Merge branch 'master' into kernel_distances

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.5
+current_version = 0.4.2
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.gitignore

@@ -154,5 +154,4 @@ scratch*
 # End of https://www.gitignore.io/api/visualstudiocode
 .vscode/
 
-reports
-artifacts
+reports

.travis.yml

@@ -4,9 +4,7 @@ language: python
 python: 3.8
 cache:
   directories:
-  - "$HOME/.cache/pip"
   - "./tests/artifacts"
-  - "$HOME/datasets"
 install:
 - pip install .[all] --progress-bar off
 

docs/source/api.rst

@@ -1,24 +1,13 @@
-.. ProtoTorch API Reference
+.. ProtoFlow API Reference
 
-ProtoTorch API Reference
+ProtoFlow API Reference
 ======================================
 
 Datasets
 --------------------------------------
-
-Common Datasets
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. automodule:: prototorch.datasets
    :members:
-
-
-Abstract Datasets
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Abstract Datasets are used to build your own datasets.
-
-.. autoclass:: prototorch.datasets.abstract.NumpyDataset
-   :members:
+   :undoc-members:
 
 Functions
 --------------------------------------

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.4.5"
+release = "0.4.2"
 
 # -- General configuration ---------------------------------------------------
 
@@ -46,7 +46,6 @@ extensions = [
     "sphinx.ext.viewcode",
     "sphinx_rtd_theme",
     "sphinxcontrib.katex",
-    'sphinx_autodoc_typehints',
 ]
 
 # katex_prerender = True
@@ -180,9 +179,6 @@ texinfo_documents = [
 intersphinx_mapping = {
     "python": ("https://docs.python.org/", None),
     "numpy": ("https://docs.scipy.org/doc/numpy/", None),
-    "torch": ('https://pytorch.org/docs/stable/', None),
-    "pytorch_lightning":
-    ("https://pytorch-lightning.readthedocs.io/en/stable/", None),
 }
 
 # -- Options for Epub output ----------------------------------------------

examples/glvq_iris.py

@@ -3,13 +3,14 @@
 import numpy as np
 import torch
 from matplotlib import pyplot as plt
+from sklearn.datasets import load_iris
+from sklearn.preprocessing import StandardScaler
+from torchinfo import summary
+
 from prototorch.functions.competitions import wtac
 from prototorch.functions.distances import euclidean_distance
 from prototorch.modules.losses import GLVQLoss
 from prototorch.modules.prototypes import Prototypes1D
-from sklearn.datasets import load_iris
-from sklearn.preprocessing import StandardScaler
-from torchinfo import summary
 
 # Prepare and preprocess the data
 scaler = StandardScaler()
@@ -27,7 +28,7 @@ class Model(torch.nn.Module):
         self.proto_layer = Prototypes1D(
             input_dim=2,
             prototypes_per_class=3,
-            num_classes=3,
+            nclasses=3,
             prototype_initializer="stratified_random",
             data=[x_train, y_train],
         )

examples/gmlvq_tecator.py

@@ -2,12 +2,13 @@
 
 import matplotlib.pyplot as plt
 import torch
+from torch.utils.data import DataLoader
+
 from prototorch.datasets.tecator import Tecator
 from prototorch.functions.distances import sed
 from prototorch.modules import Prototypes1D
 from prototorch.modules.losses import GLVQLoss
 from prototorch.utils.colors import get_legend_handles
-from torch.utils.data import DataLoader
 
 # Prepare the dataset and dataloader
 train_data = Tecator(root="./artifacts", train=True)
@@ -22,7 +23,7 @@ class Model(torch.nn.Module):
         self.p1 = Prototypes1D(
             input_dim=100,
             prototypes_per_class=2,
-            num_classes=2,
+            nclasses=2,
             prototype_initializer="stratified_random",
             data=[x, y],
         )

examples/gtlvq_mnist.py

@@ -12,13 +12,14 @@ import numpy as np
 import torch
 import torch.nn as nn
 import torchvision
+from torchvision import transforms
+
 from prototorch.functions.helper import calculate_prototype_accuracy
 from prototorch.modules.losses import GLVQLoss
 from prototorch.modules.models import GTLVQ
-from torchvision import transforms
 
 # Parameters and options
-num_epochs = 50
+n_epochs = 50
 batch_size_train = 64
 batch_size_test = 1000
 learning_rate = 0.1
@@ -140,7 +141,7 @@ optimizer = torch.optim.Adam(
 criterion = GLVQLoss(squashing="sigmoid_beta", beta=10)
 
 # Training loop
-for epoch in range(num_epochs):
+for epoch in range(n_epochs):
     for batch_idx, (x_train, y_train) in enumerate(train_loader):
         model.train()
         x_train, y_train = x_train.to(device), y_train.to(device)
@@ -160,7 +161,7 @@ for epoch in range(num_epochs):
         if batch_idx % log_interval == 0:
             acc = calculate_prototype_accuracy(distances, y_train, plabels)
             print(
-                f"Epoch: {epoch + 1:02d}/{num_epochs:02d} Epoch Progress: {100. * batch_idx / len(train_loader):02.02f} % Loss: {loss.item():02.02f} \
+                f"Epoch: {epoch + 1:02d}/{n_epochs:02d} Epoch Progress: {100. * batch_idx / len(train_loader):02.02f} % Loss: {loss.item():02.02f} \
               Train Acc: {acc.item():02.02f}")
 
     # Test

prototorch/__init__.py

@@ -1,24 +1,21 @@
 """ProtoTorch package."""
 
-import pkgutil
-
-import pkg_resources
-
-from . import components, datasets, functions, modules, utils
-from .datasets import *
-
 # Core Setup
-__version__ = "0.4.5"
+__version__ = "0.4.2"
 
 __all_core__ = [
     "datasets",
     "functions",
     "modules",
-    "components",
-    "utils",
 ]
 
+from .datasets import *
+
 # Plugin Loader
+import pkgutil
+
+import pkg_resources
+
 __path__ = pkgutil.extend_path(__path__, __name__)
 
 

prototorch/components/components.py

@@ -1,37 +1,36 @@
 """ProtoTorch components modules."""
 
 import warnings
+from typing import Tuple
 
 import torch
 from prototorch.components.initializers import (ClassAwareInitializer,
                                                 ComponentsInitializer,
-                                                CustomLabelsInitializer,
                                                 EqualLabelsInitializer,
                                                 UnequalLabelsInitializer,
                                                 ZeroReasoningsInitializer)
+from prototorch.functions.initializers import get_initializer
 from torch.nn.parameter import Parameter
 
 
 class Components(torch.nn.Module):
     """Components is a set of learnable Tensors."""
     def __init__(self,
-                 num_components=None,
+                 number_of_components=None,
                  initializer=None,
                  *,
-                 initialized_components=None):
+                 initialized_components=None,
+                 dtype=torch.float32):
         super().__init__()
 
-        self.num_components = num_components
-
         # Ignore all initialization settings if initialized_components is given.
         if initialized_components is not None:
-            self.register_parameter("_components",
-                                    Parameter(initialized_components))
-            if num_components is not None or initializer is not None:
+            self._components = Parameter(initialized_components)
+            if number_of_components is not None or initializer is not None:
                 wmsg = "Arguments ignored while initializing Components"
                 warnings.warn(wmsg)
         else:
-            self._initialize_components(initializer)
+            self._initialize_components(number_of_components, initializer)
 
     def _precheck_initializer(self, initializer):
         if not isinstance(initializer, ComponentsInitializer):
@@ -40,15 +39,15 @@ class Components(torch.nn.Module):
                 f"You have provided: {initializer=} instead."
             raise TypeError(emsg)
 
-    def _initialize_components(self, initializer):
+    def _initialize_components(self, number_of_components, initializer):
         self._precheck_initializer(initializer)
-        _components = initializer.generate(self.num_components)
-        self.register_parameter("_components", Parameter(_components))
+        self._components = Parameter(
+            initializer.generate(number_of_components))
 
     @property
     def components(self):
         """Tensor containing the component tensors."""
-        return self._components.detach()
+        return self._components.detach().cpu()
 
     def forward(self):
         return self._components
@@ -68,44 +67,36 @@ class LabeledComponents(Components):
                  *,
                  initialized_components=None):
         if initialized_components is not None:
-            components, component_labels = initialized_components
-            super().__init__(initialized_components=components)
-            self._labels = component_labels
+            super().__init__(initialized_components=initialized_components[0])
+            self._labels = initialized_components[1]
         else:
-            _labels = self._initialize_labels(distribution)
-            super().__init__(len(_labels), initializer=initializer)
-            self.register_buffer("_labels", _labels)
+            self._initialize_labels(distribution)
+            super().__init__(number_of_components=len(self._labels),
+                             initializer=initializer)
 
-    def _initialize_components(self, initializer):
+    def _initialize_components(self, number_of_components, initializer):
         if isinstance(initializer, ClassAwareInitializer):
             self._precheck_initializer(initializer)
-            _components = initializer.generate(self.num_components,
-                                               self.distribution)
-            self.register_parameter("_components", Parameter(_components))
+            self._components = Parameter(
+                initializer.generate(number_of_components, self.distribution))
         else:
-            super()._initialize_components(initializer)
+            super()._initialize_components(self, number_of_components,
+                                           initializer)
 
     def _initialize_labels(self, distribution):
-        if type(distribution) == dict:
-            if "num_classes" in distribution.keys():
-                labels = EqualLabelsInitializer(
-                    distribution["num_classes"],
-                    distribution["prototypes_per_class"])
-            else:
-                labels = CustomLabelsInitializer(distribution)
-        elif type(distribution) == tuple:
+        if type(distribution) == tuple:
             num_classes, prototypes_per_class = distribution
             labels = EqualLabelsInitializer(num_classes, prototypes_per_class)
         elif type(distribution) == list:
             labels = UnequalLabelsInitializer(distribution)
 
         self.distribution = labels.distribution
-        return labels.generate()
+        self._labels = labels.generate()
 
     @property
     def component_labels(self):
         """Tensor containing the component tensors."""
-        return self._labels.detach()
+        return self._labels.detach().cpu()
 
     def forward(self):
         return super().forward(), self._labels
@@ -132,21 +123,20 @@ class ReasoningComponents(Components):
                  *,
                  initialized_components=None):
         if initialized_components is not None:
-            components, reasonings = initialized_components
-
-            super().__init__(initialized_components=components)
-            self.register_parameter("_reasonings", reasonings)
+            super().__init__(initialized_components=initialized_components[0])
+            self._reasonings = initialized_components[1]
         else:
             self._initialize_reasonings(reasonings)
-            super().__init__(len(self._reasonings), initializer=initializer)
+            super().__init__(number_of_components=len(self._reasonings),
+                             initializer=initializer)
 
     def _initialize_reasonings(self, reasonings):
         if type(reasonings) == tuple:
-            num_classes, num_components = reasonings
-            reasonings = ZeroReasoningsInitializer(num_classes, num_components)
+            num_classes, number_of_components = reasonings
+            reasonings = ZeroReasoningsInitializer(num_classes,
+                                                   number_of_components)
 
-        _reasonings = reasonings.generate()
-        self.register_parameter("_reasonings", _reasonings)
+        self._reasonings = reasonings.generate()
 
     @property
     def reasonings(self):
@@ -155,7 +145,7 @@ class ReasoningComponents(Components):
         Dimension NxCx2
 
         """
-        return self._reasonings.detach()
+        return self._reasonings.detach().cpu()
 
     def forward(self):
         return super().forward(), self._reasonings

prototorch/components/initializers.py

@@ -7,18 +7,12 @@ import torch
 from torch.utils.data import DataLoader, Dataset
 
 
-def parse_data_arg(data_arg):
-    if isinstance(data_arg, Dataset):
-        data_arg = DataLoader(data_arg, batch_size=len(data_arg))
-
-    if isinstance(data_arg, DataLoader):
-        data = torch.tensor([])
-        labels = torch.tensor([])
-        for x, y in data_arg:
-            data = torch.cat([data, x])
-            labels = torch.cat([labels, y])
+def parse_init_arg(arg):
+    if isinstance(arg, Dataset):
+        data, labels = next(iter(DataLoader(arg, batch_size=len(arg))))
+        # data = data.view(len(arg), -1)  # flatten
     else:
-        data, labels = data_arg
+        data, labels = arg
         if not isinstance(data, torch.Tensor):
             wmsg = f"Converting data to {torch.Tensor}."
             warnings.warn(wmsg)
@@ -69,19 +63,19 @@ class UniformInitializer(DimensionAwareInitializer):
         return torch.ones(gen_dims).uniform_(self.min, self.max)
 
 
-class DataAwareInitializer(ComponentsInitializer):
-    def __init__(self, data):
+class PositionAwareInitializer(ComponentsInitializer):
+    def __init__(self, positions):
         super().__init__()
-        self.data = data
+        self.data = positions
 
 
-class SelectionInitializer(DataAwareInitializer):
+class SelectionInitializer(PositionAwareInitializer):
     def generate(self, length):
         indices = torch.LongTensor(length).random_(0, len(self.data))
         return self.data[indices]
 
 
-class MeanInitializer(DataAwareInitializer):
+class MeanInitializer(PositionAwareInitializer):
     def generate(self, length):
         mean = torch.mean(self.data, dim=0)
         repeat_dim = [length] + [1] * len(mean.shape)
@@ -89,14 +83,12 @@ class MeanInitializer(DataAwareInitializer):
 
 
 class ClassAwareInitializer(ComponentsInitializer):
-    def __init__(self, data, transform=torch.nn.Identity()):
+    def __init__(self, arg):
         super().__init__()
-        data, labels = parse_data_arg(data)
+        data, labels = parse_init_arg(arg)
         self.data = data
         self.labels = labels
 
-        self.transform = transform
-
         self.clabels = torch.unique(self.labels)
         self.num_classes = len(self.clabels)
 
@@ -104,24 +96,15 @@ class ClassAwareInitializer(ComponentsInitializer):
         if not dist:
             per_class = length // self.num_classes
             dist = self.num_classes * [per_class]
-        if type(dist) == dict:
-            dist = dist.values()
         samples_list = [
             init.generate(n) for init, n in zip(self.initializers, dist)
         ]
-        out = torch.vstack(samples_list)
-        with torch.no_grad():
-            out = self.transform(out)
-        return out
-
-    def __del__(self):
-        del self.data
-        del self.labels
+        return torch.vstack(samples_list)
 
 
 class StratifiedMeanInitializer(ClassAwareInitializer):
-    def __init__(self, data, **kwargs):
-        super().__init__(data, **kwargs)
+    def __init__(self, arg):
+        super().__init__(arg)
 
         self.initializers = []
         for clabel in self.clabels:
@@ -135,8 +118,8 @@ class StratifiedMeanInitializer(ClassAwareInitializer):
 
 
 class StratifiedSelectionInitializer(ClassAwareInitializer):
-    def __init__(self, data, noise=None, **kwargs):
-        super().__init__(data, **kwargs)
+    def __init__(self, arg, *, noise=None):
+        super().__init__(arg)
         self.noise = noise
 
         self.initializers = []
@@ -145,10 +128,7 @@ class StratifiedSelectionInitializer(ClassAwareInitializer):
             class_initializer = SelectionInitializer(class_data)
             self.initializers.append(class_initializer)
 
-    def add_noise_v1(self, x):
-        return x + self.noise
-
-    def add_noise_v2(self, x):
+    def add_noise(self, x):
         """Shifts some dimensions of the data randomly."""
         n1 = torch.rand_like(x)
         n2 = torch.rand_like(x)
@@ -158,7 +138,8 @@ class StratifiedSelectionInitializer(ClassAwareInitializer):
     def generate(self, length, dist=[]):
         samples = self._get_samples_from_initializer(length, dist)
         if self.noise is not None:
-            samples = self.add_noise_v1(samples)
+            # samples = self.add_noise(samples)
+            samples = samples + self.noise
         return samples
 
 
@@ -176,13 +157,10 @@ class UnequalLabelsInitializer(LabelsInitializer):
     def distribution(self):
         return self.dist
 
-    def generate(self, clabels=None, dist=None):
-        if not clabels:
-            clabels = range(len(self.dist))
-        if not dist:
-            dist = self.dist
-        labels = list(chain(*[[i] * n for i, n in zip(clabels, dist)]))
-        return torch.LongTensor(labels)
+    def generate(self):
+        clabels = range(len(self.dist))
+        labels = list(chain(*[[i] * n for i, n in zip(clabels, self.dist)]))
+        return torch.tensor(labels)
 
 
 class EqualLabelsInitializer(LabelsInitializer):
@@ -198,13 +176,6 @@ class EqualLabelsInitializer(LabelsInitializer):
         return torch.arange(self.classes).repeat(self.per_class, 1).T.flatten()
 
 
-class CustomLabelsInitializer(UnequalLabelsInitializer):
-    def generate(self):
-        clabels = list(self.dist.keys())
-        dist = list(self.dist.values())
-        return super().generate(clabels, dist)
-
-
 # Reasonings
 class ReasoningsInitializer:
     def generate(self, length):
@@ -224,5 +195,3 @@ class ZeroReasoningsInitializer(ReasoningsInitializer):
 SSI = StratifiedSampleInitializer = StratifiedSelectionInitializer
 SMI = StratifiedMeanInitializer
 Random = RandomInitializer = UniformInitializer
-Zeros = ZerosInitializer
-Ones = OnesInitializer

prototorch/datasets/__init__.py

@@ -1,8 +1,11 @@
 """ProtoTorch datasets."""
 
 from .abstract import NumpyDataset
-from .iris import Iris
 from .spiral import Spiral
 from .tecator import Tecator
 
-__all__ = ['Iris', 'Spiral', 'Tecator']
+__all__ = [
+    "NumpyDataset",
+    "Spiral",
+    "Tecator",
+]

prototorch/datasets/abstract.py

@@ -14,10 +14,8 @@ import torch
 
 class NumpyDataset(torch.utils.data.TensorDataset):
     """Create a PyTorch TensorDataset from NumPy arrays."""
-    def __init__(self, data, targets):
-        self.data = data
-        self.targets = targets
-        tensors = [torch.Tensor(data), torch.Tensor(targets)]
+    def __init__(self, *arrays):
+        tensors = [torch.Tensor(arr) for arr in arrays]
         super().__init__(*tensors)
 
 

prototorch/datasets/iris.py

@@ -1,40 +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 typing import Sequence
-
-from prototorch.datasets.abstract import NumpyDataset
-from sklearn.datasets import load_iris
-
-
-class Iris(NumpyDataset):
-    """
-    Iris Dataset by Ronald Fisher introduced in 1936.
-
-    The dataset contains four measurements from flowers of three species of iris.
-
-    .. list-table:: Iris
-        :header-rows: 1
-
-        * - dimensions
-          - classes
-          - training size
-          - validation size
-          - test size
-        * - 4
-          - 3
-          - 150
-          - 0
-          - 0
-
-    :param dims: select a subset of dimensions
-    """
-    def __init__(self, dims: Sequence[int] = None):
-        x, y = load_iris(return_X_y=True)
-        if dims:
-            x = x[:, dims]
-        super().__init__(x, y)

prototorch/datasets/spiral.py

@@ -4,22 +4,18 @@ import numpy as np
 import torch
 
 
-def make_spiral(num_samples=500, noise=0.3):
-    """Generates the Spiral Dataset.
-    
-    For use in Prototorch use `prototorch.datasets.Spiral` instead.
-    """
+def make_spiral(n_samples=500, noise=0.3):
     def get_samples(n, delta_t):
         points = []
         for i in range(n):
-            r = i / num_samples * 5
+            r = i / n_samples * 5
             t = 1.75 * i / n * 2 * np.pi + delta_t
             x = r * np.sin(t) + np.random.rand(1) * noise
             y = r * np.cos(t) + np.random.rand(1) * noise
             points.append([x, y])
         return points
 
-    n = num_samples // 2
+    n = n_samples // 2
     positive = get_samples(n=n, delta_t=0)
     negative = get_samples(n=n, delta_t=np.pi)
     x = np.concatenate(
@@ -31,27 +27,7 @@ def make_spiral(num_samples=500, noise=0.3):
 
 
 class Spiral(torch.utils.data.TensorDataset):
-    """Spiral dataset for binary classification.
-
-    This datasets consists of two spirals of two different classes.
-
-    .. list-table:: Spiral
-        :header-rows: 1
-
-        * - dimensions
-          - classes
-          - training size
-          - validation size
-          - test size
-        * - 2
-          - 2
-          - num_samples
-          - 0
-          - 0
-
-    :param num_samples: number of random samples
-    :param noise: noise added to the spirals
-    """
-    def __init__(self, num_samples: int = 500, noise: float = 0.3):
-        x, y = make_spiral(num_samples, noise)
+    """Spiral dataset for binary classification."""
+    def __init__(self, n_samples=500, noise=0.3):
+        x, y = make_spiral(n_samples, noise)
         super().__init__(torch.Tensor(x), torch.LongTensor(y))

prototorch/datasets/tecator.py

@@ -40,29 +40,15 @@ import os
 
 import numpy as np
 import torch
-from prototorch.datasets.abstract import ProtoDataset
 from torchvision.datasets.utils import download_file_from_google_drive
 
+from prototorch.datasets.abstract import ProtoDataset
+
 
 class Tecator(ProtoDataset):
     """
-    `Tecator Dataset <http://lib.stat.cmu.edu/datasets/tecator>`__ for classification.
-
-    The dataset contains wavelength measurements of meat.
-
-    .. list-table:: Tecator
-        :header-rows: 1
-
-        * - dimensions
-          - classes
-          - training size
-          - validation size
-          - test size
-        * - 100
-          - 2
-          - 129
-          - 43
-          - 43
+    `Tecator Dataset <http://lib.stat.cmu.edu/datasets/tecator>`__
+    for classification.
     """
 
     _resources = [

prototorch/functions/competitions.py

@@ -3,14 +3,15 @@
 import torch
 
 
+# @torch.jit.script
 def stratified_min(distances, labels):
     clabels = torch.unique(labels, dim=0)
-    num_classes = clabels.size()[0]
-    if distances.size()[1] == num_classes:
+    nclasses = clabels.size()[0]
+    if distances.size()[1] == nclasses:
         # skip if only one prototype per class
         return distances
     batch_size = distances.size()[0]
-    winning_distances = torch.zeros(num_classes, batch_size)
+    winning_distances = torch.zeros(nclasses, batch_size)
     inf = torch.full_like(distances.T, fill_value=float("inf"))
     # distances_to_wpluses = torch.where(matcher, distances, inf)
     for i, cl in enumerate(clabels):
@@ -18,7 +19,7 @@ def stratified_min(distances, labels):
         matcher = torch.eq(labels.unsqueeze(dim=1), cl)
         if labels.ndim == 2:
             # if the labels are one-hot vectors
-            matcher = torch.eq(torch.sum(matcher, dim=-1), num_classes)
+            matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
         cdists = torch.where(matcher, distances.T, inf).T
         winning_distances[i] = torch.min(cdists, dim=1,
                                          keepdim=True).values.squeeze()
@@ -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):
-    winning_indices = torch.topk(-distances, k=k, dim=1).indices
-    # winning_labels = torch.mode(labels[winning_indices].squeeze(),
-    #                             dim=1).values
-    winning_labels = torch.mode(labels[winning_indices], dim=1).values
+# @torch.jit.script
+def knnc(distances, labels, k):
+    winning_indices = torch.topk(-distances, k=k.item(), dim=1).indices
+    winning_labels = labels[winning_indices].squeeze()
     return winning_labels

prototorch/functions/distances.py

@@ -2,8 +2,12 @@
 
 import numpy as np
 import torch
-from prototorch.functions.helper import (_check_shapes, _int_and_mixed_shape,
-                                         equal_int_shape, get_flat)
+
+from prototorch.functions.helper import (
+    _check_shapes,
+    _int_and_mixed_shape,
+    equal_int_shape,
+)
 
 
 def squared_euclidean_distance(x, y):
@@ -11,10 +15,12 @@ def squared_euclidean_distance(x, y):
 
     Compute :math:`{\langle \bm x - \bm y \rangle}_2`
 
+    :param `torch.tensor` x: Two dimensional vector
+    :param `torch.tensor` y: Two dimensional vector
+
     **Alias:**
     ``prototorch.functions.distances.sed``
     """
-    x, y = get_flat(x, y)
     expanded_x = x.unsqueeze(dim=1)
     batchwise_difference = y - expanded_x
     differences_raised = torch.pow(batchwise_difference, 2)
@@ -27,17 +33,18 @@ def euclidean_distance(x, y):
 
     Compute :math:`\sqrt{{\langle \bm x - \bm y \rangle}_2}`
 
+    :param `torch.tensor` x: Input Tensor of shape :math:`X \times N`
+    :param `torch.tensor` y: Input Tensor of shape :math:`Y \times N`
+
     :returns: Distance Tensor of shape :math:`X \times Y`
     :rtype: `torch.tensor`
     """
-    x, y = get_flat(x, y)
     distances_raised = squared_euclidean_distance(x, y)
     distances = torch.sqrt(distances_raised)
     return distances
 
 
 def euclidean_distance_v2(x, y):
-    x, y = get_flat(x, y)
     diff = y - x.unsqueeze(1)
     pairwise_distances = (diff @ diff.permute((0, 2, 1))).sqrt()
     # Passing `dim1=-2` and `dim2=-1` to `diagonal()` takes the
@@ -58,9 +65,10 @@ def lpnorm_distance(x, y, p):
 
     Calls ``torch.cdist``
 
+    :param `torch.tensor` x: Two dimensional vector
+    :param `torch.tensor` y: Two dimensional vector
     :param p: p parameter of the lp norm
     """
-    x, y = get_flat(x, y)
     distances = torch.cdist(x, y, p=p)
     return distances
 
@@ -70,9 +78,10 @@ def omega_distance(x, y, omega):
 
     Compute :math:`{\| \Omega \bm x - \Omega \bm y \|}_p`
 
+    :param `torch.tensor` x: Two dimensional vector
+    :param `torch.tensor` y: Two dimensional vector
     :param `torch.tensor` omega: Two dimensional matrix
     """
-    x, y = get_flat(x, y)
     projected_x = x @ omega
     projected_y = y @ omega
     distances = squared_euclidean_distance(projected_x, projected_y)
@@ -84,9 +93,10 @@ def lomega_distance(x, y, omegas):
 
     Compute :math:`{\| \Omega_k \bm x - \Omega_k \bm y_k \|}_p`
 
+    :param `torch.tensor` x: Two dimensional vector
+    :param `torch.tensor` y: Two dimensional vector
     :param `torch.tensor` omegas: Three dimensional matrix
     """
-    x, y = get_flat(x, y)
     projected_x = x @ omegas
     projected_y = torch.diagonal(y @ omegas).T
     expanded_y = torch.unsqueeze(projected_y, dim=1)
@@ -254,5 +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
+sed = squared_euclidean_distance

prototorch/functions/helper.py

@@ -1,11 +1,6 @@
 import torch
 
 
-def get_flat(*args):
-    rv = [x.view(x.size(0), -1) for x in args]
-    return rv
-
-
 def calculate_prototype_accuracy(y_pred, y_true, plabels):
     """Computes the accuracy of a prototype based model.
     via Winner-Takes-All rule.

prototorch/functions/initializers.py

@@ -15,59 +15,59 @@ def register_initializer(function):
 
 def labels_from(distribution, one_hot=True):
     """Takes a distribution tensor and returns a labels tensor."""
-    num_classes = distribution.shape[0]
-    llist = [[i] * n for i, n in zip(range(num_classes), distribution)]
+    nclasses = distribution.shape[0]
+    llist = [[i] * n for i, n in zip(range(nclasses), distribution)]
     # labels = [l for cl in llist for l in cl]  # flatten the list of lists
     flat_llist = list(chain(*llist))  # flatten label list with itertools.chain
     plabels = torch.tensor(flat_llist, requires_grad=False)
     if one_hot:
-        return torch.eye(num_classes)[plabels]
+        return torch.eye(nclasses)[plabels]
     return plabels
 
 
 @register_initializer
 def ones(x_train, y_train, prototype_distribution, one_hot=True):
-    num_protos = torch.sum(prototype_distribution)
-    protos = torch.ones(num_protos, *x_train.shape[1:])
+    nprotos = torch.sum(prototype_distribution)
+    protos = torch.ones(nprotos, *x_train.shape[1:])
     plabels = labels_from(prototype_distribution, one_hot)
     return protos, plabels
 
 
 @register_initializer
 def zeros(x_train, y_train, prototype_distribution, one_hot=True):
-    num_protos = torch.sum(prototype_distribution)
-    protos = torch.zeros(num_protos, *x_train.shape[1:])
+    nprotos = torch.sum(prototype_distribution)
+    protos = torch.zeros(nprotos, *x_train.shape[1:])
     plabels = labels_from(prototype_distribution, one_hot)
     return protos, plabels
 
 
 @register_initializer
 def rand(x_train, y_train, prototype_distribution, one_hot=True):
-    num_protos = torch.sum(prototype_distribution)
-    protos = torch.rand(num_protos, *x_train.shape[1:])
+    nprotos = torch.sum(prototype_distribution)
+    protos = torch.rand(nprotos, *x_train.shape[1:])
     plabels = labels_from(prototype_distribution, one_hot)
     return protos, plabels
 
 
 @register_initializer
 def randn(x_train, y_train, prototype_distribution, one_hot=True):
-    num_protos = torch.sum(prototype_distribution)
-    protos = torch.randn(num_protos, *x_train.shape[1:])
+    nprotos = torch.sum(prototype_distribution)
+    protos = torch.randn(nprotos, *x_train.shape[1:])
     plabels = labels_from(prototype_distribution, one_hot)
     return protos, plabels
 
 
 @register_initializer
 def stratified_mean(x_train, y_train, prototype_distribution, one_hot=True):
-    num_protos = torch.sum(prototype_distribution)
+    nprotos = torch.sum(prototype_distribution)
     pdim = x_train.shape[1]
-    protos = torch.empty(num_protos, pdim)
+    protos = torch.empty(nprotos, pdim)
     plabels = labels_from(prototype_distribution, one_hot)
     for i, label in enumerate(plabels):
         matcher = torch.eq(label.unsqueeze(dim=0), y_train)
         if one_hot:
-            num_classes = y_train.size()[1]
-            matcher = torch.eq(torch.sum(matcher, dim=-1), num_classes)
+            nclasses = y_train.size()[1]
+            matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
         xl = x_train[matcher]
         mean_xl = torch.mean(xl, dim=0)
         protos[i] = mean_xl
@@ -81,15 +81,15 @@ def stratified_random(x_train,
                       prototype_distribution,
                       one_hot=True,
                       epsilon=1e-7):
-    num_protos = torch.sum(prototype_distribution)
+    nprotos = torch.sum(prototype_distribution)
     pdim = x_train.shape[1]
-    protos = torch.empty(num_protos, pdim)
+    protos = torch.empty(nprotos, pdim)
     plabels = labels_from(prototype_distribution, one_hot)
     for i, label in enumerate(plabels):
         matcher = torch.eq(label.unsqueeze(dim=0), y_train)
         if one_hot:
-            num_classes = y_train.size()[1]
-            matcher = torch.eq(torch.sum(matcher, dim=-1), num_classes)
+            nclasses = y_train.size()[1]
+            matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
         xl = x_train[matcher]
         rand_index = torch.zeros(1).long().random_(0, xl.shape[0] - 1)
         random_xl = xl[rand_index]

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/functions/losses.py

@@ -8,12 +8,12 @@ def _get_matcher(targets, labels):
     matcher = torch.eq(targets.unsqueeze(dim=1), labels)
     if labels.ndim == 2:
         # if the labels are one-hot vectors
-        num_classes = targets.size()[1]
-        matcher = torch.eq(torch.sum(matcher, dim=-1), num_classes)
+        nclasses = targets.size()[1]
+        matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
     return matcher
 
 
-def _get_dp_dm(distances, targets, plabels, with_indices=False):
+def _get_dp_dm(distances, targets, plabels):
     """Returns the d+ and d- values for a batch of distances."""
     matcher = _get_matcher(targets, plabels)
     not_matcher = torch.bitwise_not(matcher)
@@ -21,11 +21,9 @@ def _get_dp_dm(distances, targets, plabels, with_indices=False):
     inf = torch.full_like(distances, fill_value=float("inf"))
     d_matching = torch.where(matcher, distances, inf)
     d_unmatching = torch.where(not_matcher, distances, inf)
-    dp = torch.min(d_matching, dim=-1, keepdim=True)
-    dm = torch.min(d_unmatching, dim=-1, keepdim=True)
-    if with_indices:
-        return dp, dm
-    return dp.values, dm.values
+    dp = torch.min(d_matching, dim=1, keepdim=True).values
+    dm = torch.min(d_unmatching, dim=1, keepdim=True).values
+    return dp, dm
 
 
 def glvq_loss(distances, target_labels, prototype_labels):
@@ -49,11 +47,10 @@ def lvq1_loss(distances, target_labels, prototype_labels):
 
 def lvq21_loss(distances, target_labels, prototype_labels):
     """LVQ2.1 loss function with support for one-hot labels.
-
+    
     See Section 4 [Sado&Yamada]
     https://papers.nips.cc/paper/1995/file/9c3b1830513cc3b8fc4b76635d32e692-Paper.pdf
     """
     dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
     mu = dp - dm
-
-    return mu
+    return mu

prototorch/modules/models.py

@@ -1,8 +1,11 @@
 import torch
-from prototorch.functions.distances import euclidean_distance_matrix
+from torch import nn
+
+from prototorch.functions.distances import euclidean_distance_matrix, 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
-from torch import nn
+
 
 class GTLVQ(nn.Module):
     r""" Generalized Tangent Learning Vector Quantization
@@ -76,11 +79,22 @@ class GTLVQ(nn.Module):
         super(GTLVQ, self).__init__()
 
         self.num_protos = num_classes * prototypes_per_class
-        self.num_protos_class = prototypes_per_class
         self.subspace_size = feature_dim if subspace_size is None else subspace_size
         self.feature_dim = feature_dim
-        self.num_classes = num_classes
 
+        if subspace_data is None:
+            raise ValueError("Init Data must be specified!")
+
+        self.tpt = tangent_projection_type
+        with torch.no_grad():
+            if self.tpt == "local" or self.tpt == "local_proj":
+                self.init_local_subspace(subspace_data)
+            elif self.tpt == "global":
+                self.init_gobal_subspace(subspace_data, subspace_size)
+            else:
+                self.subspaces = None
+
+        # Hypothesis-Margin-Classifier
         self.cls = Prototypes1D(
             input_dim=feature_dim,
             prototypes_per_class=prototypes_per_class,
@@ -89,22 +103,21 @@ class GTLVQ(nn.Module):
             data=prototype_data,
         )
 
-        if subspace_data is None:
-            raise ValueError("Init Data must be specified!")
-
-        self.tpt = tangent_projection_type
-        with torch.no_grad():
-            if self.tpt == "local":
-                self.init_local_subspace(subspace_data, subspace_size,
-                                         self.num_protos)
-            elif self.tpt == "global":
-                self.init_gobal_subspace(subspace_data, subspace_size)
-            else:
-                self.subspaces = None
-
     def forward(self, x):
-        if self.tpt == "local":
-            dis = self.local_tangent_distances(x)
+        # Tangent Projection
+        if self.tpt == "local_proj":
+            x_conform = (x.unsqueeze(1).repeat_interleave(self.num_protos,
+                                                          1).unsqueeze(2))
+            dis, proj_x = self.local_tangent_projection(x_conform)
+
+            proj_x = proj_x.reshape(x.shape[0] * self.num_protos,
+                                    self.feature_dim)
+            return proj_x, dis
+        elif self.tpt == "local":
+            x_conform = (x.unsqueeze(1).repeat_interleave(self.num_protos,
+                                                          1).unsqueeze(2))
+            dis = tangent_distance(x_conform, self.cls.prototypes,
+                                   self.subspaces)
         elif self.tpt == "gloabl":
             dis = self.global_tangent_distances(x)
         else:
@@ -117,14 +130,16 @@ class GTLVQ(nn.Module):
         _, _, v = torch.svd(data)
         subspace = (torch.eye(v.shape[0]) - (v @ v.T)).T
         subspaces = subspace[:, :num_subspaces]
-        self.subspaces = nn.Parameter(subspaces, requires_grad=True)
+        self.subspaces = (torch.nn.Parameter(
+            subspaces).clone().detach().requires_grad_(True))
 
-    def init_local_subspace(self, data,num_subspaces,num_protos):
-        data = data -  torch.mean(data,dim=0)
-        _,_,v = torch.svd(data,some=False)
-        v = v[:,:num_subspaces]
-        subspaces = v.unsqueeze(0).repeat_interleave(num_protos,0)
-        self.subspaces = nn.Parameter(subspaces,requires_grad=True)
+    def init_local_subspace(self, data):
+        _, _, v = torch.svd(data)
+        inital_projector = (torch.eye(v.shape[0]) - (v @ v.T)).T
+        subspaces = inital_projector.unsqueeze(0).repeat_interleave(
+            self.num_protos, 0)
+        self.subspaces = (torch.nn.Parameter(
+            subspaces).clone().detach().requires_grad_(True))
 
     def global_tangent_distances(self, x):
         # Tangent Projection
@@ -135,21 +150,33 @@ class GTLVQ(nn.Module):
         # Euclidean Distance
         return euclidean_distance_matrix(x, projected_prototypes)
 
-    def local_tangent_distances(self, x):
+    def local_tangent_projection(self, signals):
+        # Note: subspaces is always assumed as transposed and must be orthogonal!
+        # shape(signals): batch x proto_number x channels x dim1 x dim2 x ... x dimN
+        # shape(protos): proto_number x dim1 x dim2 x ... x dimN
+        # shape(subspaces): (optional [proto_number]) x prod(dim1 * dim2 * ... * dimN)  x prod(projected_atom_shape)
+        # subspace should be orthogonalized
+        # Origin Source Code
+        # Origin Author:
+        protos = self.cls.prototypes
+        subspaces = self.subspaces
+        signal_shape, signal_int_shape = _int_and_mixed_shape(signals)
+        _, proto_int_shape = _int_and_mixed_shape(protos)
 
-        # Tangent Distance
-        x = x.unsqueeze(1).expand(x.size(0), self.cls.prototypes.size(0),
-                                  x.size(-1))
-        protos = self.cls.prototypes.unsqueeze(0).expand(
-            x.size(0), self.cls.prototypes.size(0), x.size(-1))
-        projectors = torch.eye(
-            self.subspaces.shape[-2], device=x.device) - torch.bmm(
-                self.subspaces, self.subspaces.permute([0, 2, 1]))
-        diff = (x - protos)
-        diff = diff.permute([1, 0, 2])
-        diff = torch.bmm(diff, projectors)
-        diff = torch.norm(diff,2,dim=-1).T
-        return diff
+        # check if the shapes are correct
+        _check_shapes(signal_int_shape, proto_int_shape)
+
+        # Tangent Data Projections
+        projected_protos = torch.bmm(protos.unsqueeze(1), subspaces).squeeze(1)
+        data = signals.squeeze(2).permute([1, 0, 2])
+        projected_data = torch.bmm(data, subspaces)
+        projected_data = projected_data.permute([1, 0, 2]).unsqueeze(1)
+        diff = projected_data - projected_protos
+        projected_diff = torch.reshape(
+            diff, (signal_shape[1], signal_shape[0], signal_shape[2]) +
+            signal_shape[3:])
+        diss = torch.norm(projected_diff, 2, dim=-1)
+        return diss.permute([1, 0, 2]).squeeze(-1), projected_data.squeeze(1)
 
     def get_parameters(self):
         return {

prototorch/modules/prototypes.py

@@ -3,6 +3,7 @@
 import warnings
 
 import torch
+
 from prototorch.functions.initializers import get_initializer
 
 
@@ -52,13 +53,13 @@ class Prototypes1D(_Prototypes):
                 raise NameError("`input_dim` required if "
                                 "no `data` is provided.")
             if prototype_distribution:
-                kwargs_num_classes = sum(prototype_distribution)
+                kwargs_nclasses = sum(prototype_distribution)
             else:
-                if "num_classes" not in kwargs:
+                if "nclasses" not in kwargs:
                     raise NameError("`prototype_distribution` required if "
-                                    "both `data` and `num_classes` are not "
+                                    "both `data` and `nclasses` are not "
                                     "provided.")
-                kwargs_num_classes = kwargs.pop("num_classes")
+                kwargs_nclasses = kwargs.pop("nclasses")
             input_dim = kwargs.pop("input_dim")
             if prototype_initializer in [
                     "stratified_mean", "stratified_random"
@@ -67,18 +68,18 @@ class Prototypes1D(_Prototypes):
                     f"`prototype_initializer`: `{prototype_initializer}` "
                     "requires `data`, but `data` is not provided. "
                     "Using randomly generated data instead.")
-            x_train = torch.rand(kwargs_num_classes, input_dim)
-            y_train = torch.arange(kwargs_num_classes)
+            x_train = torch.rand(kwargs_nclasses, input_dim)
+            y_train = torch.arange(kwargs_nclasses)
             if one_hot_labels:
-                y_train = torch.eye(kwargs_num_classes)[y_train]
+                y_train = torch.eye(kwargs_nclasses)[y_train]
             data = [x_train, y_train]
 
         x_train, y_train = data
         x_train = torch.as_tensor(x_train).type(dtype)
         y_train = torch.as_tensor(y_train).type(torch.int)
-        num_classes = torch.unique(y_train, dim=-1).shape[-1]
+        nclasses = torch.unique(y_train, dim=-1).shape[-1]
 
-        if num_classes == 1:
+        if nclasses == 1:
             warnings.warn("Are you sure about having one class only?")
 
         if x_train.ndim != 2:
@@ -104,20 +105,19 @@ class Prototypes1D(_Prototypes):
                                  "not match data dimension "
                                  f"`data[0].shape[1]`={x_train.shape[1]}")
 
-        # Verify the number of classes if `num_classes` is provided
-        if "num_classes" in kwargs:
-            kwargs_num_classes = kwargs.pop("num_classes")
-            if kwargs_num_classes != num_classes:
-                raise ValueError(
-                    f"Provided `num_classes={kwargs_num_classes}` does "
-                    "not match data labels "
-                    "`torch.unique(data[1]).shape[0]`"
-                    f"={num_classes}")
+        # Verify the number of classes if `nclasses` is provided
+        if "nclasses" in kwargs:
+            kwargs_nclasses = kwargs.pop("nclasses")
+            if kwargs_nclasses != nclasses:
+                raise ValueError(f"Provided `nclasses={kwargs_nclasses}` does "
+                                 "not match data labels "
+                                 "`torch.unique(data[1]).shape[0]`"
+                                 f"={nclasses}")
 
         super().__init__(**kwargs)
 
         if not prototype_distribution:
-            prototype_distribution = [prototypes_per_class] * num_classes
+            prototype_distribution = [prototypes_per_class] * nclasses
         with torch.no_grad():
             self.prototype_distribution = torch.tensor(prototype_distribution)
 

setup.py

@@ -20,7 +20,6 @@ INSTALL_REQUIRES = [
     "torch>=1.3.1",
     "torchvision>=0.5.0",
     "numpy>=1.9.1",
-    "sklearn",
 ]
 DATASETS = [
     "requests",
@@ -32,9 +31,9 @@ DOCS = [
     "sphinx",
     "sphinx_rtd_theme",
     "sphinxcontrib-katex",
-    "sphinx-autodoc-typehints",
 ]
 EXAMPLES = [
+    "sklearn",
     "matplotlib",
     "torchinfo",
 ]
@@ -43,7 +42,7 @@ ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.4.5",
+    version="0.4.2",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",

tests/test_components.py

@@ -1,25 +0,0 @@
-"""ProtoTorch components test suite."""
-
-import prototorch as pt
-import torch
-
-
-def test_labcomps_zeros_init():
-    protos = torch.zeros(3, 2)
-    c = pt.components.LabeledComponents(
-        distribution=[1, 1, 1],
-        initializer=pt.components.Zeros(2),
-    )
-    assert (c.components == protos).any() == True
-
-
-def test_labcomps_warmstart():
-    protos = torch.randn(3, 2)
-    plabels = torch.tensor([1, 2, 3])
-    c = pt.components.LabeledComponents(
-        distribution=[1, 1, 1],
-        initializer=None,
-        initialized_components=[protos, plabels],
-    )
-    assert (c.components == protos).any() == True
-    assert (c.component_labels == plabels).any() == True

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]))

tests/test_modules.py

@@ -4,6 +4,7 @@ import unittest
 
 import numpy as np
 import torch
+
 from prototorch.modules import losses, prototypes
 
 
@@ -17,20 +18,20 @@ class TestPrototypes(unittest.TestCase):
 
     def test_prototypes1d_init_without_input_dim(self):
         with self.assertRaises(NameError):
-            _ = prototypes.Prototypes1D(num_classes=2)
+            _ = prototypes.Prototypes1D(nclasses=2)
 
-    def test_prototypes1d_init_without_num_classes(self):
+    def test_prototypes1d_init_without_nclasses(self):
         with self.assertRaises(NameError):
             _ = prototypes.Prototypes1D(input_dim=1)
 
-    def test_prototypes1d_init_with_num_classes_1(self):
+    def test_prototypes1d_init_with_nclasses_1(self):
         with self.assertWarns(UserWarning):
-            _ = prototypes.Prototypes1D(num_classes=1, input_dim=1)
+            _ = prototypes.Prototypes1D(nclasses=1, input_dim=1)
 
     def test_prototypes1d_init_without_pdist(self):
         p1 = prototypes.Prototypes1D(
             input_dim=6,
-            num_classes=2,
+            nclasses=2,
             prototypes_per_class=4,
             prototype_initializer="ones",
         )
@@ -59,7 +60,7 @@ class TestPrototypes(unittest.TestCase):
         with self.assertWarns(UserWarning):
             _ = prototypes.Prototypes1D(
                 input_dim=3,
-                num_classes=2,
+                nclasses=2,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=None,
@@ -80,7 +81,7 @@ class TestPrototypes(unittest.TestCase):
 
     def test_prototypes1d_init_without_inputdim_with_data(self):
         _ = prototypes.Prototypes1D(
-            num_classes=2,
+            nclasses=2,
             prototypes_per_class=1,
             prototype_initializer="stratified_mean",
             data=[[[1.0], [0.0]], [1, 0]],
@@ -88,7 +89,7 @@ class TestPrototypes(unittest.TestCase):
 
     def test_prototypes1d_init_with_int_data(self):
         _ = prototypes.Prototypes1D(
-            num_classes=2,
+            nclasses=2,
             prototypes_per_class=1,
             prototype_initializer="stratified_mean",
             data=[[[1], [0]], [1, 0]],
@@ -97,7 +98,7 @@ class TestPrototypes(unittest.TestCase):
     def test_prototypes1d_init_one_hot_without_data(self):
         _ = prototypes.Prototypes1D(
             input_dim=1,
-            num_classes=2,
+            nclasses=2,
             prototypes_per_class=1,
             prototype_initializer="stratified_mean",
             data=None,
@@ -111,7 +112,7 @@ class TestPrototypes(unittest.TestCase):
         with self.assertRaises(ValueError):
             _ = prototypes.Prototypes1D(
                 input_dim=1,
-                num_classes=2,
+                nclasses=2,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=([[0.0], [1.0]], [[0, 1], [1, 0]]),
@@ -125,7 +126,7 @@ class TestPrototypes(unittest.TestCase):
         with self.assertRaises(ValueError):
             _ = prototypes.Prototypes1D(
                 input_dim=1,
-                num_classes=2,
+                nclasses=2,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=([[0.0], [1.0]], [0, 1]),
@@ -140,7 +141,7 @@ class TestPrototypes(unittest.TestCase):
         with self.assertRaises(ValueError):
             _ = prototypes.Prototypes1D(
                 input_dim=1,
-                num_classes=2,
+                nclasses=2,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=([[0.0], [1.0]], [[0], [1]]),
@@ -150,7 +151,7 @@ class TestPrototypes(unittest.TestCase):
     def test_prototypes1d_init_with_int_dtype(self):
         with self.assertRaises(RuntimeError):
             _ = prototypes.Prototypes1D(
-                num_classes=2,
+                nclasses=2,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=[[[1], [0]], [1, 0]],
@@ -160,7 +161,7 @@ class TestPrototypes(unittest.TestCase):
     def test_prototypes1d_inputndim_with_data(self):
         with self.assertRaises(ValueError):
             _ = prototypes.Prototypes1D(input_dim=1,
-                                        num_classes=1,
+                                        nclasses=1,
                                         prototypes_per_class=1,
                                         data=[[1.0], [1]])
 
@@ -168,20 +169,20 @@ class TestPrototypes(unittest.TestCase):
         with self.assertRaises(ValueError):
             _ = prototypes.Prototypes1D(
                 input_dim=2,
-                num_classes=2,
+                nclasses=2,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=[[[1.0], [0.0]], [1, 0]],
             )
 
-    def test_prototypes1d_num_classes_with_data(self):
-        """Test ValueError raise if provided `num_classes` is not the same
+    def test_prototypes1d_nclasses_with_data(self):
+        """Test ValueError raise if provided `nclasses` is not the same
         as the one computed from the provided `data`.
         """
         with self.assertRaises(ValueError):
             _ = prototypes.Prototypes1D(
                 input_dim=1,
-                num_classes=1,
+                nclasses=1,
                 prototypes_per_class=1,
                 prototype_initializer="stratified_mean",
                 data=[[[1.0], [2.0]], [1, 2]],
@@ -219,7 +220,7 @@ class TestPrototypes(unittest.TestCase):
 
         p1 = prototypes.Prototypes1D(
             input_dim=99,
-            num_classes=2,
+            nclasses=2,
             prototypes_per_class=1,
             prototype_initializer=my_initializer,
         )