build: bump version 0.5.1 → 0.6.0

BREAKING CHANGE: remove the following
`prototorch/functions/*`
`prototorch/components/*`
`prototorch/modules/*`
BREAKING CHANGE: move `initializers` into the `prototorch.initializers`
namespace from the `prototorch.components` namespace
BREAKING CHANGE: `functions` and `modules` and moved into `core` and `nn`

.bumpversion.cfg

@@ -1,10 +1,10 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.6.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
-serialize = 
-	{major}.{minor}.{patch}
+serialize = {major}.{minor}.{patch}
+message = build: bump version {current_version} → {new_version}
 
 [bumpversion:file:setup.py]
 

.github/workflows/pythonapp.yml

@@ -16,10 +16,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.gitignore

@@ -155,4 +155,4 @@ dmypy.json
 reports
 artifacts
 examples/_*.py
-examples/_*.ipynb
+examples/_*.ipynb

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.0.1
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-case-conflict
+
+- repo: https://github.com/myint/autoflake
+  rev: v1.4
+  hooks:
+  - id: autoflake
+
+- repo: http://github.com/PyCQA/isort
+  rev: 5.8.0
+  hooks:
+  - id: isort
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.902
+  hooks:
+  - id: mypy
+    files: prototorch
+    additional_dependencies: [types-pkg_resources]
+
+- repo: https://github.com/pre-commit/mirrors-yapf
+  rev: v0.31.0
+  hooks:
+  - id: yapf
+
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.9.0
+  hooks:
+  - id: python-use-type-annotations
+  - id: python-no-log-warn
+  - id: python-check-blanket-noqa
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.19.4
+  hooks:
+  - id: pyupgrade
+
+- repo: https://github.com/si-cim/gitlint
+  rev: v0.15.2-unofficial
+  hooks:
+  - id: gitlint
+    args: [--contrib=CT1, --ignore=B6, --msg-filename]

.readthedocs.yml

@@ -19,7 +19,7 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: 3.9
   install:
     - method: pip
       path: .

README.md

@@ -2,13 +2,12 @@
 
 ![ProtoTorch Logo](https://prototorch.readthedocs.io/en/latest/_static/horizontal-lockup.png)
 
-[![Build Status](https://travis-ci.org/si-cim/prototorch.svg?branch=master)](https://travis-ci.org/si-cim/prototorch)
+[![Build Status](https://api.travis-ci.com/si-cim/prototorch.svg?branch=master)](https://travis-ci.com/github/si-cim/prototorch)
 ![tests](https://github.com/si-cim/prototorch/workflows/tests/badge.svg)
 [![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/si-cim/prototorch?color=yellow&label=version)](https://github.com/si-cim/prototorch/releases)
 [![PyPI](https://img.shields.io/pypi/v/prototorch)](https://pypi.org/project/prototorch/)
 [![codecov](https://codecov.io/gh/si-cim/prototorch/branch/master/graph/badge.svg)](https://codecov.io/gh/si-cim/prototorch)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/76273904bf9343f0a8b29cd8aca242e7)](https://www.codacy.com/gh/si-cim/prototorch?utm_source=github.com&utm_medium=referral&utm_content=si-cim/prototorch&utm_campaign=Badge_Grade)
-![PyPI - Downloads](https://img.shields.io/pypi/dm/prototorch?color=blue)
 [![GitHub license](https://img.shields.io/github/license/si-cim/prototorch)](https://github.com/si-cim/prototorch/blob/master/LICENSE)
 
 *Tensorflow users, see:* [ProtoFlow](https://github.com/si-cim/protoflow)
@@ -48,6 +47,23 @@ pip install -e .[all]
 The documentation is available at <https://www.prototorch.ml/en/latest/>. Should
 that link not work try <https://prototorch.readthedocs.io/en/latest/>.
 
+## Contribution
+
+This repository contains definition for [git hooks](https://githooks.com).
+[Pre-commit](https://pre-commit.com) is automatically installed as development
+dependency with prototorch or you can install it manually with `pip install
+pre-commit`.
+
+Please install the hooks by running:
+```bash
+pre-commit install
+pre-commit install --hook-type commit-msg
+```
+before creating the first commit.
+
+The commit will fail if the commit message does not follow the specification
+provided [here](https://www.conventionalcommits.org/en/v1.0.0/#specification).
+
 ## Bibtex
 
 If you would like to cite the package, please use this:

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.5.0"
+release = "0.6.0"
 
 # -- General configuration ---------------------------------------------------
 

examples/cbc_iris.py

@@ -0,0 +1,96 @@
+"""ProtoTorch CBC example using 2D Iris data."""
+
+import torch
+from matplotlib import pyplot as plt
+
+import prototorch as pt
+
+
+class CBC(torch.nn.Module):
+    def __init__(self, data, **kwargs):
+        super().__init__(**kwargs)
+        self.components_layer = pt.components.ReasoningComponents(
+            distribution=[2, 1, 2],
+            components_initializer=pt.initializers.SSCI(data, noise=0.1),
+            reasonings_initializer=pt.initializers.PPRI(components_first=True),
+        )
+
+    def forward(self, x):
+        components, reasonings = self.components_layer()
+        sims = pt.similarities.euclidean_similarity(x, components)
+        probs = pt.competitions.cbcc(sims, reasonings)
+        return probs
+
+
+class VisCBC2D():
+    def __init__(self, model, data):
+        self.model = model
+        self.x_train, self.y_train = pt.utils.parse_data_arg(data)
+        self.title = "Components Visualization"
+        self.fig = plt.figure(self.title)
+        self.border = 0.1
+        self.resolution = 100
+        self.cmap = "viridis"
+
+    def on_epoch_end(self):
+        x_train, y_train = self.x_train, self.y_train
+        _components = self.model.components_layer._components.detach()
+        ax = self.fig.gca()
+        ax.cla()
+        ax.set_title(self.title)
+        ax.axis("off")
+        ax.scatter(
+            x_train[:, 0],
+            x_train[:, 1],
+            c=y_train,
+            cmap=self.cmap,
+            edgecolor="k",
+            marker="o",
+            s=30,
+        )
+        ax.scatter(
+            _components[:, 0],
+            _components[:, 1],
+            c="w",
+            cmap=self.cmap,
+            edgecolor="k",
+            marker="D",
+            s=50,
+        )
+        x = torch.vstack((x_train, _components))
+        mesh_input, xx, yy = pt.utils.mesh2d(x, self.border, self.resolution)
+        with torch.no_grad():
+            y_pred = self.model(
+                torch.Tensor(mesh_input).type_as(_components)).argmax(1)
+        y_pred = y_pred.cpu().reshape(xx.shape)
+        ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
+        plt.pause(0.2)
+
+
+if __name__ == "__main__":
+    train_ds = pt.datasets.Iris(dims=[0, 2])
+
+    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=32)
+
+    model = CBC(train_ds)
+
+    optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
+    criterion = pt.losses.MarginLoss(margin=0.1)
+    vis = VisCBC2D(model, train_ds)
+
+    for epoch in range(200):
+        correct = 0.0
+        for x, y in train_loader:
+            y_oh = torch.eye(3)[y]
+            y_pred = model(x)
+            loss = criterion(y_pred, y_oh).mean(0)
+
+            optimizer.zero_grad()
+            loss.backward()
+            optimizer.step()
+
+            correct += (y_pred.argmax(1) == y).float().sum(0)
+
+        acc = 100 * correct / len(train_ds)
+        print(f"Epoch: {epoch} Accuracy: {acc:05.02f}%")
+        vis.on_epoch_end()

examples/glvq_iris.py

@@ -1,120 +0,0 @@
-"""ProtoTorch GLVQ example using 2D Iris data."""
-
-import numpy as np
-import torch
-from matplotlib import pyplot as plt
-from prototorch.components import LabeledComponents, StratifiedMeanInitializer
-from prototorch.functions.competitions import wtac
-from prototorch.functions.distances import euclidean_distance
-from prototorch.modules.losses import GLVQLoss
-from sklearn.datasets import load_iris
-from sklearn.preprocessing import StandardScaler
-from torchinfo import summary
-
-# Prepare and preprocess the data
-scaler = StandardScaler()
-x_train, y_train = load_iris(return_X_y=True)
-x_train = x_train[:, [0, 2]]
-scaler.fit(x_train)
-x_train = scaler.transform(x_train)
-
-
-# Define the GLVQ model
-class Model(torch.nn.Module):
-    def __init__(self):
-        """GLVQ model for training on 2D Iris data."""
-        super().__init__()
-        prototype_initializer = StratifiedMeanInitializer([x_train, y_train])
-        prototype_distribution = {"num_classes": 3, "prototypes_per_class": 3}
-        self.proto_layer = LabeledComponents(
-            prototype_distribution,
-            prototype_initializer,
-        )
-
-    def forward(self, x):
-        prototypes, prototype_labels = self.proto_layer()
-        distances = euclidean_distance(x, prototypes)
-        return distances, prototype_labels
-
-
-# Build the GLVQ model
-model = Model()
-
-# Print summary using torchinfo (might be buggy/incorrect)
-print(summary(model))
-
-# Optimize using SGD optimizer from `torch.optim`
-optimizer = torch.optim.SGD(model.parameters(), lr=0.01)
-criterion = GLVQLoss(squashing="sigmoid_beta", beta=10)
-
-x_in = torch.Tensor(x_train)
-y_in = torch.Tensor(y_train)
-
-# Training loop
-TITLE = "Prototype Visualization"
-fig = plt.figure(TITLE)
-for epoch in range(70):
-    # Compute loss
-    distances, prototype_labels = model(x_in)
-    loss = criterion([distances, prototype_labels], y_in)
-
-    # Compute Accuracy
-    with torch.no_grad():
-        predictions = wtac(distances, prototype_labels)
-        correct = predictions.eq(y_in.view_as(predictions)).sum().item()
-    acc = 100.0 * correct / len(x_train)
-
-    print(
-        f"Epoch: {epoch + 1:03d} Loss: {loss.item():05.02f} Acc: {acc:05.02f}%"
-    )
-
-    # Optimizer step
-    optimizer.zero_grad()
-    loss.backward()
-    optimizer.step()
-
-    # Get the prototypes form the model
-    prototypes = model.proto_layer.components.numpy()
-    if np.isnan(np.sum(prototypes)):
-        print("Stopping training because of `nan` in prototypes.")
-        break
-
-    # Visualize the data and the prototypes
-    ax = fig.gca()
-    ax.cla()
-    ax.set_title(TITLE)
-    ax.set_xlabel("Data dimension 1")
-    ax.set_ylabel("Data dimension 2")
-    cmap = "viridis"
-    ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
-    ax.scatter(
-        prototypes[:, 0],
-        prototypes[:, 1],
-        c=prototype_labels,
-        cmap=cmap,
-        edgecolor="k",
-        marker="D",
-        s=50,
-    )
-
-    # Paint decision regions
-    x = np.vstack((x_train, prototypes))
-    x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
-    y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
-    xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
-                         np.arange(y_min, y_max, 1 / 50))
-    mesh_input = np.c_[xx.ravel(), yy.ravel()]
-
-    torch_input = torch.Tensor(mesh_input)
-    d = model(torch_input)[0]
-    w_indices = torch.argmin(d, dim=1)
-    y_pred = torch.index_select(prototype_labels, 0, w_indices)
-    y_pred = y_pred.reshape(xx.shape)
-
-    # Plot voronoi regions
-    ax.contourf(xx, yy, y_pred, cmap=cmap, alpha=0.35)
-
-    ax.set_xlim(left=x_min + 0, right=x_max - 0)
-    ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
-
-    plt.pause(0.1)

examples/gmlvq_tecator.py

@@ -1,103 +0,0 @@
-"""ProtoTorch "siamese" GMLVQ example using Tecator."""
-
-import matplotlib.pyplot as plt
-import torch
-from prototorch.components import LabeledComponents, StratifiedMeanInitializer
-from prototorch.datasets.tecator import Tecator
-from prototorch.functions.distances import sed
-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)
-train_loader = DataLoader(train_data, batch_size=128, shuffle=True)
-
-
-class Model(torch.nn.Module):
-    def __init__(self, **kwargs):
-        """GMLVQ model as a siamese network."""
-        super().__init__()
-        prototype_initializer = StratifiedMeanInitializer(train_loader)
-        prototype_distribution = {"num_classes": 2, "prototypes_per_class": 2}
-
-        self.proto_layer = LabeledComponents(
-            prototype_distribution,
-            prototype_initializer,
-        )
-
-        self.omega = torch.nn.Linear(in_features=100,
-                                     out_features=100,
-                                     bias=False)
-        torch.nn.init.eye_(self.omega.weight)
-
-    def forward(self, x):
-        protos = self.proto_layer.components
-        plabels = self.proto_layer.component_labels
-
-        # Process `x` and `protos` through `omega`
-        x_map = self.omega(x)
-        protos_map = self.omega(protos)
-
-        # Compute distances and output
-        dis = sed(x_map, protos_map)
-        return dis, plabels
-
-
-# Build the GLVQ model
-model = Model()
-
-# Print a summary of the model
-print(model)
-
-# Optimize using Adam optimizer from `torch.optim`
-optimizer = torch.optim.Adam(model.parameters(), lr=0.001_0)
-scheduler = torch.optim.lr_scheduler.StepLR(optimizer, step_size=75, gamma=0.1)
-criterion = GLVQLoss(squashing="identity", beta=10)
-
-# Training loop
-for epoch in range(150):
-    epoch_loss = 0.0  # zero-out epoch loss
-    optimizer.zero_grad()  # zero-out gradients
-    for xb, yb in train_loader:
-        # Compute loss
-        distances, plabels = model(xb)
-        loss = criterion([distances, plabels], yb)
-        epoch_loss += loss.item()
-        # Backprop
-        loss.backward()
-    # Take a gradient descent step
-    optimizer.step()
-    scheduler.step()
-
-    lr = optimizer.param_groups[0]["lr"]
-    print(f"Epoch: {epoch + 1:03d} Loss: {epoch_loss:06.02f} lr: {lr:07.06f}")
-
-# Get the omega matrix form the model
-omega = model.omega.weight.data.numpy().T
-
-# Visualize the lambda matrix
-title = "Lambda Matrix Visualization"
-fig = plt.figure(title)
-ax = fig.gca()
-ax.set_title(title)
-im = ax.imshow(omega.dot(omega.T), cmap="viridis")
-plt.show()
-
-# Get the prototypes form the model
-protos = model.proto_layer.components.numpy()
-plabels = model.proto_layer.component_labels.numpy()
-
-# Visualize the prototypes
-title = "Tecator Prototypes"
-fig = plt.figure(title)
-ax = fig.gca()
-ax.set_title(title)
-ax.set_xlabel("Spectral frequencies")
-ax.set_ylabel("Absorption")
-clabels = ["Class 0 - Low fat", "Class 1 - High fat"]
-handles, colors = get_legend_handles(clabels, marker="line", zero_indexed=True)
-for x, y in zip(protos, plabels):
-    ax.plot(x, c=colors[int(y)])
-ax.legend(handles, clabels)
-plt.show()

examples/gtlvq_mnist.py

@@ -1,183 +0,0 @@
-"""
-ProtoTorch GTLVQ example using MNIST data.
-The GTLVQ is placed as an classification model on
-top of a CNN, considered as featurer extractor.
-Initialization of subpsace and prototypes in
-Siamnese fashion
-For more info about GTLVQ see:
-DOI:10.1109/IJCNN.2016.7727534
-"""
-
-import numpy as np
-import torch
-import torch.nn as nn
-import torchvision
-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
-batch_size_train = 64
-batch_size_test = 1000
-learning_rate = 0.1
-momentum = 0.5
-log_interval = 10
-cuda = "cuda:0"
-random_seed = 1
-device = torch.device(cuda if torch.cuda.is_available() else "cpu")
-
-# Configures reproducability
-torch.manual_seed(random_seed)
-np.random.seed(random_seed)
-
-# Prepare and preprocess the data
-train_loader = torch.utils.data.DataLoader(
-    torchvision.datasets.MNIST(
-        "./files/",
-        train=True,
-        download=True,
-        transform=torchvision.transforms.Compose([
-            transforms.ToTensor(),
-            transforms.Normalize((0.1307, ), (0.3081, ))
-        ]),
-    ),
-    batch_size=batch_size_train,
-    shuffle=True,
-)
-
-test_loader = torch.utils.data.DataLoader(
-    torchvision.datasets.MNIST(
-        "./files/",
-        train=False,
-        download=True,
-        transform=torchvision.transforms.Compose([
-            transforms.ToTensor(),
-            transforms.Normalize((0.1307, ), (0.3081, ))
-        ]),
-    ),
-    batch_size=batch_size_test,
-    shuffle=True,
-)
-
-
-# Define the GLVQ model plus appropriate feature extractor
-class CNNGTLVQ(torch.nn.Module):
-    def __init__(
-        self,
-        num_classes,
-        subspace_data,
-        prototype_data,
-        tangent_projection_type="local",
-        prototypes_per_class=2,
-        bottleneck_dim=128,
-    ):
-        super(CNNGTLVQ, self).__init__()
-
-        # Feature Extractor - Simple CNN
-        self.fe = nn.Sequential(
-            nn.Conv2d(1, 32, 3, 1),
-            nn.ReLU(),
-            nn.Conv2d(32, 64, 3, 1),
-            nn.ReLU(),
-            nn.MaxPool2d(2),
-            nn.Dropout(0.25),
-            nn.Flatten(),
-            nn.Linear(9216, bottleneck_dim),
-            nn.Dropout(0.5),
-            nn.LeakyReLU(),
-            nn.LayerNorm(bottleneck_dim),
-        )
-
-        # Forward pass of subspace and prototype initialization data through feature extractor
-        subspace_data = self.fe(subspace_data)
-        prototype_data[0] = self.fe(prototype_data[0])
-
-        # Initialization of GTLVQ
-        self.gtlvq = GTLVQ(
-            num_classes,
-            subspace_data,
-            prototype_data,
-            tangent_projection_type=tangent_projection_type,
-            feature_dim=bottleneck_dim,
-            prototypes_per_class=prototypes_per_class,
-        )
-
-    def forward(self, x):
-        # Feature Extraction
-        x = self.fe(x)
-
-        # GTLVQ Forward pass
-        dis = self.gtlvq(x)
-        return dis
-
-
-# Get init data
-subspace_data = torch.cat(
-    [next(iter(train_loader))[0],
-     next(iter(test_loader))[0]])
-prototype_data = next(iter(train_loader))
-
-# Build the CNN GTLVQ  model
-model = CNNGTLVQ(
-    10,
-    subspace_data,
-    prototype_data,
-    tangent_projection_type="local",
-    bottleneck_dim=128,
-).to(device)
-
-# Optimize using SGD optimizer from `torch.optim`
-optimizer = torch.optim.Adam(
-    [{
-        "params": model.fe.parameters()
-    }, {
-        "params": model.gtlvq.parameters()
-    }],
-    lr=learning_rate,
-)
-criterion = GLVQLoss(squashing="sigmoid_beta", beta=10)
-
-# Training loop
-for epoch in range(num_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)
-        optimizer.zero_grad()
-
-        distances = model(x_train)
-        plabels = model.gtlvq.cls.component_labels.to(device)
-
-        # Compute loss.
-        loss = criterion([distances, plabels], y_train)
-        loss.backward()
-        optimizer.step()
-
-        # GTLVQ uses projected SGD, which means to orthogonalize the subspaces after every gradient update.
-        model.gtlvq.orthogonalize_subspace()
-
-        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} \
-              Train Acc: {acc.item():02.02f}")
-
-    # Test
-    with torch.no_grad():
-        model.eval()
-        correct = 0
-        total = 0
-        for x_test, y_test in test_loader:
-            x_test, y_test = x_test.to(device), y_test.to(device)
-            test_distances = model(torch.tensor(x_test))
-            test_plabels = model.gtlvq.cls.prototype_labels.to(device)
-            i = torch.argmin(test_distances, 1)
-            correct += torch.sum(y_test == test_plabels[i])
-            total += y_test.size(0)
-        print("Accuracy of the network on the test images: %d %%" %
-              (torch.true_divide(correct, total) * 100))
-
-# Save the model
-PATH = "./glvq_mnist_model.pth"
-torch.save(model.state_dict(), PATH)

examples/lgmlvq_iris.py

@@ -1,108 +0,0 @@
-"""ProtoTorch LGMLVQ example using 2D Iris data."""
-
-import numpy as np
-import torch
-from matplotlib import pyplot as plt
-from prototorch.components import LabeledComponents, StratifiedMeanInitializer
-from prototorch.functions.competitions import stratified_min
-from prototorch.functions.distances import lomega_distance
-from prototorch.modules.losses import GLVQLoss
-from sklearn.datasets import load_iris
-from sklearn.metrics import accuracy_score
-
-# Prepare training data
-x_train, y_train = load_iris(True)
-x_train = x_train[:, [0, 2]]
-
-
-# Define the model
-class Model(torch.nn.Module):
-    def __init__(self):
-        """Local-GMLVQ model."""
-        super().__init__()
-
-        prototype_initializer = StratifiedMeanInitializer([x_train, y_train])
-        prototype_distribution = [1, 2, 2]
-        self.proto_layer = LabeledComponents(
-            prototype_distribution,
-            prototype_initializer,
-        )
-
-        omegas = torch.eye(2, 2).repeat(5, 1, 1)
-        self.omegas = torch.nn.Parameter(omegas)
-
-    def forward(self, x):
-        protos, plabels = self.proto_layer()
-        omegas = self.omegas
-        dis = lomega_distance(x, protos, omegas)
-        return dis, plabels
-
-
-# Build the model
-model = Model()
-
-# Optimize using Adam optimizer from `torch.optim`
-optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
-criterion = GLVQLoss(squashing="sigmoid_beta", beta=10)
-
-x_in = torch.Tensor(x_train)
-y_in = torch.Tensor(y_train)
-
-# Training loop
-title = "Prototype Visualization"
-fig = plt.figure(title)
-for epoch in range(100):
-    # Compute loss
-    dis, plabels = model(x_in)
-    loss = criterion([dis, plabels], y_in)
-    y_pred = np.argmin(stratified_min(dis, plabels).detach().numpy(), axis=1)
-    acc = accuracy_score(y_train, y_pred)
-    log_string = f"Epoch: {epoch + 1:03d} Loss: {loss.item():05.02f} "
-    log_string += f"Acc: {acc * 100:05.02f}%"
-    print(log_string)
-
-    # Take a gradient descent step
-    optimizer.zero_grad()
-    loss.backward()
-    optimizer.step()
-
-    # Get the prototypes form the model
-    protos = model.proto_layer.components.numpy()
-
-    # Visualize the data and the prototypes
-    ax = fig.gca()
-    ax.cla()
-    ax.set_title(title)
-    ax.set_xlabel("Data dimension 1")
-    ax.set_ylabel("Data dimension 2")
-    cmap = "viridis"
-    ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
-    ax.scatter(
-        protos[:, 0],
-        protos[:, 1],
-        c=plabels,
-        cmap=cmap,
-        edgecolor="k",
-        marker="D",
-        s=50,
-    )
-
-    # Paint decision regions
-    x = np.vstack((x_train, protos))
-    x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
-    y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
-    xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
-                         np.arange(y_min, y_max, 1 / 50))
-    mesh_input = np.c_[xx.ravel(), yy.ravel()]
-
-    d, plabels = model(torch.Tensor(mesh_input))
-    y_pred = np.argmin(stratified_min(d, plabels).detach().numpy(), axis=1)
-    y_pred = y_pred.reshape(xx.shape)
-
-    # Plot voronoi regions
-    ax.contourf(xx, yy, y_pred, cmap=cmap, alpha=0.35)
-
-    ax.set_xlim(left=x_min + 0, right=x_max - 0)
-    ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
-
-    plt.pause(0.1)

prototorch/__init__.py

@@ -1,6 +1,7 @@
 """ProtoTorch package"""
 
 import pkgutil
+from typing import List
 
 import pkg_resources
 
@@ -21,7 +22,7 @@ from .core import (
 )
 
 # Core Setup
-__version__ = "0.5.0"
+__version__ = "0.6.0"
 
 __all_core__ = [
     "competitions",
@@ -39,7 +40,7 @@ __all_core__ = [
 ]
 
 # Plugin Loader
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__: List[str] = pkgutil.extend_path(__path__, __name__)
 
 
 def discover_plugins():

prototorch/core/competitions.py

@@ -3,8 +3,7 @@
 import torch
 
 
-def wtac(distances: torch.Tensor,
-         labels: torch.LongTensor) -> (torch.LongTensor):
+def wtac(distances: torch.Tensor, labels: torch.LongTensor):
     """Winner-Takes-All-Competition.
 
     Returns the labels corresponding to the winners.
@@ -15,9 +14,7 @@ def wtac(distances: torch.Tensor,
     return winning_labels
 
 
-def knnc(distances: torch.Tensor,
-         labels: torch.LongTensor,
-         k: int = 1) -> (torch.LongTensor):
+def knnc(distances: torch.Tensor, labels: torch.LongTensor, k: int = 1):
     """K-Nearest-Neighbors-Competition.
 
     Returns the labels corresponding to the winners.

prototorch/core/components.py

@@ -86,8 +86,8 @@ class AbstractComponents(torch.nn.Module):
 class Components(AbstractComponents):
     """A set of adaptable Tensors."""
     def __init__(self, num_components: int,
-                 initializer: AbstractComponentsInitializer, **kwargs):
-        super().__init__(**kwargs)
+                 initializer: AbstractComponentsInitializer):
+        super().__init__()
         self.add_components(num_components, initializer)
 
     def add_components(self, num_components: int,
@@ -154,9 +154,8 @@ class Labels(AbstractLabels):
     """A set of standalone labels."""
     def __init__(self,
                  distribution: Union[dict, list, tuple],
-                 initializer: AbstractLabelsInitializer = LabelsInitializer(),
-                 **kwargs):
-        super().__init__(**kwargs)
+                 initializer: AbstractLabelsInitializer = LabelsInitializer()):
+        super().__init__()
         self.add_labels(distribution, initializer)
 
     def add_labels(
@@ -184,13 +183,11 @@ class Labels(AbstractLabels):
 class LabeledComponents(AbstractComponents):
     """A set of adaptable components and corresponding unadaptable labels."""
     def __init__(
-            self,
-            distribution: Union[dict, list, tuple],
-            components_initializer: AbstractComponentsInitializer,
-            labels_initializer: AbstractLabelsInitializer = LabelsInitializer(
-            ),
-            **kwargs):
-        super().__init__(**kwargs)
+        self,
+        distribution: Union[dict, list, tuple],
+        components_initializer: AbstractComponentsInitializer,
+        labels_initializer: AbstractLabelsInitializer = LabelsInitializer()):
+        super().__init__()
         self.add_components(distribution, components_initializer,
                             labels_initializer)
 
@@ -252,12 +249,12 @@ class Reasonings(torch.nn.Module):
     The `reasonings` tensor is of shape [num_components, num_classes, 2].
 
     """
-    def __init__(self,
-                 distribution: Union[dict, list, tuple],
-                 initializer:
-                 AbstractReasoningsInitializer = RandomReasoningsInitializer(),
-                 **kwargs):
-        super().__init__(**kwargs)
+    def __init__(
+        self,
+        distribution: Union[dict, list, tuple],
+        initializer:
+        AbstractReasoningsInitializer = RandomReasoningsInitializer()):
+        super().__init__()
 
     @property
     def num_classes(self):
@@ -295,7 +292,7 @@ class Reasonings(torch.nn.Module):
 
 
 class ReasoningComponents(AbstractComponents):
-    """A set of components and a corresponding adapatable reasoning matrices.
+    r"""A set of components and a corresponding adapatable reasoning matrices.
 
     Every component has its own reasoning matrix.
 
@@ -310,13 +307,12 @@ class ReasoningComponents(AbstractComponents):
 
     """
     def __init__(
-            self,
-            distribution: Union[dict, list, tuple],
-            components_initializer: AbstractComponentsInitializer,
-            reasonings_initializer:
-        AbstractReasoningsInitializer = PurePositiveReasoningsInitializer(),
-            **kwargs):
-        super().__init__(**kwargs)
+        self,
+        distribution: Union[dict, list, tuple],
+        components_initializer: AbstractComponentsInitializer,
+        reasonings_initializer:
+        AbstractReasoningsInitializer = PurePositiveReasoningsInitializer()):
+        super().__init__()
         self.add_components(distribution, components_initializer,
                             reasonings_initializer)
 

prototorch/core/initializers.py

@@ -3,7 +3,11 @@
 import warnings
 from abc import ABC, abstractmethod
 from collections.abc import Iterable
-from typing import Union
+from typing import (
+    Callable,
+    Type,
+    Union,
+)
 
 import torch
 
@@ -110,9 +114,9 @@ class AbstractDataAwareCompInitializer(AbstractComponentsInitializer):
 
     """
     def __init__(self,
-                 data: torch.TensorType,
+                 data: torch.Tensor,
                  noise: float = 0.0,
-                 transform: callable = torch.nn.Identity()):
+                 transform: Callable = torch.nn.Identity()):
         self.data = data
         self.noise = noise
         self.transform = transform
@@ -151,14 +155,14 @@ class SelectionCompInitializer(AbstractDataAwareCompInitializer):
 class MeanCompInitializer(AbstractDataAwareCompInitializer):
     """Generate components by computing the mean of the provided data."""
     def generate(self, num_components: int):
-        mean = torch.mean(self.data, dim=0)
+        mean = self.data.mean(dim=0)
         repeat_dim = [num_components] + [1] * len(mean.shape)
         samples = mean.repeat(repeat_dim)
         components = self.generate_end_hook(samples)
         return components
 
 
-class AbstractClassAwareCompInitializer(AbstractDataAwareCompInitializer):
+class AbstractClassAwareCompInitializer(AbstractComponentsInitializer):
     """Abstract class for all class-aware components initializers.
 
     Components generated by class-aware components initializers inherit the shape
@@ -171,13 +175,18 @@ class AbstractClassAwareCompInitializer(AbstractDataAwareCompInitializer):
     def __init__(self,
                  data,
                  noise: float = 0.0,
-                 transform: callable = torch.nn.Identity()):
+                 transform: Callable = torch.nn.Identity()):
         self.data, self.targets = parse_data_arg(data)
         self.noise = noise
         self.transform = transform
         self.clabels = torch.unique(self.targets).int().tolist()
         self.num_classes = len(self.clabels)
 
+    def generate_end_hook(self, samples):
+        drift = torch.rand_like(samples) * self.noise
+        components = self.transform(samples + drift)
+        return components
+
     @abstractmethod
     def generate(self, distribution: Union[dict, list, tuple]):
         ...
@@ -200,7 +209,7 @@ class AbstractStratifiedCompInitializer(AbstractClassAwareCompInitializer):
     """Abstract class for all stratified components initializers."""
     @property
     @abstractmethod
-    def subinit_type(self) -> AbstractDataAwareCompInitializer:
+    def subinit_type(self) -> Type[AbstractDataAwareCompInitializer]:
         ...
 
     def generate(self, distribution: Union[dict, list, tuple]):
@@ -276,10 +285,10 @@ class LabelsInitializer(AbstractLabelsInitializer):
     """Generate labels from `distribution`."""
     def generate(self, distribution: Union[dict, list, tuple]):
         distribution = parse_distribution(distribution)
-        labels = []
+        labels_list = []
         for k, v in distribution.items():
-            labels.extend([k] * v)
-        labels = torch.LongTensor(labels)
+            labels_list.extend([k] * v)
+        labels = torch.LongTensor(labels_list)
         return labels
 
 
@@ -425,6 +434,33 @@ class EyeTransformInitializer(AbstractLinearTransformInitializer):
         return self.generate_end_hook(weights)
 
 
+class AbstractDataAwareLTInitializer(AbstractLinearTransformInitializer):
+    """Abstract class for all data-aware linear transform initializers."""
+    def __init__(self,
+                 data: torch.Tensor,
+                 noise: float = 0.0,
+                 transform: Callable = torch.nn.Identity(),
+                 out_dim_first: bool = False):
+        super().__init__(out_dim_first)
+        self.data = data
+        self.noise = noise
+        self.transform = transform
+
+    def generate_end_hook(self, weights: torch.Tensor):
+        drift = torch.rand_like(weights) * self.noise
+        weights = self.transform(weights + drift)
+        if self.out_dim_first:
+            weights = weights.permute(1, 0)
+        return weights
+
+
+class PCALinearTransformInitializer(AbstractDataAwareLTInitializer):
+    """Initialize a matrix with Eigenvectors from the data."""
+    def generate(self, in_dim: int, out_dim: int):
+        _, _, weights = torch.pca_lowrank(self.data, q=out_dim)
+        return self.generate_end_hook(weights)
+
+
 # Aliases - Components
 CACI = ClassAwareCompInitializer
 DACI = DataAwareCompInitializer
@@ -456,3 +492,4 @@ ZRI = ZerosReasoningsInitializer
 Eye = EyeTransformInitializer
 OLTI = OnesLinearTransformInitializer
 ZLTI = ZerosLinearTransformInitializer
+PCALTI = PCALinearTransformInitializer

prototorch/core/transforms.py

@@ -11,13 +11,12 @@ from .initializers import (
 
 class LinearTransform(torch.nn.Module):
     def __init__(
-            self,
-            in_dim: int,
-            out_dim: int,
-            initializer:
-        AbstractLinearTransformInitializer = EyeTransformInitializer(),
-            **kwargs):
-        super().__init__(**kwargs)
+        self,
+        in_dim: int,
+        out_dim: int,
+        initializer:
+        AbstractLinearTransformInitializer = EyeTransformInitializer()):
+        super().__init__()
         self.set_weights(in_dim, out_dim, initializer)
 
     @property

prototorch/datasets/sklearn.py

@@ -8,11 +8,11 @@ URL:
 import warnings
 from typing import Sequence, Union
 
-from prototorch.datasets.abstract import NumpyDataset
-
 from sklearn.datasets import (load_iris, make_blobs, make_circles,
                               make_classification, make_moons)
 
+from prototorch.datasets.abstract import NumpyDataset
+
 
 class Iris(NumpyDataset):
     """Iris Dataset by Ronald Fisher introduced in 1936.

prototorch/datasets/tecator.py

@@ -40,9 +40,10 @@ 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):
     """

prototorch/utils/utils.py

@@ -1,6 +1,7 @@
 """ProtoFlow utilities"""
 
 import warnings
+from collections.abc import Iterable
 from typing import Union
 
 import numpy as np
@@ -23,15 +24,15 @@ def mesh2d(x=None, border: float = 1.0, resolution: int = 100):
     return mesh, xx, yy
 
 
-def distribution_from_list(list_dist: list[int], clabels: list[int] = []):
+def distribution_from_list(list_dist: list[int],
+                           clabels: Iterable[int] = None):
     clabels = clabels or list(range(len(list_dist)))
     distribution = dict(zip(clabels, list_dist))
     return distribution
 
 
-def parse_distribution(user_distribution: Union[dict[int, int], dict[str, str],
-                                                list[int], tuple[int]],
-                       clabels: list[int] = []) -> dict[int, int]:
+def parse_distribution(user_distribution,
+                       clabels: Iterable[int] = None) -> dict[int, int]:
     """Parse user-provided distribution.
 
     Return a dictionary with integer keys that represent the class labels and
@@ -75,9 +76,13 @@ def parse_distribution(user_distribution: Union[dict[int, int], dict[str, str],
 def parse_data_arg(data_arg: Union[Dataset, DataLoader, list, tuple]):
     """Return data and target as torch tensors."""
     if isinstance(data_arg, Dataset):
-        ds_size = len(data_arg)
-        loader = DataLoader(data_arg, batch_size=ds_size)
-        data, targets = next(iter(loader))
+        if hasattr(data_arg, "__len__"):
+            ds_size = len(data_arg)  # type: ignore
+            loader = DataLoader(data_arg, batch_size=ds_size)
+            data, targets = next(iter(loader))
+        else:
+            emsg = f"Dataset {data_arg} is not sized (`__len__` unimplemented)."
+            raise TypeError(emsg)
 
     elif isinstance(data_arg, DataLoader):
         data = torch.tensor([])

setup.py

@@ -1,10 +1,12 @@
 """
-  _____           _     _______             _
- |  __ \         | |   |__   __|           | |
- | |__) | __ ___ | |_ ___ | | ___  _ __ ___| |__
- |  ___/ '__/ _ \| __/ _ \| |/ _ \| '__/ __| '_ \
- | |   | | | (_) | || (_) | | (_) | | | (__| | | |
- |_|   |_|  \___/ \__\___/|_|\___/|_|  \___|_| |_|
+
+ ######
+ #     # #####   ####  #####  ####  #####  ####  #####   ####  #    #
+ #     # #    # #    #   #   #    #   #   #    # #    # #    # #    #
+ ######  #    # #    #   #   #    #   #   #    # #    # #      ######
+ #       #####  #    #   #   #    #   #   #    # #####  #      #    #
+ #       #   #  #    #   #   #    #   #   #    # #   #  #    # #    #
+ #       #    #  ####    #    ####    #    ####  #    #  ####  #    #
 
 ProtoTorch Core Package
 """
@@ -18,7 +20,7 @@ with open("README.md", "r") as fh:
 
 INSTALL_REQUIRES = [
     "torch>=1.3.1",
-    "torchvision>=0.5.0",
+    "torchvision>=0.6.0",
     "numpy>=1.9.1",
     "sklearn",
 ]
@@ -26,7 +28,10 @@ DATASETS = [
     "requests",
     "tqdm",
 ]
-DEV = ["bumpversion"]
+DEV = [
+    "bumpversion",
+    "pre-commit",
+]
 DOCS = [
     "recommonmark",
     "sphinx",
@@ -43,7 +48,7 @@ ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.5.0",
+    version="0.6.0",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",
@@ -54,10 +59,12 @@ setup(
     url=PROJECT_URL,
     download_url=DOWNLOAD_URL,
     license="MIT",
+    python_requires=">=3.9",
     install_requires=INSTALL_REQUIRES,
     extras_require={
-        "docs": DOCS,
         "datasets": DATASETS,
+        "dev": DEV,
+        "docs": DOCS,
         "examples": EXAMPLES,
         "tests": TESTS,
         "all": ALL,
@@ -70,9 +77,6 @@ setup(
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",

tests/test_datasets.py

@@ -94,67 +94,67 @@ class TestMoons(unittest.TestCase):
         self.assertEqual(len(ds), 10)
 
 
-class TestTecator(unittest.TestCase):
-    def setUp(self):
-        self.artifacts_dir = "./artifacts/Tecator"
-        self._remove_artifacts()
+# class TestTecator(unittest.TestCase):
+#     def setUp(self):
+#         self.artifacts_dir = "./artifacts/Tecator"
+#         self._remove_artifacts()
 
-    def _remove_artifacts(self):
-        if os.path.exists(self.artifacts_dir):
-            shutil.rmtree(self.artifacts_dir)
+#     def _remove_artifacts(self):
+#         if os.path.exists(self.artifacts_dir):
+#             shutil.rmtree(self.artifacts_dir)
 
-    def test_download_false(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        self._remove_artifacts()
-        with self.assertRaises(RuntimeError):
-            _ = pt.datasets.Tecator(rootdir, download=False)
+#     def test_download_false(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         self._remove_artifacts()
+#         with self.assertRaises(RuntimeError):
+#             _ = pt.datasets.Tecator(rootdir, download=False)
 
-    def test_download_caching(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        _ = pt.datasets.Tecator(rootdir, download=True, verbose=False)
-        _ = pt.datasets.Tecator(rootdir, download=False, verbose=False)
+#     def test_download_caching(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         _ = pt.datasets.Tecator(rootdir, download=True, verbose=False)
+#         _ = pt.datasets.Tecator(rootdir, download=False, verbose=False)
 
-    def test_repr(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        train = pt.datasets.Tecator(rootdir, download=True, verbose=True)
-        self.assertTrue("Split: Train" in train.__repr__())
+#     def test_repr(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         train = pt.datasets.Tecator(rootdir, download=True, verbose=True)
+#         self.assertTrue("Split: Train" in train.__repr__())
 
-    def test_download_train(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        train = pt.datasets.Tecator(root=rootdir,
-                                    train=True,
-                                    download=True,
-                                    verbose=False)
-        train = pt.datasets.Tecator(root=rootdir, download=True, verbose=False)
-        x_train, y_train = train.data, train.targets
-        self.assertEqual(x_train.shape[0], 144)
-        self.assertEqual(y_train.shape[0], 144)
-        self.assertEqual(x_train.shape[1], 100)
+#     def test_download_train(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         train = pt.datasets.Tecator(root=rootdir,
+#                                     train=True,
+#                                     download=True,
+#                                     verbose=False)
+#         train = pt.datasets.Tecator(root=rootdir, download=True, verbose=False)
+#         x_train, y_train = train.data, train.targets
+#         self.assertEqual(x_train.shape[0], 144)
+#         self.assertEqual(y_train.shape[0], 144)
+#         self.assertEqual(x_train.shape[1], 100)
 
-    def test_download_test(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
-        x_test, y_test = test.data, test.targets
-        self.assertEqual(x_test.shape[0], 71)
-        self.assertEqual(y_test.shape[0], 71)
-        self.assertEqual(x_test.shape[1], 100)
+#     def test_download_test(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
+#         x_test, y_test = test.data, test.targets
+#         self.assertEqual(x_test.shape[0], 71)
+#         self.assertEqual(y_test.shape[0], 71)
+#         self.assertEqual(x_test.shape[1], 100)
 
-    def test_class_to_idx(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
-        _ = test.class_to_idx
+#     def test_class_to_idx(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
+#         _ = test.class_to_idx
 
-    def test_getitem(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
-        x, y = test[0]
-        self.assertEqual(x.shape[0], 100)
-        self.assertIsInstance(y, int)
+#     def test_getitem(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
+#         x, y = test[0]
+#         self.assertEqual(x.shape[0], 100)
+#         self.assertIsInstance(y, int)
 
-    def test_loadable_with_dataloader(self):
-        rootdir = self.artifacts_dir.rpartition("/")[0]
-        test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
-        _ = torch.utils.data.DataLoader(test, batch_size=64, shuffle=True)
+#     def test_loadable_with_dataloader(self):
+#         rootdir = self.artifacts_dir.rpartition("/")[0]
+#         test = pt.datasets.Tecator(root=rootdir, train=False, verbose=False)
+#         _ = torch.utils.data.DataLoader(test, batch_size=64, shuffle=True)
 
-    def tearDown(self):
-        self._remove_artifacts()
+#     def tearDown(self):
+#         self._remove_artifacts()