Eccentricity Lifting (Graph to Complex)

configs/transforms/liftings/graph2simplicial/graph_induced_lifting.yaml → configs/transforms/liftings/graph2simplicial/eccentricity_lifting.yaml

@@ -1,5 +1,5 @@
 transform_type: 'lifting'
-transform_name: "SimplicialGraphInducedLifting"
+transform_name: "SimplicialEccentricityLifting"
 complex_dim: 3
 preserve_edge_attr: False
 signed: True

modules/transforms/data_transform.py

@@ -23,8 +23,8 @@
 from modules.transforms.liftings.graph2simplicial.clique_lifting import (
     SimplicialCliqueLifting,
 )
-from modules.transforms.liftings.graph2simplicial.graph_induced_lifting import (
-    SimplicialGraphInducedLifting,
+from modules.transforms.liftings.graph2simplicial.eccentricity_lifting import (
+    SimplicialEccentricityLifting,
 )
 from modules.transforms.liftings.graph2simplicial.line_lifting import (
     SimplicialLineLifting,
@@ -45,9 +45,9 @@
     "ExpanderGraphLifting": ExpanderGraphLifting,
     # Graph -> Simplicial Complex
     "SimplicialCliqueLifting": SimplicialCliqueLifting,
+    "SimplicialEccentricityLifting": SimplicialEccentricityLifting,
     "SimplicialLineLifting": SimplicialLineLifting,
     "SimplicialVietorisRipsLifting": SimplicialVietorisRipsLifting,
-    "SimplicialGraphInducedLifting": SimplicialGraphInducedLifting,
     # Graph -> Cell Complex
     "CellCycleLifting": CellCycleLifting,
     # Point Cloud -> Simplicial Complex,

modules/transforms/liftings/graph2simplicial/graph_induced_lifting.py → modules/transforms/liftings/graph2simplicial/eccentricity_lifting.py

@@ -9,8 +9,8 @@
 )
 
 
-class SimplicialGraphInducedLifting(Graph2SimplicialLifting):
-    r"""Lifts graphs to simplicial complex domain by identifying connected subgraphs as simplices.
+class SimplicialEccentricityLifting(Graph2SimplicialLifting):
+    r"""Lifts graphs to simplicial complex domain using eccentricity.
 
     Parameters
     ----------
@@ -35,15 +35,20 @@ def lift_topology(self, data: torch_geometric.data.Data) -> dict:
             The lifted topology.
         """
         graph = self._generate_graph_from_data(data)
-        simplicial_complex = SimplicialComplex(graph)
-        all_nodes = list(graph.nodes)
+        simplicial_complex = SimplicialComplex()
+        eccentricities = nx.eccentricity(graph)
         simplices = [set() for _ in range(2, self.complex_dim + 1)]
 
-        for k in range(2, self.complex_dim + 1):
-            for combination in combinations(all_nodes, k + 1):
-                subgraph = graph.subgraph(combination)
-                if nx.is_connected(subgraph):
-                    simplices[k - 2].add(tuple(sorted(combination)))
+        for node in graph.nodes:
+            simplicial_complex.add_node(node, features=data.x[node])
+
+        for node, ecc in eccentricities.items():
+            neighborhood = list(
+                nx.single_source_shortest_path_length(graph, node, cutoff=ecc).keys()
+            )
+            for k in range(1, self.complex_dim):
+                for combination in combinations(neighborhood, k + 1):
+                    simplices[k - 1].add(tuple(sorted(combination)))
 
         for set_k_simplices in simplices:
             simplicial_complex.add_simplices_from(list(set_k_simplices))

pr_tutorial.sh

@@ -0,0 +1,16 @@
+# <fork_name> - is a name of the person who created the PR
+# <PR_name> - is a name of the PR
+# Example: Jonas-Verhellen:eccentricity-lifting --> 
+# --> <fork_name> = jonas-verhellen <PR_name> = eccentricity-lifting
+
+# First it is required to fetch the PR
+git fetch <fork_name> <PR_name>
+
+# Check that the PR is fetched
+git branch -r
+
+# Checkout to the PR 
+git checkout <fork_name>/<PR_name>
+
+# Push to the PR
+git push <fork_name> <PR_name>

test/transforms/liftings/graph2simplicial/test_graph_induced_lifting.py → test/transforms/liftings/graph2simplicial/test_eccentricity_lifting.py

@@ -3,21 +3,21 @@
 import torch
 
 from modules.data.utils.utils import load_manual_graph
-from modules.transforms.liftings.graph2simplicial.graph_induced_lifting import (
-    SimplicialGraphInducedLifting,
+from modules.transforms.liftings.graph2simplicial.eccentricity_lifting import (
+    SimplicialEccentricityLifting,
 )
 
 
-class TestSimplicialCliqueLifting:
-    """Test the SimplicialCliqueLifting class."""
+class TestSimplicialEccentricityLifting:
+    """Test the SimplicialEccentricityLifting class."""
 
     def setup_method(self):
         # Load the graph
         self.data = load_manual_graph()
 
         # Initialise the SimplicialCliqueLifting class
-        self.lifting_signed = SimplicialGraphInducedLifting(complex_dim=3, signed=True)
-        self.lifting_unsigned = SimplicialGraphInducedLifting(
+        self.lifting_signed = SimplicialEccentricityLifting(complex_dim=3, signed=True)
+        self.lifting_unsigned = SimplicialEccentricityLifting(
             complex_dim=3, signed=False
         )
 
@@ -57,14 +57,19 @@ def test_lift_topology(self):
 
         expected_incidence_2_singular_values_unsigned = torch.tensor(
             [
-                4.1190,
+                4.2426,
                 3.1623,
                 3.1623,
                 3.1623,
-                3.0961,
-                3.0000,
-                3.0000,
-                2.7564,
+                3.1623,
+                3.1623,
+                3.1623,
+                3.1623,
+                2.0000,
+                2.0000,
+                2.0000,
+                2.0000,
+                2.0000,
                 2.0000,
                 2.0000,
                 2.0000,
@@ -80,11 +85,6 @@ def test_lift_topology(self):
                 2.0000,
                 2.0000,
                 2.0000,
-                1.7321,
-                1.6350,
-                1.4142,
-                1.4142,
-                1.0849,
             ]
         )
 
@@ -106,18 +106,18 @@ def test_lift_topology(self):
                 2.8284e00,
                 2.8284e00,
                 2.8284e00,
-                2.6458e00,
-                2.6458e00,
-                2.2361e00,
-                1.7321e00,
-                1.7321e00,
-                9.3758e-07,
-                4.7145e-07,
-                4.3417e-07,
-                4.0241e-07,
-                3.1333e-07,
-                2.2512e-07,
-                1.9160e-07,
+                2.8284e00,
+                2.8284e00,
+                2.8284e00,
+                2.8284e00,
+                2.8284e00,
+                7.0866e-07,
+                4.0955e-07,
+                3.2154e-07,
+                2.9976e-07,
+                2.8069e-07,
+                2.3097e-07,
+                9.4821e-08,
             ]
         )
 
@@ -129,91 +129,3 @@ def test_lift_topology(self):
         assert torch.allclose(
             expected_incidence_2_singular_values_signed, S_signed, atol=1.0e-04
         ), "Something is wrong with signed incidence_2 (edges to triangles)."
-
-        expected_incidence_3_singular_values_unsigned = torch.tensor(
-            [
-                3.8466,
-                3.1379,
-                3.0614,
-                2.8749,
-                2.8392,
-                2.8125,
-                2.5726,
-                2.3709,
-                2.2858,
-                2.2369,
-                2.1823,
-                2.0724,
-                2.0000,
-                2.0000,
-                2.0000,
-                1.8937,
-                1.7814,
-                1.7321,
-                1.7256,
-                1.5469,
-                1.5340,
-                1.4834,
-                1.4519,
-                1.4359,
-                1.4142,
-                1.0525,
-                1.0000,
-                1.0000,
-                1.0000,
-                1.0000,
-                0.9837,
-                0.9462,
-                0.8853,
-                0.7850,
-            ]
-        )
-
-        expected_incidence_3_singular_values_signed = torch.tensor(
-            [
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.8284e00,
-                2.6933e00,
-                2.6458e00,
-                2.6458e00,
-                2.6280e00,
-                2.4495e00,
-                2.3040e00,
-                1.9475e00,
-                1.7321e00,
-                1.7321e00,
-                1.7321e00,
-                1.4823e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                1.0000e00,
-                7.3584e-01,
-                2.7959e-07,
-                2.1776e-07,
-                1.4498e-07,
-                5.5373e-08,
-            ]
-        )
-
-        U, S_unsigned, V = torch.svd(lifted_data_unsigned.incidence_3.to_dense())
-        U, S_signed, V = torch.svd(lifted_data_signed.incidence_3.to_dense())
-
-        assert torch.allclose(
-            expected_incidence_3_singular_values_unsigned, S_unsigned, atol=1.0e-04
-        ), "Something is wrong with unsigned incidence_3 (triangles to tetrahedrons)."
-        assert torch.allclose(
-            expected_incidence_3_singular_values_signed, S_signed, atol=1.0e-04
-        ), "Something is wrong with signed incidence_3 (triangles to tetrahedrons)."