nystrom-ncut 0.0.8__py3-none-any.whl → 0.0.9__py3-none-any.whl

nystrom_ncut/common.py

@@ -22,3 +22,40 @@ def lazy_normalize(x: torch.Tensor, n: int = 1000, **normalize_kwargs: Any) -> t
         return x
     else:
         return Fn.normalize(x, **normalize_kwargs)
+
+
+def quantile_min_max(x, q1=0.01, q2=0.99, n_sample=10000):
+    if x.shape[0] > n_sample:
+        np.random.seed(0)
+        random_idx = np.random.choice(x.shape[0], n_sample, replace=False)
+        vmin, vmax = x[random_idx].quantile(q1), x[random_idx].quantile(q2)
+    else:
+        vmin, vmax = x.quantile(q1), x.quantile(q2)
+    return vmin, vmax
+
+
+def quantile_normalize(x, q=0.95):
+    """normalize each dimension of x to [0, 1], take 95-th percentage, this robust to outliers
+        </br> 1. sort x
+        </br> 2. take q-th quantile
+        </br>     min_value -> (1-q)-th quantile
+        </br>     max_value -> q-th quantile
+        </br> 3. normalize
+        </br> x = (x - min_value) / (max_value - min_value)
+
+    Args:
+        x (torch.Tensor): input tensor, shape (n_samples, n_features)
+            normalize each feature to 0-1 range
+        q (float): quantile, default 0.95
+
+    Returns:
+        torch.Tensor: quantile normalized tensor
+    """
+    # normalize x to 0-1 range, max value is q-th quantile
+    # quantile makes the normalization robust to outliers
+    if isinstance(x, np.ndarray):
+        x = torch.tensor(x)
+    vmax, vmin = quantile_min_max(x, q, 1 - q)
+    x = (x - vmin) / (vmax - vmin)
+    x = x.clamp(0, 1)
+    return x

nystrom_ncut/nystrom.py

@@ -2,7 +2,9 @@ from typing import Literal, Tuple
 
 import torch
 
-from .common import ceildiv
+from .common import (
+    ceildiv,
+)
 
 
 EigSolverOptions = Literal["svd_lowrank", "lobpcg", "svd", "eigh"]

nystrom_ncut/propagation_utils.py

@@ -1,5 +1,4 @@
 import logging
-from typing import Literal
 
 import numpy as np
 import torch
@@ -256,40 +255,3 @@ def extrapolate_knn_with_subsampling(
         device=device
     )
     return new_eigenvectors
-
-
-def quantile_min_max(x, q1=0.01, q2=0.99, n_sample=10000):
-    if x.shape[0] > n_sample:
-        np.random.seed(0)
-        random_idx = np.random.choice(x.shape[0], n_sample, replace=False)
-        vmin, vmax = x[random_idx].quantile(q1), x[random_idx].quantile(q2)
-    else:
-        vmin, vmax = x.quantile(q1), x.quantile(q2)
-    return vmin, vmax
-
-
-def quantile_normalize(x, q=0.95):
-    """normalize each dimension of x to [0, 1], take 95-th percentage, this robust to outliers
-        </br> 1. sort x
-        </br> 2. take q-th quantile
-        </br>     min_value -> (1-q)-th quantile
-        </br>     max_value -> q-th quantile
-        </br> 3. normalize
-        </br> x = (x - min_value) / (max_value - min_value)
-
-    Args:
-        x (torch.Tensor): input tensor, shape (n_samples, n_features)
-            normalize each feature to 0-1 range
-        q (float): quantile, default 0.95
-
-    Returns:
-        torch.Tensor: quantile normalized tensor
-    """
-    # normalize x to 0-1 range, max value is q-th quantile
-    # quantile makes the normalization robust to outliers
-    if isinstance(x, np.ndarray):
-        x = torch.tensor(x)
-    vmax, vmin = quantile_min_max(x, q, 1 - q)
-    x = (x - vmin) / (vmax - vmin)
-    x = x.clamp(0, 1)
-    return x

nystrom_ncut/visualize_utils.py

@@ -7,15 +7,13 @@ import torch.nn.functional as F
 from sklearn.base import BaseEstimator
 
 from .common import (
-    DistanceOptions,
     lazy_normalize,
+    quantile_min_max,
+    quantile_normalize,
 )
 from .propagation_utils import (
     run_subgraph_sampling,
     extrapolate_knn,
-    extrapolate_knn_with_subsampling,
-    quantile_min_max,
-    quantile_normalize
 )
 
 
@@ -28,22 +26,22 @@ def _rgb_with_dimensionality_reduction(
     num_sample: int,
     metric: Literal["cosine", "euclidean"],
     rgb_func: Callable[[torch.Tensor, float], torch.Tensor],
-    q: float, knn: int,
-    seed: int, device: str,
+    q: float,
+    knn: int,
     reduction: Callable[..., BaseEstimator],
     reduction_dim: int,
     reduction_kwargs: Dict[str, Any],
-    transform_func: Callable[[torch.Tensor], torch.Tensor] = _identity,
-    pre_smooth: bool = True,
+    transform_func: Callable[[torch.Tensor], torch.Tensor],
+    seed: int,
+    device: str,
 ) -> Tuple[torch.Tensor, torch.Tensor]:
 
-    if pre_smooth:
-        features = extrapolate_knn(
-            features,
-            features,
-            features,
-            distance="cosine",
-        )
+    features = extrapolate_knn(
+        features,
+        features,
+        features,
+        distance="cosine",
+    )
 
     subgraph_indices = run_subgraph_sampling(
         features,
@@ -78,10 +76,10 @@ def rgb_from_tsne_2d(
     num_sample: int = 1000,
     perplexity: int = 150,
     metric: Literal["cosine", "euclidean"] = "cosine",
-    device: str = None,
-    seed: int = 0,
     q: float = 0.95,
     knn: int = 10,
+    seed: int = 0,
+    device: str = None,
 ):
     """
     Returns:
@@ -106,11 +104,13 @@ def rgb_from_tsne_2d(
         num_sample=num_sample,
         metric=metric,
         rgb_func=rgb_from_2d_colormap,
-        q=q, knn=knn,
-        seed=seed, device=device,
+        q=q,
+        knn=knn,
         reduction=TSNE, reduction_dim=2, reduction_kwargs={
             "perplexity": perplexity,
-        },
+        }, transform_func=_identity,
+        seed=seed,
+        device=device,
     )
     return x2d, rgb
 
@@ -120,10 +120,10 @@ def rgb_from_tsne_3d(
     num_sample: int = 1000,
     perplexity: int = 150,
     metric: Literal["cosine", "euclidean"] = "cosine",
-    device: str = None,
-    seed: int = 0,
     q: float = 0.95,
     knn: int = 10,
+    seed: int = 0,
+    device: str = None,
 ):
     """
     Returns:
@@ -148,11 +148,13 @@ def rgb_from_tsne_3d(
         num_sample=num_sample,
         metric=metric,
         rgb_func=rgb_from_3d_rgb_cube,
-        q=q, knn=knn,
-        seed=seed, device=device,
+        q=q,
+        knn=knn,
         reduction=TSNE, reduction_dim=3, reduction_kwargs={
             "perplexity": perplexity,
-        },
+        }, transform_func=_identity,
+        seed=seed,
+        device=device,
     )
     return x3d, rgb
 
@@ -161,10 +163,10 @@ def rgb_from_cosine_tsne_3d(
     features: torch.Tensor,
     num_sample: int = 1000,
     perplexity: int = 150,
-    device: str = None,
-    seed: int = 0,
     q: float = 0.95,
     knn: int = 10,
+    seed: int = 0,
+    device: str = None
 ):
     """
     Returns:
@@ -205,11 +207,13 @@ def rgb_from_cosine_tsne_3d(
         num_sample=num_sample,
         metric="cosine",
         rgb_func=rgb_from_cosine,
-        q=q, knn=knn,
-        seed=seed, device=device,
+        q=q,
+        knn=knn,
         reduction=TSNE, reduction_dim=3, reduction_kwargs={
             "perplexity": perplexity,
-        },
+        }, transform_func=_identity,
+        seed=seed,
+        device=device,
     )
     return x3d, rgb
 
@@ -220,10 +224,10 @@ def rgb_from_umap_2d(
     n_neighbors: int = 150,
     min_dist: float = 0.1,
     metric: Literal["cosine", "euclidean"] = "cosine",
-    device: str = None,
-    seed: int = 0,
     q: float = 0.95,
     knn: int = 10,
+    seed: int = 0,
+    device: str = None,
 ):
     """
     Returns:
@@ -240,12 +244,14 @@ def rgb_from_umap_2d(
         num_sample=num_sample,
         metric=metric,
         rgb_func=rgb_from_2d_colormap,
-        q=q, knn=knn,
-        seed=seed, device=device,
+        q=q,
+        knn=knn,
         reduction=UMAP, reduction_dim=2, reduction_kwargs={
             "n_neighbors": n_neighbors,
             "min_dist": min_dist,
-        },
+        }, transform_func=_identity,
+        seed=seed,
+        device=device,
     )
     return x2d, rgb
 
@@ -256,10 +262,10 @@ def rgb_from_umap_sphere(
     n_neighbors: int = 150,
     min_dist: float = 0.1,
     metric: Literal["cosine", "euclidean"] = "cosine",
-    device: str = None,
-    seed: int = 0,
     q: float = 0.95,
     knn: int = 10,
+    seed: int = 0,
+    device: str = None,
 ):
     """
     Returns:
@@ -283,14 +289,15 @@ def rgb_from_umap_sphere(
         num_sample=num_sample,
         metric=metric,
         rgb_func=rgb_from_3d_rgb_cube,
-        q=q, knn=knn,
-        seed=seed, device=device,
+        q=q,
+        knn=knn,
         reduction=UMAP, reduction_dim=2, reduction_kwargs={
             "n_neighbors": n_neighbors,
             "min_dist": min_dist,
             "output_metric": "haversine",
-        },
-        transform_func=transform_func
+        }, transform_func=transform_func,
+        seed=seed,
+        device=device,
     )
     return x3d, rgb
 
@@ -301,10 +308,10 @@ def rgb_from_umap_3d(
     n_neighbors: int = 150,
     min_dist: float = 0.1,
     metric: Literal["cosine", "euclidean"] = "cosine",
-    device: str = None,
-    seed: int = 0,
     q: float = 0.95,
     knn: int = 10,
+    seed: int = 0,
+    device: str = None,
 ):
     """
     Returns:
@@ -321,12 +328,14 @@ def rgb_from_umap_3d(
         num_sample=num_sample,
         metric=metric,
         rgb_func=rgb_from_3d_rgb_cube,
-        q=q, knn=knn,
-        seed=seed, device=device,
+        q=q,
+        knn=knn,
         reduction=UMAP, reduction_dim=3, reduction_kwargs={
             "n_neighbors": n_neighbors,
             "min_dist": min_dist,
-        },
+        }, transform_func=_identity,
+        seed=seed,
+        device=device,
     )
     return x3d, rgb
 

{nystrom_ncut-0.0.8.dist-info → nystrom_ncut-0.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nystrom_ncut
-Version: 0.0.8
+Version: 0.0.9
 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-0.0.9.dist-info/RECORD

@@ -0,0 +1,11 @@
+nystrom_ncut/__init__.py,sha256=Vlc_iAlfvTNUiJXpZLWUOaL2Q-YqZqgr7WoG6cVnD0g,439
+nystrom_ncut/common.py,sha256=RMPQvg9R2s7V-q7zAStN9YCZt7gpc5Ut-KSKtvELBQ4,1934
+nystrom_ncut/ncut_pytorch.py,sha256=-SKs9AdkafJSGkeYt4LwhbKZr8oq9JA5caAqjiVDAzU,11220
+nystrom_ncut/nystrom.py,sha256=1ngKzRrY9i2jEDo0EP8I9RsNTQzy4S7pmvkpayIkUOQ,8811
+nystrom_ncut/propagation_utils.py,sha256=AEKgWVw7x_podLEzELdCQeMmTJfAYfG4TiPuKbrN8Sw,10279
+nystrom_ncut/visualize_utils.py,sha256=p4wXXg47vqMn8c1N6NxGxtmPNwOzqquDvpMEjZVdq34,17196
+nystrom_ncut-0.0.9.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
+nystrom_ncut-0.0.9.dist-info/METADATA,sha256=umrvGtKsci280oi3D5I_BeLIt8ajBogC5veHYrRln48,6058
+nystrom_ncut-0.0.9.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nystrom_ncut-0.0.9.dist-info/top_level.txt,sha256=j7g_j0S048EvguFFnGgD5Ewd3r2H6klsxd5A4dd-wHw,13
+nystrom_ncut-0.0.9.dist-info/RECORD,,

nystrom_ncut-0.0.8.dist-info/RECORD

@@ -1,11 +0,0 @@
-nystrom_ncut/__init__.py,sha256=Vlc_iAlfvTNUiJXpZLWUOaL2Q-YqZqgr7WoG6cVnD0g,439
-nystrom_ncut/common.py,sha256=G6w_8_BfBUMc6r8WFgA0NH4K6am7AzZCSdrQEVjra7U,671
-nystrom_ncut/ncut_pytorch.py,sha256=-SKs9AdkafJSGkeYt4LwhbKZr8oq9JA5caAqjiVDAzU,11220
-nystrom_ncut/nystrom.py,sha256=-l26oiJ0oPReSGlMlYV3gftszgFdAAHAi7OFtGPZ4Ic,8802
-nystrom_ncut/propagation_utils.py,sha256=0d2VhT0JrLRurd44hZbnxBvBh-QscPKxtV7VrwYtTdo,11569
-nystrom_ncut/visualize_utils.py,sha256=jDjuyZ9rdd25jqrPObJgK8zCLHc3Oms0fQnaIetHk-U,17112
-nystrom_ncut-0.0.8.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
-nystrom_ncut-0.0.8.dist-info/METADATA,sha256=zQpx3REOOckpJSuc7N6UNpXZoqgsM5UoFWV6__DuaRQ,6058
-nystrom_ncut-0.0.8.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nystrom_ncut-0.0.8.dist-info/top_level.txt,sha256=j7g_j0S048EvguFFnGgD5Ewd3r2H6klsxd5A4dd-wHw,13
-nystrom_ncut-0.0.8.dist-info/RECORD,,