@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/torch_geometric/references/datasets_reference.md

@@ -0,0 +1,574 @@
+# PyTorch Geometric Datasets Reference
+
+This document provides a comprehensive catalog of all datasets available in `torch_geometric.datasets`.
+
+## Citation Networks
+
+### Planetoid
+**Usage**: Node classification, semi-supervised learning
+**Networks**: Cora, CiteSeer, PubMed
+**Description**: Citation networks where nodes are papers and edges are citations
+- **Cora**: 2,708 nodes, 5,429 edges, 7 classes, 1,433 features
+- **CiteSeer**: 3,327 nodes, 4,732 edges, 6 classes, 3,703 features
+- **PubMed**: 19,717 nodes, 44,338 edges, 3 classes, 500 features
+
+```python
+from torch_geometric.datasets import Planetoid
+dataset = Planetoid(root='/tmp/Cora', name='Cora')
+```
+
+### Coauthor
+**Usage**: Node classification on collaboration networks
+**Networks**: CS, Physics
+**Description**: Co-authorship networks from Microsoft Academic Graph
+- **CS**: 18,333 nodes, 81,894 edges, 15 classes (computer science)
+- **Physics**: 34,493 nodes, 247,962 edges, 5 classes (physics)
+
+```python
+from torch_geometric.datasets import Coauthor
+dataset = Coauthor(root='/tmp/CS', name='CS')
+```
+
+### Amazon
+**Usage**: Node classification on product networks
+**Networks**: Computers, Photo
+**Description**: Amazon co-purchase networks where nodes are products
+- **Computers**: 13,752 nodes, 245,861 edges, 10 classes
+- **Photo**: 7,650 nodes, 119,081 edges, 8 classes
+
+```python
+from torch_geometric.datasets import Amazon
+dataset = Amazon(root='/tmp/Computers', name='Computers')
+```
+
+### CitationFull
+**Usage**: Citation network analysis
+**Networks**: Cora, Cora_ML, DBLP, PubMed
+**Description**: Full citation networks without sampling
+
+```python
+from torch_geometric.datasets import CitationFull
+dataset = CitationFull(root='/tmp/Cora', name='Cora')
+```
+
+## Graph Classification
+
+### TUDataset
+**Usage**: Graph classification, graph kernel benchmarks
+**Description**: Collection of 120+ graph classification datasets
+- **MUTAG**: 188 graphs, 2 classes (molecular compounds)
+- **PROTEINS**: 1,113 graphs, 2 classes (protein structures)
+- **ENZYMES**: 600 graphs, 6 classes (protein enzymes)
+- **IMDB-BINARY**: 1,000 graphs, 2 classes (social networks)
+- **REDDIT-BINARY**: 2,000 graphs, 2 classes (discussion threads)
+- **COLLAB**: 5,000 graphs, 3 classes (scientific collaborations)
+- **NCI1**: 4,110 graphs, 2 classes (chemical compounds)
+- **DD**: 1,178 graphs, 2 classes (protein structures)
+
+```python
+from torch_geometric.datasets import TUDataset
+dataset = TUDataset(root='/tmp/ENZYMES', name='ENZYMES')
+```
+
+### MoleculeNet
+**Usage**: Molecular property prediction
+**Datasets**: Over 10 molecular benchmark datasets
+**Description**: Comprehensive molecular machine learning benchmarks
+- **ESOL**: Aqueous solubility (regression)
+- **FreeSolv**: Hydration free energy (regression)
+- **Lipophilicity**: Octanol/water distribution (regression)
+- **BACE**: Binding results (classification)
+- **BBBP**: Blood-brain barrier penetration (classification)
+- **HIV**: HIV inhibition (classification)
+- **Tox21**: Toxicity prediction (multi-task classification)
+- **ToxCast**: Toxicology forecasting (multi-task classification)
+- **SIDER**: Side effects (multi-task classification)
+- **ClinTox**: Clinical trial toxicity (multi-task classification)
+
+```python
+from torch_geometric.datasets import MoleculeNet
+dataset = MoleculeNet(root='/tmp/ESOL', name='ESOL')
+```
+
+## Molecular and Chemical Datasets
+
+### QM7b
+**Usage**: Molecular property prediction (quantum mechanics)
+**Description**: 7,211 molecules with up to 7 heavy atoms
+- Properties: Atomization energies, electronic properties
+
+```python
+from torch_geometric.datasets import QM7b
+dataset = QM7b(root='/tmp/QM7b')
+```
+
+### QM9
+**Usage**: Molecular property prediction (quantum mechanics)
+**Description**: ~130,000 molecules with up to 9 heavy atoms (C, O, N, F)
+- Properties: 19 quantum chemical properties including HOMO, LUMO, gap, energy
+
+```python
+from torch_geometric.datasets import QM9
+dataset = QM9(root='/tmp/QM9')
+```
+
+### ZINC
+**Usage**: Molecular generation, property prediction
+**Description**: ~250,000 drug-like molecular graphs
+- Properties: Constrained solubility, molecular weight
+
+```python
+from torch_geometric.datasets import ZINC
+dataset = ZINC(root='/tmp/ZINC', subset=True)
+```
+
+### AQSOL
+**Usage**: Aqueous solubility prediction
+**Description**: ~10,000 molecules with solubility measurements
+
+```python
+from torch_geometric.datasets import AQSOL
+dataset = AQSOL(root='/tmp/AQSOL')
+```
+
+### MD17
+**Usage**: Molecular dynamics, force field learning
+**Description**: Molecular dynamics trajectories for small molecules
+- Molecules: Benzene, Uracil, Naphthalene, Aspirin, Salicylic acid, etc.
+
+```python
+from torch_geometric.datasets import MD17
+dataset = MD17(root='/tmp/MD17', name='benzene')
+```
+
+### PCQM4Mv2
+**Usage**: Large-scale molecular property prediction
+**Description**: 3.8M molecules from PubChem for quantum chemistry
+- Part of OGB Large-Scale Challenge
+
+```python
+from torch_geometric.datasets import PCQM4Mv2
+dataset = PCQM4Mv2(root='/tmp/PCQM4Mv2')
+```
+
+## Social Networks
+
+### Reddit
+**Usage**: Large-scale node classification
+**Description**: Reddit posts from September 2014
+- 232,965 nodes, 11,606,919 edges, 41 classes
+- Features: TF-IDF of post content
+
+```python
+from torch_geometric.datasets import Reddit
+dataset = Reddit(root='/tmp/Reddit')
+```
+
+### Reddit2
+**Usage**: Large-scale node classification
+**Description**: Updated Reddit dataset with more posts
+
+```python
+from torch_geometric.datasets import Reddit2
+dataset = Reddit2(root='/tmp/Reddit2')
+```
+
+### Twitch
+**Usage**: Node classification, social network analysis
+**Networks**: DE, EN, ES, FR, PT, RU
+**Description**: Twitch user networks by language
+
+```python
+from torch_geometric.datasets import Twitch
+dataset = Twitch(root='/tmp/Twitch', name='DE')
+```
+
+### Facebook
+**Usage**: Social network analysis, node classification
+**Description**: Facebook page-page networks
+
+```python
+from torch_geometric.datasets import FacebookPagePage
+dataset = FacebookPagePage(root='/tmp/Facebook')
+```
+
+### GitHub
+**Usage**: Social network analysis
+**Description**: GitHub developer networks
+
+```python
+from torch_geometric.datasets import GitHub
+dataset = GitHub(root='/tmp/GitHub')
+```
+
+## Knowledge Graphs
+
+### Entities
+**Usage**: Link prediction, knowledge graph embeddings
+**Datasets**: AIFB, MUTAG, BGS, AM
+**Description**: RDF knowledge graphs with typed relations
+
+```python
+from torch_geometric.datasets import Entities
+dataset = Entities(root='/tmp/AIFB', name='AIFB')
+```
+
+### WordNet18
+**Usage**: Link prediction on semantic networks
+**Description**: Subset of WordNet with 18 relations
+- 40,943 entities, 151,442 triplets
+
+```python
+from torch_geometric.datasets import WordNet18
+dataset = WordNet18(root='/tmp/WordNet18')
+```
+
+### WordNet18RR
+**Usage**: Link prediction (no inverse relations)
+**Description**: Refined version without inverse relations
+
+```python
+from torch_geometric.datasets import WordNet18RR
+dataset = WordNet18RR(root='/tmp/WordNet18RR')
+```
+
+### FB15k-237
+**Usage**: Link prediction on Freebase
+**Description**: Subset of Freebase with 237 relations
+- 14,541 entities, 310,116 triplets
+
+```python
+from torch_geometric.datasets import FB15k_237
+dataset = FB15k_237(root='/tmp/FB15k')
+```
+
+## Heterogeneous Graphs
+
+### OGB_MAG
+**Usage**: Heterogeneous graph learning, node classification
+**Description**: Microsoft Academic Graph with multiple node/edge types
+- Node types: paper, author, institution, field of study
+- 1M+ nodes, 21M+ edges
+
+```python
+from torch_geometric.datasets import OGB_MAG
+dataset = OGB_MAG(root='/tmp/OGB_MAG')
+```
+
+### MovieLens
+**Usage**: Recommendation systems, link prediction
+**Versions**: 100K, 1M, 10M, 20M
+**Description**: User-movie rating networks
+- Node types: user, movie
+- Edge types: rates
+
+```python
+from torch_geometric.datasets import MovieLens
+dataset = MovieLens(root='/tmp/MovieLens', model_name='100k')
+```
+
+### IMDB
+**Usage**: Heterogeneous graph learning
+**Description**: IMDB movie network
+- Node types: movie, actor, director
+
+```python
+from torch_geometric.datasets import IMDB
+dataset = IMDB(root='/tmp/IMDB')
+```
+
+### DBLP
+**Usage**: Heterogeneous graph learning, node classification
+**Description**: DBLP bibliography network
+- Node types: author, paper, term, conference
+
+```python
+from torch_geometric.datasets import DBLP
+dataset = DBLP(root='/tmp/DBLP')
+```
+
+### LastFM
+**Usage**: Heterogeneous recommendation
+**Description**: LastFM music network
+- Node types: user, artist, tag
+
+```python
+from torch_geometric.datasets import LastFM
+dataset = LastFM(root='/tmp/LastFM')
+```
+
+## Temporal Graphs
+
+### BitcoinOTC
+**Usage**: Temporal link prediction, trust networks
+**Description**: Bitcoin OTC trust network over time
+
+```python
+from torch_geometric.datasets import BitcoinOTC
+dataset = BitcoinOTC(root='/tmp/BitcoinOTC')
+```
+
+### ICEWS18
+**Usage**: Temporal knowledge graph completion
+**Description**: Integrated Crisis Early Warning System events
+
+```python
+from torch_geometric.datasets import ICEWS18
+dataset = ICEWS18(root='/tmp/ICEWS18')
+```
+
+### GDELT
+**Usage**: Temporal event forecasting
+**Description**: Global Database of Events, Language, and Tone
+
+```python
+from torch_geometric.datasets import GDELT
+dataset = GDELT(root='/tmp/GDELT')
+```
+
+### JODIEDataset
+**Usage**: Dynamic graph learning
+**Datasets**: Reddit, Wikipedia, MOOC, LastFM
+**Description**: Temporal interaction networks
+
+```python
+from torch_geometric.datasets import JODIEDataset
+dataset = JODIEDataset(root='/tmp/JODIE', name='Reddit')
+```
+
+## 3D Meshes and Point Clouds
+
+### ShapeNet
+**Usage**: 3D shape classification and segmentation
+**Description**: Large-scale 3D CAD model dataset
+- 16,881 models across 16 categories
+- Part-level segmentation labels
+
+```python
+from torch_geometric.datasets import ShapeNet
+dataset = ShapeNet(root='/tmp/ShapeNet', categories=['Airplane'])
+```
+
+### ModelNet
+**Usage**: 3D shape classification
+**Versions**: ModelNet10, ModelNet40
+**Description**: CAD models for 3D object classification
+- ModelNet10: 4,899 models, 10 categories
+- ModelNet40: 12,311 models, 40 categories
+
+```python
+from torch_geometric.datasets import ModelNet
+dataset = ModelNet(root='/tmp/ModelNet', name='10')
+```
+
+### FAUST
+**Usage**: 3D shape matching, correspondence
+**Description**: Human body scans for shape analysis
+- 100 meshes of 10 people in 10 poses
+
+```python
+from torch_geometric.datasets import FAUST
+dataset = FAUST(root='/tmp/FAUST')
+```
+
+### CoMA
+**Usage**: 3D mesh deformation
+**Description**: Facial expression meshes
+- 20,466 3D face scans with expressions
+
+```python
+from torch_geometric.datasets import CoMA
+dataset = CoMA(root='/tmp/CoMA')
+```
+
+### S3DIS
+**Usage**: 3D semantic segmentation
+**Description**: Stanford Large-Scale 3D Indoor Spaces
+- 6 areas, 271 rooms, point cloud data
+
+```python
+from torch_geometric.datasets import S3DIS
+dataset = S3DIS(root='/tmp/S3DIS', test_area=6)
+```
+
+## Image and Vision Datasets
+
+### MNISTSuperpixels
+**Usage**: Graph-based image classification
+**Description**: MNIST images as superpixel graphs
+- 70,000 graphs (60k train, 10k test)
+
+```python
+from torch_geometric.datasets import MNISTSuperpixels
+dataset = MNISTSuperpixels(root='/tmp/MNIST')
+```
+
+### Flickr
+**Usage**: Image description, node classification
+**Description**: Flickr image network
+- 89,250 nodes, 899,756 edges
+
+```python
+from torch_geometric.datasets import Flickr
+dataset = Flickr(root='/tmp/Flickr')
+```
+
+### PPI
+**Usage**: Protein-protein interaction prediction
+**Description**: Multi-graph protein interaction networks
+- 24 graphs, 2,373 nodes total
+
+```python
+from torch_geometric.datasets import PPI
+dataset = PPI(root='/tmp/PPI', split='train')
+```
+
+## Small Classic Graphs
+
+### KarateClub
+**Usage**: Community detection, visualization
+**Description**: Zachary's karate club network
+- 34 nodes, 78 edges, 2 communities
+
+```python
+from torch_geometric.datasets import KarateClub
+dataset = KarateClub()
+```
+
+## Open Graph Benchmark (OGB)
+
+PyG integrates seamlessly with OGB datasets:
+
+### Node Property Prediction
+- **ogbn-products**: Amazon product network (2.4M nodes)
+- **ogbn-proteins**: Protein association network (132K nodes)
+- **ogbn-arxiv**: Citation network (169K nodes)
+- **ogbn-papers100M**: Large citation network (111M nodes)
+- **ogbn-mag**: Heterogeneous academic graph
+
+### Link Property Prediction
+- **ogbl-ppa**: Protein association networks
+- **ogbl-collab**: Collaboration networks
+- **ogbl-ddi**: Drug-drug interaction network
+- **ogbl-citation2**: Citation network
+- **ogbl-wikikg2**: Wikidata knowledge graph
+
+### Graph Property Prediction
+- **ogbg-molhiv**: Molecular HIV activity prediction
+- **ogbg-molpcba**: Molecular bioassays (multi-task)
+- **ogbg-ppa**: Protein function prediction
+- **ogbg-code2**: Code abstract syntax trees
+
+```python
+from torch_geometric.datasets import OGB_MAG, OGB_PPA
+# or
+from ogb.nodeproppred import PygNodePropPredDataset
+dataset = PygNodePropPredDataset(name='ogbn-arxiv')
+```
+
+## Synthetic Datasets
+
+### FakeDataset
+**Usage**: Testing, debugging
+**Description**: Generates random graph data
+
+```python
+from torch_geometric.datasets import FakeDataset
+dataset = FakeDataset(num_graphs=100, avg_num_nodes=50)
+```
+
+### StochasticBlockModelDataset
+**Usage**: Community detection benchmarks
+**Description**: Graphs generated from stochastic block models
+
+```python
+from torch_geometric.datasets import StochasticBlockModelDataset
+dataset = StochasticBlockModelDataset(root='/tmp/SBM', num_graphs=1000)
+```
+
+### ExplainerDataset
+**Usage**: Testing explainability methods
+**Description**: Synthetic graphs with known explanation ground truth
+
+```python
+from torch_geometric.datasets import ExplainerDataset
+dataset = ExplainerDataset(num_graphs=1000)
+```
+
+## Materials Science
+
+### QM8
+**Usage**: Molecular property prediction
+**Description**: Electronic properties of small molecules
+
+```python
+from torch_geometric.datasets import QM8
+dataset = QM8(root='/tmp/QM8')
+```
+
+## Biological Networks
+
+### PPI (Protein-Protein Interaction)
+Already listed above under Image and Vision Datasets
+
+### STRING
+**Usage**: Protein interaction networks
+**Description**: Known and predicted protein-protein interactions
+
+```python
+# Available through external sources or custom loading
+```
+
+## Usage Tips
+
+1. **Start with small datasets**: Use Cora, KarateClub, or ENZYMES for prototyping
+2. **Citation networks**: Planetoid datasets are perfect for node classification
+3. **Graph classification**: TUDataset provides diverse benchmarks
+4. **Molecular**: QM9, ZINC, MoleculeNet for chemistry applications
+5. **Large-scale**: Use Reddit, OGB datasets with NeighborLoader
+6. **Heterogeneous**: OGB_MAG, MovieLens, IMDB for multi-type graphs
+7. **Temporal**: JODIE, ICEWS for dynamic graph learning
+8. **3D**: ShapeNet, ModelNet, S3DIS for geometric learning
+
+## Common Patterns
+
+### Loading with Transforms
+```python
+from torch_geometric.datasets import Planetoid
+from torch_geometric.transforms import NormalizeFeatures
+
+dataset = Planetoid(root='/tmp/Cora', name='Cora',
+                    transform=NormalizeFeatures())
+```
+
+### Train/Val/Test Splits
+```python
+# For datasets with pre-defined splits
+data = dataset[0]
+train_data = data[data.train_mask]
+val_data = data[data.val_mask]
+test_data = data[data.test_mask]
+
+# For graph classification
+from torch_geometric.loader import DataLoader
+train_dataset = dataset[:int(len(dataset) * 0.8)]
+test_dataset = dataset[int(len(dataset) * 0.8):]
+train_loader = DataLoader(train_dataset, batch_size=32)
+```
+
+### Custom Data Loading
+```python
+from torch_geometric.data import Data, Dataset
+
+class MyCustomDataset(Dataset):
+    def __init__(self, root, transform=None):
+        super().__init__(root, transform)
+        # Your initialization
+
+    def len(self):
+        return len(self.data_list)
+
+    def get(self, idx):
+        # Load and return data object
+        return self.data_list[idx]
+```