Re-structure torch_geometric.nn.aggr and torch_geometric.nn.norm documentation

CHANGELOG.md

@@ -57,7 +57,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Changed
 
-- Re-structured the documentation ([#6420](https://github.com/pyg-team/pytorch_geometric/pull/6420), [#6423](https://github.com/pyg-team/pytorch_geometric/pull/6423), [#6429](https://github.com/pyg-team/pytorch_geometric/pull/6429), [#6440](https://github.com/pyg-team/pytorch_geometric/pull/6440), [#6443](https://github.com/pyg-team/pytorch_geometric/pull/6443))
+- Re-structured the documentation ([#6420](https://github.com/pyg-team/pytorch_geometric/pull/6420), [#6423](https://github.com/pyg-team/pytorch_geometric/pull/6423), [#6429](https://github.com/pyg-team/pytorch_geometric/pull/6429), [#6440](https://github.com/pyg-team/pytorch_geometric/pull/6440), [#6443](https://github.com/pyg-team/pytorch_geometric/pull/6443), [#6445](https://github.com/pyg-team/pytorch_geometric/pull/6445))
 - Fix the default arguments of `DataParallel` class ([#6376](https://github.com/pyg-team/pytorch_geometric/pull/6376))
 - Fix `ImbalancedSampler` on sliced `InMemoryDataset` ([#6374](https://github.com/pyg-team/pytorch_geometric/pull/6374))
 - Breaking Change: Changed the interface and implementation of `GraphMultisetTransformer` ([#6343](https://github.com/pyg-team/pytorch_geometric/pull/6343))

README.md

@@ -70,7 +70,7 @@ In this quick tour, we highlight the ease of creating and training a GNN model w
 ### Train your own GNN model
 
 In the first glimpse of PyG, we implement the training of a GNN for classifying papers in a citation graph.
-For this, we load the [Cora](https://pytorch-geometric.readthedocs.io/en/latest/modules/datasets.html#torch_geometric.datasets.Planetoid) dataset, and create a simple 2-layer GCN model using the pre-defined [`GCNConv`](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.conv.GCNConv):
+For this, we load the [Cora](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.datasets.Planetoid.html) dataset, and create a simple 2-layer GCN model using the pre-defined [`GCNConv`](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.conv.GCNConv):
 
 ```python
 import torch
@@ -253,9 +253,9 @@ It is commonly applied to graph-level tasks, which require combining node featur
 <details>
 <summary><b>Expand to see all implemented pooling layers...</b></summary>
 
-* **[Attentional Aggregation](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.aggr.AttentionalAggregation)** from Li *et al.*: [Graph Matching Networks for Learning the Similarity of Graph Structured Objects](https://arxiv.org/abs/1904.12787) (ICML 2019) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/global_attention.py)]
-* **[Set2Set](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.aggr.Set2Set)** from Vinyals *et al.*: [Order Matters: Sequence to Sequence for Sets](https://arxiv.org/abs/1511.06391) (ICLR 2016) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/set2set.py)]
-* **[Sort Aggregation](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.aggr.SortAggregation)** from Zhang *et al.*: [An End-to-End Deep Learning Architecture for Graph Classification](https://www.cse.wustl.edu/~muhan/papers/AAAI_2018_DGCNN.pdf) (AAAI 2018) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/sort_pool.py)]
+* **[Attentional Aggregation](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.aggr.AttentionalAggregation.html)** from Li *et al.*: [Graph Matching Networks for Learning the Similarity of Graph Structured Objects](https://arxiv.org/abs/1904.12787) (ICML 2019) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/global_attention.py)]
+* **[Set2Set](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.aggr.Set2Set.html)** from Vinyals *et al.*: [Order Matters: Sequence to Sequence for Sets](https://arxiv.org/abs/1511.06391) (ICLR 2016) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/set2set.py)]
+* **[Sort Aggregation](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.aggr.SortAggregation.html)** from Zhang *et al.*: [An End-to-End Deep Learning Architecture for Graph Classification](https://www.cse.wustl.edu/~muhan/papers/AAAI_2018_DGCNN.pdf) (AAAI 2018) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/sort_pool.py)]
 * **[MinCut Pooling](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.dense.mincut_pool.dense_mincut_pool)** from Bianchi *et al.*: [Spectral Clustering with Graph Neural Networks for Graph Pooling](https://arxiv.org/abs/1907.00481) (ICML 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/proteins_mincut_pool.py)]
 * **[DMoN Pooling](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.dense.dmon_pool.DMoNPooling)** from Tsitsulin *et al.*: [Graph Clustering with Graph Neural Networks](https://arxiv.org/abs/2006.16904) (CoRR 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/proteins_dmon_pool.py)]
 * **[Graclus Pooling](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.pool.graclus)** from Dhillon *et al.*: [Weighted Graph Cuts without Eigenvectors: A Multilevel Approach](http://www.cs.utexas.edu/users/inderjit/public_papers/multilevel_pami.pdf) (PAMI 2007) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/mnist_graclus.py)]
@@ -265,8 +265,8 @@ It is commonly applied to graph-level tasks, which require combining node featur
 * **[ASAPooling](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.pool.ASAPooling)** from Ranjan *et al.*: [ASAP: Adaptive Structure Aware Pooling for Learning Hierarchical Graph Representations](https://arxiv.org/abs/1911.07979) (AAAI 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/benchmark/kernel/asap.py)]
 * **[PANPooling](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.pool.PANPooling)** from Ma *et al.*: [Path Integral Based Convolution and Pooling for Graph Neural Networks](https://arxiv.org/abs/2006.16811) (NeurIPS 2020)
 * **[MemPooling](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.pool.MemPooling)** from Khasahmadi *et al.*: [Memory-Based Graph Networks](https://arxiv.org/abs/2002.09518) (ICLR 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/mem_pool.py)]
-* **[Graph Multiset Transformer](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.aggr.GraphMultisetTransformer)** from Baek *et al.*: [Accurate Learning of Graph Representations with Graph Multiset Pooling](https://arxiv.org/abs/2102.11533) (ICLR 2021) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/proteins_gmt.py)]
-* **[Equilibrium Aggregation](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.aggr.EquilibriumAggregation)** from Bartunov *et al.*: [](https://arxiv.org/abs/2202.12795) (UAI 2022) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/equilibrium_median.py)]
+* **[Graph Multiset Transformer](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.aggr.GraphMultisetTransformer.html)** from Baek *et al.*: [Accurate Learning of Graph Representations with Graph Multiset Pooling](https://arxiv.org/abs/2102.11533) (ICLR 2021) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/proteins_gmt.py)]
+* **[Equilibrium Aggregation](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.aggr.EquilibriumAggregation.html)** from Bartunov *et al.*: [](https://arxiv.org/abs/2202.12795) (UAI 2022) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/equilibrium_median.py)]
 </details>
 
 **GNN models:**
@@ -311,16 +311,16 @@ They follow an extensible design: It is easy to apply these operators and graph
 * **[DropNode](https://pytorch-geometric.readthedocs.io/en/latest/modules/utils.html#torch_geometric.utils.dropout_node)**, **[MaskFeature](https://pytorch-geometric.readthedocs.io/en/latest/modules/utils.html#torch_geometric.utils.mask_feature)** and **[AddRandomEdge](https://pytorch-geometric.readthedocs.io/en/latest/modules/utils.html#torch_geometric.utils.add_random_edge)** from You *et al.*: [Graph Contrastive Learning with Augmentations](https://arxiv.org/abs/2010.13902) (NeurIPS 2020)
 * **[DropPath](https://pytorch-geometric.readthedocs.io/en/latest/modules/utils.html#torch_geometric.utils.dropout_path)** from Li *et al.*: [MaskGAE: Masked Graph Modeling Meets Graph Autoencoders](https://arxiv.org/abs/2205.10053) (arXiv 2022)
 * **[ShuffleNode](https://pytorch-geometric.readthedocs.io/en/latest/modules/utils.html#torch_geometric.utils.shuffle_node)** from Veličković *et al.*: [Deep Graph Infomax](https://arxiv.org/abs/1809.10341) (ICLR 2019)
-* **[GraphNorm](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.norm.GraphNorm)** from Cai *et al.*: [GraphNorm: A Principled Approach to Accelerating Graph Neural Network Training](https://proceedings.mlr.press/v139/cai21e.html) (ICML 2021)
-* **[GDC](https://pytorch-geometric.readthedocs.io/en/latest/modules/transforms.html#torch_geometric.transforms.GDC)** from Klicpera *et al.*: [Diffusion Improves Graph Learning](https://arxiv.org/abs/1911.05485) (NeurIPS 2019) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/gcn.py)]
+* **[GraphNorm](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.norm.GraphNorm.html)** from Cai *et al.*: [GraphNorm: A Principled Approach to Accelerating Graph Neural Network Training](https://proceedings.mlr.press/v139/cai21e.html) (ICML 2021)
+* **[GDC](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.transforms.GDC.html)** from Klicpera *et al.*: [Diffusion Improves Graph Learning](https://arxiv.org/abs/1911.05485) (NeurIPS 2019) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/gcn.py)]
 
 <details>
 <summary><b>Expand to see all implemented GNN operators and utilities...</b></summary>
 
-* **[GraphSizeNorm](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.norm.GraphSizeNorm)** from Dwivedi *et al.*: [Benchmarking Graph Neural Networks](https://arxiv.org/abs/2003.00982) (CoRR 2020)
-* **[PairNorm](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.norm.PairNorm)** from Zhao and Akoglu: [PairNorm: Tackling Oversmoothing in GNNs](https://arxiv.org/abs/1909.12223) (ICLR 2020)
-* **[MeanSubtractionNorm](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.norm.MeanSubtractionNorm)** from Yang *et al.*: [Revisiting "Over-smoothing" in Deep GCNs](https://arxiv.org/abs/2003.13663) (CoRR 2020)
-* **[DiffGroupNorm](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.norm.DiffGroupNorm)** from Zhou *et al.*: [Towards Deeper Graph Neural Networks with Differentiable Group Normalization](https://arxiv.org/abs/2006.06972) (NeurIPS 2020)
+* **[GraphSizeNorm](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.norm.GraphSizeNorm.html)** from Dwivedi *et al.*: [Benchmarking Graph Neural Networks](https://arxiv.org/abs/2003.00982) (CoRR 2020)
+* **[PairNorm](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.norm.PairNorm.html)** from Zhao and Akoglu: [PairNorm: Tackling Oversmoothing in GNNs](https://arxiv.org/abs/1909.12223) (ICLR 2020)
+* **[MeanSubtractionNorm](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.norm.MeanSubtractionNorm.html)** from Yang *et al.*: [Revisiting "Over-smoothing" in Deep GCNs](https://arxiv.org/abs/2003.13663) (CoRR 2020)
+* **[DiffGroupNorm](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.norm.DiffGroupNorm.html)** from Zhou *et al.*: [Towards Deeper Graph Neural Networks with Differentiable Group Normalization](https://arxiv.org/abs/2006.06972) (NeurIPS 2020)
 * **[Tree Decomposition](https://pytorch-geometric.readthedocs.io/en/latest/modules/utils.html#torch_geometric.utils.tree_decomposition)** from Jin *et al.*: [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://arxiv.org/abs/1802.04364) (ICML 2018)
 * **[TGN](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.models.TGNMemory)** from Rossi *et al.*: [Temporal Graph Networks for Deep Learning on Dynamic Graphs](https://arxiv.org/abs/2006.10637) (GRL+ 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/tgn.py)]
 * **[Weisfeiler Lehman Operator](https://pytorch-geometric.readthedocs.io/en/latest/modules/nn.html#torch_geometric.nn.conv.WLConv)** from Weisfeiler and Lehman: [A Reduction of a Graph to a Canonical Form and an Algebra Arising During this Reduction](https://www.iti.zcu.cz/wl2018/pdf/wl_paper_translation.pdf) (Nauchno-Technicheskaya Informatsia 1968) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/wl_kernel.py)]
@@ -347,8 +347,8 @@ These approaches have been implemented in PyG, and can benefit from the above GN
 <summary><b>Expand to see all implemented scalable GNNs...</b></summary>
 
 * **[ShaDow](https://pytorch-geometric.readthedocs.io/en/latest/modules/loader.html#torch_geometric.loader.ShaDowKHopSampler)** from Zeng *et al.*: [Decoupling the Depth and Scope of Graph Neural Networks](https://arxiv.org/abs/2201.07858) (NeurIPS 2021) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/shadow.py)]
-* **[SIGN](https://pytorch-geometric.readthedocs.io/en/latest/modules/transforms.html#torch_geometric.transforms.SIGN)** from Rossi *et al.*: [SIGN: Scalable Inception Graph Neural Networks](https://arxiv.org/abs/2004.11198) (CoRR 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/sign.py)]
-* **[HGTLoader](https://pytorch-geometric.readthedocs.io/en/latest/modules/transforms.html#torch_geometric.loader.HGTLoader)** from Hu *et al.*: [Heterogeneous Graph Transformer](https://arxiv.org/abs/2003.01332) (WWW 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/hetero/to_hetero_mag.py)]
+* **[SIGN](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.transforms.SIGN.html)** from Rossi *et al.*: [SIGN: Scalable Inception Graph Neural Networks](https://arxiv.org/abs/2004.11198) (CoRR 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/sign.py)]
+* **[HGTLoader](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.loader.HGTLoader.html)** from Hu *et al.*: [Heterogeneous Graph Transformer](https://arxiv.org/abs/2003.01332) (WWW 2020) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/hetero/to_hetero_mag.py)]
 </details>
 
 ## Installation

docs/source/_templates/autosummary/class.rst

@@ -5,5 +5,3 @@
 .. autoclass:: {{ objname }}
    :show-inheritance:
    :members:
-   :inherited-members:
-   :special-members: __cat_dim__, __inc__

docs/source/_templates/autosummary/inherited_class.rst

@@ -0,0 +1,9 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :show-inheritance:
+   :members:
+   :inherited-members:
+   :special-members: __cat_dim__, __inc__

docs/source/modules/data.rst

@@ -12,6 +12,7 @@ Data Objects
 .. autosummary::
    :nosignatures:
    :toctree: ../generated
+   :template: autosummary/inherited_class.rst
 
    {% for name in torch_geometric.data.data_classes %}
      {{ name }}

docs/source/modules/nn.rst

@@ -85,7 +85,7 @@ For this, an :obj:`index` vector defines the mapping from input elements to thei
 
    output = mean_aggr(x, index)  #  Output shape: [100, 64]
 
-Notably, all aggregations share the same set of forward arguments, as described in detail in :class:`torch_geometric.nn.aggr.Aggregation`.
+Notably, all aggregations share the same set of forward arguments, as described in detail in the :class:`torch_geometric.nn.aggr.Aggregation` base class.
 
 Each of the provided aggregations can be used within :class:`~torch_geometric.nn.conv.MessagePassing` as well as for hierachical/global pooling to obtain graph-level representations:
 
@@ -155,31 +155,24 @@ Finally, we added full support for customization of aggregations into the :class
 
 .. autosummary::
    :nosignatures:
-   {% for cls in torch_geometric.nn.aggr.classes %}
-     {{ cls }}
-   {% endfor %}
-
-.. autoclass:: torch_geometric.nn.aggr.Aggregation
-   :members:
+   :toctree: ../generated
 
-.. automodule:: torch_geometric.nn.aggr
-   :members:
-   :exclude-members: Aggregation, forward
+   {% for name in torch_geometric.nn.aggr.classes %}
+     {{ name }}
+   {% endfor %}
 
 Normalization Layers
 --------------------
 
 .. currentmodule:: torch_geometric.nn.norm
+
 .. autosummary::
    :nosignatures:
-   {% for cls in torch_geometric.nn.norm.classes %}
-     {{ cls }}
-   {% endfor %}
+   :toctree: ../generated
 
-.. automodule:: torch_geometric.nn.norm
-   :members:
-   :undoc-members:
-   :exclude-members: training
+   {% for name in torch_geometric.nn.norm.classes %}
+     {{ name }}
+   {% endfor %}
 
 Pooling Layers
 --------------

torch_geometric/nn/aggr/base.py

@@ -22,7 +22,8 @@ class Aggregation(torch.nn.Module):
 
     |
 
-    Notably, :obj:`index` does not have to be sorted:
+    Notably, :obj:`index` does not have to be sorted (for most aggregation
+    operators):
 
     .. code-block::
 
@@ -52,26 +53,24 @@ class Aggregation(torch.nn.Module):
 
     Shapes:
         - **input:**
-          node features :math:`(|\mathcal{V}|, F_{in})` or edge features
-          :math:`(|\mathcal{E}|, F_{in})`,
+          node features :math:`(*, |\mathcal{V}|, F_{in})` or edge features
+          :math:`(*, |\mathcal{E}|, F_{in})`,
           index vector :math:`(|\mathcal{V}|)` or :math:`(|\mathcal{E}|)`,
-        - **output:** graph features :math:`(|\mathcal{G}|, F_{out})` or node
-          features :math:`(|\mathcal{V}|, F_{out})`
+        - **output:** graph features :math:`(*, |\mathcal{G}|, F_{out})` or
+          node features :math:`(*, |\mathcal{V}|, F_{out})`
     """
-
-    # @abstractmethod
     def forward(self, x: Tensor, index: Optional[Tensor] = None,
                 ptr: Optional[Tensor] = None, dim_size: Optional[int] = None,
                 dim: int = -2) -> Tensor:
         r"""
         Args:
             x (torch.Tensor): The source tensor.
-            index (torch.LongTensor, optional): The indices of elements for
+            index (torch.Tensor, optional): The indices of elements for
                 applying the aggregation.
                 One of :obj:`index` or :obj:`ptr` must be defined.
                 (default: :obj:`None`)
-            ptr (torch.LongTensor, optional): If given, computes the
-                aggregation based on sorted inputs in CSR representation.
+            ptr (torch.Tensor, optional): If given, computes the aggregation
+                based on sorted inputs in CSR representation.
                 One of :obj:`index` or :obj:`ptr` must be defined.
                 (default: :obj:`None`)
             dim_size (int, optional): The size of the output tensor at
@@ -82,6 +81,7 @@ def forward(self, x: Tensor, index: Optional[Tensor] = None,
         pass
 
     def reset_parameters(self):
+        r"""Resets all learnable parameters of the module."""
         pass
 
     def __call__(self, x: Tensor, index: Optional[Tensor] = None,