github.com/ChEB-AI/python-chebai-graph.git
```

The dependencies `torch`, `torch_geometric` and `torch_scatter` cannot be installed automatically.

Use the following command:

```bash
pip install torch torch_scatter torch_geometric -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
```

Replace:
- `${TORCH}` with a PyTorch version (e.g., `2.8.0`; for later versions, check first if they are compatible with torch_scatter and [torch_geometric](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html))
- `${CUDA}` with `cpu`, `cu118`, `cu121` (or other, depending on your system and CUDA version)

If you already have `torch` installed, make sure that `torch_scatter` and `torch_geometric` are compatible with your
PyTorch version and are installed with the same CUDA version.

For a full list of currently available PyTorch versions and CUDA compatibility, please refer to libraries' official documentation:
- [torch](https://pytorch.org/get-started/locally/)
- [torch_geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html#installation)
- [torch-scatter](https://github.com/rusty1s/pytorch_scatter)

_Note for developers_: If you want to install the package in editable mode, use the following command instead:

```bash
pip install -e .
```

## Recommended Folder Structure

ChEB-AI Graph is not a standalone library. Instead, it provides additional models and datasets for [`python-chebai`](https://github.com/ChEB-AI/python-chebai).
The training relies on config files that are located either in `python-chebai` or in this repository.

Therefore, for training, we recommend to clone both repositories into a common parent directory. For instance, your project can look like this:

```
my_projects/
├── python-chebai/
│   ├── chebai/
│   ├── configs/
│   └── ...
└── python-chebai-graph/
    ├── chebai_graph/
    ├── configs/
    └── ...
```

## Training & Pretraining

### Ontology Prediction


This example command trains a Residual Gated Graph Convolutional Network on the ChEBI50 dataset (see [wiki](https://github.com/ChEB-AI/python-chebai/wiki/Data-Management)).
The dataset has a customizable list of properties for atoms, bonds and molecules that are added to the graph.
The list can be found in the `configs/data/chebi50_graph_properties.yml` file.

```bash
python -m chebai fit --trainer=configs/training/default_trainer.yml --trainer.logger=configs/training/csv_logger.yml --model=../python-chebai-graph/configs/model/gnn_res_gated.yml --model.train_metrics=configs/metrics/micro-macro-f1.yml --model.test_metrics=configs/metrics/micro-macro-f1.yml --model.val_metrics=configs/metrics/micro-macro-f1.yml --data=../python-chebai-graph/configs/data/chebi50_graph_properties.yml --data.init_args.batch_size=128 --trainer.accumulate_grad_batches=4 --data.init_args.num_workers=10 --model.pass_loss_kwargs=false --data.init_args.chebi_version=241 --trainer.min_epochs=200 --trainer.max_epochs=200 --model.criterion=configs/loss/bce_weighted.yml
```

## Augmented Graphs 
_See thesis related to this work [here](https://www.uni-osnabrueck.de/fileadmin/informatik/Arbeitsgruppen/Hybride_KI/mt_aditya_khedekar.pdf)_.

Graph Neural Networks (GNNs) often fail to explicitly leverage the chemically meaningful substructures present within molecules (i.e. **functional groups (FGs)**).  To make this implicit information explicitly accessible to GNNs, we augment molecular graphs with **artificial nodes** that represent these substructures. The resulting graph are referred to as **augmented graphs**.
> Note: Rings are also treated as functional groups in our work.

In these augmented graphs, each functional group node is connected to the atoms that constitute the group. Additionally, two functional group nodes are connected if any atom belonging to one group shares a bond with an atom from the other group. We further introduce a **graph node**, an extra node connected to all functional group nodes.

Among all the connection schemes we evaluated, this configuration delivered the strongest performance. We denote it using the abbreviation **WFG_WFGE_WGN** in our work and is shown in below figure.

<img width="1220" height="668" alt="mol_to_aug_mol" src="https://github.com/user-attachments/assets/0aba6b80-765b-45a6-913a-7d628f14a5db" />

</br>
</br>

Below is the command for the model and data configuration that achieved the best classification performance using augmented graphs.

```bash
python -m chebai fit --trainer=configs/training/default_trainer.yml --trainer.logger=configs/training/wandb_logger.yml --model=../python-chebai-graph/configs/model/gat_aug_amgpool.yml --model.train_metrics=configs/metrics/micro-macro-f1.yml --model.test_metrics=configs/metrics/micro-macro-f1.yml --model.val_metrics=configs/metrics/micro-macro-f1.yml --data=../python-chebai-graph/configs/data/chebi50_aug_prop_as_per_node.yml --data.init_args.batch_size=128 --trainer.accumulate_grad_batches=4 --data.init_args.num_workers=10 --model.pass_loss_kwargs=false --data.init_args.chebi_version=241 --trainer.min_epochs=200 --trainer.max_epochs=200 --model.criterion=configs/loss/bce_weighted.yml --trainer.logger.init_args.name=gatv2_amg_s0
```

### Model Hyperparameters

#### **GAT Architecture**

To use a GAT-based model, choose **one** of the following configs:

- **Standard Pooling**: `--model=../python-chebai-graph/configs/model/gat.yml`
   > Standard pooling sums the learned representations from all the nodes to produce a single representation which is used for classification.

- **Atom-Augmented Node Pooling**: `--model=../python-chebai-graph/configs/model/gat_aug_aagpool.yml`
   > With this pooling stratergy, the learned representations are first separated into **two distinct sets**: those from atom nodes and those from all artificial nodes (both functional groups and the graph node). The representations within each set are aggregated separately (using summation) to yield two distinct single vectors. These two resulting vectors are then concatenated before being passed to the classification layer.

- **Atom–Motif–Graph Node Pooling**: `--model=../python-chebai-graph/configs/model/gat_aug_amgpool.yml`
   >  This approach employs a finer granularity of separation, distinguishing learned representations into **three distinct sets**: atom nodes, Functional Group (FG) nodes, and the single graph node. Summation is performed separately on the atom node set and the FG node set, yielding two vectors. These two vectors are then concatenated along with the single vector corresponding to the graph node before the final linear layer.

#### GAT-specific hyperparameters

- **Number of message-passing layers**: `--model.config.num_layers=5`        (default: 4)
- **Attention heads**: `--model.config.heads=4`             (default: 8)
  > **Note**: The number of heads should be divisible by the output channels (or hidden channels if output channels are not specified).

- **To Use different GAT versions**:
    - **Use GAT**: `--model.config.v2=False`

    - **Use GATv2**: `--model.config.v2=True`             (__default__)
      > **Note**: GATv2 addresses the limitation of static attention in GAT by introducing a dynamic attention mechanism. For further details, please refer to the [original GATv2 paper](https://arxiv.org/abs/2105.14491).

#### **ResGated Architecture**

To use a ResGated GNN model, choose **one** of the following configs:

- **Atom–Motif–Graph Node Pooling**: `--model=../python-chebai-graph/configs/model/res_aug_amgpool.yml`
- **Atom-Augmented Node Pooling**: `--model=../python-chebai-graph/configs/model/res_aug_aagpool.yml`
- **Standard Pooling**: `--model=../python-chebai-graph/configs/model/resgated.yml`

#### **Common Hyperparameters**

These can be used for both GAT and ResGated architectures:

- **Dropout**: `--model.config.dropout=0.1`         (default: 0)
- **Number of final linear layers**: `--model.n_linear_layers=2`         (default: 1)

## Random Node Initialization

### Static Node Initialization

In this type of node initialization, the node features (and/or edge features) of the given molecular graph are initialized only once during dataset creation with the given initialization scheme.

```bash
python -m chebai fit --trainer=configs/training/default_trainer.yml --trainer.logger=configs/training/wandb_logger.yml --model=../python-chebai-graph/configs/model/resgated.yml --model.config.in_channels=203 --model.config.edge_dim=11 --model.train_metrics=configs/metrics/micro-macro-f1.yml --model.test_metrics=configs/metrics/micro-macro-f1.yml --model.val_metrics=configs/metrics/micro-macro-f1.yml --data=../python-chebai-graph/configs/data/chebi50_graph_properties.yml --data.pad_node_features=45 --data.pad_edge_features=4 --data.init_args.batch_size=128 --trainer.accumulate_grad_batches=4 --data.init_args.num_workers=10 --data.init_args.persistent_workers=False --model.pass_loss_kwargs=false --data.init_args.chebi_version=241 --trainer.min_epochs=200 --trainer.max_epochs=200 --model.criterion=configs/loss/bce_weighted.yml --trainer.logger.init_args.name=gni_res_props+zeros_s0
```

In the above command, for each node we use the 158 node features (corresponding the node properties defined in `chebi50_graph_properties.yml`) which are retrieved from RDKit and additional 45 additional features (specified by `--data.pad_node_features=45`) drawn from a normal distribution (default).

You can change the distribution from which additional are drawn by using the following config in above command: `--data.distribution=zeros`

Available distributions: `"normal", "uniform", "xavier_normal", "xavier_uniform", "zeros"`


Similarly, each edge is initialized with 7 RDKit features and 4 additional features drawn from the given distribution.


If you want all node (and edge) features to be drawn from a given distribution (i.e., ignore RDKit features), use: `--data=../python-chebai-graph/configs/data/chebi50_static_gni.yml`


Refer to the data class code for details.


### Dynamic Node Initialization

In this type of node initialization, the node features (and/or edge features) of the molecular graph are initialized at **each forward pass** of the model using the given initialization scheme.



Currently, dynamic node initialization is implemented only for the **resgated** architecture by specifying: `--model=../python-chebai-graph/configs/model/resgated_dynamic_gni.yml`

To keep RDKit features and *add* dynamically initialized features use the following config in the command:

```
--model.config.complete_randomness=False
--model.config.pad_node_features=45
```

The additional features are drawn from normal distribution (default). You can change it using:`--model.config.distribution=uniform`

If all features should be initialized from the given distribution, remove the complete_randomness flag (default is True).


Please find below the command for a typical dynamic node initialization:

```bash
python -m chebai fit --trainer=configs/training/default_trainer.yml --trainer.logger=configs/training/wandb_logger.yml --model=../python-chebai-graph/configs/model/resgated_dynamic_gni.yml --model.config.in_channels=203 --model.config.edge_dim=11 --model.config.complete_randomness=False --model.config.pad_node_features=45 --model.config.pad_edge_features=4 --model.train_metrics=configs/metrics/micro-macro-f1.yml --model.test_metrics=configs/metrics/micro-macro-f1.yml --model.val_metrics=configs/metrics/micro-macro-f1.yml --data=../python-chebai-graph/configs/data/chebi50_graph_properties.yml --data.init_args.batch_size=128 --trainer.accumulate_grad_batches=4 --data.init_args.num_workers=10 --data.init_args.persistent_workers=False --model.pass_loss_kwargs=false --data.init_args.chebi_version=241 --trainer.min_epochs=200 --trainer.max_epochs=200 --model.criterion=configs/loss/bce_weighted.yml --trainer.logger.init_args.name=gni_dres_props+rand_s0
```

