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Pyg 2.3.0: PyTorch 2.0 support, native sparse tensor support, explainability and accelerations
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@wsad1 wsad1 released this 23 Mar 09:00
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2.3.0
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We are thrilled to announce the release of PyG 2.3 🎉

PyG 2.3 is the culmination of work from 59 contributors who have worked on features and bug-fixes for a total of over 470 commits since torch-geometric==2.2.0.

Highlights

PyTorch 2.0 Support

PyG 2.3 is fully compatible with the next generation release of PyTorch, bringing many new innovations and features such as torch.compile() and Python 3.11 support to PyG out-of-the-box. In particular, many PyG models and functions are speeded up significantly using torch.compile() in torch >= 2.0.0.

We have prepared a full tutorial and a set of examples to get you going with torch.compile() immediately:

import torch_geometric
from torch_geometric.nn import GraphSAGE

model = GraphSAGE(in_channels, hidden_channels, num_layers, out_channels)
model = model.to(device)

model = torch_geometric.compile(model)

Overall, we observed runtime improvements of nearly up to 300%:

Model Mode Forward Backward Total Speedup
GCN Eager 2.6396s 2.1697s 4.8093s  
GCN Compiled 1.1082s 0.5896s 1.6978s 2.83x
GraphSAGE Eager 1.6023s 1.6428s 3.2451s  
GraphSAGE Compiled 0.7033s 0.7465s 1.4498s 2.24x
GIN Eager 1.6701s 1.6990s 3.3690s  
GIN Compiled 0.7320s 0.7407s 1.4727s 2.29x

Please note that torch.compile() within PyG is in beta mode and under active development. For example, currently torch.compile(model, dynamic=True) does not yet work seamlessly, but fixes are on its way. We are very eager to improve its support across the whole PyG code base, so do not hesitate to reach out if you notice anything unexpected.

Infrastructure Changes

With the recent upstreams of torch-scatter and torch-sparse to native PyTorch, we are happy to announce that any installation of the extension packages torch-scatter, torch-sparse, torch-cluster and torch-spline-conv is now fully optional.

All it takes to install PyG is now encapsulated into a single command

pip install torch-geometric

and finally resolves a lot of previous installation issues.

Extension packages are still picked up for the following use-cases (if installed):

We recommend to start with a minimal installation, and only install additional dependencies once you actually get notified about them being missing during PyG usage.

Native PyTorch Sparse Tensor Support

With the recent additions of torch.sparse_csr_tensor and torch.sparse_csc_tensor classes and accelerated sparse matrix multiplication routines to PyTorch, we finally enable MessagePassing on pure PyTorch sparse tensors as well. In particular, you can now use torch.sparse_csr_tensor and torch.sparse_csc_tensor as a drop-in replacement for torch_sparse.SparseTensor:

from torch_geometric.nn import GCN
import torch_geometric.transforms as T
from torch_geometric.datasets import Planetoid

transform = T.ToSparseTensor(layout=torch.sparse_csr)
dataset = Planetoid("Planetoid", name="Cora", transform=transform)

model = GCN(in_channels, hidden_channels, num_layers=2)
model = model(data.x, data.adj_t)

Nearly all of the native PyG layers have been tested to work seamlessly with native PyTorch sparse tensors (#5906, #5944, #6003, #6033, #6514, #6532, #6748, #6847, #6868, #6874, #6897, #6930, #6932, #6936, #6937, #6939, #6947, #6950, #6951, #6957).

Explainability Framework

In PyG 2.2 we introduced the torch_geometric.explain package that provides a flexible interface to generate and visualize GNN explanations using various algorithms. We are happy to add the following key improvements on this front:

  1. Support for explaining heterogeneous GNNs via HeteroExplanation
  2. New visualization tools to visualize_feature_importance and to visualize_graph explanations
  3. May new datasets and metrics to evaluate explanation algorithms
  4. Several new explanation algorithms such as CaptumExplainer, PGExplainer, AttentionExplainer, PGMExplainer, and GraphMaskExplainer
  5. Support for node-level, link-level and graph-level explanations

Using the new explainer interface is as simple as:

explainer = Explainer(
    model=model,
    algorithm=CaptumExplainer('IntegratedGradients'),
    explanation_type='model',
    model_config=dict(
        mode='multiclass_classification',
        task_level='node',
        return_type='log_probs',
    ),
    node_mask_type='attributes',
    edge_mask_type='object',
)

explanation = explainer(data.x, data.edge_index)

Read more about torch_geometric.explain in our newly added tutorial and example scripts. We also added a blog post that describes the new interface and functionality in depth.

Accelerations

Together with Intel and NVIDIA, we are excited about new PyG accelerations:

  • [Experimental] Support for native cugraph-based GNN layers for commonly used layers such as CuGraphSAGEConv, CuGraphGATConv, and CuGraphRGCNConv (#6278, #6388, #6412):

    RGCN with neighbor sampling:

    Dataset CuGraphRGCNConv (ms) FastRGCNConv (ms) RGCNConv (ms)
    AIFB 7,2 13,4 70
    BGS 7,1 8,8 146,9
    MUTAG 8,3 21,8 47,6
    AM 17,5 51 330,1

    Full-batch GAT:

    Dataset CuGraphGATConv (ms) GATConv (ms)
    Cora 7 8,7
    Citeseer 7 9
    Pubmed 8,2 11,4

    GraphSAGE with neighbor sampling:

    Dataset CuGraphSAGEConv (ms) SAGEConv (ms)
    ogbn-products 2591,8 3040,3

  • A fast alternative to HGTConv via FastHGTConv that utilizes pyg-lib integration for improved runtimes. Overall, FastHGTConv achieves a speed-up of approximately 300% compared to the original implementation (#6178).

  • A fast implementation of HeteroDictLinear that utilizes pyg-lib integration for improved runtimes (#6178).

  • GNN inference and training optimizations on CPU within native PyTorch 2.0. Optimizations include:

    • scatter_reduce: performance hotspot in message passing when edge_index is stored in Coordinate format (COO).
    • gather: backward of scatter_reduce, specially tuned for the GNN compute when the index is an expanded tensor.
    • torch.sparse.mm with reduce flag: performance hotspot in message passing when the edge_index is stored in Compressed Sparse Row (CSR). Supported reduce flags are "sum", "mean", "amax" and "amin".
      On OGB benchmarks, a 1.12x - 4.07x performance speedup is measured (PyTorch 1.13.1 vs PyTorch 2.0) for single node inference and training.

  • Introduction of index_sort via pyg-lib>=0.2.0, which implements a (way) faster alternative to sorting one-dimensional indices compared to torch.sort (#6554). Overall, this achieves speed-ups in dataset loading times by up to 600%.

  • Introduction of AffinityMixin to accelerate PyG workflows on CPU. CPU affinity can be enabled via the AffinityMixin.enable_cpu_affinity() method for num_workers > 0 data loading use-cases, and will guarantee that a separate core is assigned to each worker at initialization. Over all benchmarked model/dataset samples, the average training time is decreased by up to 1.85x. We added an in-depth tutorial on how to speed-up your PyG workflows on CPU.

Additional Highlights

Documentation Revamp

The documentation has undergone a revision of design and structure, making it faster to load and easier to navigate. Take a look at its new design here.

Community Sprint: Improving Code Coverage

We had our third community sprint in the last two weeks of January. The goal was to improve code coverage by writing more thorough tests. Thanks to the efforts of many contributors, the total code coverage went from ~85% to ~92% (#6528, #6523, #6538, #6555, #6558, #6568, #6573, #6578, #6597, #6600, #6618, #6619, #6621, #6623, #6637, #6638, #6640, #6645, #6648, #6647, #6653, #6657, #6662, #6664, #6667, #6668, #6669, #6670, #6671, #6673, #6675, #6676, #6677, #6678, #6681, #6683, #6703, #6720, #6735, #6736, #6763, #6781, #6797, #6799, #6824, #6858)

Breaking Changes

Deprecations

Features

Layers, Models and Examples

Datasets

Loaders

Transformations

General Improvements

Bug Fixes

Full Changelog

Added
  • Added a memory-efficient utils.one_hot implementation (#7005)
  • Added HeteroDictLinear and an optimized FastHGTConv module (#6178, #6998)
  • Added the DenseGATConv module (#6928)
  • Added trim_to_layer utility function for more efficient NeighborLoader use-cases (#6661)
  • Added the DistMult KGE model (#6958)
  • Added HeteroData.set_value_dict functionality (#6961, #6974)
  • Added PyTorch >= 2.0 support (#6934, #7000)
  • Added PyTorch Lightning >= 2.0 support (#6929)
  • Added the ComplEx KGE model (#6898)
  • Added option to write benchmark results to csv (#6888)
  • Added HeteroLayerNorm and HeteroBatchNorm layers (#6838)
  • Added the HeterophilousGraphDataset suite (#6846)
  • Added support for sparse tensor in full batch mode inference benchmark (#6843)
  • Enabled NeighborLoader to return number of sampled nodes and edges per hop (#6834)
  • Added ZipLoader to execute multiple NodeLoader or LinkLoader instances (#6829)
  • Added common utils.select and utils.narrow functionality to support filtering of both tensors and lists (#6162)
  • Support normalization customization in get_mesh_laplacian (#6790)
  • Added the TemporalEncoding module (#6785)
  • Added CPU-optimized spmm_reduce functionality via CSR format (#6699, #6759)
  • Added support for the revised version of the MD17 dataset (#6734)
  • Added TorchScript support to the RECT_L model (#6727)
  • Added TorchScript support to the Node2Vec model (#6726)
  • Added utils.to_edge_index to convert sparse tensors to edge indices and edge attributes (#6728)
  • Fixed expected data format in PolBlogs dataset (#6714)
  • Added SimpleConv to perform non-trainable propagation (#6718)
  • Added a RemoveDuplicatedEdges transform (#6709)
  • Added TorchScript support to the LINKX model (#6712)
  • Added torch.jit examples for example/film.py and example/gcn.py(#6602)
  • Added Pad transform (#5940, #6697, #6731, #6758)
  • Added full batch mode to the inference benchmark (#6631)
  • Added cat aggregation type to the HeteroConv class so that features can be concatenated during grouping (#6634)
  • Added torch.compile support and benchmark study (#6610, #6952, #6953, #6980, #6983, #6984, #6985, #6986, #6989, #7002)
  • Added the AntiSymmetricConv layer (#6577)
  • Added a mixin for Huggingface model hub integration (#5930, #6591)
  • Added support for accelerated GNN layers in nn.conv.cugraph via cugraph-ops (#6278, #6388, #6412)
  • Added accelerated index_sort function from pyg-lib for faster sorting (#6554)
  • Fix incorrect device in EquilibriumAggregration (#6560)
  • Added bipartite graph support in dense_to_sparse() (#6546)
  • Add CPU affinity support for more data loaders (#6534, #6922)
  • Added the BAMultiShapesDataset (#6541)
  • Added the interfaces of a graph pooling framework (#6540)
  • Added automatic n_id and e_id attributes to mini-batches produced by NodeLoader and LinkLoader (#6524)
  • Added PGMExplainer to torch_geometric.contrib (#6149, #6588, #6589)
  • Added a NumNeighbors helper class for specifying the number of neighbors when sampling (#6501, #6505, #6690)
  • Added caching to is_node_attr() and is_edge_attr() calls (#6492)
  • Added ToHeteroLinear and ToHeteroMessagePassing modules to accelerate to_hetero functionality (#5992, #6456)
  • Added GraphMaskExplainer (#6284)
  • Added the GRBCD and PRBCD adversarial attack models (#5972)
  • Added dropout option to SetTransformer and GraphMultisetTransformer (#6484)
  • Added option to customize loader arguments for evaluation in LightningNodeData and LightningLinkData (#6450, #6456)
  • Added option to customize num_neighbors in NeighborSampler after instantiation (#6446)
  • Added the Taobao dataset and a corresponding example for it (#6144)
  • Added pyproject.toml (#6431)
  • Added the torch_geometric.contrib sub-package (#6422)
  • Warn on using latest documentation (#6418)
  • Added basic pyright type checker support (#6415)
  • Added a new external resource for link prediction (#6396)
  • Added CaptumExplainer (#6383, #6387, #6433, #6487, #6966)
  • Added support for custom HeteroData mini-batch class in remote backends (#6377)
  • Added the GNNFF model (#5866)
  • Added MLPAggregation, SetTransformerAggregation, GRUAggregation, and DeepSetsAggregation as adaptive readout functions (#6301, #6336, #6338)
  • Added Dataset.to_datapipe for converting PyG datasets into a torchdata DataPipe(#6141)
  • Added to_nested_tensor and from_nested_tensor functionality (#6329, #6330, #6331, #6332)
  • Added the GPSConv Graph Transformer layer and example (#6326, #6327)
  • Added networkit conversion utilities (#6321)
  • Added global dataset attribute access via dataset.{attr_name} (#6319)
  • Added the TransE KGE model and example (#6314)
  • Added the Freebase FB15k_237 dataset (#3204)
  • Added Data.update() and HeteroData.update() functionality (#6313)
  • Added PGExplainer (#6204)
  • Added the AirfRANS dataset (#6287)
  • Added AttentionExplainer (#6279)
  • Added (un)faithfulness explainability metric (#6090)
  • Added fidelity explainability metric (#6116, #6510)
  • Added subgraph visualization of GNN explanations (#6235, #6271)
  • Added weighted negative sampling option in LinkNeighborLoader (#6264)
  • Added the BA2MotifDataset explainer dataset (#6257)
  • Added CycleMotif motif generator to generate n-node cycle shaped motifs (#6256)
  • Added the InfectionDataset to evaluate explanations (#6222)
  • Added characterization_score and fidelity_curve_auc explainer metrics (#6188)
  • Added get_message_passing_embeddings (#6201)
  • Added the PointGNNConv layer (#6194)
  • Added GridGraph graph generator to generate grid graphs (#6220
  • Added explainability metrics for when ground truth is available (#6137)
  • Added visualize_feature_importance to support node feature visualizations (#6094)
  • Added heterogeneous graph support to Explanation framework (#6091, #6218)
  • Added a CustomMotif motif generator (#6179)
  • Added ERGraph graph generator to generate Ergos-Renyi (ER) graphs (#6073)
  • Added BAGraph graph generator to generate Barabasi-Albert graphs - the usage of datasets.BAShapes is now deprecated (#6072
  • Added explainability benchmark dataset framework (#6104)
  • Added seed_time attribute to temporal NodeLoader outputs in case input_time is given (#6196)
  • Added Data.edge_subgraph and HeteroData.edge_subgraph functionalities (#6193)
  • Added input_time option to LightningNodeData and transform_sampler_output to NodeLoader and LinkLoader (#6187)
  • Added summary for PyG/PyTorch models (#5859, #6161)
  • Started adding torch.sparse support to PyG (#5906, #5944, #6003, #6033, #6514, #6532, #6748, #6847, #6868, #6874, #6897, #6930, #6932, #6936, #6937, #6939, #6947, #6950, #6951, #6957)
  • Add inputs_channels back in training benchmark (#6154)
  • Added support for dropping nodes in utils.to_dense_batch in case max_num_nodes is smaller than the number of nodes (#6124)
  • Added the RandLA-Net architecture as an example (#5117)
Changed
  • Drop internal usage of __dunder__ names (#6999)
  • Changed the interface of sort_edge_index, coalesce and to_undirected to only return single edge_index information in case the edge_attr argument is not specified (#6875, #6879, #6893)
  • Fixed a bug in to_hetero when using an uninitialized submodule without implementing reset_parameters (#6863)
  • Fixed a bug in get_mesh_laplacian (#6790)
  • Fixed a bug in which masks were not properly masked in GNNExplainer on link prediction tasks (#6787)
  • Allow the usage of ChebConv within GNNExplainer (#6778)
  • Allow setting the EdgeStorage.num_edges property (#6710)
  • Fixed a bug in utils.bipartite_subgraph() and updated docs of HeteroData.subgraph() (#6654)
  • Properly reset the data_list cache of an InMemoryDataset when accessing dataset.data (#6685)
  • Fixed a bug in Data.subgraph() and HeteroData.subgraph() (#6613)
  • Fixed a bug in PNAConv and DegreeScalerAggregation to correctly incorporate degree statistics of isolated nodes (#6609)
  • Improved code coverage (#6523, #6538, #6555, #6558, #6568, #6573, #6578, #6597, #6600, #6618, #6619, #6621, #6623, #6637, #6638, #6640, #6645, #6648, #6647, #6653, #6657, #6662, #6664, #6667, #6668, #6669, #6670, #6671, #6673, #6675, #6676, #6677, #6678, #6681, #6683, #6703, #6720, #6735, #6736, #6763, #6781, #6797, #6799, #6824, #6858)
  • Fixed a bug in which data.to_heterogeneous() filtered attributs in the wrong dimension (#6522)
  • Breaking Change: Temporal sampling will now also sample nodes with an equal timestamp to the seed time (requires pyg-lib>0.1.0) (#6517)
  • Changed DataLoader workers with affinity to start at cpu0 (#6512)
  • Allow 1D input to global_*_pool functions (#6504)
  • Add information about dynamic shapes in RGCNConv (#6482)
  • Fixed the use of types removed in numpy 1.24.0 (#6495)
  • Fixed keyword parameters in examples/mnist_voxel_grid.py (#6478)
  • Unified LightningNodeData and LightningLinkData code paths (#6473)
  • Allow indices with any integer type in RGCNConv (#6463)
  • Re-structured the documentation (#6420, #6423, #6429, #6440, #6443, #6445, #6452, #6453, #6458, #6459, #6460, #6490, #6491, #6693, #6744)
  • Fix the default arguments of DataParallel class (#6376)
  • Fix ImbalancedSampler on sliced InMemoryDataset (#6374)
  • Breaking Change: Changed the interface and implementation of GraphMultisetTransformer (#6343)
  • Fixed the approximate PPR variant in transforms.GDC to not crash on graphs with isolated nodes (#6242)
  • Added a warning when accesing InMemoryDataset.data (#6318)
  • Drop SparseTensor dependency in GraphStore (#5517)
  • Replace NeighborSampler with NeighborLoader in the distributed sampling example (#6204)
  • Fixed the filtering of node features in transforms.RemoveIsolatedNodes (#6308)
  • Fixed a bug in DimeNet that causes a output dimension mismatch (#6305)
  • Fixed Data.to_heterogeneous() with empty edge_index (#6304)
  • Unify Explanation.node_mask and Explanation.node_feat_mask (#6267)
  • Moved thresholding config of the Explainer to Explanation (#6215)
  • Fixed a bug in the output order in HeteroLinear for un-sorted type vectors (#6198)
  • Breaking Change: Move ExplainerConfig arguments to the Explainer class (#6176)
  • Refactored NeighborSampler to be input-type agnostic (#6173)
  • Infer correct CUDA device ID in profileit decorator (#6164)
  • Correctly use edge weights in GDC example (#6159)
  • Breaking Change: Moved PyTorch Lightning data modules to torch_geometric.data.lightning (#6140)
  • Make torch_sparse an optional dependency (#6132, #6134, #6138, #6139)
  • Optimized utils.softmax implementation (#6113, #6155, #6805)
  • Optimized topk implementation for large enough graphs (#6123)
Removed
  • torch-sparse is now an optional dependency (#6625, #6626, #6627, #6628, #6629, #6630)
  • Removed most of the torch-scatter dependencies (#6394, #6395, #6399, #6400, #6615, #6617)
  • Removed the deprecated classes GNNExplainer and Explainer from nn.models (#6382)
  • Removed target_index argument in the Explainer interface (#6270)
  • Removed Aggregation.set_validate_args option (#6175)

Full Changelog: 2.2.0...2.3.0

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