nystrom-ncut 0.0.3__tar.gz → 0.0.5__tar.gz

{nystrom_ncut-0.0.3/src/nystrom_ncut.egg-info → nystrom_ncut-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nystrom_ncut
-Version: 0.0.3
+Version: 0.0.5
 Summary: Normalized Cut and Nyström Approximation
 Author-email: Huzheng Yang <huze.yann@gmail.com>, Wentinn Liao <wentinn.liao@gmail.com>
 Project-URL: Documentation, https://github.com/JophiArcana/Nystrom-NCUT/

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nystrom_ncut"
-version = "0.0.3"
+version = "0.0.5"
 authors = [
     { name = "Huzheng Yang", email = "huze.yann@gmail.com" },
     { name = "Wentinn Liao", email = "wentinn.liao@gmail.com" },

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5}/src/nystrom_ncut/ncut_pytorch.py

@@ -173,9 +173,10 @@ class NCUT(OnlineNystrom):
         else:
             sampled_indices = run_subgraph_sampling(
                 features,
-                num_sample=self.num_sample,
+                self.num_sample,
                 sample_method=self.sample_method,
             )
+        sampled_indices = torch.sort(sampled_indices).values
         sampled_features = features[sampled_indices]
         OnlineNystrom.fit(self, sampled_features)
 

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5}/src/nystrom_ncut/nystrom.py

@@ -52,6 +52,18 @@ class OnlineNystrom:
         self.transform_matrix: torch.Tensor = None  # [n x n_components]
         self.LS: torch.Tensor = None                # [n]
 
+    def _update_to_kernel(self) -> Tuple[torch.Tensor, torch.Tensor]:
+        self.A = self.S = self.kernel.transform()
+        U, L = solve_eig(
+            self.A,
+            num_eig=self.inverse_approximation_dim,
+            eig_solver=self.eig_solver,
+        )                                                                                           # [n x (? + 1)], [? + 1]
+        self.Ahinv_UL = U * (L ** -0.5)                                                             # [n x (? + 1)]
+        self.Ahinv_VT = U.mT                                                                        # [(? + 1) x n]
+        self.Ahinv = self.Ahinv_UL @ self.Ahinv_VT                                                  # [n x n]
+        return U, L
+
     def fit(self, features: torch.Tensor):
         OnlineNystrom.fit_transform(self, features)
         return self
@@ -60,17 +72,8 @@ class OnlineNystrom:
         self.anchor_features = features
 
         self.kernel.fit(self.anchor_features)
-        self.A = self.S = self.kernel.transform()                                                   # [n x n]
-
         self.inverse_approximation_dim = max(self.n_components, features.shape[-1]) + 1
-        U, L = solve_eig(
-            self.A,
-            num_eig=self.inverse_approximation_dim,
-            eig_solver=self.eig_solver,
-        )                                                                                           # [n x (? + 1)], [? + 1]
-        self.Ahinv_UL = U * (L ** -0.5)                                                             # [n x (? + 1)]
-        self.Ahinv_VT = U.mT                                                                        # [(? + 1) x n]
-        self.Ahinv = self.Ahinv_UL @ self.Ahinv_VT                                                  # [n x n]
+        U, L = self._update_to_kernel()                                                             # [n x (? + 1)], [? + 1]
 
         self.transform_matrix = (U / L)[:, :self.n_components]                                      # [n x n_components]
         self.LS = L[:self.n_components]                                                             # [n_components]
@@ -83,6 +86,7 @@ class OnlineNystrom:
             chunks = torch.chunk(features, n_chunks, dim=0)
             for chunk in chunks:
                 self.kernel.update(chunk)
+            self._update_to_kernel()
 
             compressed_BBT = torch.zeros((self.inverse_approximation_dim, self.inverse_approximation_dim))  # [(? + 1) x (? + 1))]
             for i, chunk in enumerate(chunks):
@@ -101,6 +105,7 @@ class OnlineNystrom:
         else:
             """ Unchunked version """
             B = self.kernel.update(features).mT                                                         # [n x m]
+            self._update_to_kernel()
             compressed_B = self.Ahinv_VT @ B                                                            # [indirect_pca_dim x m]
 
             self.S = self.S + self.Ahinv_UL @ (compressed_B @ compressed_B.mT) @ self.Ahinv_UL.mT       # [n x n]

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5}/src/nystrom_ncut/propagation_utils.py

@@ -11,7 +11,7 @@ from .common import ceildiv, lazy_normalize
 @torch.no_grad()
 def run_subgraph_sampling(
     features: torch.Tensor,
-    num_sample: int = 300,
+    num_sample: int,
     max_draw: int = 1000000,
     sample_method: Literal["farthest", "random"] = "farthest",
 ):
@@ -272,7 +272,7 @@ def propagate_eigenvectors(
     # sample subgraph
     subgraph_indices = run_subgraph_sampling(
         features,
-        num_sample=num_sample,
+        num_sample,
         sample_method=sample_method,
     )
 

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5}/src/nystrom_ncut/visualize_utils.py

@@ -34,7 +34,7 @@ def _rgb_with_dimensionality_reduction(
 ) -> Tuple[torch.Tensor, torch.Tensor]:
     subgraph_indices = run_subgraph_sampling(
         features,
-        num_sample=num_sample,
+        num_sample,
         sample_method="farthest",
     )
 

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5/src/nystrom_ncut.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nystrom_ncut
-Version: 0.0.3
+Version: 0.0.5
 Summary: Normalized Cut and Nyström Approximation
 Author-email: Huzheng Yang <huze.yann@gmail.com>, Wentinn Liao <wentinn.liao@gmail.com>
 Project-URL: Documentation, https://github.com/JophiArcana/Nystrom-NCUT/

{nystrom_ncut-0.0.3 → nystrom_ncut-0.0.5}/tests/test.py

@@ -1,5 +1,7 @@
 import numpy as np
 import torch
+import torch.nn.functional as Fn
+
 from src.nystrom_ncut.ncut_pytorch import NCUT, axis_align
 # from ncut_pytorch.src import rgb_from_umap_sphere
 # from ncut_pytorch.src.new_ncut_pytorch import NewNCUT
@@ -35,28 +37,36 @@ if __name__ == "__main__":
     # # ))
     # raise Exception(
 
-    torch.set_printoptions(precision=12, sci_mode=False, linewidth=400)
+    torch.set_printoptions(precision=8, sci_mode=False, linewidth=400)
+    torch.set_default_dtype(torch.float64)
     torch.manual_seed(1212)
     np.random.seed(1212)
 
-    M = torch.rand((10000, 12))
-    # NC = NCUT(num_eig=5, knn=None, verbose=True)
-    kwargs = dict(num_eig=7, sample_method="random")
-    nNC = NCUT(**kwargs)
+    M = torch.rand((12000, 12))
+    NC = NCUT(n_components=12, num_sample=10000, sample_method="farthest")
 
     torch.manual_seed(1212)
     np.random.seed(1212)
-    nX, neigs = nNC.fit_transform(M)
-    # print(neigs)
-    # print(nX.mT @ nX)
+    X, eigs = NC.fit_transform(M)
+    print(eigs)
 
-    torch.manual_seed(1212)
-    np.random.seed(1212)
+    normalized_M = Fn.normalize(M, p=2, dim=-1)
+    A = torch.exp(-(1 - normalized_M @ normalized_M.mT))
+    R = torch.diag(torch.sum(A, dim=-1) ** -0.5)
+    L = R @ A @ R
+    # print(L)
+    # print(X @ torch.diag(eigs) @ X.mT)
+    # print(L)
+    RE = torch.abs(X @ torch.diag(eigs) @ X.mT / L - 1)
+    print(RE.max().item(), RE.mean().item())
 
-    aX, R = axis_align(nX)
-    print(aX[:3])
-    print(R)
-    print(R @ R.mT)
+    # torch.manual_seed(1212)
+    # np.random.seed(1212)
+    #
+    # aX, R = axis_align(X)
+    # print(aX[:3])
+    # print(R)
+    # print(R @ R.mT)
     raise Exception()