Add sgw_torch package.

.github/workflows/publish.yml

@@ -18,6 +18,12 @@ jobs:
         pip
         install
         -r requirements.txt
+    - name: Install torch dependencies
+      run: >-
+        python3 -m
+        pip
+        install
+        -r requirements-torch.txt
     - name: Tests
       run: >-
         python3 -m

requirements-torch.txt

@@ -0,0 +1,2 @@
+torch
+torch-geometric

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="sgw_tools",
-    version="2.5.5",
+    version="3.0",
     author="Mark Hale",
     license="MIT",
     description="Spectral graph wavelet tools",

sgw_torch/__init__.py

@@ -0,0 +1,40 @@
+from typing import Optional
+
+import numpy as np
+import torch
+from torch import Tensor
+import torch_geometric.utils as torch_utils
+from torch_geometric.typing import OptTensor
+from sgw_tools import util
+
+from . import layers
+
+def edge_tensors(G):
+    edge_list = G.get_edge_list()
+    edge_index = np.array([
+        np.concatenate((edge_list[0], edge_list[1])),
+        np.concatenate((edge_list[1], edge_list[0]))
+    ])
+    edge_weight = np.concatenate((edge_list[2], edge_list[2]))
+    return torch.from_numpy(edge_index).long(), torch.from_numpy(edge_weight)
+
+
+def get_laplacian(edge_index: Tensor,
+        edge_weight: OptTensor = None,
+        lap_type: str = "normalized",
+        dtype: Optional[torch.dtype] = None,
+        num_nodes: Optional[int] = None):
+    if lap_type == "adjacency":
+        if edge_weight is None:
+            edge_weight = torch.ones(edge_index.size[1], dtype=dtype, device=edge_index.device)
+        op_norm = util.operator_norm(torch_utils.to_scipy_sparse_matrix(edge_index, edge_weight))
+        num_nodes = torch_utils.num_nodes.maybe_num_nodes(edge_index, num_nodes)
+        return torch_utils.add_self_loops(edge_index, -edge_weight/op_norm, fill_value=1.0, num_nodes=num_nodes)
+    else:
+        normalization_mapping = {
+            "combinatorial": None,
+            "normalized": "sym"
+        }
+        normalization = normalization_mapping[lap_type]
+        return torch_utils.get_laplacian(edge_index, edge_weight=edge_weight, normalization=normalization, dtype=dtype, num_nodes=num_nodes)
+

sgw_torch/layers.py

@@ -0,0 +1,216 @@
+from typing import Optional
+
+import torch
+from torch import Tensor
+from torch.nn import Parameter
+import torch.nn.functional as F
+
+from torch_geometric.nn.conv import MessagePassing
+from torch_geometric.nn.dense.linear import Linear
+from torch_geometric.nn.inits import zeros
+from torch_geometric.typing import OptTensor
+import sgw_torch
+import numpy as np
+
+
+class SpectralLayer(MessagePassing):
+    def __init__(self,
+        in_channels: int,
+        out_channels: int,
+        lap_type: str,
+    ):
+        super().__init__(aggr="add")
+        self.in_channels = in_channels
+        self.out_channels = out_channels
+        self.lap_type = lap_type
+
+    def get_laplacian(self,
+        edge_index: Tensor,
+        edge_weight: OptTensor = None,
+        lap_type: str = "normalized",
+        dtype: Optional[torch.dtype] = None,
+        num_nodes: Optional[int] = None
+    ):
+        return sgw_torch.get_laplacian(edge_index, edge_weight=edge_weight, lap_type=lap_type, dtype=dtype, num_nodes=num_nodes)
+
+    def get_lambda_max(self, edge_weight: Tensor, num_nodes: int) -> Tensor:
+        if self.lap_type == "normalized" or self.lap_type == "adjacency":
+            return torch.tensor(2.0, dtype=edge_weight.dtype)
+        elif self.lap_type == "combinatorial":
+            D = edge_weight[edge_weight > 0]
+            A = -edge_weight[edge_weight < 0]
+            return min(num_nodes*A.max(), 2.0 * D.max())
+        else:
+            raise ValueError(f"Unsupported lap_type {self.lap_type}")
+
+    def message(self, x_j: Tensor, norm: Tensor) -> Tensor:
+        return norm.view(-1, 1) * x_j
+
+
+class ChebLayer(SpectralLayer):
+    def __init__(
+        self,
+        in_channels: int,
+        out_channels: int,
+        K: int,
+        lap_type: str ='normalized',
+        bias: bool = True,
+    ):
+        super().__init__(in_channels, out_channels, lap_type)
+        self.lins = torch.nn.ModuleList([
+            Linear(in_channels, out_channels, bias=False,
+                   weight_initializer='glorot') for _ in range(K)
+        ])
+
+        if bias:
+            self.bias = Parameter(Tensor(out_channels))
+        else:
+            self.register_parameter('bias', None)
+
+        self.reset_parameters()
+
+    def reset_parameters(self):
+        super().reset_parameters()
+        for lin in self.lins:
+            lin.reset_parameters()
+        zeros(self.bias)
+
+    def __norm__(
+        self,
+        edge_index: Tensor,
+        num_nodes: int,
+        edge_weight: OptTensor,
+        lambda_max: OptTensor = None,
+        dtype: Optional[int] = None,
+        batch: OptTensor = None,
+    ):
+        edge_index, edge_weight = self.get_laplacian(edge_index, edge_weight,
+                                                self.lap_type, dtype,
+                                                num_nodes)
+        assert edge_weight is not None
+
+        if lambda_max is None:
+            lambda_max = self.get_lambda_max(edge_weight, num_nodes)
+        elif not isinstance(lambda_max, Tensor):
+            lambda_max = torch.tensor(lambda_max, dtype=dtype,
+                                      device=edge_index.device)
+        assert lambda_max is not None
+
+        if batch is not None and lambda_max.numel() > 1:
+            lambda_max = lambda_max[batch[edge_index[0]]]
+
+        edge_weight = (2.0 * edge_weight) / lambda_max
+        edge_weight.masked_fill_(edge_weight == float('inf'), 0)
+
+        loop_mask = edge_index[0] == edge_index[1]
+        edge_weight[loop_mask] -= 1
+
+        return edge_index, edge_weight
+
+    def _weight_op(self, x: Tensor, weight: Tensor):
+        return F.linear(x, weight)
+
+    def _evaluate_chebyshev(
+        self,
+        coeffs: list[Tensor],
+        x: Tensor,
+        edge_index: Tensor,
+        edge_weight: OptTensor = None,
+        batch: OptTensor = None,
+        lambda_max: OptTensor = None,
+    ) -> Tensor:
+
+        edge_index, norm = self.__norm__(
+            edge_index,
+            x.size(self.node_dim),
+            edge_weight,
+            lambda_max,
+            dtype=x.dtype,
+            batch=batch,
+        )
+
+        Tx_0 = x
+        out = self._weight_op(Tx_0, coeffs[0])
+
+        # propagate_type: (x: Tensor, norm: Tensor)
+        if len(coeffs) > 1:
+            Tx_1 = self.propagate(edge_index, x=x, norm=norm)
+            out = out + self._weight_op(Tx_1, coeffs[1])
+
+        for coeff in coeffs[2:]:
+            Tx_2 = self.propagate(edge_index, x=Tx_1, norm=norm)
+            Tx_2 = 2.0 * Tx_2 - Tx_0
+            out = out + self._weight_op(Tx_2, coeff)
+            Tx_0, Tx_1 = Tx_1, Tx_2
+
+        if self.bias is not None:
+            out = out + self.bias
+
+        return out
+
+    def forward(
+        self,
+        x: Tensor,
+        edge_index: Tensor,
+        edge_weight: OptTensor = None,
+        batch: OptTensor = None,
+        lambda_max: OptTensor = None,
+    ) -> Tensor:
+        ws = [lin.weight for lin in self.lins]
+        return self._evaluate_chebyshev(ws, x, edge_index, edge_weight, batch, lambda_max)
+
+    def __repr__(self) -> str:
+        return (f'{self.__class__.__name__}({self.in_channels}, '
+                f'{self.out_channels}, K={len(self.lins)}, '
+                f'lap_type={self.lap_type})')
+
+
+class ChebIILayer(ChebLayer):
+    """
+    https://github.com/ivam-he/ChebNetII
+    """
+    def __init__(
+        self,
+        in_channels: int,
+        out_channels: int,
+        K: int,
+        lap_type: str ='normalized',
+        bias: bool = True,
+    ):
+        super().__init__(in_channels, out_channels, K, lap_type, bias)
+
+    def convert_coefficients(self, ys):
+        k1 = len(self.lins)
+
+        def transform(Ts):
+            itr = zip(ys, Ts)
+            first = next(itr)
+            w = first[0] * first[1]  # initialise with correct shape
+            for y, T in itr:
+                w += y*T
+            return 2*w/k1
+
+        ws = []
+        x = torch.from_numpy(np.polynomial.chebyshev.chebpts1(k1))
+        a = torch.ones(k1)
+        b = x
+        ws.append(transform(a/2))
+        ws.append(transform(b))
+        for _ in range(2, k1):
+            T = 2*x*b - a
+            ws.append(transform(T))
+            a = b
+            b = T
+        return ws
+
+    def forward(
+        self,
+        x: Tensor,
+        edge_index: Tensor,
+        edge_weight: OptTensor = None,
+        batch: OptTensor = None,
+        lambda_max: OptTensor = None,
+    ) -> Tensor:
+        ys = [lin.weight for lin in self.lins]
+        ws = self.convert_coefficients(ys)
+        return self._evaluate_cheb(ws, x, edge_index, edge_weight, batch, lambda_max)

tests/test_torch.py

@@ -0,0 +1,36 @@
+import unittest
+
+import numpy as np
+import sgw_tools as sgw
+import sgw_torch
+import pygsp as gsp
+import torch
+import torch_geometric.utils as torch_utils
+
+
+class TestCase(unittest.TestCase):
+    def test_get_laplacian(self):
+        G = sgw.BigGraph.create_from(gsp.graphs.Sensor(50, seed=32), lap_type="adjacency")
+        edge_index, edge_weight = sgw_torch.edge_tensors(G)
+        L_index, L_weight = sgw_torch.get_laplacian(edge_index, edge_weight, lap_type="adjacency", num_nodes=G.N)
+        torch_L = torch_utils.to_scipy_sparse_matrix(L_index, L_weight)
+        np.testing.assert_allclose(G.L.toarray(), torch_L.toarray())
+
+    def test_ChebLayer(self):
+        G = gsp.graphs.Sensor(34, seed=506, lap_type="normalized")
+        K = 5
+        domain = [0, 2]
+        coeffs = sgw.approximations.compute_cheby_coeff(gsp.filters.Heat(G, tau=5), m=K, domain=domain)
+        coeffs[0] /= 2
+
+        s = sgw.createSignal(G, nodes=[0])
+        g = sgw.ChebyshevFilter(G, coeffs, domain, coeff_normalization="numpy")
+        expected = g.filter(s)
+
+        layer = sgw_torch.layers.ChebLayer(1, 1, K+1, lap_type="normalized", bias=False)
+        for c, p in zip(coeffs, layer.parameters()):
+            p.data = torch.tensor([[c]])
+        edge_index, edge_weight = sgw_torch.edge_tensors(G)
+        y = layer(torch.from_numpy(s), edge_index, edge_weight)
+
+        np.testing.assert_allclose(expected, y.detach().numpy().squeeze())