ngab 0.1.1
Noisy Graph Alignment Benchmark (NGAB) - a library for benchmarking GNNs on graph alignment tasks and generating positional encodings.
Requires Python: >=3.12
Keywords: Benchmark, Combinatorial Optimization, GNN, Graph Alignment, Graph Neural Networks, Graphs, Positional Encodings, Pre-training, Pytorch, Torch-Geometric

### ngab — Noisy Graph Alignment Benchmark

NGAB is a lightweight Python library for benchmarking graph neural networks (GNNs) on noisy graph alignment and matching tasks, and for pretraining GNNs with alignment-oriented objectives.

It provides:
- A lightweight dataset format (safetensors) for graph pairs, and utilities to download prepared datasets from the Hugging Face Hub.
- Utilities to create your own graph-alignment datasets from existing datasets.
- A consistent `torch`-based training loop and metrics for graph alignment (loss, LAP accuracy, top-k accuracy), enabling fast benchmarking of new architectures and pretraining GNNs for high-quality positional encodings.
- A suite of GNN backbones (GCN, GAT, GATv2, GatedGCN, GIN, TAGCN, SGC, GraphGPS, PNA, PAN).


This repository accompanies the paper `Graph Alignment for Benchmarking Graph Neural Networks and Learning Positional Encodings`. The GitHub repository is available at [Graph-Alignment-Benchmark](https://github.com/adrien-lagesse/graph-alignment-benchmark), where you can see how we used `ngab` to run the experiments. It includes helper scripts to generate datasets and Hydra-parameterized experiments for full reproducibility and automation.

### Install

Requirements: Python 3.12+, PyTorch 2.8+, and PyTorch Geometric 2.6+

You can install the package with your preferred tool.

```bash
pip install ngab
uv add ngab
```

This project uses additional PyG wheel links (see `pyproject.toml`) and depends on `torch-scatter`, `torch-sparse`, `torch-cluster`, and `torch-spline-conv`. Ensure that your PyTorch and CUDA versions are compatible with your environment.


### Datasets

Prepared datasets are hosted on the Hugging Face Hub under `alagesse/graph-alignment-benchmark-data`.

- Hugging Face dataset page: `https://huggingface.co/datasets/alagesse/graph-alignment-benchmark-data`

You can programmatically download a dataset by name using the package API:

```python
from ngab import download_dataset

dataset_dir = download_dataset("zinc")  # returns a local path string
print(dataset_dir)
```

This fetches the required `*.safetensors` files for both the training and validation splits into a local directory (by default `graph-alignment-benchmark-data/zinc`). If the files already exist locally and are complete, no download occurs.


#### Generate your own datasets with `ngab.random`

Use `ngab.random` to synthesize graph pairs for alignment tasks, or build new datasets from existing graphs.

Available helpers:
- `erdos_renyi(nb_graphs, order, p, directed=False, self_loops=False)`
- `bernoulli_corruption(graphs, noise, directed=False, self_loops=False, type="add"|"add_remove")`
- `uniform_sub_sampling(graph, n, num_nodes)`
- `bfs_sub_sampling(graph, n, num_nodes, p=1.0)`

Example: build equal-size graph pairs suitable for alignment training:

```python
import torch
import ngab
from ngab.random import erdos_renyi, bernoulli_corruption

# 1) Generate base graphs (Erdős–Rényi)
base_graphs = erdos_renyi(nb_graphs=10_000, order=64, p=0.08, directed=False, self_loops=False)

# 2) Corrupt them (add/remove edges) to form paired graphs
corrupted_graphs = bernoulli_corruption(base_graphs, noise=0.10, directed=False, self_loops=False, type="add_remove")

# Now (base_graphs[i], corrupted_graphs[i]) form an aligned pair with the same number of nodes.
# You can serialize pairs into `safetensors` using your own pipeline to match the `GADataset` file layout.
```

Example: derive many small graphs from a large graph:

```python
from ngab.random import uniform_sub_sampling, bfs_sub_sampling

# Given a PyG Data object `big_graph`, create a batch of small induced subgraphs
uniform_batch = uniform_sub_sampling(big_graph, n=512, num_nodes=64)
bfs_batch = bfs_sub_sampling(big_graph, n=512, num_nodes=64, p=0.5)
```

### Benchmarking and Metrics

During training, NGAB logs to Weights & Biases:
- **loss**: alignment cross-entropy over the diagonal after masked softmax.
- **LAP**: assignment accuracy from the Hungarian algorithm on softmax-normalized similarities.
- **top_k**: mean recall at k for node assignments (top_1, top_3, top_5).

#### Quick training with `TrainConfig`

Use the built-in training loop to quickly benchmark or pretrain a custom model on any downloaded dataset.

```python
import pathlib
import torch
import ngab
from ngab import TrainConfig, train_loop

# 1) Download dataset locally (from Hugging Face)
dataset_dir = ngab.download_dataset("zinc")

# 2) Define your model (any class from ngab.models or your own torch.nn.Module)
model = ngab.models.GCN(in_features=1, features=128, out_features=64, layers=4)

# 3) Build the training configuration
config = TrainConfig()
config.model = model
config.dataset = pathlib.Path(dataset_dir)
config.experiment = "graph-alignment-benchmark-zinc"
config.run_name = "gcn-zinc"
config.epochs = 50
config.batch_size = 128
config.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
config.log_frequency = 5
config.profile = False
config.optimizer = torch.optim.Adam(model.parameters(), lr=1e-3)
config.scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(config.optimizer, T_max=config.epochs)
config.grad_clip = 1.0

# 4) Train
train_loop(config)
```
### Available Models

Models are implemented with PyTorch Geometric and share a simple constructor interface; typical arguments include `in_features`, `features`, `out_features`, and `layers`. Available classes are exposed under `ngab.models`:

- `GCN`, `GAT`, `GATv2`, `GatedGCN`, `GIN`, `TAGCN`, `SGC`, `GraphGPS`, `PNA`, `PAN`

Example:

```python
import ngab
model = ngab.models.GCN(in_features=1, features=128, out_features=64, layers=4)
```


### Links

- GitHub repository: `https://github.com/adrien-lagesse/graph-alignment-benchmark`
- Hugging Face dataset: `https://huggingface.co/datasets/alagesse/graph-alignment-benchmark-data`


### License

MIT License — see `LICENSE`.