Merge branch 'master' into kernel_distances

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.4
+current_version = 0.4.2
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.4.4"
+release = "0.4.2"
 
 # -- General configuration ---------------------------------------------------
 

prototorch/__init__.py

@@ -1,7 +1,7 @@
 """ProtoTorch package."""
 
 # Core Setup
-__version__ = "0.4.4"
+__version__ = "0.4.2"
 
 __all_core__ = [
     "datasets",

prototorch/components/components.py

@@ -67,9 +67,8 @@ class LabeledComponents(Components):
                  *,
                  initialized_components=None):
         if initialized_components is not None:
-            components, component_labels = initialized_components
+            super().__init__(initialized_components=initialized_components[0])
-            super().__init__(initialized_components=components)
+            self._labels = initialized_components[1]
-            self._labels = component_labels
         else:
             self._initialize_labels(distribution)
             super().__init__(number_of_components=len(self._labels),

prototorch/datasets/__init__.py

@@ -1,6 +1,11 @@
 """ProtoTorch datasets."""
 
 from .abstract import NumpyDataset
-from .iris import Iris
 from .spiral import Spiral
 from .tecator import Tecator
+
+__all__ = [
+    "NumpyDataset",
+    "Spiral",
+    "Tecator",
+]

prototorch/datasets/iris.py

@@ -1,15 +0,0 @@
-"""Thin wrapper for the Iris classification dataset from sklearn.
-
-URL:
-    https://scikit-learn.org/stable/modules/generated/sklearn.datasets.load_iris.html
-
-"""
-
-from prototorch.datasets.abstract import NumpyDataset
-from sklearn.datasets import load_iris
-
-
-class Iris(NumpyDataset):
-    def __init__(self):
-        x, y = load_iris(return_X_y=True)
-        super().__init__(x, y)

prototorch/functions/competitions.py

@@ -3,6 +3,7 @@
 import torch
 
 
+# @torch.jit.script
 def stratified_min(distances, labels):
     clabels = torch.unique(labels, dim=0)
     nclasses = clabels.size()[0]
@@ -30,15 +31,15 @@ def stratified_min(distances, labels):
     return winning_distances.T  # return with `batch_size` first
 
 
+# @torch.jit.script
 def wtac(distances, labels):
     winning_indices = torch.min(distances, dim=1).indices
     winning_labels = labels[winning_indices].squeeze()
     return winning_labels
 
 
-def knnc(distances, labels, k=1):
+# @torch.jit.script
-    winning_indices = torch.topk(-distances, k=k, dim=1).indices
+def knnc(distances, labels, k):
-    # winning_labels = torch.mode(labels[winning_indices].squeeze(),
+    winning_indices = torch.topk(-distances, k=k.item(), dim=1).indices
-    #                             dim=1).values
+    winning_labels = labels[winning_indices].squeeze()
-    winning_labels = torch.mode(labels[winning_indices], dim=1).values
     return winning_labels

prototorch/functions/distances.py

@@ -3,8 +3,11 @@
 import numpy as np
 import torch
 
-from prototorch.functions.helper import (_check_shapes, _int_and_mixed_shape,
+from prototorch.functions.helper import (
-                                         equal_int_shape)
+    _check_shapes,
+    _int_and_mixed_shape,
+    equal_int_shape,
+)
 
 
 def squared_euclidean_distance(x, y):
@@ -261,5 +264,86 @@ def tangent_distance(signals, protos, subspaces, squared=False, epsilon=1e-10):
             return diss.permute([1, 0, 2]).squeeze(-1)
 
 
+class KernelDistance:
+    r"""Kernel Distance
+
+    Distance based on a kernel function.
+    """
+    def __init__(self, kernel_fn):
+        self.kernel_fn = kernel_fn
+
+    def __call__(self, x_batch: torch.Tensor, y_batch: torch.Tensor):
+        return self._single_call(x_batch, y_batch)
+
+    def _single_call(self, x, y):
+        remove_dims = []
+        if len(x.shape) == 1:
+            x = x.unsqueeze(0)
+            remove_dims.append(0)
+        if len(y.shape) == 1:
+            y = y.unsqueeze(0)
+            remove_dims.append(-1)
+
+        output = self.kernel_fn(x, x).diag().unsqueeze(1) - 2 * self.kernel_fn(
+            x, y) + self.kernel_fn(y, y).diag()
+
+        for dim in remove_dims:
+            output.squeeze_(dim)
+
+        return torch.sqrt(output)
+
+
+class BatchKernelDistance:
+    r"""Kernel Distance
+
+    Distance based on a kernel function.
+    """
+    def __init__(self, kernel_fn):
+        self.kernel_fn = kernel_fn
+
+    def __call__(self, x_batch: torch.Tensor, y_batch: torch.Tensor):
+        remove_dims = 0
+        # Extend Single inputs
+        if len(x_batch.shape) == 1:
+            x_batch = x_batch.unsqueeze(0)
+            remove_dims += 1
+        if len(y_batch.shape) == 1:
+            y_batch = y_batch.unsqueeze(0)
+            remove_dims += 1
+
+        # Loop over batches
+        output = torch.FloatTensor(len(x_batch), len(y_batch))
+        for i, x in enumerate(x_batch):
+            for j, y in enumerate(y_batch):
+                output[i][j] = self._single_call(x, y)
+
+        for _ in range(remove_dims):
+            output.squeeze_(0)
+
+        return output
+
+    def _single_call(self, x, y):
+        kappa_xx = self.kernel_fn(x, x)
+        kappa_xy = self.kernel_fn(x, y)
+        kappa_yy = self.kernel_fn(y, y)
+
+        squared_distance = kappa_xx - 2 * kappa_xy + kappa_yy
+
+        return torch.sqrt(squared_distance)
+
+
+class SquaredKernelDistance(KernelDistance):
+    r"""Squared Kernel Distance
+
+    Kernel distance without final squareroot.
+    """
+    def single_call(self, x, y):
+        kappa_xx = self.kernel_fn(x, x)
+        kappa_xy = self.kernel_fn(x, y)
+        kappa_yy = self.kernel_fn(y, y)
+
+        return kappa_xx - 2 * kappa_xy + kappa_yy
+
+
 # Aliases
 sed = squared_euclidean_distance

prototorch/functions/kernels.py

@@ -0,0 +1,28 @@
+"""
+Experimental Kernels
+"""
+
+import torch
+
+
+class ExplicitKernel:
+    def __init__(self, projection=torch.nn.Identity()):
+        self.projection = projection
+
+    def __call__(self, x, y):
+        return self.projection(x) @ self.projection(y).T
+
+
+class RadialBasisFunctionKernel:
+    def __init__(self, sigma) -> None:
+        self.s2 = sigma * sigma
+
+    def __call__(self, x, y):
+        remove_dim = False
+        if len(x.shape) > 1:
+            x = x.unsqueeze(1)
+            remove_dim = True
+        output = torch.exp(-torch.sum((x - y)**2, dim=-1) / (2 * self.s2))
+        if remove_dim:
+            output = output.squeeze(1)
+        return output

prototorch/modules/models.py

@@ -1,8 +1,7 @@
 import torch
 from torch import nn
 
-from prototorch.functions.distances import (euclidean_distance_matrix,
+from prototorch.functions.distances import euclidean_distance_matrix, tangent_distance
-                                            tangent_distance)
 from prototorch.functions.helper import _check_shapes, _int_and_mixed_shape
 from prototorch.functions.normalization import orthogonalization
 from prototorch.modules.prototypes import Prototypes1D

setup.py

@@ -23,7 +23,6 @@ INSTALL_REQUIRES = [
 ]
 DATASETS = [
     "requests",
-    "sklearn",
     "tqdm",
 ]
 DEV = ["bumpversion"]
@@ -43,7 +42,7 @@ ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.4.4",
+    version="0.4.2",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",

tests/test_functions.py

@@ -4,8 +4,14 @@ import unittest
 
 import numpy as np
 import torch
-from prototorch.functions import (activations, competitions, distances,
+
-                                  initializers, losses)
+from prototorch.functions import (
+    activations,
+    competitions,
+    distances,
+    initializers,
+    losses,
+)
 
 
 class TestActivations(unittest.TestCase):
@@ -138,7 +144,7 @@ class TestCompetitions(unittest.TestCase):
     def test_knnc_k1(self):
         d = torch.tensor([[2.0, 3.0, 1.99, 3.01], [2.0, 3.0, 2.01, 3.0]])
         labels = torch.tensor([0, 1, 2, 3])
-        actual = competitions.knnc(d, labels, k=1)
+        actual = competitions.knnc(d, labels, k=torch.tensor([1]))
         desired = torch.tensor([2, 0])
         mismatch = np.testing.assert_array_almost_equal(actual,
                                                         desired,

tests/test_kernels.py

@@ -0,0 +1,98 @@
+"""ProtoTorch kernels test suite."""
+
+import unittest
+
+import numpy as np
+import torch
+
+from prototorch.functions.distances import KernelDistance
+from prototorch.functions.kernels import ExplicitKernel, RadialBasisFunctionKernel
+
+
+class TestExplicitKernel(unittest.TestCase):
+    def setUp(self):
+        self.single_x = torch.randn(1024)
+        self.single_y = torch.randn(1024)
+
+        self.batch_x = torch.randn(32, 1024)
+        self.batch_y = torch.randn(32, 1024)
+
+    def test_single_values(self):
+        kernel = ExplicitKernel()
+        self.assertEqual(
+            kernel(self.single_x, self.single_y).shape, torch.Size([]))
+
+    def test_single_batch(self):
+        kernel = ExplicitKernel()
+        self.assertEqual(
+            kernel(self.single_x, self.batch_y).shape, torch.Size([32]))
+
+    def test_batch_single(self):
+        kernel = ExplicitKernel()
+        self.assertEqual(
+            kernel(self.batch_x, self.single_y).shape, torch.Size([32]))
+
+    def test_batch_values(self):
+        kernel = ExplicitKernel()
+        self.assertEqual(
+            kernel(self.batch_x, self.batch_y).shape, torch.Size([32, 32]))
+
+
+class TestRadialBasisFunctionKernel(unittest.TestCase):
+    def setUp(self):
+        self.single_x = torch.randn(1024)
+        self.single_y = torch.randn(1024)
+
+        self.batch_x = torch.randn(32, 1024)
+        self.batch_y = torch.randn(32, 1024)
+
+    def test_single_values(self):
+        kernel = RadialBasisFunctionKernel(1)
+        self.assertEqual(
+            kernel(self.single_x, self.single_y).shape, torch.Size([]))
+
+    def test_single_batch(self):
+        kernel = RadialBasisFunctionKernel(1)
+        self.assertEqual(
+            kernel(self.single_x, self.batch_y).shape, torch.Size([32]))
+
+    def test_batch_single(self):
+        kernel = RadialBasisFunctionKernel(1)
+        self.assertEqual(
+            kernel(self.batch_x, self.single_y).shape, torch.Size([32]))
+
+    def test_batch_values(self):
+        kernel = RadialBasisFunctionKernel(1)
+        self.assertEqual(
+            kernel(self.batch_x, self.batch_y).shape, torch.Size([32, 32]))
+
+
+class TestKernelDistance(unittest.TestCase):
+    def setUp(self):
+        self.single_x = torch.randn(1024)
+        self.single_y = torch.randn(1024)
+
+        self.batch_x = torch.randn(32, 1024)
+        self.batch_y = torch.randn(32, 1024)
+
+        self.kernel = ExplicitKernel()
+
+    def test_single_values(self):
+        distance = KernelDistance(self.kernel)
+        self.assertEqual(
+            distance(self.single_x, self.single_y).shape, torch.Size([]))
+
+    def test_single_batch(self):
+        distance = KernelDistance(self.kernel)
+        self.assertEqual(
+            distance(self.single_x, self.batch_y).shape, torch.Size([32]))
+
+    def test_batch_single(self):
+        distance = KernelDistance(self.kernel)
+        self.assertEqual(
+            distance(self.batch_x, self.single_y).shape, torch.Size([32]))
+
+    def test_batch_values(self):
+        distance = KernelDistance(self.kernel)
+        self.assertEqual(
+            distance(self.batch_x, self.batch_y).shape, torch.Size([32, 32]))