Added spectral lifting

configs/transforms/liftings/graph2hypergraph/spectral_lifting.yaml

@@ -0,0 +1,6 @@
+transform_type: 'lifting'
+transform_name: "SpectralLifting"
+n_c: null
+cluster_alg: "KMeans"
+eps: 1e-9
+feature_lifting: ProjectionSum

modules/transforms/data_transform.py

@@ -12,13 +12,17 @@
 from modules.transforms.liftings.graph2hypergraph.knn_lifting import (
     HypergraphKNNLifting,
 )
+from modules.transforms.liftings.graph2hypergraph.spectral_lifting import (
+    SpectralLifting,
+)
 from modules.transforms.liftings.graph2simplicial.clique_lifting import (
     SimplicialCliqueLifting,
 )
 
 TRANSFORMS = {
     # Graph -> Hypergraph
     "HypergraphKNNLifting": HypergraphKNNLifting,
+    "SpectralLifting": SpectralLifting,
     # Graph -> Simplicial Complex
     "SimplicialCliqueLifting": SimplicialCliqueLifting,
     # Graph -> Cell Complex

modules/transforms/liftings/graph2hypergraph/spectral_lifting.py

@@ -0,0 +1,177 @@
+import warnings
+
+import torch
+import torch_geometric
+from sklearn.cluster import KMeans
+
+from modules.transforms.liftings.graph2hypergraph.base import Graph2HypergraphLifting
+
+
+class SpectralLifting(Graph2HypergraphLifting):
+    r"""Lifts graphs to hypergraph domain by finding clusters using spectral clustering [Ng, Jordan, and Weiss (2002) [[1]](https://proceedings.neurips.cc/paper/2001/hash/801272ee79cfde7fa5960571fee36b9b-Abstract.html)]
+
+    Parameters
+    ----------
+    n_c : int, optional
+        The number of clusters. Default is None.
+    cluster_alg : str, optional
+        The clustering algorithm to use after spectral projection. Default is KMeans.
+    eps : float, optional
+        The threshold to use on the eigenvalues before inverting the matrix to avoid division by 0. Default is 1e-
+    **kwargs : optional
+        Additional arguments for the class.
+    """
+
+    def __init__(
+        self,
+        n_c=None,
+        cluster_alg="KMeans",
+        eps=1e-9,
+        **kwargs,
+    ):
+        super().__init__(**kwargs)
+        self.n_c = n_c
+        self.eps = eps
+        self.init_clust_alg(cluster_alg)
+
+    def init_clust_alg(self, cluster_alg: str):
+        cluster_algs = {"KMeans": KMeans}
+        if cluster_alg not in cluster_algs:
+            warnings.warn(
+                f"KMeans will be used since the algorithm {cluster_alg} was not recognized. Available algorithms: {list(cluster_algs.values())}"
+            )
+        self.cluster_alg = cluster_algs.get(cluster_alg, KMeans)
+
+    def get_degree_matrix(self, W: torch.Tensor):
+        return torch.diag(W.sum(1))
+
+    def get_sqrt_inv(self, D: torch.Tensor):
+        degrees = torch.clamp(torch.diag(D), min=self.eps)
+        return torch.diag(degrees ** (-0.5))
+
+    def to_dense(self, m: torch.Tensor):
+        M = torch.zeros(self.num_nodes, self.num_nodes)
+        n_edges = m.shape[1]
+        for i in range(n_edges):
+            M[m[0, i], m[1, i]] = 1
+            M[m[1, i], m[0, i]] = 1
+        return M
+
+    def get_normalized_laplacian(self, W: torch.Tensor):
+        # Retrieve dense representation of W
+        W = self.to_dense(W)
+
+        # Compute degree matrix
+        D = self.get_degree_matrix(W)
+
+        # Compute unnormalized Laplacian
+        L = D - W
+
+        # Compute the square root of the inverse of the degree matrix
+        Dinv = self.get_sqrt_inv(D)
+
+        # Return normalized Laplacian
+        return Dinv @ L @ Dinv
+
+    def find_gaps(self, v: torch.Tensor, a_max: int = 6, a_min: int = 2):
+        def find_gap(a):
+            """Finds index largest gap using the eigengap heuristic"""
+            for k in range(1, len(v)):
+                m = v[:k].mean()
+                s = v[:k].std()
+                if v[k] > m + s * a:
+                    return k - 1
+
+        def find_k_largest_diff():
+            """Finds index largest gap usings absolute differences"""
+            max_diff = 0
+            max_index = 0
+            for i in range(1, len(v)):
+                diff = abs(v[i] - v[i - 1])
+                if diff > max_diff:
+                    max_diff = diff
+                    max_index = i
+            return max_index - 1
+
+        # Attempt to find index largest gap using eigengap heuristic
+        for a in range(a_max, a_min - 1, -1):
+            k = find_gap(a)
+            if k and k > 1:
+                break
+
+        if k is None or k == 1:
+            # Fall back to using largest absolute difference in case gap heuristic did not work
+            warnings.warn(
+                "Unable to confidently determine the number of clusters n_c. The largest difference between consecutive eigenvalues was used to determine the number of clusters. Please provide n_c."
+            )
+            k = find_k_largest_diff()
+        if k == 1:
+            warnings.warn(
+                "Please provide the number of clusters n_c. The heuristics identified a single cluster and n_c was set to 2."
+            )
+            k += 1
+        return k
+
+    def get_first_eigenvectors(self, Lsym: torch.Tensor):
+        # Compute eigenvectors
+        Lambdas, V = torch.linalg.eig(Lsym)
+        Lambdas, ind_sort = torch.sort(torch.abs(Lambdas))
+
+        # Filter eigenvectors
+        if not self.n_c:
+            self.n_c = self.find_gaps(Lambdas)
+
+        # Return eigenvectors associated to the self.nc smallest eigenvalues
+        return torch.abs(V[:, ind_sort[: self.n_c + 1]])
+
+    def normalize_rows(self, U: torch.Tensor):
+        return U / ((U**2).sum(1, keepdims=True).sqrt())
+
+    def build_clusters(self, U: torch.Tensor):
+        return torch.tensor(self.cluster_alg(n_clusters=self.n_c).fit(U).labels_)
+
+    def build_incidence_hyperedges(self, indices_clusters):
+        A = torch.zeros(self.n_c, self.num_nodes)
+        for c in range(self.n_c):
+            ind_curr_clust = torch.nonzero(indices_clusters == c)
+            A[c, ind_curr_clust] = 1
+        return A
+
+    def transform(self, data: torch_geometric.data.Data) -> dict:
+        # Compute normalized Laplacian
+        self.num_nodes = data.x.shape[0]
+        Lsym = self.get_normalized_laplacian(data.edge_index)
+
+        # Compute eigenvectors matrix
+        U = self.get_first_eigenvectors(Lsym)
+
+        # Normalize rows
+        U = self.normalize_rows(U)
+
+        # Build clusters
+        indices_clusters = self.build_clusters(U)
+
+        # Return incidence_hyperedges matrix
+        return self.build_incidence_hyperedges(indices_clusters=indices_clusters).T
+
+    def lift_topology(self, data: torch_geometric.data.Data) -> dict:
+        r"""Lifts graphs to hypergraph domain by finding clusters using spectral clustering [Ng, Jordan, and Weiss (2002) [[1]](https://proceedings.neurips.cc/paper/2001/hash/801272ee79cfde7fa5960571fee36b9b-Abstract.html)]
+
+        Parameters
+        ----------
+        data : torch_geometric.data.Data
+            The input data to be lifted.
+
+        Returns
+        -------
+        dict
+            The lifted topology.
+        """
+
+        data.pos = data.x
+        incidence_1 = self.transform(data).to_sparse_coo()
+        return {
+            "incidence_hyperedges": incidence_1,
+            "num_hyperedges": self.n_c,
+            "x_0": data.x,
+        }

test/transforms/liftings/graph2hypergraph/test_spectral_lifting.py

@@ -0,0 +1,29 @@
+"""Test the message passing module."""
+
+import torch
+
+from modules.data.utils.utils import load_manual_graph
+from modules.transforms.liftings.graph2hypergraph.spectral_lifting import (
+    SpectralLifting,
+)
+
+
+class TestSpectralLifting:
+    """Test the SpectralLifting class."""
+
+    def setup_method(self):
+        # Load the graph
+        self.data = load_manual_graph()
+
+        # Initialise the SpectralLifting class
+        self.num_hyperedges = 3
+        self.lifting = SpectralLifting(n_c=self.num_hyperedges)
+
+    def test_lift_topology(self):
+        # Test the lift_topology method
+        lifted_data_k = self.lifting.forward(self.data.clone())
+
+        assert list(lifted_data_k.incidence_hyperedges.shape) == [
+            self.data.num_nodes,
+            self.num_hyperedges,
+        ], "There were issues computing the incidence_hyperedges matrix"