Add assortativity to torch_geometric.utils (#5587)

* add assortativity

* test

* doc-string

* doc-string

* Update torch_geometric/utils/assortativity.py

Co-authored-by: Matthias Fey <[email protected]>

* Update torch_geometric/utils/assortativity.py

Co-authored-by: Matthias Fey <[email protected]>

* Update torch_geometric/utils/assortativity.py

Co-authored-by: Padarn Wilson <[email protected]>

* update test

* doc-string

* fix test

* changelog

Co-authored-by: Matthias Fey <[email protected]>
Co-authored-by: Padarn Wilson <[email protected]>

Author: 3 people

CHANGELOG.md

@@ -5,6 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [2.2.0] - 2022-MM-DD
 ### Added
+- Added `assortativity` that computes degree assortativity coefficient ([#5587](https://github.com/pyg-team/pytorch_geometric/pull/5587))
 - Added `SSGConv` layer ([#5599](https://github.com/pyg-team/pytorch_geometric/pull/5599))
 - Added `shuffle_node`, `mask_feature` and `add_random_edge` augmentation methdos ([#5548](https://github.com/pyg-team/pytorch_geometric/pull/5548))
 - Added `dropout_path` augmentation that drops edges from a graph based on random walks ([#5531](https://github.com/pyg-team/pytorch_geometric/pull/5531))

test/utils/test_assortativity.py

@@ -0,0 +1,18 @@
+import pytest
+import torch
+
+from torch_geometric.utils import assortativity
+
+
+def test_assortativity():
+    # completely assortative graph
+    edge_index = torch.tensor([[0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 5],
+                               [1, 2, 3, 0, 2, 3, 0, 1, 3, 0, 1, 2, 5, 4]])
+    out = assortativity(edge_index)
+    assert pytest.approx(out, abs=1e-5) == 1.0
+
+    # completely disassortative graph
+    edge_index = torch.tensor([[0, 1, 2, 3, 4, 5, 5, 5, 5, 5],
+                               [5, 5, 5, 5, 5, 0, 1, 2, 3, 4]])
+    out = assortativity(edge_index)
+    assert pytest.approx(out, abs=1e-5) == -1.0

torch_geometric/utils/__init__.py

@@ -1,6 +1,7 @@
 from .degree import degree
 from .softmax import softmax
 from .dropout import dropout_adj, dropout_node, dropout_edge, dropout_path
+from .augmentation import shuffle_node, mask_feature, add_random_edge
 from .sort_edge_index import sort_edge_index
 from .coalesce import coalesce
 from .undirected import is_undirected, to_undirected
@@ -11,6 +12,7 @@
 from .subgraph import (get_num_hops, subgraph, k_hop_subgraph,
                        bipartite_subgraph)
 from .homophily import homophily
+from .assortativity import assortativity
 from .get_laplacian import get_laplacian
 from .get_mesh_laplacian import get_mesh_laplacian
 from .mask import index_to_mask, mask_to_index
@@ -34,7 +36,6 @@
                                 structured_negative_sampling_feasible)
 from .train_test_split_edges import train_test_split_edges
 from .scatter import scatter
-from .augmentation import shuffle_node, mask_feature, add_random_edge
 
 __all__ = [
     'degree',
@@ -63,6 +64,7 @@
     'bipartite_subgraph',
     'k_hop_subgraph',
     'homophily',
+    'assortativity',
     'get_laplacian',
     'get_mesh_laplacian',
     'index_to_mask',

torch_geometric/utils/assortativity.py

@@ -0,0 +1,66 @@
+import torch
+from torch_sparse import SparseTensor
+
+from torch_geometric.typing import Adj
+from torch_geometric.utils import coalesce, degree
+
+from .to_dense_adj import to_dense_adj
+
+
+def assortativity(edge_index: Adj) -> float:
+    r"""The degree assortativity coefficient from the
+    `"Mixing patterns in networks"
+    <https://arxiv.org/abs/cond-mat/0209450>`_ paper.
+    Assortativity in a network refers to the tendency of nodes to
+    connect with other similar nodes over dissimilar nodes.
+    It is computed from Pearson correlation coefficient of the node degrees.
+
+    Args:
+        edge_index (Tensor or SparseTensor): The graph connectivity.
+
+    Returns:
+        The value of the degree assortativity coefficient for the input
+        graph :math:`\in [-1, 1]`
+
+    Example:
+
+        >>> edge_index = torch.tensor([[0, 1, 2, 3, 2],
+        ...                            [1, 2, 0, 1, 3]])
+        >>> assortativity(edge_index)
+        -0.666667640209198
+    """
+    if isinstance(edge_index, SparseTensor):
+        row, col, _ = edge_index.coo()
+    else:
+        row, col = edge_index
+
+    device = row.device
+    out_deg = degree(row, dtype=torch.long)
+    in_deg = degree(col, dtype=torch.long)
+    degrees = torch.unique(torch.cat([out_deg, in_deg]))
+    mapping = row.new_zeros(degrees.max().item() + 1)
+    mapping[degrees] = torch.arange(degrees.size(0), device=device)
+
+    # Compute degree mixing matrix (joint probability distribution) `M`
+    num_degrees = degrees.size(0)
+    src_deg = mapping[out_deg[row]]
+    dst_deg = mapping[in_deg[col]]
+
+    pairs = torch.stack([src_deg, dst_deg], dim=0)
+    occurrence = torch.ones(pairs.size(1), device=device)
+    pairs, occurrence = coalesce(pairs, occurrence)
+    M = to_dense_adj(pairs, edge_attr=occurrence, max_num_nodes=num_degrees)[0]
+    # normalization
+    M /= M.sum()
+
+    # numeric assortativity coefficient, computed by
+    # Pearson correlation coefficient of the node degrees
+    x = y = degrees.float()
+    a, b = M.sum(0), M.sum(1)
+
+    vara = (a * x**2).sum() - ((a * x).sum())**2
+    varb = (b * x**2).sum() - ((b * x).sum())**2
+    xy = torch.outer(x, y)
+    ab = torch.outer(a, b)
+    out = (xy * (M - ab)).sum() / (vara * varb).sqrt()
+    return out.item()