nystrom-ncut 0.0.4__tar.gz → 0.0.6__tar.gz

{nystrom_ncut-0.0.4/src/nystrom_ncut.egg-info → nystrom_ncut-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nystrom_ncut
-Version: 0.0.4
+Version: 0.0.6
 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-0.0.4 → nystrom_ncut-0.0.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nystrom_ncut"
-version = "0.0.4"
+version = "0.0.6"
 authors = [
     { name = "Huzheng Yang", email = "huze.yann@gmail.com" },
     { name = "Wentinn Liao", email = "wentinn.liao@gmail.com" },

{nystrom_ncut-0.0.4 → nystrom_ncut-0.0.6}/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-0.0.4 → nystrom_ncut-0.0.6}/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",
 ):
@@ -96,7 +96,6 @@ def distance_from_features(
         D = D / (2 * features.var(dim=0).sum())
     else:
         raise ValueError("distance should be 'cosine' or 'euclidean', 'rbf'")
-
     return D
 
 
@@ -184,13 +183,37 @@ def propagate_knn(
     V_list = []
     for _v in torch.chunk(inp_features, n_chunks, dim=0):
         _v = _v.to(device)
-        _A = affinity_from_features(subgraph_features, _v, affinity_focal_gamma, distance).mT
 
-        if knn is not None:
-            mask = torch.full_like(_A, True, dtype=torch.bool)
-            mask[torch.arange(len(_v))[:, None], _A.topk(knn, dim=-1, largest=True).indices] = False
-            _A[mask] = 0.0
-        _A = F.normalize(_A, p=1, dim=-1)
+        # _A = affinity_from_features(subgraph_features, _v, affinity_focal_gamma, distance).mT
+        # if knn is not None:
+        #     mask = torch.full_like(_A, True, dtype=torch.bool)
+        #     mask[torch.arange(len(_v))[:, None], _A.topk(knn, dim=-1, largest=True).indices] = False
+        #     _A[mask] = 0.0
+        # _A = F.normalize(_A, p=1, dim=-1)
+
+        if distance == 'cosine':
+            _A = _v @ subgraph_features.T
+        elif distance == 'euclidean':
+            _A = - torch.cdist(_v, subgraph_features, p=2)
+        elif distance == 'rbf':
+            _A = - torch.cdist(_v, subgraph_features, p=2) ** 2
+        else:
+            raise ValueError("distance should be 'cosine' or 'euclidean', 'rbf'")
+
+        # keep topk KNN for each row
+        topk_sim, topk_idx = _A.topk(knn, dim=-1, largest=True)
+        row_id = torch.arange(topk_idx.shape[0], device=_A.device)[:, None].expand(
+            -1, topk_idx.shape[1]
+        )
+        _A = torch.sparse_coo_tensor(
+            torch.stack([row_id, topk_idx], dim=-1).reshape(-1, 2).T,
+            topk_sim.reshape(-1),
+            size=(_A.shape[0], _A.shape[1]),
+            device=_A.device,
+        )
+        _A = _A.to_dense().to(dtype=subgraph_output.dtype)
+        _D = _A.sum(-1)
+        _A /= _D[:, None]
 
         _V = _A @ subgraph_output
         if move_output_to_cpu:
@@ -272,7 +295,7 @@ def propagate_eigenvectors(
     # sample subgraph
     subgraph_indices = run_subgraph_sampling(
         features,
-        num_sample=num_sample,
+        num_sample,
         sample_method=sample_method,
     )
 

{nystrom_ncut-0.0.4 → nystrom_ncut-0.0.6}/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-0.0.4 → nystrom_ncut-0.0.6/src/nystrom_ncut.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nystrom_ncut
-Version: 0.0.4
+Version: 0.0.6
 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-0.0.4 → nystrom_ncut-0.0.6}/tests/test.py

@@ -38,27 +38,28 @@ if __name__ == "__main__":
     # raise Exception(
 
     torch.set_printoptions(precision=8, sci_mode=False, linewidth=400)
-    torch.set_default_dtype(torch.float64)
-    # torch.manual_seed(1212)
-    # np.random.seed(1212)
+    torch.set_default_dtype(torch.float32)
+    torch.manual_seed(1212)
+    np.random.seed(1212)
 
-    M = torch.rand((200, 12))
-    NC = NCUT(n_components=12, num_sample=80, sample_method="random", chunk_size=20)
+    M = torch.rand((1200, 12))
+    NC = NCUT(n_components=30, num_sample=1000, sample_method="farthest", eig_solver="svd")
 
     torch.manual_seed(1212)
     np.random.seed(1212)
     X, eigs = NC.fit_transform(M)
     print(eigs)
-    raise Exception()
+    # print(X.mT @ X)
 
     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)
-    print(torch.abs(X @ torch.diag(eigs) @ X.mT / L - 1))
+    # 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())
 
     # torch.manual_seed(1212)
     # np.random.seed(1212)