nystrom-ncut 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

nystrom_ncut/__init__.py

@@ -8,6 +8,7 @@ from .distance_utils import (
 )
 from .sampling_utils import (
     SampleConfig,
+    subsample_features,
 )
 from .visualize_utils import (
     extrapolate_knn,

nystrom_ncut/distance_utils.py

@@ -41,7 +41,9 @@ def distance_from_features(
         D = torch.cdist(features, features_B, p=2) ** 2
 
         # Outlier-robust scale invariance using quantiles to estimate standard deviation
-        stds = torch.quantile(features, q=torch.tensor((0.158655, 0.841345), device=features.device), dim=0)
+        c = 2.0
+        p = torch.erf(torch.tensor((-c, c), device=features.device) * (2 ** -0.5))
+        stds = torch.quantile(features, q=(p + 1) / 2, dim=0)
         stds = (stds[1] - stds[0]) / 2
         D = D / (2 * torch.linalg.norm(stds) ** 2)
     else:

nystrom_ncut/nystrom/nystrom_utils.py

@@ -12,7 +12,7 @@ from ..distance_utils import (
 )
 from ..sampling_utils import (
     SampleConfig,
-    run_subgraph_sampling,
+    subsample_features,
 )
 
 
@@ -180,7 +180,7 @@ class OnlineNystromSubsampleFit(OnlineNystrom):
         if precomputed_sampled_indices is not None:
             self.anchor_indices = precomputed_sampled_indices
         else:
-            self.anchor_indices = run_subgraph_sampling(
+            self.anchor_indices = subsample_features(
                 features=features,
                 disttype=self.distance,
                 config=self.sample_config,

nystrom_ncut/sampling_utils.py

@@ -3,11 +3,10 @@ from dataclasses import dataclass
 from typing import Literal
 
 import torch
-from dgl.geometry import farthest_point_sampler
+from pytorch3d.ops import sample_farthest_points
 
 from .distance_utils import (
     DistanceOptions,
-    affinity_from_features,
     to_euclidean,
 )
 
@@ -25,7 +24,7 @@ class SampleConfig:
 
 
 @torch.no_grad()
-def run_subgraph_sampling(
+def subsample_features(
     features: torch.Tensor,
     disttype: DistanceOptions,
     config: SampleConfig,
@@ -57,25 +56,15 @@ def run_subgraph_sampling(
 
         elif config.method == "fps_recursive":
             features = to_euclidean(features, disttype)
-            sampled_indices = run_subgraph_sampling(
+            sampled_indices = subsample_features(
                 features=features,
                 disttype=disttype,
                 config=SampleConfig(method="fps", num_sample=config.num_sample, fps_dim=config.fps_dim)
             )
-
             nc = config._ncut_obj
-
-            A = affinity_from_features(features, affinity_focal_gamma=nc.kernel.affinity_focal_gamma, distance=nc.kernel.distance)
-            R = torch.diag(torch.sum(A, dim=-1) ** -0.5)
-            L = R @ A @ R
-
             for _ in range(config.n_iter):
                 fps_features, eigenvalues = nc.fit_transform(features, precomputed_sampled_indices=sampled_indices)
 
-                _L = fps_features @ torch.diag(eigenvalues) @ fps_features.mT
-                RE = torch.abs(_L / L - 1)
-
-                print(f"Iteration {_} --- max: {RE.max().item()}, mean: {RE.mean().item()}, min: {RE.min().item()}")
                 fps_features = to_euclidean(fps_features[:, :config.fps_dim], "cosine")
                 sampled_indices = torch.sort(fpsample(fps_features, config)).values
         else:
@@ -93,4 +82,4 @@ def fpsample(
         U, S, V = torch.pca_lowrank(features, q=config.fps_dim)
         features = U * S
 
-    return farthest_point_sampler(features[None], config.num_sample)[0]
+    return sample_farthest_points(features[None], K=config.num_sample)[1][0]

nystrom_ncut/visualize_utils.py

@@ -19,7 +19,7 @@ from .distance_utils import (
 )
 from .sampling_utils import (
     SampleConfig,
-    run_subgraph_sampling,
+    subsample_features,
 )
 
 
@@ -120,7 +120,7 @@ def extrapolate_knn_with_subsampling(
     device = full_output.device if device is None else device
 
     # sample subgraph
-    anchor_indices = run_subgraph_sampling(
+    anchor_indices = subsample_features(
         features=full_features,
         disttype=distance,
         config=sample_config,
@@ -160,7 +160,7 @@ def _rgb_with_dimensionality_reduction(
 ) -> torch.Tensor:
 
     if True:
-        _subgraph_indices = run_subgraph_sampling(
+        _subgraph_indices = subsample_features(
             features=features,
             disttype=disttype,
             config=SampleConfig(method="fps"),
@@ -172,7 +172,7 @@ def _rgb_with_dimensionality_reduction(
             distance=disttype,
         )
 
-    subgraph_indices = run_subgraph_sampling(
+    subgraph_indices = subsample_features(
         features=features,
         disttype=disttype,
         config=SampleConfig(method="fps", num_sample=num_sample),

{nystrom_ncut-0.1.2.dist-info → nystrom_ncut-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nystrom_ncut
-Version: 0.1.2
+Version: 0.1.3
 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-0.1.3.dist-info/RECORD

@@ -0,0 +1,15 @@
+__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+nystrom_ncut/__init__.py,sha256=HifrTcqX2-hYjBDe6xIThHvuIBYMPBA3EzjR8-qPMUM,512
+nystrom_ncut/common.py,sha256=_PGJoImSk_Fb_5Ri-e_IsFoCcSfbGS8CxYUUHVoNM50,2036
+nystrom_ncut/distance_utils.py,sha256=xSMKL-sFGrz0EL106vhVx0qSk3iSdSLRFhGL0KmAOnU,3121
+nystrom_ncut/sampling_utils.py,sha256=7zCneqmkaA_fUkaZcykFjHtn7pxdZdsjAbKxJplegc0,2960
+nystrom_ncut/visualize_utils.py,sha256=RsQVjPhxoIdxDOQ2PI7ifFDuEL23YXpZBdJ0wjjafek,22970
+nystrom_ncut/nystrom/__init__.py,sha256=4EpxD3Cmc8Fif4vo8DG-6FpTfCnNanD5zCZxK3WrMwQ,121
+nystrom_ncut/nystrom/distance_realization.py,sha256=9GX_XSISTvsEWUu8bG5AxtlkYYNItFspcH5wXiwSOKY,5789
+nystrom_ncut/nystrom/normalized_cut.py,sha256=ZxFV8Sckp6wtpNyoA15DS7Vfu9QLvzNpwrwY0n9_GNs,6953
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+nystrom_ncut-0.1.3.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
+nystrom_ncut-0.1.3.dist-info/METADATA,sha256=tK9gbt1b0c5mGNm2e0OdAKQm7rFUWCuhn9myh_Vf408,6058
+nystrom_ncut-0.1.3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nystrom_ncut-0.1.3.dist-info/top_level.txt,sha256=gM8IWWHYysIRTCvCTcdS4RShOyl9pxpylgSwPUZR2XM,22
+nystrom_ncut-0.1.3.dist-info/RECORD,,

nystrom_ncut-0.1.2.dist-info/RECORD

@@ -1,15 +0,0 @@
-__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nystrom_ncut/__init__.py,sha256=Wgud0tGaNkK2m_qVU47rXQqKdoR-4ztDXXD9UKzc4c8,488
-nystrom_ncut/common.py,sha256=_PGJoImSk_Fb_5Ri-e_IsFoCcSfbGS8CxYUUHVoNM50,2036
-nystrom_ncut/distance_utils.py,sha256=U1223ri8OuIzj0wjhAUhHWcsEvREDitgz8i1rRlCfj8,3069
-nystrom_ncut/sampling_utils.py,sha256=uoWWSyfttv5fnOSq8KFXomWiNO-THiPPbLXfupnVar0,3444
-nystrom_ncut/visualize_utils.py,sha256=xDlkE5sMXehK5hNz9U1twqgHZVzmV5tf5O9bL96AiaM,22982
-nystrom_ncut/nystrom/__init__.py,sha256=4EpxD3Cmc8Fif4vo8DG-6FpTfCnNanD5zCZxK3WrMwQ,121
-nystrom_ncut/nystrom/distance_realization.py,sha256=9GX_XSISTvsEWUu8bG5AxtlkYYNItFspcH5wXiwSOKY,5789
-nystrom_ncut/nystrom/normalized_cut.py,sha256=ZxFV8Sckp6wtpNyoA15DS7Vfu9QLvzNpwrwY0n9_GNs,6953
-nystrom_ncut/nystrom/nystrom_utils.py,sha256=MEmW5xgOu8u2HCwjFapHAOFFXhoVslBbLG4Cn-mYMDU,12995
-nystrom_ncut-0.1.2.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
-nystrom_ncut-0.1.2.dist-info/METADATA,sha256=0wsHYtW3cY4Bzq-lH_y_Blazt6YMrwWxsmR7SOHMyzs,6058
-nystrom_ncut-0.1.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nystrom_ncut-0.1.2.dist-info/top_level.txt,sha256=gM8IWWHYysIRTCvCTcdS4RShOyl9pxpylgSwPUZR2XM,22
-nystrom_ncut-0.1.2.dist-info/RECORD,,