build: bump version 0.7.0 → 0.7.1

Necessary for different optimizer runs

.bumpversion.cfg

@@ -1,13 +1,13 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.7.1
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
 serialize = {major}.{minor}.{patch}
 message = build: bump version {current_version} → {new_version}
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
-[bumpversion:file:./prototorch/models/__init__.py]
+[bumpversion:file:./src/prototorch/models/__init__.py]
 
 [bumpversion:file:./docs/source/conf.py]

.codacy.yml

@@ -1,15 +0,0 @@
-# To validate the contents of your configuration file
-# run the following command in the folder where the configuration file is located:
-# codacy-analysis-cli validate-configuration --directory `pwd`
-# To analyse, run:
-# codacy-analysis-cli analyse --tool remark-lint --directory `pwd`
----
-engines:
-  pylintpython3:
-    exclude_paths:
-      - config/engines.yml
-  remark-lint:
-    exclude_paths:
-      - config/engines.yml
-exclude_paths:
-  - 'tests/**'

.codecov.yml

@@ -1,2 +0,0 @@
-comment:
-  require_changes: yes

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Steps to reproduce the behavior**
+1. ...
+2. Run script '...' or this snippet:
+```python
+import prototorch as pt
+
+...
+```
+3. See errors
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Observed behavior**
+A clear and concise description of what actually happened.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**System and version information**
+- OS: [e.g. Ubuntu 20.10]
+- ProtoTorch Version: [e.g. 0.4.0]
+- Python Version: [e.g. 3.9.5]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/examples.yml

@@ -0,0 +1,25 @@
+# Thi workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: examples
+
+on:
+  push:
+    paths:
+      - "examples/**.py"
+jobs:
+  cpu:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[all]
+      - name: Run examples
+        run: |
+          ./tests/test_examples.sh examples/

.github/workflows/pythonapp.yml

@@ -0,0 +1,75 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: tests
+
+on:
+  push:
+  pull_request:
+    branches: [master]
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[all]
+      - uses: pre-commit/action@v3.0.0
+  compatibility:
+    needs: style
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest]
+        exclude:
+          - os: windows-latest
+            python-version: "3.8"
+          - os: windows-latest
+            python-version: "3.9"
+          - os: windows-latest
+            python-version: "3.10"
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[all]
+      - name: Test with pytest
+        run: |
+          pytest
+  publish_pypi:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    needs: compatibility
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[all]
+          pip install build
+      - name: Build package
+        run: python -m build . -C verbose
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -2,52 +2,53 @@
 # 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/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    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: https://github.com/myint/autoflake
+    rev: v2.1.1
+    hooks:
+      - id: autoflake
 
-- repo: http://github.com/PyCQA/isort
-  rev: 5.8.0
-  hooks:
-  - id: isort
+  - repo: http://github.com/PyCQA/isort
+    rev: 5.12.0
+    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-mypy
+    rev: v1.3.0
+    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/mirrors-yapf
+    rev: v0.32.0
+    hooks:
+      - id: yapf
+        additional_dependencies: ["toml"]
 
-- 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/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    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/asottile/pyupgrade
+    rev: v3.7.0
+    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]
+  - repo: https://github.com/si-cim/gitlint
+    rev: v0.15.2-unofficial
+    hooks:
+      - id: gitlint
+        args: [--contrib=CT1, --ignore=B6, --msg-filename]

.travis.yml

@@ -1,25 +0,0 @@
-dist: bionic
-sudo: false
-language: python
-python: 3.9
-cache:
-  directories:
-  - "$HOME/.cache/pip"
-  - "./tests/artifacts"
-  - "$HOME/datasets"
-install:
-- pip install git+git://github.com/si-cim/prototorch@dev --progress-bar off
-- pip install .[all] --progress-bar off
-script:
-- coverage run -m pytest
-- ./tests/test_examples.sh examples/
-after_success:
-- bash <(curl -s https://codecov.io/bash)
-deploy:
-  provider: pypi
-  username: __token__
-  password:
-    secure: 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
-  on:
-    tags: true
-    skip_existing: true

README.md

@@ -1,6 +1,5 @@
 # ProtoTorch Models
 
-[![Build Status](https://api.travis-ci.com/si-cim/prototorch_models.svg?branch=main)](https://travis-ci.com/github/si-cim/prototorch_models)
 [![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/si-cim/prototorch_models?color=yellow&label=version)](https://github.com/si-cim/prototorch_models/releases)
 [![PyPI](https://img.shields.io/pypi/v/prototorch_models)](https://pypi.org/project/prototorch_models/)
 [![GitHub license](https://img.shields.io/github/license/si-cim/prototorch_models)](https://github.com/si-cim/prototorch_models/blob/master/LICENSE)
@@ -36,6 +35,7 @@ be available for use in your Python environment as `prototorch.models`.
 - Soft Learning Vector Quantization (SLVQ)
 - Robust Soft Learning Vector Quantization (RSLVQ)
 - Probabilistic Learning Vector Quantization (PLVQ)
+- Median-LVQ
 
 ### Other
 
@@ -51,7 +51,6 @@ be available for use in your Python environment as `prototorch.models`.
 
 ## Planned models
 
-- Median-LVQ
 - Generalized Tangent Learning Vector Quantization (GTLVQ)
 - Self-Incremental Learning Vector Quantization (SILVQ)
 

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.2.0"
+release = "0.7.1"
 
 # -- General configuration ---------------------------------------------------
 

examples/cbc_iris.py

@@ -1,25 +1,32 @@
 """CBC example using the Iris dataset."""
-
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
-import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import CBC, VisCBC2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
+
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
     train_ds = pt.datasets.Iris(dims=[0, 2])
 
-    # Reproducibility
-    pl.utilities.seed.seed_everything(seed=42)
-
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=32)
+    train_loader = DataLoader(train_ds, batch_size=32)
 
     # Hyperparameters
     hparams = dict(
@@ -30,23 +37,32 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.CBC(
+    model = CBC(
         hparams,
-        components_initializer=pt.initializers.SSCI(train_ds, noise=0.01),
-        reasonings_iniitializer=pt.initializers.
+        components_initializer=pt.initializers.SSCI(train_ds, noise=0.1),
+        reasonings_initializer=pt.initializers.
         PurePositiveReasoningsInitializer(),
     )
 
     # Callbacks
-    vis = pt.models.VisCBC2D(data=train_ds,
-                             title="CBC Iris Example",
-                             resolution=100,
-                             axis_off=True)
+    vis = VisCBC2D(
+        data=train_ds,
+        title="CBC Iris Example",
+        resolution=100,
+        axis_off=True,
+    )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
-        callbacks=[vis],
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        detect_anomaly=True,
+        log_every_n_steps=1,
+        max_epochs=1000,
     )
 
     # Training loop

examples/cli/README.md

@@ -1,8 +0,0 @@
-# Examples using Lightning CLI
-
-Examples in this folder use the experimental [Lightning CLI](https://pytorch-lightning.readthedocs.io/en/latest/common/lightning_cli.html).
-
-To use the example run
-```
-python gmlvq.py --config gmlvq.yaml
-```

examples/cli/gmlvq.py

@@ -1,20 +0,0 @@
-"""GMLVQ example using the MNIST dataset."""
-
-import torch
-from pytorch_lightning.utilities.cli import LightningCLI
-
-import prototorch as pt
-from prototorch.models import ImageGMLVQ
-from prototorch.models.abstract import PrototypeModel
-from prototorch.models.data import MNISTDataModule
-
-
-class ExperimentClass(ImageGMLVQ):
-    def __init__(self, hparams, **kwargs):
-        super().__init__(hparams,
-                         optimizer=torch.optim.Adam,
-                         prototype_initializer=pt.components.zeros(28 * 28),
-                         **kwargs)
-
-
-cli = LightningCLI(ImageGMLVQ, MNISTDataModule)

examples/cli/gmlvq.yaml

@@ -1,11 +0,0 @@
-model:
-  hparams:
-    input_dim: 784
-    latent_dim: 784
-    distribution:
-      num_classes: 10
-      prototypes_per_class: 2
-    proto_lr: 0.01
-    bb_lr: 0.01
-data:
-  batch_size: 32

examples/dynamic_pruning.py

@@ -1,30 +1,50 @@
 """Dynamically prune 'loser' prototypes in GLVQ-type models."""
 
 import argparse
+import logging
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import (
+    CELVQ,
+    PruneLoserPrototypes,
+    VisGLVQ2D,
+)
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
+
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
     num_classes = 4
     num_features = 2
     num_clusters = 1
-    train_ds = pt.datasets.Random(num_samples=500,
-                                  num_classes=num_classes,
-                                  num_features=num_features,
-                                  num_clusters=num_clusters,
-                                  separation=3.0,
-                                  seed=42)
+    train_ds = pt.datasets.Random(
+        num_samples=500,
+        num_classes=num_classes,
+        num_features=num_features,
+        num_clusters=num_clusters,
+        separation=3.0,
+        seed=42,
+    )
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=256)
+    train_loader = DataLoader(train_ds, batch_size=256)
 
     # Hyperparameters
     prototypes_per_class = num_clusters * 5
@@ -34,7 +54,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.CELVQ(
+    model = CELVQ(
         hparams,
         prototypes_initializer=pt.initializers.FVCI(2, 3.0),
     )
@@ -43,18 +63,18 @@ if __name__ == "__main__":
     model.example_input_array = torch.zeros(4, 2)
 
     # Summary
-    print(model)
+    logging.info(model)
 
     # Callbacks
-    vis = pt.models.VisGLVQ2D(train_ds)
-    pruning = pt.models.PruneLoserPrototypes(
+    vis = VisGLVQ2D(train_ds)
+    pruning = PruneLoserPrototypes(
         threshold=0.01,  # prune prototype if it wins less than 1%
         idle_epochs=20,  # pruning too early may cause problems
         prune_quota_per_epoch=2,  # prune at most 2 prototypes per epoch
         frequency=1,  # prune every epoch
         verbose=True,
     )
-    es = pl.callbacks.EarlyStopping(
+    es = EarlyStopping(
         monitor="train_loss",
         min_delta=0.001,
         patience=20,
@@ -64,17 +84,18 @@ if __name__ == "__main__":
     )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         callbacks=[
             vis,
             pruning,
             es,
         ],
-        progress_bar_refresh_rate=0,
-        terminate_on_nan=True,
-        weights_summary="full",
-        accelerator="ddp",
+        detect_anomaly=True,
+        log_every_n_steps=1,
+        max_epochs=1000,
     )
 
     # Training loop

examples/glvq_iris.py

@@ -1,23 +1,35 @@
 """GLVQ example using the Iris dataset."""
 
 import argparse
+import logging
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import GLVQ, VisGLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.optim.lr_scheduler import ExponentialLR
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=UserWarning)
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
 
 if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
     train_ds = pt.datasets.Iris(dims=[0, 2])
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=64)
+    train_loader = DataLoader(train_ds, batch_size=64, num_workers=4)
 
     # Hyperparameters
     hparams = dict(
@@ -29,7 +41,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.GLVQ(
+    model = GLVQ(
         hparams,
         optimizer=torch.optim.Adam,
         prototypes_initializer=pt.initializers.SMCI(train_ds),
@@ -41,15 +53,30 @@ if __name__ == "__main__":
     model.example_input_array = torch.zeros(4, 2)
 
     # Callbacks
-    vis = pt.models.VisGLVQ2D(data=train_ds)
+    vis = VisGLVQ2D(data=train_ds)
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
-        callbacks=[vis],
-        weights_summary="full",
-        accelerator="ddp",
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        max_epochs=100,
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop
     trainer.fit(model, train_loader)
+
+    # Manual save
+    trainer.save_checkpoint("./glvq_iris.ckpt")
+
+    # Load saved model
+    new_model = GLVQ.load_from_checkpoint(
+        checkpoint_path="./glvq_iris.ckpt",
+        strict=False,
+    )
+    logging.info(new_model)

examples/gmlvq_iris.py

@@ -0,0 +1,78 @@
+"""GMLVQ example using the Iris dataset."""
+
+import argparse
+import warnings
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import GMLVQ, VisGMLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.optim.lr_scheduler import ExponentialLR
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+if __name__ == "__main__":
+
+    # Reproducibility
+    seed_everything(seed=4)
+
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
+    args = parser.parse_args()
+
+    # Dataset
+    train_ds = pt.datasets.Iris()
+
+    # Dataloaders
+    train_loader = DataLoader(train_ds, batch_size=64)
+
+    # Hyperparameters
+    hparams = dict(
+        input_dim=4,
+        latent_dim=4,
+        distribution={
+            "num_classes": 3,
+            "per_class": 2
+        },
+        proto_lr=0.01,
+        bb_lr=0.01,
+    )
+
+    # Initialize the model
+    model = GMLVQ(
+        hparams,
+        optimizer=torch.optim.Adam,
+        prototypes_initializer=pt.initializers.SMCI(train_ds),
+        lr_scheduler=ExponentialLR,
+        lr_scheduler_kwargs=dict(gamma=0.99, verbose=False),
+    )
+
+    # Compute intermediate input and output sizes
+    model.example_input_array = torch.zeros(4, 4)
+
+    # Callbacks
+    vis = VisGMLVQ2D(data=train_ds)
+
+    # Setup trainer
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        max_epochs=100,
+        log_every_n_steps=1,
+        detect_anomaly=True,
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)
+
+    torch.save(model, "iris.pth")

examples/gmlvq_mnist.py

@@ -1,17 +1,33 @@
 """GMLVQ example using the MNIST dataset."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import (
+    ImageGMLVQ,
+    PruneLoserPrototypes,
+    VisImgComp,
+)
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
 from torchvision import transforms
 from torchvision.datasets import MNIST
 
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
 if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
@@ -33,12 +49,8 @@ if __name__ == "__main__":
     )
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds,
-                                               num_workers=0,
-                                               batch_size=256)
-    test_loader = torch.utils.data.DataLoader(test_ds,
-                                              num_workers=0,
-                                              batch_size=256)
+    train_loader = DataLoader(train_ds, num_workers=4, batch_size=256)
+    test_loader = DataLoader(test_ds, num_workers=4, batch_size=256)
 
     # Hyperparameters
     num_classes = 10
@@ -52,14 +64,14 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.ImageGMLVQ(
+    model = ImageGMLVQ(
         hparams,
         optimizer=torch.optim.Adam,
         prototypes_initializer=pt.initializers.SMCI(train_ds),
     )
 
     # Callbacks
-    vis = pt.models.VisImgComp(
+    vis = VisImgComp(
         data=train_ds,
         num_columns=10,
         show=False,
@@ -69,14 +81,14 @@ if __name__ == "__main__":
         embedding_data=200,
         flatten_data=False,
     )
-    pruning = pt.models.PruneLoserPrototypes(
+    pruning = PruneLoserPrototypes(
         threshold=0.01,
         idle_epochs=1,
         prune_quota_per_epoch=10,
         frequency=1,
         verbose=True,
     )
-    es = pl.callbacks.EarlyStopping(
+    es = EarlyStopping(
         monitor="train_loss",
         min_delta=0.001,
         patience=15,
@@ -85,16 +97,18 @@ if __name__ == "__main__":
     )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         callbacks=[
             vis,
             pruning,
-            # es,
+            es,
         ],
-        terminate_on_nan=True,
-        weights_summary=None,
-        # accelerator="ddp",
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/gmlvq_spiral.py

@@ -1,22 +1,39 @@
-"""GLVQ example using the spiral dataset."""
+"""GMLVQ example using the spiral dataset."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import (
+    GMLVQ,
+    PruneLoserPrototypes,
+    VisGLVQ2D,
+)
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
+
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
     train_ds = pt.datasets.Spiral(num_samples=500, noise=0.5)
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=256)
+    train_loader = DataLoader(train_ds, batch_size=256)
 
     # Hyperparameters
     num_classes = 2
@@ -32,19 +49,19 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.GMLVQ(
+    model = GMLVQ(
         hparams,
         optimizer=torch.optim.Adam,
         prototypes_initializer=pt.initializers.SSCI(train_ds, noise=1e-2),
     )
 
     # Callbacks
-    vis = pt.models.VisGLVQ2D(
+    vis = VisGLVQ2D(
         train_ds,
         show_last_only=False,
         block=False,
     )
-    pruning = pt.models.PruneLoserPrototypes(
+    pruning = PruneLoserPrototypes(
         threshold=0.01,
         idle_epochs=10,
         prune_quota_per_epoch=5,
@@ -53,7 +70,7 @@ if __name__ == "__main__":
         prototypes_initializer=pt.initializers.SSCI(train_ds, noise=1e-1),
         verbose=True,
     )
-    es = pl.callbacks.EarlyStopping(
+    es = EarlyStopping(
         monitor="train_loss",
         min_delta=1.0,
         patience=5,
@@ -62,14 +79,18 @@ if __name__ == "__main__":
     )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         callbacks=[
             vis,
-            # es, # FIXME
+            es,
             pruning,
         ],
-        terminate_on_nan=True,
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/gng_iris.py

@@ -1,23 +1,33 @@
 """Growing Neural Gas example using the Iris dataset."""
 
 import argparse
+import logging
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import GrowingNeuralGas, VisNG2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Reproducibility
-    pl.utilities.seed.seed_everything(seed=42)
+    seed_everything(seed=42)
 
     # Prepare the data
     train_ds = pt.datasets.Iris(dims=[0, 2])
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=64)
+    train_loader = DataLoader(train_ds, batch_size=64)
 
     # Hyperparameters
     hparams = dict(
@@ -27,7 +37,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.GrowingNeuralGas(
+    model = GrowingNeuralGas(
         hparams,
         prototypes_initializer=pt.initializers.ZCI(2),
     )
@@ -36,17 +46,22 @@ if __name__ == "__main__":
     model.example_input_array = torch.zeros(4, 2)
 
     # Model summary
-    print(model)
+    logging.info(model)
 
     # Callbacks
-    vis = pt.models.VisNG2D(data=train_loader)
+    vis = VisNG2D(data=train_loader)
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
         max_epochs=100,
-        callbacks=[vis],
-        weights_summary="full",
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/grlvq_iris.py

@@ -0,0 +1,77 @@
+"""GMLVQ example using the Iris dataset."""
+
+import argparse
+import warnings
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import GRLVQ, VisSiameseGLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.optim.lr_scheduler import ExponentialLR
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+if __name__ == "__main__":
+
+    # Reproducibility
+    seed_everything(seed=4)
+
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
+    args = parser.parse_args()
+
+    # Dataset
+    train_ds = pt.datasets.Iris([0, 1])
+
+    # Dataloaders
+    train_loader = DataLoader(train_ds, batch_size=64)
+
+    # Hyperparameters
+    hparams = dict(
+        input_dim=2,
+        distribution={
+            "num_classes": 3,
+            "per_class": 2
+        },
+        proto_lr=0.01,
+        bb_lr=0.01,
+    )
+
+    # Initialize the model
+    model = GRLVQ(
+        hparams,
+        optimizer=torch.optim.Adam,
+        prototypes_initializer=pt.initializers.SMCI(train_ds),
+        lr_scheduler=ExponentialLR,
+        lr_scheduler_kwargs=dict(gamma=0.99, verbose=False),
+    )
+
+    # Compute intermediate input and output sizes
+    model.example_input_array = torch.zeros(4, 2)
+
+    # Callbacks
+    vis = VisSiameseGLVQ2D(data=train_ds)
+
+    # Setup trainer
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        max_epochs=5,
+        log_every_n_steps=1,
+        detect_anomaly=True,
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)
+
+    torch.save(model, "iris.pth")

examples/gtlvq_mnist.py

@@ -0,0 +1,119 @@
+"""GTLVQ example using the MNIST dataset."""
+
+import argparse
+import warnings
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import (
+    ImageGTLVQ,
+    PruneLoserPrototypes,
+    VisImgComp,
+)
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+from torchvision import transforms
+from torchvision.datasets import MNIST
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
+
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
+    args = parser.parse_args()
+
+    # Dataset
+    train_ds = MNIST(
+        "~/datasets",
+        train=True,
+        download=True,
+        transform=transforms.Compose([
+            transforms.ToTensor(),
+        ]),
+    )
+    test_ds = MNIST(
+        "~/datasets",
+        train=False,
+        download=True,
+        transform=transforms.Compose([
+            transforms.ToTensor(),
+        ]),
+    )
+
+    # Dataloaders
+    train_loader = DataLoader(train_ds, num_workers=0, batch_size=256)
+    test_loader = DataLoader(test_ds, num_workers=0, batch_size=256)
+
+    # Hyperparameters
+    num_classes = 10
+    prototypes_per_class = 1
+    hparams = dict(
+        input_dim=28 * 28,
+        latent_dim=28,
+        distribution=(num_classes, prototypes_per_class),
+        proto_lr=0.01,
+        bb_lr=0.01,
+    )
+
+    # Initialize the model
+    model = ImageGTLVQ(
+        hparams,
+        optimizer=torch.optim.Adam,
+        prototypes_initializer=pt.initializers.SMCI(train_ds),
+        #Use one batch of data for subspace initiator.
+        omega_initializer=pt.initializers.PCALinearTransformInitializer(
+            next(iter(train_loader))[0].reshape(256, 28 * 28)))
+
+    # Callbacks
+    vis = VisImgComp(
+        data=train_ds,
+        num_columns=10,
+        show=False,
+        tensorboard=True,
+        random_data=100,
+        add_embedding=True,
+        embedding_data=200,
+        flatten_data=False,
+    )
+    pruning = PruneLoserPrototypes(
+        threshold=0.01,
+        idle_epochs=1,
+        prune_quota_per_epoch=10,
+        frequency=1,
+        verbose=True,
+    )
+    es = EarlyStopping(
+        monitor="train_loss",
+        min_delta=0.001,
+        patience=15,
+        mode="min",
+        check_on_train_epoch_end=True,
+    )
+
+    # Setup trainer
+    # using GPUs here is strongly recommended!
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+            pruning,
+            es,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)

examples/gtlvq_moons.py

@@ -0,0 +1,79 @@
+"""Localized-GTLVQ example using the Moons dataset."""
+
+import argparse
+import logging
+import warnings
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import GTLVQ, VisGLVQ2D
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+if __name__ == "__main__":
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
+    args = parser.parse_args()
+
+    # Reproducibility
+    seed_everything(seed=2)
+
+    # Dataset
+    train_ds = pt.datasets.Moons(num_samples=300, noise=0.2, seed=42)
+
+    # Dataloaders
+    train_loader = DataLoader(
+        train_ds,
+        batch_size=256,
+        shuffle=True,
+    )
+
+    # Hyperparameters
+    # Latent_dim should be lower than input dim.
+    hparams = dict(distribution=[1, 3], input_dim=2, latent_dim=1)
+
+    # Initialize the model
+    model = GTLVQ(hparams,
+                  prototypes_initializer=pt.initializers.SMCI(train_ds))
+
+    # Compute intermediate input and output sizes
+    model.example_input_array = torch.zeros(4, 2)
+
+    # Summary
+    logging.info(model)
+
+    # Callbacks
+    vis = VisGLVQ2D(data=train_ds)
+    es = EarlyStopping(
+        monitor="train_acc",
+        min_delta=0.001,
+        patience=20,
+        mode="max",
+        verbose=False,
+        check_on_train_epoch_end=True,
+    )
+
+    # Setup trainer
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+            es,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)

examples/knn_iris.py

@@ -1,52 +1,75 @@
 """k-NN example using the Iris dataset from scikit-learn."""
 
 import argparse
-
-import pytorch_lightning as pl
-import torch
-from sklearn.datasets import load_iris
+import logging
+import warnings
 
 import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from prototorch.models import KNN, VisGLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from sklearn.datasets import load_iris
+from sklearn.model_selection import train_test_split
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
 
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
-    x_train, y_train = load_iris(return_X_y=True)
-    x_train = x_train[:, [0, 2]]
-    train_ds = pt.datasets.NumpyDataset(x_train, y_train)
+    X, y = load_iris(return_X_y=True)
+    X = X[:, 0:3:2]
+
+    X_train, X_test, y_train, y_test = train_test_split(
+        X,
+        y,
+        test_size=0.5,
+        random_state=42,
+    )
+
+    train_ds = pt.datasets.NumpyDataset(X_train, y_train)
+    test_ds = pt.datasets.NumpyDataset(X_test, y_test)
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=150)
+    train_loader = DataLoader(train_ds, batch_size=16)
+    test_loader = DataLoader(test_ds, batch_size=16)
 
     # Hyperparameters
     hparams = dict(k=5)
 
     # Initialize the model
-    model = pt.models.KNN(hparams, data=train_ds)
+    model = KNN(hparams, data=train_ds)
 
     # Compute intermediate input and output sizes
     model.example_input_array = torch.zeros(4, 2)
 
     # Summary
-    print(model)
+    logging.info(model)
 
     # Callbacks
-    vis = pt.models.VisGLVQ2D(
-        data=(x_train, y_train),
+    vis = VisGLVQ2D(
+        data=(X_train, y_train),
         resolution=200,
         block=True,
     )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         max_epochs=1,
-        callbacks=[vis],
-        weights_summary="full",
+        callbacks=[
+            vis,
+        ],
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop
@@ -54,5 +77,8 @@ if __name__ == "__main__":
     trainer.fit(model, train_loader)
 
     # Recall
-    y_pred = model.predict(torch.tensor(x_train))
-    print(y_pred)
+    y_pred = model.predict(torch.tensor(X_train))
+    logging.info(y_pred)
+
+    # Test
+    trainer.test(model, dataloaders=test_loader)

examples/ksom_colors.py

@@ -1,15 +1,25 @@
 """Kohonen Self Organizing Map."""
 
 import argparse
+import logging
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
 from matplotlib import pyplot as plt
+from prototorch.models import KohonenSOM
 from prototorch.utils.colors import hex_to_rgb
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader, TensorDataset
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 
 class Vis2DColorSOM(pl.Callback):
+
     def __init__(self, data, title="ColorSOMe", pause_time=0.1):
         super().__init__()
         self.title = title
@@ -17,7 +27,7 @@ class Vis2DColorSOM(pl.Callback):
         self.data = data
         self.pause_time = pause_time
 
-    def on_epoch_end(self, trainer, pl_module):
+    def on_train_epoch_end(self, trainer, pl_module: KohonenSOM):
         ax = self.fig.gca()
         ax.cla()
         ax.set_title(self.title)
@@ -30,12 +40,14 @@ class Vis2DColorSOM(pl.Callback):
         d = pl_module.compute_distances(self.data)
         wp = pl_module.predict_from_distances(d)
         for i, iloc in enumerate(wp):
-            plt.text(iloc[1],
-                     iloc[0],
-                     cnames[i],
-                     ha="center",
-                     va="center",
-                     bbox=dict(facecolor="white", alpha=0.5, lw=0))
+            plt.text(
+                iloc[1],
+                iloc[0],
+                color_names[i],
+                ha="center",
+                va="center",
+                bbox=dict(facecolor="white", alpha=0.5, lw=0),
+            )
 
         if trainer.current_epoch != trainer.max_epochs - 1:
             plt.pause(self.pause_time)
@@ -46,11 +58,12 @@ class Vis2DColorSOM(pl.Callback):
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Reproducibility
-    pl.utilities.seed.seed_everything(seed=42)
+    seed_everything(seed=42)
 
     # Prepare the data
     hex_colors = [
@@ -58,15 +71,15 @@ if __name__ == "__main__":
         "#00ff00", "#ff0000", "#00ffff", "#ff00ff", "#ffff00", "#ffffff",
         "#545454", "#7f7f7f", "#a8a8a8", "#808000", "#800080", "#ffa500"
     ]
-    cnames = [
+    color_names = [
         "black", "blue", "darkblue", "skyblue", "greyblue", "lilac", "green",
         "red", "cyan", "magenta", "yellow", "white", "darkgrey", "mediumgrey",
         "lightgrey", "olive", "purple", "orange"
     ]
     colors = list(hex_to_rgb(hex_colors))
     data = torch.Tensor(colors) / 255.0
-    train_ds = torch.utils.data.TensorDataset(data)
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=8)
+    train_ds = TensorDataset(data)
+    train_loader = DataLoader(train_ds, batch_size=8)
 
     # Hyperparameters
     hparams = dict(
@@ -77,7 +90,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.KohonenSOM(
+    model = KohonenSOM(
         hparams,
         prototypes_initializer=pt.initializers.RNCI(3),
     )
@@ -86,17 +99,22 @@ if __name__ == "__main__":
     model.example_input_array = torch.zeros(4, 3)
 
     # Model summary
-    print(model)
+    logging.info(model)
 
     # Callbacks
     vis = Vis2DColorSOM(data=data)
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         max_epochs=500,
-        callbacks=[vis],
-        weights_summary="full",
+        callbacks=[
+            vis,
+        ],
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/lgmlvq_moons.py

@@ -1,27 +1,36 @@
 """Localized-GMLVQ example using the Moons dataset."""
 
 import argparse
+import logging
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import LGMLVQ, VisGLVQ2D
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Reproducibility
-    pl.utilities.seed.seed_everything(seed=2)
+    seed_everything(seed=2)
 
     # Dataset
     train_ds = pt.datasets.Moons(num_samples=300, noise=0.2, seed=42)
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds,
-                                               batch_size=256,
-                                               shuffle=True)
+    train_loader = DataLoader(train_ds, batch_size=256, shuffle=True)
 
     # Hyperparameters
     hparams = dict(
@@ -31,7 +40,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.LGMLVQ(
+    model = LGMLVQ(
         hparams,
         prototypes_initializer=pt.initializers.SMCI(train_ds),
     )
@@ -40,11 +49,11 @@ if __name__ == "__main__":
     model.example_input_array = torch.zeros(4, 2)
 
     # Summary
-    print(model)
+    logging.info(model)
 
     # Callbacks
-    vis = pt.models.VisGLVQ2D(data=train_ds)
-    es = pl.callbacks.EarlyStopping(
+    vis = VisGLVQ2D(data=train_ds)
+    es = EarlyStopping(
         monitor="train_acc",
         min_delta=0.001,
         patience=20,
@@ -54,14 +63,17 @@ if __name__ == "__main__":
     )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         callbacks=[
             vis,
             es,
         ],
-        weights_summary="full",
-        accelerator="ddp",
+        log_every_n_steps=1,
+        max_epochs=1000,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/lvqmln_iris.py

@@ -1,13 +1,26 @@
 """LVQMLN example using all four dimensions of the Iris dataset."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import (
+    LVQMLN,
+    PruneLoserPrototypes,
+    VisSiameseGLVQ2D,
+)
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 
 class Backbone(torch.nn.Module):
+
     def __init__(self, input_size=4, hidden_size=10, latent_size=2):
         super().__init__()
         self.input_size = input_size
@@ -26,17 +39,18 @@ class Backbone(torch.nn.Module):
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
     train_ds = pt.datasets.Iris()
 
     # Reproducibility
-    pl.utilities.seed.seed_everything(seed=42)
+    seed_everything(seed=42)
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=150)
+    train_loader = DataLoader(train_ds, batch_size=150)
 
     # Hyperparameters
     hparams = dict(
@@ -49,7 +63,7 @@ if __name__ == "__main__":
     backbone = Backbone()
 
     # Initialize the model
-    model = pt.models.LVQMLN(
+    model = LVQMLN(
         hparams,
         prototypes_initializer=pt.initializers.SSCI(
             train_ds,
@@ -58,18 +72,15 @@ if __name__ == "__main__":
         backbone=backbone,
     )
 
-    # Model summary
-    print(model)
-
     # Callbacks
-    vis = pt.models.VisSiameseGLVQ2D(
+    vis = VisSiameseGLVQ2D(
         data=train_ds,
         map_protos=False,
         border=0.1,
         resolution=500,
         axis_off=True,
     )
-    pruning = pt.models.PruneLoserPrototypes(
+    pruning = PruneLoserPrototypes(
         threshold=0.01,
         idle_epochs=20,
         prune_quota_per_epoch=2,
@@ -78,12 +89,17 @@ if __name__ == "__main__":
     )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
         callbacks=[
             vis,
             pruning,
         ],
+        log_every_n_steps=1,
+        max_epochs=1000,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/median_lvq_iris.py

@@ -0,0 +1,71 @@
+"""Median-LVQ example using the Iris dataset."""
+
+import argparse
+import warnings
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import MedianLVQ, VisGLVQ2D
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
+    args = parser.parse_args()
+
+    # Dataset
+    train_ds = pt.datasets.Iris(dims=[0, 2])
+
+    # Dataloaders
+    train_loader = DataLoader(
+        train_ds,
+        batch_size=len(train_ds),  # MedianLVQ cannot handle mini-batches
+    )
+
+    # Initialize the model
+    model = MedianLVQ(
+        hparams=dict(distribution=(3, 2), lr=0.01),
+        prototypes_initializer=pt.initializers.SSCI(train_ds),
+    )
+
+    # Compute intermediate input and output sizes
+    model.example_input_array = torch.zeros(4, 2)
+
+    # Callbacks
+    vis = VisGLVQ2D(data=train_ds)
+    es = EarlyStopping(
+        monitor="train_acc",
+        min_delta=0.01,
+        patience=5,
+        mode="max",
+        verbose=True,
+        check_on_train_epoch_end=True,
+    )
+
+    # Setup trainer
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+            es,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)

examples/ng_iris.py

@@ -1,23 +1,35 @@
 """Neural Gas example using the Iris dataset."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import NeuralGas, VisNG2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from sklearn.datasets import load_iris
 from sklearn.preprocessing import StandardScaler
 from torch.optim.lr_scheduler import ExponentialLR
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
+    # Reproducibility
+    seed_everything(seed=4)
+
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Prepare and pre-process the dataset
     x_train, y_train = load_iris(return_X_y=True)
-    x_train = x_train[:, [0, 2]]
+    x_train = x_train[:, 0:3:2]
     scaler = StandardScaler()
     scaler.fit(x_train)
     x_train = scaler.transform(x_train)
@@ -25,7 +37,7 @@ if __name__ == "__main__":
     train_ds = pt.datasets.NumpyDataset(x_train, y_train)
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=150)
+    train_loader = DataLoader(train_ds, batch_size=150)
 
     # Hyperparameters
     hparams = dict(
@@ -35,7 +47,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.NeuralGas(
+    model = NeuralGas(
         hparams,
         prototypes_initializer=pt.core.ZCI(2),
         lr_scheduler=ExponentialLR,
@@ -45,17 +57,20 @@ if __name__ == "__main__":
     # Compute intermediate input and output sizes
     model.example_input_array = torch.zeros(4, 2)
 
-    # Model summary
-    print(model)
-
     # Callbacks
-    vis = pt.models.VisNG2D(data=train_ds)
+    vis = VisNG2D(data=train_ds)
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
-        callbacks=[vis],
-        weights_summary="full",
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/rslvq_iris.py

@@ -1,25 +1,34 @@
 """RSLVQ example using the Iris dataset."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import RSLVQ, VisGLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Reproducibility
-    pl.utilities.seed.seed_everything(seed=42)
+    seed_everything(seed=42)
 
     # Dataset
     train_ds = pt.datasets.Iris(dims=[0, 2])
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=64)
+    train_loader = DataLoader(train_ds, batch_size=64)
 
     # Hyperparameters
     hparams = dict(
@@ -33,7 +42,7 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.RSLVQ(
+    model = RSLVQ(
         hparams,
         optimizer=torch.optim.Adam,
         prototypes_initializer=pt.initializers.SSCI(train_ds, noise=0.2),
@@ -42,19 +51,20 @@ if __name__ == "__main__":
     # Compute intermediate input and output sizes
     model.example_input_array = torch.zeros(4, 2)
 
-    # Summary
-    print(model)
-
     # Callbacks
-    vis = pt.models.VisGLVQ2D(data=train_ds)
+    vis = VisGLVQ2D(data=train_ds)
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
-        callbacks=[vis],
-        terminate_on_nan=True,
-        weights_summary="full",
-        accelerator="ddp",
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        detect_anomaly=True,
+        max_epochs=100,
+        log_every_n_steps=1,
     )
 
     # Training loop

examples/siamese_glvq_iris.py

@@ -1,13 +1,22 @@
 """Siamese GLVQ example using all four dimensions of the Iris dataset."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import SiameseGLVQ, VisSiameseGLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 
 class Backbone(torch.nn.Module):
+
     def __init__(self, input_size=4, hidden_size=10, latent_size=2):
         super().__init__()
         self.input_size = input_size
@@ -26,46 +35,50 @@ class Backbone(torch.nn.Module):
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Dataset
     train_ds = pt.datasets.Iris()
 
     # Reproducibility
-    pl.utilities.seed.seed_everything(seed=2)
+    seed_everything(seed=2)
 
     # Dataloaders
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=150)
+    train_loader = DataLoader(train_ds, batch_size=150)
 
     # Hyperparameters
     hparams = dict(
         distribution=[1, 2, 3],
-        proto_lr=0.01,
-        bb_lr=0.01,
+        lr=0.01,
     )
 
     # Initialize the backbone
     backbone = Backbone()
 
     # Initialize the model
-    model = pt.models.SiameseGLVQ(
+    model = SiameseGLVQ(
         hparams,
         prototypes_initializer=pt.initializers.SMCI(train_ds),
         backbone=backbone,
         both_path_gradients=False,
     )
 
-    # Model summary
-    print(model)
-
     # Callbacks
-    vis = pt.models.VisSiameseGLVQ2D(data=train_ds, border=0.1)
+    vis = VisSiameseGLVQ2D(data=train_ds, border=0.1)
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
-        callbacks=[vis],
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

examples/siamese_gtlvq_iris.py

@@ -0,0 +1,87 @@
+"""Siamese GTLVQ example using all four dimensions of the Iris dataset."""
+
+import argparse
+import warnings
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import SiameseGTLVQ, VisSiameseGLVQ2D
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+
+class Backbone(torch.nn.Module):
+
+    def __init__(self, input_size=4, hidden_size=10, latent_size=2):
+        super().__init__()
+        self.input_size = input_size
+        self.hidden_size = hidden_size
+        self.latent_size = latent_size
+        self.dense1 = torch.nn.Linear(self.input_size, self.hidden_size)
+        self.dense2 = torch.nn.Linear(self.hidden_size, self.latent_size)
+        self.activation = torch.nn.Sigmoid()
+
+    def forward(self, x):
+        x = self.activation(self.dense1(x))
+        out = self.activation(self.dense2(x))
+        return out
+
+
+if __name__ == "__main__":
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
+    args = parser.parse_args()
+
+    # Dataset
+    train_ds = pt.datasets.Iris()
+
+    # Reproducibility
+    seed_everything(seed=2)
+
+    # Dataloaders
+    train_loader = DataLoader(train_ds, batch_size=150)
+
+    # Hyperparameters
+    hparams = dict(
+        distribution=[1, 2, 3],
+        lr=0.01,
+        input_dim=2,
+        latent_dim=1,
+    )
+
+    # Initialize the backbone
+    backbone = Backbone(latent_size=hparams["input_dim"])
+
+    # Initialize the model
+    model = SiameseGTLVQ(
+        hparams,
+        prototypes_initializer=pt.initializers.SMCI(train_ds),
+        backbone=backbone,
+        both_path_gradients=False,
+    )
+
+    # Callbacks
+    vis = VisSiameseGLVQ2D(data=train_ds, border=0.1)
+
+    # Setup trainer
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)

examples/warm_starting.py

@@ -1,24 +1,42 @@
 """Warm-starting GLVQ with prototypes from Growing Neural Gas."""
 
 import argparse
+import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
 import torch
+from lightning_fabric.utilities.seed import seed_everything
+from prototorch.models import (
+    GLVQ,
+    KNN,
+    GrowingNeuralGas,
+    PruneLoserPrototypes,
+    VisGLVQ2D,
+)
+from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.optim.lr_scheduler import ExponentialLR
+from torch.utils.data import DataLoader
+
+warnings.filterwarnings("ignore", category=PossibleUserWarning)
 
 if __name__ == "__main__":
+
+    # Reproducibility
+    seed_everything(seed=4)
     # Command-line arguments
     parser = argparse.ArgumentParser()
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--gpus", type=int, default=0)
+    parser.add_argument("--fast_dev_run", type=bool, default=False)
     args = parser.parse_args()
 
     # Prepare the data
     train_ds = pt.datasets.Iris(dims=[0, 2])
-    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=64)
+    train_loader = DataLoader(train_ds, batch_size=64, num_workers=0)
 
     # Initialize the gng
-    gng = pt.models.GrowingNeuralGas(
+    gng = GrowingNeuralGas(
         hparams=dict(num_prototypes=5, insert_freq=2, lr=0.1),
         prototypes_initializer=pt.initializers.ZCI(2),
         lr_scheduler=ExponentialLR,
@@ -26,7 +44,7 @@ if __name__ == "__main__":
     )
 
     # Callbacks
-    es = pl.callbacks.EarlyStopping(
+    es = EarlyStopping(
         monitor="loss",
         min_delta=0.001,
         patience=20,
@@ -37,9 +55,14 @@ if __name__ == "__main__":
 
     # Setup trainer for GNG
     trainer = pl.Trainer(
-        max_epochs=200,
-        callbacks=[es],
-        weights_summary=None,
+        accelerator="cpu",
+        max_epochs=50 if args.fast_dev_run else
+        1000,  # 10 epochs fast dev run reproducible DIV error.
+        callbacks=[
+            es,
+        ],
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop
@@ -52,12 +75,12 @@ if __name__ == "__main__":
     )
 
     # Warm-start prototypes
-    knn = pt.models.KNN(dict(k=1), data=train_ds)
+    knn = KNN(dict(k=1), data=train_ds)
     prototypes = gng.prototypes
     plabels = knn.predict(prototypes)
 
     # Initialize the model
-    model = pt.models.GLVQ(
+    model = GLVQ(
         hparams,
         optimizer=torch.optim.Adam,
         prototypes_initializer=pt.initializers.LCI(prototypes),
@@ -70,14 +93,36 @@ if __name__ == "__main__":
     model.example_input_array = torch.zeros(4, 2)
 
     # Callbacks
-    vis = pt.models.VisGLVQ2D(data=train_ds)
+    vis = VisGLVQ2D(data=train_ds)
+    pruning = PruneLoserPrototypes(
+        threshold=0.02,
+        idle_epochs=2,
+        prune_quota_per_epoch=5,
+        frequency=1,
+        verbose=True,
+    )
+    es = EarlyStopping(
+        monitor="train_loss",
+        min_delta=0.001,
+        patience=10,
+        mode="min",
+        verbose=True,
+        check_on_train_epoch_end=True,
+    )
 
     # Setup trainer
-    trainer = pl.Trainer.from_argparse_args(
-        args,
-        callbacks=[vis],
-        weights_summary="full",
-        accelerator="ddp",
+    trainer = pl.Trainer(
+        accelerator="cuda" if args.gpus else "cpu",
+        devices=args.gpus if args.gpus else "auto",
+        fast_dev_run=args.fast_dev_run,
+        callbacks=[
+            vis,
+            pruning,
+            es,
+        ],
+        max_epochs=1000,
+        log_every_n_steps=1,
+        detect_anomaly=True,
     )
 
     # Training loop

prototorch/models/data.py

@@ -1,124 +0,0 @@
-"""Prototorch Data Modules
-
-This allows to store the used dataset inside a Lightning Module.
-Mainly used for PytorchLightningCLI configurations.
-"""
-from typing import Any, Optional, Type
-
-import pytorch_lightning as pl
-from torch.utils.data import DataLoader, Dataset, random_split
-from torchvision import transforms
-from torchvision.datasets import MNIST
-
-import prototorch as pt
-
-
-# MNIST
-class MNISTDataModule(pl.LightningDataModule):
-    def __init__(self, batch_size=32):
-        super().__init__()
-        self.batch_size = batch_size
-
-    # Download mnist dataset as side-effect, only called on the first cpu
-    def prepare_data(self):
-        MNIST("~/datasets", train=True, download=True)
-        MNIST("~/datasets", train=False, download=True)
-
-    # called for every GPU/machine (assigning state is OK)
-    def setup(self, stage=None):
-        # Transforms
-        transform = transforms.Compose([
-            transforms.ToTensor(),
-        ])
-        # Split dataset
-        if stage in (None, "fit"):
-            mnist_train = MNIST("~/datasets", train=True, transform=transform)
-            self.mnist_train, self.mnist_val = random_split(
-                mnist_train,
-                [55000, 5000],
-            )
-        if stage == (None, "test"):
-            self.mnist_test = MNIST(
-                "~/datasets",
-                train=False,
-                transform=transform,
-            )
-
-    # Dataloaders
-    def train_dataloader(self):
-        mnist_train = DataLoader(self.mnist_train, batch_size=self.batch_size)
-        return mnist_train
-
-    def val_dataloader(self):
-        mnist_val = DataLoader(self.mnist_val, batch_size=self.batch_size)
-        return mnist_val
-
-    def test_dataloader(self):
-        mnist_test = DataLoader(self.mnist_test, batch_size=self.batch_size)
-        return mnist_test
-
-
-# def train_on_mnist(batch_size=256) -> type:
-#     class DataClass(pl.LightningModule):
-#         datamodule = MNISTDataModule(batch_size=batch_size)
-
-#         def __init__(self, *args, **kwargs):
-#             prototype_initializer = kwargs.pop(
-#                 "prototype_initializer", pt.components.Zeros((28, 28, 1)))
-#             super().__init__(*args,
-#                              prototype_initializer=prototype_initializer,
-#                              **kwargs)
-
-#     dc: Type[DataClass] = DataClass
-#     return dc
-
-
-# ABSTRACT
-class GeneralDataModule(pl.LightningDataModule):
-    def __init__(self, dataset: Dataset, batch_size: int = 32) -> None:
-        super().__init__()
-        self.train_dataset = dataset
-        self.batch_size = batch_size
-
-    def train_dataloader(self) -> DataLoader:
-        return DataLoader(self.train_dataset, batch_size=self.batch_size)
-
-
-# def train_on_dataset(dataset: Dataset, batch_size: int = 256):
-#     class DataClass(pl.LightningModule):
-#         datamodule = GeneralDataModule(dataset, batch_size)
-#         datashape = dataset[0][0].shape
-#         example_input_array = torch.zeros_like(dataset[0][0]).unsqueeze(0)
-
-#         def __init__(self, *args: Any, **kwargs: Any) -> None:
-#             prototype_initializer = kwargs.pop(
-#                 "prototype_initializer",
-#                 pt.components.Zeros(self.datashape),
-#             )
-#             super().__init__(*args,
-#                              prototype_initializer=prototype_initializer,
-#                              **kwargs)
-
-#     return DataClass
-
-# if __name__ == "__main__":
-#     from prototorch.models import GLVQ
-
-#     demo_dataset = pt.datasets.Iris()
-
-#     TrainingClass: Type = train_on_dataset(demo_dataset)
-
-#     class DemoGLVQ(TrainingClass, GLVQ):
-#         """Model Definition."""
-
-#     # Hyperparameters
-#     hparams = dict(
-#         distribution={
-#             "num_classes": 3,
-#             "prototypes_per_class": 4
-#         },
-#         lr=0.01,
-#     )
-
-#     initialized = DemoGLVQ(hparams)
-#     print(initialized)

prototorch/models/lvq.py

@@ -1,69 +0,0 @@
-"""LVQ models that are optimized using non-gradient methods."""
-
-from ..core.losses import _get_dp_dm
-from .abstract import NonGradientMixin
-from .glvq import GLVQ
-
-
-class LVQ1(NonGradientMixin, GLVQ):
-    """Learning Vector Quantization 1."""
-    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
-        protos = self.proto_layer.components
-        plabels = self.proto_layer.labels
-
-        x, y = train_batch
-        dis = self.compute_distances(x)
-        # TODO Vectorized implementation
-
-        for xi, yi in zip(x, y):
-            d = self.compute_distances(xi.view(1, -1))
-            preds = self.competition_layer(d, plabels)
-            w = d.argmin(1)
-            if yi == preds:
-                shift = xi - protos[w]
-            else:
-                shift = protos[w] - xi
-            updated_protos = protos + 0.0
-            updated_protos[w] = protos[w] + (self.hparams.lr * shift)
-            self.proto_layer.load_state_dict({"_components": updated_protos},
-                                             strict=False)
-
-        print(f"{dis=}")
-        print(f"{y=}")
-        # Logging
-        self.log_acc(dis, y, tag="train_acc")
-
-        return None
-
-
-class LVQ21(NonGradientMixin, GLVQ):
-    """Learning Vector Quantization 2.1."""
-    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
-        protos = self.proto_layer.components
-        plabels = self.proto_layer.labels
-
-        x, y = train_batch
-        dis = self.compute_distances(x)
-        # TODO Vectorized implementation
-
-        for xi, yi in zip(x, y):
-            xi = xi.view(1, -1)
-            yi = yi.view(1, )
-            d = self.compute_distances(xi)
-            (_, wp), (_, wn) = _get_dp_dm(d, yi, plabels, with_indices=True)
-            shiftp = xi - protos[wp]
-            shiftn = protos[wn] - xi
-            updated_protos = protos + 0.0
-            updated_protos[wp] = protos[wp] + (self.hparams.lr * shiftp)
-            updated_protos[wn] = protos[wn] + (self.hparams.lr * shiftn)
-            self.proto_layer.load_state_dict({"_components": updated_protos},
-                                             strict=False)
-
-        # Logging
-        self.log_acc(dis, y, tag="train_acc")
-
-        return None
-
-
-class MedianLVQ(NonGradientMixin, GLVQ):
-    """Median LVQ"""

pyproject.toml

@@ -0,0 +1,90 @@
+
+[project]
+name = "prototorch-models"
+version = "0.7.1"
+description = "Pre-packaged prototype-based machine learning models using ProtoTorch and PyTorch-Lightning."
+authors = [
+    { name = "Jensun Ravichandran", email = "jjensun@gmail.com" },
+    { name = "Alexander Engelsberger", email = "engelsbe@hs-mittweida.de" },
+]
+dependencies = ["lightning>=2.0.0", "prototorch>=0.7.5"]
+requires-python = ">=3.8"
+readme = "README.md"
+license = { text = "MIT" }
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Environment :: Plugins",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+
+[project.urls]
+Homepage = "https://github.com/si-cim/prototorch_models"
+Downloads = "https://github.com/si-cim/prototorch_models.git"
+
+[project.optional-dependencies]
+dev = ["bumpversion", "pre-commit", "yapf", "toml"]
+examples = ["matplotlib", "scikit-learn"]
+ci = ["pytest", "pre-commit"]
+docs = [
+    "recommonmark",
+    "nbsphinx",
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-bibtex",
+    "sphinxcontrib-katex",
+    "ipykernel",
+]
+all = [
+    "bumpversion",
+    "pre-commit",
+    "yapf",
+    "toml",
+    "pytest",
+    "matplotlib",
+    "scikit-learn",
+    "recommonmark",
+    "nbsphinx",
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-bibtex",
+    "sphinxcontrib-katex",
+    "ipykernel",
+]
+
+[build-system]
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.yapf]
+based_on_style = "pep8"
+spaces_before_comment = 2
+split_before_logical_operator = true
+
+[tool.pylint]
+disable = ["too-many-arguments", "too-few-public-methods", "fixme"]
+
+[tool.isort]
+profile = "hug"
+src_paths = ["isort", "test"]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 3
+use_parentheses = true
+line_length = 79
+
+[tool.mypy]
+explicit_package_bases = true
+namespace_packages = true

setup.cfg

@@ -1,8 +0,0 @@
-[isort]
-profile = hug
-src_paths = isort, test
-
-[yapf]
-based_on_style = pep8
-spaces_before_comment = 2
-split_before_logical_operator = true

setup.py

@@ -1,93 +0,0 @@
-"""
-
- ######
- #     # #####   ####  #####  ####  #####  ####  #####   ####  #    #
- #     # #    # #    #   #   #    #   #   #    # #    # #    # #    #
- ######  #    # #    #   #   #    #   #   #    # #    # #      ######
- #       #####  #    #   #   #    #   #   #    # #####  #      #    #
- #       #   #  #    #   #   #    #   #   #    # #   #  #    # #    #
- #       #    #  ####    #    ####    #    ####  #    #  ####  #    #Plugin
-
-ProtoTorch models Plugin Package
-"""
-from pkg_resources import safe_name
-from setuptools import find_namespace_packages, setup
-
-PLUGIN_NAME = "models"
-
-PROJECT_URL = "https://github.com/si-cim/prototorch_models"
-DOWNLOAD_URL = "https://github.com/si-cim/prototorch_models.git"
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-INSTALL_REQUIRES = [
-    "prototorch>=0.6.0",
-    "pytorch_lightning>=1.3.5",
-    "torchmetrics",
-]
-CLI = [
-    "jsonargparse",
-]
-DEV = [
-    "bumpversion",
-    "pre-commit",
-]
-DOCS = [
-    "recommonmark",
-    "sphinx",
-    "nbsphinx",
-    "sphinx_rtd_theme",
-    "sphinxcontrib-katex",
-    "sphinxcontrib-bibtex",
-]
-EXAMPLES = [
-    "matplotlib",
-    "scikit-learn",
-]
-TESTS = [
-    "codecov",
-    "pytest",
-]
-ALL = CLI + DEV + DOCS + EXAMPLES + TESTS
-
-setup(
-    name=safe_name("prototorch_" + PLUGIN_NAME),
-    version="0.2.0",
-    description="Pre-packaged prototype-based "
-    "machine learning models using ProtoTorch and PyTorch-Lightning.",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author="Alexander Engelsberger",
-    author_email="engelsbe@hs-mittweida.de",
-    url=PROJECT_URL,
-    download_url=DOWNLOAD_URL,
-    license="MIT",
-    python_requires=">=3.9",
-    install_requires=INSTALL_REQUIRES,
-    extras_require={
-        "dev": DEV,
-        "examples": EXAMPLES,
-        "tests": TESTS,
-        "all": ALL,
-    },
-    classifiers=[
-        "Development Status :: 2 - Pre-Alpha",
-        "Environment :: Plugins",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Education",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: MIT License",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3.9",
-        "Operating System :: OS Independent",
-        "Topic :: Scientific/Engineering :: Artificial Intelligence",
-        "Topic :: Software Development :: Libraries",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-    ],
-    entry_points={
-        "prototorch.plugins": f"{PLUGIN_NAME} = prototorch.{PLUGIN_NAME}"
-    },
-    packages=find_namespace_packages(include=["prototorch.*"]),
-    zip_safe=False,
-)

src/prototorch/models/__init__.py

@@ -1,7 +1,5 @@
 """`models` plugin for the `prototorch` package."""
 
-from importlib.metadata import PackageNotFoundError, version
-
 from .callbacks import PrototypeConvergence, PruneLoserPrototypes
 from .cbc import CBC, ImageCBC
 from .glvq import (
@@ -10,17 +8,32 @@ from .glvq import (
     GLVQ21,
     GMLVQ,
     GRLVQ,
+    GTLVQ,
     LGMLVQ,
     LVQMLN,
     ImageGLVQ,
     ImageGMLVQ,
+    ImageGTLVQ,
     SiameseGLVQ,
     SiameseGMLVQ,
+    SiameseGTLVQ,
 )
 from .knn import KNN
-from .lvq import LVQ1, LVQ21, MedianLVQ
-from .probabilistic import CELVQ, PLVQ, RSLVQ, SLVQ
-from .unsupervised import GrowingNeuralGas, HeskesSOM, KohonenSOM, NeuralGas
+from .lvq import (
+    LVQ1,
+    LVQ21,
+    MedianLVQ,
+)
+from .probabilistic import (
+    CELVQ,
+    RSLVQ,
+    SLVQ,
+)
+from .unsupervised import (
+    GrowingNeuralGas,
+    KohonenSOM,
+    NeuralGas,
+)
 from .vis import *
 
-__version__ = "0.2.0"
+__version__ = "0.7.1"

src/prototorch/models/abstract.py

@@ -1,33 +1,29 @@
 """Abstract classes to be inherited by prototorch models."""
 
-from typing import Final, final
+import logging
 
 import pytorch_lightning as pl
 import torch
+import torch.nn.functional as F
 import torchmetrics
-
-from ..core.competitions import WTAC
-from ..core.components import Components, LabeledComponents
-from ..core.distances import euclidean_distance
-from ..core.initializers import LabelsInitializer
-from ..core.pooling import stratified_min_pooling
-from ..nn.wrappers import LambdaLayer
-
-
-class ProtoTorchMixin(object):
-    pass
+from prototorch.core.competitions import WTAC
+from prototorch.core.components import (
+    AbstractComponents,
+    Components,
+    LabeledComponents,
+)
+from prototorch.core.distances import euclidean_distance
+from prototorch.core.initializers import (
+    LabelsInitializer,
+    ZerosCompInitializer,
+)
+from prototorch.core.pooling import stratified_min_pooling
+from prototorch.nn.wrappers import LambdaLayer
 
 
 class ProtoTorchBolt(pl.LightningModule):
     """All ProtoTorch models are ProtoTorch Bolts."""
-    def __repr__(self):
-        surep = super().__repr__()
-        indented = "".join([f"\t{line}\n" for line in surep.splitlines()])
-        wrapped = f"ProtoTorch Bolt(\n{indented})"
-        return wrapped
 
-
-class PrototypeModel(ProtoTorchBolt):
     def __init__(self, hparams, **kwargs):
         super().__init__()
 
@@ -42,8 +38,40 @@ class PrototypeModel(ProtoTorchBolt):
         self.lr_scheduler = kwargs.get("lr_scheduler", None)
         self.lr_scheduler_kwargs = kwargs.get("lr_scheduler_kwargs", dict())
 
+    def configure_optimizers(self):
+        optimizer = self.optimizer(self.parameters(), lr=self.hparams["lr"])
+        if self.lr_scheduler is not None:
+            scheduler = self.lr_scheduler(optimizer,
+                                          **self.lr_scheduler_kwargs)
+            sch = {
+                "scheduler": scheduler,
+                "interval": "step",
+            }  # called after each training step
+            return [optimizer], [sch]
+        else:
+            return optimizer
+
+    def reconfigure_optimizers(self):
+        if self.trainer:
+            self.trainer.strategy.setup_optimizers(self.trainer)
+        else:
+            logging.warning("No trainer to reconfigure optimizers!")
+
+    def __repr__(self):
+        surep = super().__repr__()
+        indented = "".join([f"\t{line}\n" for line in surep.splitlines()])
+        wrapped = f"ProtoTorch Bolt(\n{indented})"
+        return wrapped
+
+
+class PrototypeModel(ProtoTorchBolt):
+    proto_layer: AbstractComponents
+
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+
         distance_fn = kwargs.get("distance_fn", euclidean_distance)
-        self.distance_layer = LambdaLayer(distance_fn)
+        self.distance_layer = LambdaLayer(distance_fn, name="distance_fn")
 
     @property
     def num_prototypes(self):
@@ -58,33 +86,20 @@ class PrototypeModel(ProtoTorchBolt):
         """Only an alias for the prototypes."""
         return self.prototypes
 
-    def configure_optimizers(self):
-        optimizer = self.optimizer(self.parameters(), lr=self.hparams.lr)
-        if self.lr_scheduler is not None:
-            scheduler = self.lr_scheduler(optimizer,
-                                          **self.lr_scheduler_kwargs)
-            sch = {
-                "scheduler": scheduler,
-                "interval": "step",
-            }  # called after each training step
-            return [optimizer], [sch]
-        else:
-            return optimizer
-
-    @final
-    def reconfigure_optimizers(self):
-        self.trainer.accelerator_backend.setup_optimizers(self.trainer)
-
     def add_prototypes(self, *args, **kwargs):
         self.proto_layer.add_components(*args, **kwargs)
+        self.hparams["distribution"] = self.proto_layer.distribution
         self.reconfigure_optimizers()
 
     def remove_prototypes(self, indices):
         self.proto_layer.remove_components(indices)
+        self.hparams["distribution"] = self.proto_layer.distribution
         self.reconfigure_optimizers()
 
 
 class UnsupervisedPrototypeModel(PrototypeModel):
+    proto_layer: Components
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
@@ -92,12 +107,12 @@ class UnsupervisedPrototypeModel(PrototypeModel):
         prototypes_initializer = kwargs.get("prototypes_initializer", None)
         if prototypes_initializer is not None:
             self.proto_layer = Components(
-                self.hparams.num_prototypes,
+                self.hparams["num_prototypes"],
                 initializer=prototypes_initializer,
             )
 
     def compute_distances(self, x):
-        protos = self.proto_layer()
+        protos = self.proto_layer().type_as(x)
         distances = self.distance_layer(x, protos)
         return distances
 
@@ -107,19 +122,34 @@ class UnsupervisedPrototypeModel(PrototypeModel):
 
 
 class SupervisedPrototypeModel(PrototypeModel):
-    def __init__(self, hparams, **kwargs):
+    proto_layer: LabeledComponents
+
+    def __init__(self, hparams, skip_proto_layer=False, **kwargs):
         super().__init__(hparams, **kwargs)
 
         # Layers
+        distribution = hparams.get("distribution", None)
         prototypes_initializer = kwargs.get("prototypes_initializer", None)
         labels_initializer = kwargs.get("labels_initializer",
                                         LabelsInitializer())
-        if prototypes_initializer is not None:
-            self.proto_layer = LabeledComponents(
-                distribution=self.hparams.distribution,
-                components_initializer=prototypes_initializer,
-                labels_initializer=labels_initializer,
-            )
+        if not skip_proto_layer:
+            # when subclasses do not need a customized prototype layer
+            if prototypes_initializer is not None:
+                # when building a new model
+                self.proto_layer = LabeledComponents(
+                    distribution=distribution,
+                    components_initializer=prototypes_initializer,
+                    labels_initializer=labels_initializer,
+                )
+                proto_shape = self.proto_layer.components.shape[1:]
+                self.hparams["initialized_proto_shape"] = proto_shape
+            else:
+                # when restoring a checkpointed model
+                self.proto_layer = LabeledComponents(
+                    distribution=distribution,
+                    components_initializer=ZerosCompInitializer(
+                        self.hparams["initialized_proto_shape"]),
+                )
         self.competition_layer = WTAC()
 
     @property
@@ -137,14 +167,14 @@ class SupervisedPrototypeModel(PrototypeModel):
 
     def forward(self, x):
         distances = self.compute_distances(x)
-        plabels = self.proto_layer.labels
+        _, plabels = self.proto_layer()
         winning = stratified_min_pooling(distances, plabels)
-        y_pred = torch.nn.functional.softmin(winning)
+        y_pred = F.softmin(winning, dim=1)
         return y_pred
 
     def predict_from_distances(self, distances):
         with torch.no_grad():
-            plabels = self.proto_layer.labels
+            _, plabels = self.proto_layer()
             y_pred = self.competition_layer(distances, plabels)
         return y_pred
 
@@ -156,31 +186,57 @@ class SupervisedPrototypeModel(PrototypeModel):
 
     def log_acc(self, distances, targets, tag):
         preds = self.predict_from_distances(distances)
-        accuracy = torchmetrics.functional.accuracy(preds.int(), targets.int())
-        # `.int()` because FloatTensors are assumed to be class probabilities
+        accuracy = torchmetrics.functional.accuracy(
+            preds.int(),
+            targets.int(),
+            "multiclass",
+            num_classes=self.num_classes,
+        )
 
-        self.log(tag,
-                 accuracy,
-                 on_step=False,
-                 on_epoch=True,
-                 prog_bar=True,
-                 logger=True)
+        self.log(
+            tag,
+            accuracy,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+
+    def test_step(self, batch, batch_idx):
+        x, targets = batch
+
+        preds = self.predict(x)
+        accuracy = torchmetrics.functional.accuracy(
+            preds.int(),
+            targets.int(),
+            "multiclass",
+            num_classes=self.num_classes,
+        )
+
+        self.log("test_acc", accuracy)
+
+
+class ProtoTorchMixin:
+    """All mixins are ProtoTorchMixins."""
 
 
 class NonGradientMixin(ProtoTorchMixin):
     """Mixin for custom non-gradient optimization."""
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.automatic_optimization: Final = False
+        self.automatic_optimization = False
 
-    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
+    def training_step(self, train_batch, batch_idx):
         raise NotImplementedError
 
 
 class ImagePrototypesMixin(ProtoTorchMixin):
     """Mixin for models with image prototypes."""
-    @final
-    def on_train_batch_end(self, outputs, batch, batch_idx, dataloader_idx):
+    proto_layer: Components
+    components: torch.Tensor
+
+    def on_train_batch_end(self, outputs, batch, batch_idx):
         """Constrain the components to the range [0, 1] by clamping after updates."""
         self.proto_layer.components.data.clamp_(0.0, 1.0)
 

src/prototorch/models/callbacks.py

@@ -1,24 +1,30 @@
 """Lightning Callbacks."""
 
 import logging
+from typing import TYPE_CHECKING
 
 import pytorch_lightning as pl
 import torch
+from prototorch.core.initializers import LiteralCompInitializer
 
-from ..core.components import Components
-from ..core.initializers import LiteralCompInitializer
 from .extras import ConnectionTopology
 
+if TYPE_CHECKING:
+    from prototorch.models import GLVQ, GrowingNeuralGas
+
 
 class PruneLoserPrototypes(pl.Callback):
-    def __init__(self,
-                 threshold=0.01,
-                 idle_epochs=10,
-                 prune_quota_per_epoch=-1,
-                 frequency=1,
-                 replace=False,
-                 prototypes_initializer=None,
-                 verbose=False):
+
+    def __init__(
+        self,
+        threshold=0.01,
+        idle_epochs=10,
+        prune_quota_per_epoch=-1,
+        frequency=1,
+        replace=False,
+        prototypes_initializer=None,
+        verbose=False,
+    ):
         self.threshold = threshold  # minimum win ratio
         self.idle_epochs = idle_epochs  # epochs to wait before pruning
         self.prune_quota_per_epoch = prune_quota_per_epoch
@@ -27,7 +33,7 @@ class PruneLoserPrototypes(pl.Callback):
         self.verbose = verbose
         self.prototypes_initializer = prototypes_initializer
 
-    def on_epoch_end(self, trainer, pl_module):
+    def on_train_epoch_end(self, trainer, pl_module: "GLVQ"):
         if (trainer.current_epoch + 1) < self.idle_epochs:
             return None
         if (trainer.current_epoch + 1) % self.frequency:
@@ -42,41 +48,44 @@ class PruneLoserPrototypes(pl.Callback):
             prune_labels = prune_labels[:self.prune_quota_per_epoch]
 
         if len(to_prune) > 0:
-            if self.verbose:
-                print(f"\nPrototype win ratios: {ratios}")
-                print(f"Pruning prototypes at: {to_prune}")
-                print(f"Corresponding labels are: {prune_labels.tolist()}")
+            logging.debug(f"\nPrototype win ratios: {ratios}")
+            logging.debug(f"Pruning prototypes at: {to_prune}")
+            logging.debug(f"Corresponding labels are: {prune_labels.tolist()}")
+
             cur_num_protos = pl_module.num_prototypes
             pl_module.remove_prototypes(indices=to_prune)
+
             if self.replace:
                 labels, counts = torch.unique(prune_labels,
                                               sorted=True,
                                               return_counts=True)
                 distribution = dict(zip(labels.tolist(), counts.tolist()))
-                if self.verbose:
-                    print(f"Re-adding pruned prototypes...")
-                    print(f"{distribution=}")
+
+                logging.info(f"Re-adding pruned prototypes...")
+                logging.debug(f"distribution={distribution}")
+
                 pl_module.add_prototypes(
                     distribution=distribution,
                     components_initializer=self.prototypes_initializer)
             new_num_protos = pl_module.num_prototypes
-            if self.verbose:
-                print(f"`num_prototypes` changed from {cur_num_protos} "
-                      f"to {new_num_protos}.")
+
+            logging.info(f"`num_prototypes` changed from {cur_num_protos} "
+                         f"to {new_num_protos}.")
         return True
 
 
 class PrototypeConvergence(pl.Callback):
+
     def __init__(self, min_delta=0.01, idle_epochs=10, verbose=False):
         self.min_delta = min_delta
         self.idle_epochs = idle_epochs  # epochs to wait
         self.verbose = verbose
 
-    def on_epoch_end(self, trainer, pl_module):
+    def on_train_epoch_end(self, trainer, pl_module):
         if (trainer.current_epoch + 1) < self.idle_epochs:
             return None
-        if self.verbose:
-            print("Stopping...")
+
+        logging.info("Stopping...")
         # TODO
         return True
 
@@ -89,16 +98,21 @@ class GNGCallback(pl.Callback):
     Based on "A Growing Neural Gas Network Learns Topologies" by Bernd Fritzke.
 
     """
+
     def __init__(self, reduction=0.1, freq=10):
         self.reduction = reduction
         self.freq = freq
 
-    def on_epoch_end(self, trainer: pl.Trainer, pl_module):
+    def on_train_epoch_end(
+        self,
+        trainer: pl.Trainer,
+        pl_module: "GrowingNeuralGas",
+    ):
         if (trainer.current_epoch + 1) % self.freq == 0:
             # Get information
             errors = pl_module.errors
             topology: ConnectionTopology = pl_module.topology_layer
-            components: Components = pl_module.proto_layer.components
+            components = pl_module.proto_layer.components
 
             # Insertion point
             worst = torch.argmax(errors)
@@ -118,8 +132,9 @@ class GNGCallback(pl.Callback):
 
             # Add component
             pl_module.proto_layer.add_components(
-                None,
-                initializer=LiteralCompInitializer(new_component.unsqueeze(0)))
+                1,
+                initializer=LiteralCompInitializer(new_component.unsqueeze(0)),
+            )
 
             # Adjust Topology
             topology.add_prototype()
@@ -134,4 +149,4 @@ class GNGCallback(pl.Callback):
             pl_module.errors[
                 worst_neighbor] = errors[worst_neighbor] * self.reduction
 
-            trainer.accelerator_backend.setup_optimizers(trainer)
+            trainer.strategy.setup_optimizers(trainer)

src/prototorch/models/cbc.py

@@ -1,20 +1,21 @@
 import torch
 import torchmetrics
+from prototorch.core.competitions import CBCC
+from prototorch.core.components import ReasoningComponents
+from prototorch.core.initializers import RandomReasoningsInitializer
+from prototorch.core.losses import MarginLoss
+from prototorch.core.similarities import euclidean_similarity
+from prototorch.nn.wrappers import LambdaLayer
 
-from ..core.competitions import CBCC
-from ..core.components import ReasoningComponents
-from ..core.initializers import RandomReasoningsInitializer
-from ..core.losses import MarginLoss
-from ..core.similarities import euclidean_similarity
-from ..nn.wrappers import LambdaLayer
 from .abstract import ImagePrototypesMixin
 from .glvq import SiameseGLVQ
 
 
 class CBC(SiameseGLVQ):
     """Classification-By-Components."""
+
     def __init__(self, hparams, **kwargs):
-        super().__init__(hparams, **kwargs)
+        super().__init__(hparams, skip_proto_layer=True, **kwargs)
 
         similarity_fn = kwargs.get("similarity_fn", euclidean_similarity)
         components_initializer = kwargs.get("components_initializer", None)
@@ -43,25 +44,31 @@ class CBC(SiameseGLVQ):
         probs = self.competition_layer(detections, reasonings)
         return probs
 
-    def shared_step(self, batch, batch_idx, optimizer_idx=None):
+    def shared_step(self, batch, batch_idx):
         x, y = batch
         y_pred = self(x)
         num_classes = self.num_classes
         y_true = torch.nn.functional.one_hot(y.long(), num_classes=num_classes)
-        loss = self.loss(y_pred, y_true).mean(dim=0)
+        loss = self.loss(y_pred, y_true).mean()
         return y_pred, loss
 
-    def training_step(self, batch, batch_idx, optimizer_idx=None):
-        y_pred, train_loss = self.shared_step(batch, batch_idx, optimizer_idx)
+    def training_step(self, batch, batch_idx):
+        y_pred, train_loss = self.shared_step(batch, batch_idx)
         preds = torch.argmax(y_pred, dim=1)
-        accuracy = torchmetrics.functional.accuracy(preds.int(),
-                                                    batch[1].int())
-        self.log("train_acc",
-                 accuracy,
-                 on_step=False,
-                 on_epoch=True,
-                 prog_bar=True,
-                 logger=True)
+        accuracy = torchmetrics.functional.accuracy(
+            preds.int(),
+            batch[1].int(),
+            "multiclass",
+            num_classes=self.num_classes,
+        )
+        self.log(
+            "train_acc",
+            accuracy,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
         return train_loss
 
     def predict(self, x):

src/prototorch/models/extras.py

@@ -5,8 +5,7 @@ Modules not yet available in prototorch go here temporarily.
 """
 
 import torch
-
-from ..core.similarities import gaussian
+from prototorch.core.similarities import gaussian
 
 
 def rank_scaled_gaussian(distances, lambd):
@@ -15,7 +14,46 @@ def rank_scaled_gaussian(distances, lambd):
     return torch.exp(-torch.exp(-ranks / lambd) * distances)
 
 
+def orthogonalization(tensors):
+    """Orthogonalization via polar decomposition """
+    u, _, v = torch.svd(tensors, compute_uv=True)
+    u_shape = tuple(list(u.shape))
+    v_shape = tuple(list(v.shape))
+
+    # reshape to (num x N x M)
+    u = torch.reshape(u, (-1, u_shape[-2], u_shape[-1]))
+    v = torch.reshape(v, (-1, v_shape[-2], v_shape[-1]))
+
+    out = u @ v.permute([0, 2, 1])
+
+    out = torch.reshape(out, u_shape[:-1] + (v_shape[-2], ))
+
+    return out
+
+
+def ltangent_distance(x, y, omegas):
+    r"""Localized Tangent distance.
+    Compute Orthogonal Complement: math:`\bm P_k = \bm I - \Omega_k \Omega_k^T`
+    Compute Tangent Distance: math:`{\| \bm P \bm x - \bm P_k \bm y_k \|}_2`
+
+    :param `torch.tensor` omegas: Three dimensional matrix
+    :rtype: `torch.tensor`
+    """
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
+    p = torch.eye(omegas.shape[-2], device=omegas.device) - torch.bmm(
+        omegas, omegas.permute([0, 2, 1]))
+    projected_x = x @ p
+    projected_y = torch.diagonal(y @ p).T
+    expanded_y = torch.unsqueeze(projected_y, dim=1)
+    batchwise_difference = expanded_y - projected_x
+    differences_squared = batchwise_difference**2
+    distances = torch.sqrt(torch.sum(differences_squared, dim=2))
+    distances = distances.permute(1, 0)
+    return distances
+
+
 class GaussianPrior(torch.nn.Module):
+
     def __init__(self, variance):
         super().__init__()
         self.variance = variance
@@ -25,6 +63,7 @@ class GaussianPrior(torch.nn.Module):
 
 
 class RankScaledGaussianPrior(torch.nn.Module):
+
     def __init__(self, lambd):
         super().__init__()
         self.lambd = lambd
@@ -34,6 +73,7 @@ class RankScaledGaussianPrior(torch.nn.Module):
 
 
 class ConnectionTopology(torch.nn.Module):
+
     def __init__(self, agelimit, num_prototypes):
         super().__init__()
         self.agelimit = agelimit

src/prototorch/models/glvq.py

@@ -1,39 +1,54 @@
 """Models based on the GLVQ framework."""
 
 import torch
+from prototorch.core.competitions import wtac
+from prototorch.core.distances import (
+    lomega_distance,
+    omega_distance,
+    squared_euclidean_distance,
+)
+from prototorch.core.initializers import EyeLinearTransformInitializer
+from prototorch.core.losses import (
+    GLVQLoss,
+    lvq1_loss,
+    lvq21_loss,
+)
+from prototorch.core.transforms import LinearTransform
+from prototorch.nn.wrappers import LambdaLayer, LossLayer
 from torch.nn.parameter import Parameter
 
-from ..core.competitions import wtac
-from ..core.distances import lomega_distance, omega_distance, squared_euclidean_distance
-from ..core.initializers import EyeTransformInitializer
-from ..core.losses import glvq_loss, lvq1_loss, lvq21_loss
-from ..nn.activations import get_activation
-from ..nn.wrappers import LambdaLayer, LossLayer
 from .abstract import ImagePrototypesMixin, SupervisedPrototypeModel
+from .extras import ltangent_distance, orthogonalization
 
 
 class GLVQ(SupervisedPrototypeModel):
     """Generalized Learning Vector Quantization."""
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
         # Default hparams
+        self.hparams.setdefault("margin", 0.0)
         self.hparams.setdefault("transfer_fn", "identity")
         self.hparams.setdefault("transfer_beta", 10.0)
 
-        # Layers
-        transfer_fn = get_activation(self.hparams.transfer_fn)
-        self.transfer_layer = LambdaLayer(transfer_fn)
-
         # Loss
-        self.loss = LossLayer(glvq_loss)
+        self.loss = GLVQLoss(
+            margin=self.hparams["margin"],
+            transfer_fn=self.hparams["transfer_fn"],
+            beta=self.hparams["transfer_beta"],
+        )
+
+    # def on_save_checkpoint(self, checkpoint):
+    #     if "prototype_win_ratios" in checkpoint["state_dict"]:
+    #         del checkpoint["state_dict"]["prototype_win_ratios"]
 
     def initialize_prototype_win_ratios(self):
         self.register_buffer(
             "prototype_win_ratios",
             torch.zeros(self.num_prototypes, device=self.device))
 
-    def on_epoch_start(self):
+    def on_train_epoch_start(self):
         self.initialize_prototype_win_ratios()
 
     def log_prototype_win_ratios(self, distances):
@@ -51,17 +66,15 @@ class GLVQ(SupervisedPrototypeModel):
             prototype_wr,
         ])
 
-    def shared_step(self, batch, batch_idx, optimizer_idx=None):
+    def shared_step(self, batch, batch_idx):
         x, y = batch
         out = self.compute_distances(x)
-        plabels = self.proto_layer.labels
-        mu = self.loss(out, y, prototype_labels=plabels)
-        batch_loss = self.transfer_layer(mu, beta=self.hparams.transfer_beta)
-        loss = batch_loss.sum(dim=0)
+        _, plabels = self.proto_layer()
+        loss = self.loss(out, y, plabels)
         return out, loss
 
-    def training_step(self, batch, batch_idx, optimizer_idx=None):
-        out, train_loss = self.shared_step(batch, batch_idx, optimizer_idx)
+    def training_step(self, batch, batch_idx):
+        out, train_loss = self.shared_step(batch, batch_idx)
         self.log_prototype_win_ratios(out)
         self.log("train_loss", train_loss)
         self.log_acc(out, batch[-1], tag="train_acc")
@@ -86,10 +99,6 @@ class GLVQ(SupervisedPrototypeModel):
             test_loss += batch_loss.item()
         self.log("test_loss", test_loss)
 
-    # TODO
-    # def predict_step(self, batch, batch_idx, dataloader_idx=None):
-    #     pass
-
 
 class SiameseGLVQ(GLVQ):
     """GLVQ in a Siamese setting.
@@ -99,6 +108,7 @@ class SiameseGLVQ(GLVQ):
     transformation pipeline are only learned from the inputs.
 
     """
+
     def __init__(self,
                  hparams,
                  backbone=torch.nn.Identity(),
@@ -109,32 +119,17 @@ class SiameseGLVQ(GLVQ):
         self.backbone = backbone
         self.both_path_gradients = both_path_gradients
 
-    def configure_optimizers(self):
-        proto_opt = self.optimizer(self.proto_layer.parameters(),
-                                   lr=self.hparams.proto_lr)
-        # Only add a backbone optimizer if backbone has trainable parameters
-        if (bb_params := list(self.backbone.parameters())):
-            bb_opt = self.optimizer(bb_params, lr=self.hparams.bb_lr)
-            optimizers = [proto_opt, bb_opt]
-        else:
-            optimizers = [proto_opt]
-        if self.lr_scheduler is not None:
-            schedulers = []
-            for optimizer in optimizers:
-                scheduler = self.lr_scheduler(optimizer,
-                                              **self.lr_scheduler_kwargs)
-                schedulers.append(scheduler)
-            return optimizers, schedulers
-        else:
-            return optimizers
-
     def compute_distances(self, x):
         protos, _ = self.proto_layer()
-        x, protos = [arr.view(arr.size(0), -1) for arr in (x, protos)]
+        x, protos = (arr.view(arr.size(0), -1) for arr in (x, protos))
         latent_x = self.backbone(x)
-        self.backbone.requires_grad_(self.both_path_gradients)
+
+        bb_grad = any([el.requires_grad for el in self.backbone.parameters()])
+
+        self.backbone.requires_grad_(bb_grad and self.both_path_gradients)
         latent_protos = self.backbone(protos)
-        self.backbone.requires_grad_(True)
+        self.backbone.requires_grad_(bb_grad)
+
         distances = self.distance_layer(latent_x, latent_protos)
         return distances
 
@@ -164,6 +159,7 @@ class LVQMLN(SiameseGLVQ):
     rather in the embedding space.
 
     """
+
     def compute_distances(self, x):
         latent_protos, _ = self.proto_layer()
         latent_x = self.backbone(x)
@@ -179,17 +175,22 @@ class GRLVQ(SiameseGLVQ):
     TODO Make a RelevanceLayer. `bb_lr` is ignored otherwise.
 
     """
+    _relevances: torch.Tensor
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
         # Additional parameters
-        relevances = torch.ones(self.hparams.input_dim, device=self.device)
+        relevances = torch.ones(self.hparams["input_dim"], device=self.device)
         self.register_parameter("_relevances", Parameter(relevances))
 
         # Override the backbone
-        self.backbone = LambdaLayer(lambda x: x @ torch.diag(self._relevances),
+        self.backbone = LambdaLayer(self._apply_relevances,
                                     name="relevance scaling")
 
+    def _apply_relevances(self, x):
+        return x @ torch.diag(self._relevances)
+
     @property
     def relevance_profile(self):
         return self._relevances.detach().cpu()
@@ -204,22 +205,27 @@ class SiameseGMLVQ(SiameseGLVQ):
     Implemented as a Siamese network with a linear transformation backbone.
 
     """
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
         # Override the backbone
-        self.backbone = torch.nn.Linear(self.hparams.input_dim,
-                                        self.hparams.latent_dim,
-                                        bias=False)
+        omega_initializer = kwargs.get("omega_initializer",
+                                       EyeLinearTransformInitializer())
+        self.backbone = LinearTransform(
+            self.hparams["input_dim"],
+            self.hparams["latent_dim"],
+            initializer=omega_initializer,
+        )
 
     @property
     def omega_matrix(self):
-        return self.backbone.weight.detach().cpu()
+        return self.backbone.weights
 
     @property
     def lambda_matrix(self):
-        omega = self.backbone.weight  # (latent_dim, input_dim)
-        lam = omega.T @ omega
+        omega = self.backbone.weights  # (input_dim, latent_dim)
+        lam = omega @ omega.T
         return lam.detach().cpu()
 
 
@@ -230,23 +236,31 @@ class GMLVQ(GLVQ):
     function. This makes it easier to implement a localized variant.
 
     """
+
+    # Parameters
+    _omega: torch.Tensor
+
     def __init__(self, hparams, **kwargs):
         distance_fn = kwargs.pop("distance_fn", omega_distance)
         super().__init__(hparams, distance_fn=distance_fn, **kwargs)
 
         # Additional parameters
         omega_initializer = kwargs.get("omega_initializer",
-                                       EyeTransformInitializer())
-        omega = omega_initializer.generate(self.hparams.input_dim,
-                                           self.hparams.latent_dim)
+                                       EyeLinearTransformInitializer())
+        omega = omega_initializer.generate(self.hparams["input_dim"],
+                                           self.hparams["latent_dim"])
         self.register_parameter("_omega", Parameter(omega))
-        self.backbone = LambdaLayer(lambda x: x @ self._omega,
-                                    name="omega matrix")
 
     @property
     def omega_matrix(self):
         return self._omega.detach().cpu()
 
+    @property
+    def lambda_matrix(self):
+        omega = self._omega.detach()  # (input_dim, latent_dim)
+        lam = omega @ omega.T
+        return lam.detach().cpu()
+
     def compute_distances(self, x):
         protos, _ = self.proto_layer()
         distances = self.distance_layer(x, protos, self._omega)
@@ -258,6 +272,7 @@ class GMLVQ(GLVQ):
 
 class LGMLVQ(GMLVQ):
     """Localized and Generalized Matrix Learning Vector Quantization."""
+
     def __init__(self, hparams, **kwargs):
         distance_fn = kwargs.pop("distance_fn", lomega_distance)
         super().__init__(hparams, distance_fn=distance_fn, **kwargs)
@@ -265,15 +280,59 @@ class LGMLVQ(GMLVQ):
         # Re-register `_omega` to override the one from the super class.
         omega = torch.randn(
             self.num_prototypes,
-            self.hparams.input_dim,
-            self.hparams.latent_dim,
+            self.hparams["input_dim"],
+            self.hparams["latent_dim"],
             device=self.device,
         )
         self.register_parameter("_omega", Parameter(omega))
 
 
+class GTLVQ(LGMLVQ):
+    """Localized and Generalized Tangent Learning Vector Quantization."""
+
+    def __init__(self, hparams, **kwargs):
+        distance_fn = kwargs.pop("distance_fn", ltangent_distance)
+        super().__init__(hparams, distance_fn=distance_fn, **kwargs)
+
+        omega_initializer = kwargs.get("omega_initializer")
+
+        if omega_initializer is not None:
+            subspace = omega_initializer.generate(
+                self.hparams["input_dim"],
+                self.hparams["latent_dim"],
+            )
+            omega = torch.repeat_interleave(
+                subspace.unsqueeze(0),
+                self.num_prototypes,
+                dim=0,
+            )
+        else:
+            omega = torch.rand(
+                self.num_prototypes,
+                self.hparams["input_dim"],
+                self.hparams["latent_dim"],
+                device=self.device,
+            )
+
+        # Re-register `_omega` to override the one from the super class.
+        self.register_parameter("_omega", Parameter(omega))
+
+    def on_train_batch_end(self, outputs, batch, batch_idx):
+        with torch.no_grad():
+            self._omega.copy_(orthogonalization(self._omega))
+
+
+class SiameseGTLVQ(SiameseGLVQ, GTLVQ):
+    """Generalized Tangent Learning Vector Quantization.
+
+    Implemented as a Siamese network with a linear transformation backbone.
+
+    """
+
+
 class GLVQ1(GLVQ):
     """Generalized Learning Vector Quantization 1."""
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
         self.loss = LossLayer(lvq1_loss)
@@ -282,6 +341,7 @@ class GLVQ1(GLVQ):
 
 class GLVQ21(GLVQ):
     """Generalized Learning Vector Quantization 2.1."""
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
         self.loss = LossLayer(lvq21_loss)
@@ -304,3 +364,18 @@ class ImageGMLVQ(ImagePrototypesMixin, GMLVQ):
     after updates.
 
     """
+
+
+class ImageGTLVQ(ImagePrototypesMixin, GTLVQ):
+    """GTLVQ for training on image data.
+
+    GTLVQ model that constrains the prototypes to the range [0, 1] by clamping
+    after updates.
+
+    """
+
+    def on_train_batch_end(self, outputs, batch, batch_idx):
+        """Constrain the components to the range [0, 1] by clamping after updates."""
+        self.proto_layer.components.data.clamp_(0.0, 1.0)
+        with torch.no_grad():
+            self._omega.copy_(orthogonalization(self._omega))

src/prototorch/models/knn.py

@@ -2,17 +2,22 @@
 
 import warnings
 
-from ..core.competitions import KNNC
-from ..core.components import LabeledComponents
-from ..core.initializers import LiteralCompInitializer, LiteralLabelsInitializer
-from ..utils.utils import parse_data_arg
+from prototorch.core.competitions import KNNC
+from prototorch.core.components import LabeledComponents
+from prototorch.core.initializers import (
+    LiteralCompInitializer,
+    LiteralLabelsInitializer,
+)
+from prototorch.utils.utils import parse_data_arg
+
 from .abstract import SupervisedPrototypeModel
 
 
 class KNN(SupervisedPrototypeModel):
     """K-Nearest-Neighbors classification algorithm."""
+
     def __init__(self, hparams, **kwargs):
-        super().__init__(hparams, **kwargs)
+        super().__init__(hparams, skip_proto_layer=True, **kwargs)
 
         # Default hparams
         self.hparams.setdefault("k", 1)
@@ -24,18 +29,15 @@ class KNN(SupervisedPrototypeModel):
 
         # Layers
         self.proto_layer = LabeledComponents(
-            distribution=[],
+            distribution=len(data) * [1],
             components_initializer=LiteralCompInitializer(data),
             labels_initializer=LiteralLabelsInitializer(targets))
         self.competition_layer = KNNC(k=self.hparams.k)
 
-    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
+    def training_step(self, train_batch, batch_idx):
         return 1  # skip training step
 
-    def on_train_batch_start(self,
-                             train_batch,
-                             batch_idx,
-                             dataloader_idx=None):
+    def on_train_batch_start(self, train_batch, batch_idx):
         warnings.warn("k-NN has no training, skipping!")
         return -1
 

src/prototorch/models/lvq.py

@@ -0,0 +1,128 @@
+"""LVQ models that are optimized using non-gradient methods."""
+
+import logging
+
+from prototorch.core.losses import _get_dp_dm
+from prototorch.nn.activations import get_activation
+from prototorch.nn.wrappers import LambdaLayer
+
+from .abstract import NonGradientMixin
+from .glvq import GLVQ
+
+
+class LVQ1(NonGradientMixin, GLVQ):
+    """Learning Vector Quantization 1."""
+
+    def training_step(self, train_batch, batch_idx):
+        protos, plables = self.proto_layer()
+        x, y = train_batch
+        dis = self.compute_distances(x)
+        # TODO Vectorized implementation
+
+        for xi, yi in zip(x, y):
+            d = self.compute_distances(xi.view(1, -1))
+            preds = self.competition_layer(d, plabels)
+            w = d.argmin(1)
+            if yi == preds:
+                shift = xi - protos[w]
+            else:
+                shift = protos[w] - xi
+            updated_protos = protos + 0.0
+            updated_protos[w] = protos[w] + (self.hparams.lr * shift)
+            self.proto_layer.load_state_dict({"_components": updated_protos},
+                                             strict=False)
+
+        logging.debug(f"dis={dis}")
+        logging.debug(f"y={y}")
+        # Logging
+        self.log_acc(dis, y, tag="train_acc")
+
+        return None
+
+
+class LVQ21(NonGradientMixin, GLVQ):
+    """Learning Vector Quantization 2.1."""
+
+    def training_step(self, train_batch, batch_idx):
+        protos, plabels = self.proto_layer()
+
+        x, y = train_batch
+        dis = self.compute_distances(x)
+        # TODO Vectorized implementation
+
+        for xi, yi in zip(x, y):
+            xi = xi.view(1, -1)
+            yi = yi.view(1, )
+            d = self.compute_distances(xi)
+            (_, wp), (_, wn) = _get_dp_dm(d, yi, plabels, with_indices=True)
+            shiftp = xi - protos[wp]
+            shiftn = protos[wn] - xi
+            updated_protos = protos + 0.0
+            updated_protos[wp] = protos[wp] + (self.hparams.lr * shiftp)
+            updated_protos[wn] = protos[wn] + (self.hparams.lr * shiftn)
+            self.proto_layer.load_state_dict({"_components": updated_protos},
+                                             strict=False)
+
+        # Logging
+        self.log_acc(dis, y, tag="train_acc")
+
+        return None
+
+
+class MedianLVQ(NonGradientMixin, GLVQ):
+    """Median LVQ
+
+    # TODO Avoid computing distances over and over
+
+    """
+
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+
+        self.transfer_layer = LambdaLayer(
+            get_activation(self.hparams.transfer_fn))
+
+    def _f(self, x, y, protos, plabels):
+        d = self.distance_layer(x, protos)
+        dp, dm = _get_dp_dm(d, y, plabels)
+        mu = (dp - dm) / (dp + dm)
+        invmu = -1.0 * mu
+        f = self.transfer_layer(invmu, beta=self.hparams.transfer_beta) + 1.0
+        return f
+
+    def expectation(self, x, y, protos, plabels):
+        f = self._f(x, y, protos, plabels)
+        gamma = f / f.sum()
+        return gamma
+
+    def lower_bound(self, x, y, protos, plabels, gamma):
+        f = self._f(x, y, protos, plabels)
+        lower_bound = (gamma * f.log()).sum()
+        return lower_bound
+
+    def training_step(self, train_batch, batch_idx):
+        protos, plabels = self.proto_layer()
+
+        x, y = train_batch
+        dis = self.compute_distances(x)
+
+        for i, _ in enumerate(protos):
+            # Expectation step
+            gamma = self.expectation(x, y, protos, plabels)
+            lower_bound = self.lower_bound(x, y, protos, plabels, gamma)
+
+            # Maximization step
+            _protos = protos + 0
+            for k, xk in enumerate(x):
+                _protos[i] = xk
+                _lower_bound = self.lower_bound(x, y, _protos, plabels, gamma)
+                if _lower_bound > lower_bound:
+                    logging.debug(f"Updating prototype {i} to data {k}...")
+                    self.proto_layer.load_state_dict({"_components": _protos},
+                                                     strict=False)
+                    break
+
+        # Logging
+        self.log_acc(dis, y, tag="train_acc")
+
+        return None

src/prototorch/models/probabilistic.py

@@ -1,48 +1,60 @@
 """Probabilistic GLVQ methods"""
 
 import torch
+from prototorch.core.losses import nllr_loss, rslvq_loss
+from prototorch.core.pooling import (
+    stratified_min_pooling,
+    stratified_sum_pooling,
+)
+from prototorch.nn.wrappers import LossLayer
 
-from ..core.losses import nllr_loss, rslvq_loss
-from ..core.pooling import stratified_min_pooling, stratified_sum_pooling
-from ..nn.wrappers import LambdaLayer, LossLayer
 from .extras import GaussianPrior, RankScaledGaussianPrior
 from .glvq import GLVQ, SiameseGMLVQ
 
 
 class CELVQ(GLVQ):
     """Cross-Entropy Learning Vector Quantization."""
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
         # Loss
         self.loss = torch.nn.CrossEntropyLoss()
 
-    def shared_step(self, batch, batch_idx, optimizer_idx=None):
+    def shared_step(self, batch, batch_idx):
         x, y = batch
         out = self.compute_distances(x)  # [None, num_protos]
-        plabels = self.proto_layer.labels
+        _, plabels = self.proto_layer()
         winning = stratified_min_pooling(out, plabels)  # [None, num_classes]
         probs = -1.0 * winning
         batch_loss = self.loss(probs, y.long())
-        loss = batch_loss.sum(dim=0)
+        loss = batch_loss.sum()
         return out, loss
 
 
 class ProbabilisticLVQ(GLVQ):
+
     def __init__(self, hparams, rejection_confidence=0.0, **kwargs):
         super().__init__(hparams, **kwargs)
 
-        self.conditional_distribution = None
         self.rejection_confidence = rejection_confidence
+        self._conditional_distribution = None
 
     def forward(self, x):
         distances = self.compute_distances(x)
+
         conditional = self.conditional_distribution(distances)
         prior = (1. / self.num_prototypes) * torch.ones(self.num_prototypes,
                                                         device=self.device)
         posterior = conditional * prior
+
         plabels = self.proto_layer._labels
-        y_pred = stratified_sum_pooling(posterior, plabels)
+        if isinstance(plabels, torch.LongTensor) or isinstance(
+                plabels, torch.cuda.LongTensor):  # type: ignore
+            y_pred = stratified_sum_pooling(posterior, plabels)  # type: ignore
+        else:
+            raise ValueError("Labels must be LongTensor.")
+
         return y_pred
 
     def predict(self, x):
@@ -51,29 +63,47 @@ class ProbabilisticLVQ(GLVQ):
         prediction[confidence < self.rejection_confidence] = -1
         return prediction
 
-    def training_step(self, batch, batch_idx, optimizer_idx=None):
+    def training_step(self, batch, batch_idx):
         x, y = batch
         out = self.forward(x)
-        plabels = self.proto_layer.labels
+        _, plabels = self.proto_layer()
         batch_loss = self.loss(out, y, plabels)
-        loss = batch_loss.sum(dim=0)
+        loss = batch_loss.sum()
         return loss
 
+    def conditional_distribution(self, distances):
+        """Conditional distribution of distances."""
+        if self._conditional_distribution is None:
+            raise ValueError("Conditional distribution is not set.")
+        return self._conditional_distribution(distances)
+
 
 class SLVQ(ProbabilisticLVQ):
     """Soft Learning Vector Quantization."""
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+
+        # Default hparams
+        self.hparams.setdefault("variance", 1.0)
+        variance = self.hparams.get("variance")
+
+        self._conditional_distribution = GaussianPrior(variance)
         self.loss = LossLayer(nllr_loss)
-        self.conditional_distribution = GaussianPrior(self.hparams.variance)
 
 
 class RSLVQ(ProbabilisticLVQ):
     """Robust Soft Learning Vector Quantization."""
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+
+        # Default hparams
+        self.hparams.setdefault("variance", 1.0)
+        variance = self.hparams.get("variance")
+
+        self._conditional_distribution = GaussianPrior(variance)
         self.loss = LossLayer(rslvq_loss)
-        self.conditional_distribution = GaussianPrior(self.hparams.variance)
 
 
 class PLVQ(ProbabilisticLVQ, SiameseGMLVQ):
@@ -81,16 +111,21 @@ class PLVQ(ProbabilisticLVQ, SiameseGMLVQ):
 
     TODO: Use Backbone LVQ instead
     """
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.conditional_distribution = RankScaledGaussianPrior(
-            self.hparams.lambd)
+
+        # Default hparams
+        self.hparams.setdefault("lambda", 1.0)
+        lam = self.hparams.get("lambda", 1.0)
+
+        self.conditional_distribution = RankScaledGaussianPrior(lam)
         self.loss = torch.nn.KLDivLoss()
 
     # FIXME
-    # def training_step(self, batch, batch_idx, optimizer_idx=None):
+    # def training_step(self, batch, batch_idx):
     #     x, y = batch
     #     y_pred = self(x)
     #     batch_loss = self.loss(y_pred, y)
-    #     loss = batch_loss.sum(dim=0)
+    #     loss = batch_loss.sum()
     #     return loss

src/prototorch/models/unsupervised.py

@@ -2,11 +2,10 @@
 
 import numpy as np
 import torch
+from prototorch.core.competitions import wtac
+from prototorch.core.distances import squared_euclidean_distance
+from prototorch.core.losses import NeuralGasEnergy
 
-from ..core.competitions import wtac
-from ..core.distances import squared_euclidean_distance
-from ..core.losses import NeuralGasEnergy
-from ..nn.wrappers import LambdaLayer
 from .abstract import NonGradientMixin, UnsupervisedPrototypeModel
 from .callbacks import GNGCallback
 from .extras import ConnectionTopology
@@ -18,6 +17,8 @@ class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
     TODO Allow non-2D grids
 
     """
+    _grid: torch.Tensor
+
     def __init__(self, hparams, **kwargs):
         h, w = hparams.get("shape")
         # Ignore `num_prototypes`
@@ -34,7 +35,7 @@ class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
 
         # Additional parameters
         x, y = torch.arange(h), torch.arange(w)
-        grid = torch.stack(torch.meshgrid(x, y), dim=-1)
+        grid = torch.stack(torch.meshgrid(x, y, indexing="ij"), dim=-1)
         self.register_buffer("_grid", grid)
         self._sigma = self.hparams.sigma
         self._lr = self.hparams.lr
@@ -53,14 +54,16 @@ class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
         grid = self._grid.view(-1, 2)
         gd = squared_euclidean_distance(wp, grid)
         nh = torch.exp(-gd / self._sigma**2)
-        protos = self.proto_layer.components
+        protos = self.proto_layer()
         diff = x.unsqueeze(dim=1) - protos
         delta = self._lr * self.hparams.alpha * nh.unsqueeze(-1) * diff
         updated_protos = protos + delta.sum(dim=0)
-        self.proto_layer.load_state_dict({"_components": updated_protos},
-                                         strict=False)
+        self.proto_layer.load_state_dict(
+            {"_components": updated_protos},
+            strict=False,
+        )
 
-    def training_epoch_end(self, training_step_outputs):
+    def on_training_epoch_end(self, training_step_outputs):
         self._sigma = self.hparams.sigma * np.exp(
             -self.current_epoch / self.trainer.max_epochs)
 
@@ -69,6 +72,7 @@ class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
 
 
 class HeskesSOM(UnsupervisedPrototypeModel):
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
@@ -78,6 +82,7 @@ class HeskesSOM(UnsupervisedPrototypeModel):
 
 
 class NeuralGas(UnsupervisedPrototypeModel):
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
@@ -85,13 +90,13 @@ class NeuralGas(UnsupervisedPrototypeModel):
         self.save_hyperparameters(hparams)
 
         # Default hparams
-        self.hparams.setdefault("agelimit", 10)
+        self.hparams.setdefault("age_limit", 10)
         self.hparams.setdefault("lm", 1)
 
-        self.energy_layer = NeuralGasEnergy(lm=self.hparams.lm)
+        self.energy_layer = NeuralGasEnergy(lm=self.hparams["lm"])
         self.topology_layer = ConnectionTopology(
-            agelimit=self.hparams.agelimit,
-            num_prototypes=self.hparams.num_prototypes,
+            agelimit=self.hparams["age_limit"],
+            num_prototypes=self.hparams["num_prototypes"],
         )
 
     def training_step(self, train_batch, batch_idx):
@@ -104,12 +109,10 @@ class NeuralGas(UnsupervisedPrototypeModel):
         self.log("loss", loss)
         return loss
 
-    # def training_epoch_end(self, training_step_outputs):
-    #     print(f"{self.trainer.lr_schedulers}")
-    #     print(f"{self.trainer.lr_schedulers[0]['scheduler'].optimizer}")
-
 
 class GrowingNeuralGas(NeuralGas):
+    errors: torch.Tensor
+
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
@@ -118,7 +121,10 @@ class GrowingNeuralGas(NeuralGas):
         self.hparams.setdefault("insert_reduction", 0.1)
         self.hparams.setdefault("insert_freq", 10)
 
-        errors = torch.zeros(self.hparams.num_prototypes, device=self.device)
+        errors = torch.zeros(
+            self.hparams["num_prototypes"],
+            device=self.device,
+        )
         self.register_buffer("errors", errors)
 
     def training_step(self, train_batch, _batch_idx):
@@ -132,8 +138,8 @@ class GrowingNeuralGas(NeuralGas):
         mask[torch.arange(len(mask)), winner] = 1.0
         dp = d * mask
 
-        self.errors += torch.sum(dp * dp, dim=0)
-        self.errors *= self.hparams.step_reduction
+        self.errors += torch.sum(dp * dp)
+        self.errors *= self.hparams["step_reduction"]
 
         self.topology_layer(d)
         self.log("loss", loss)
@@ -141,6 +147,8 @@ class GrowingNeuralGas(NeuralGas):
 
     def configure_callbacks(self):
         return [
-            GNGCallback(reduction=self.hparams.insert_reduction,
-                        freq=self.hparams.insert_freq)
+            GNGCallback(
+                reduction=self.hparams["insert_reduction"],
+                freq=self.hparams["insert_freq"],
+            )
         ]

src/prototorch/models/vis.py

@@ -1,20 +1,28 @@
 """Visualization Callbacks."""
 
+import warnings
+from typing import Sized
+
 import numpy as np
 import pytorch_lightning as pl
 import torch
 import torchvision
 from matplotlib import pyplot as plt
+from prototorch.utils.colors import get_colors, get_legend_handles
+from prototorch.utils.utils import mesh2d
+from pytorch_lightning.loggers import TensorBoardLogger
 from torch.utils.data import DataLoader, Dataset
 
-from ..utils.utils import mesh2d
-
 
 class Vis2DAbstract(pl.Callback):
+
     def __init__(self,
-                 data,
+                 data=None,
                  title="Prototype Visualization",
                  cmap="viridis",
+                 xlabel="Data dimension 1",
+                 ylabel="Data dimension 2",
+                 legend_labels=None,
                  border=0.1,
                  resolution=100,
                  flatten_data=True,
@@ -27,24 +35,36 @@ class Vis2DAbstract(pl.Callback):
                  block=False):
         super().__init__()
 
-        if isinstance(data, Dataset):
-            x, y = next(iter(DataLoader(data, batch_size=len(data))))
-        elif isinstance(data, torch.utils.data.DataLoader):
-            x = torch.tensor([])
-            y = torch.tensor([])
-            for x_b, y_b in data:
-                x = torch.cat([x, x_b])
-                y = torch.cat([y, y_b])
+        if data:
+            if isinstance(data, Dataset):
+                if isinstance(data, Sized):
+                    x, y = next(iter(DataLoader(data, batch_size=len(data))))
+                else:
+                    # TODO: Add support for non-sized datasets
+                    raise NotImplementedError(
+                        "Data must be a dataset with a __len__ method.")
+            elif isinstance(data, DataLoader):
+                x = torch.tensor([])
+                y = torch.tensor([])
+                for x_b, y_b in data:
+                    x = torch.cat([x, x_b])
+                    y = torch.cat([y, y_b])
+            else:
+                x, y = data
+
+            if flatten_data:
+                x = x.reshape(len(x), -1)
+
+            self.x_train = x
+            self.y_train = y
         else:
-            x, y = data
-
-        if flatten_data:
-            x = x.reshape(len(x), -1)
-
-        self.x_train = x
-        self.y_train = y
+            self.x_train = None
+            self.y_train = None
 
         self.title = title
+        self.xlabel = xlabel
+        self.ylabel = ylabel
+        self.legend_labels = legend_labels
         self.fig = plt.figure(self.title)
         self.cmap = cmap
         self.border = border
@@ -63,14 +83,12 @@ class Vis2DAbstract(pl.Callback):
                 return False
         return True
 
-    def setup_ax(self, xlabel=None, ylabel=None):
+    def setup_ax(self):
         ax = self.fig.gca()
         ax.cla()
         ax.set_title(self.title)
-        if xlabel:
-            ax.set_xlabel("Data dimension 1")
-        if ylabel:
-            ax.set_ylabel("Data dimension 2")
+        ax.set_xlabel(self.xlabel)
+        ax.set_ylabel(self.ylabel)
         if self.axis_off:
             ax.axis("off")
         return ax
@@ -113,42 +131,47 @@ class Vis2DAbstract(pl.Callback):
             else:
                 plt.show(block=self.block)
 
+    def on_train_epoch_end(self, trainer, pl_module):
+        if not self.precheck(trainer):
+            return True
+        self.visualize(pl_module)
+        self.log_and_display(trainer, pl_module)
+
     def on_train_end(self, trainer, pl_module):
         plt.close()
 
+    def visualize(self, pl_module):
+        raise NotImplementedError
+
 
 class VisGLVQ2D(Vis2DAbstract):
-    def on_epoch_end(self, trainer, pl_module):
-        if not self.precheck(trainer):
-            return True
 
+    def visualize(self, pl_module):
         protos = pl_module.prototypes
         plabels = pl_module.prototype_labels
         x_train, y_train = self.x_train, self.y_train
-        ax = self.setup_ax(xlabel="Data dimension 1",
-                           ylabel="Data dimension 2")
-        self.plot_data(ax, x_train, y_train)
+        ax = self.setup_ax()
         self.plot_protos(ax, protos, plabels)
-        x = np.vstack((x_train, protos))
-        mesh_input, xx, yy = mesh2d(x, self.border, self.resolution)
+        if x_train is not None:
+            self.plot_data(ax, x_train, y_train)
+            mesh_input, xx, yy = mesh2d(np.vstack([x_train, protos]),
+                                        self.border, self.resolution)
+        else:
+            mesh_input, xx, yy = mesh2d(protos, self.border, self.resolution)
         _components = pl_module.proto_layer._components
         mesh_input = torch.from_numpy(mesh_input).type_as(_components)
         y_pred = pl_module.predict(mesh_input)
         y_pred = y_pred.cpu().reshape(xx.shape)
         ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
 
-        self.log_and_display(trainer, pl_module)
-
 
 class VisSiameseGLVQ2D(Vis2DAbstract):
+
     def __init__(self, *args, map_protos=True, **kwargs):
         super().__init__(*args, **kwargs)
         self.map_protos = map_protos
 
-    def on_epoch_end(self, trainer, pl_module):
-        if not self.precheck(trainer):
-            return True
-
+    def visualize(self, pl_module):
         protos = pl_module.prototypes
         plabels = pl_module.prototype_labels
         x_train, y_train = self.x_train, self.y_train
@@ -175,18 +198,42 @@ class VisSiameseGLVQ2D(Vis2DAbstract):
         y_pred = y_pred.cpu().reshape(xx.shape)
         ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
 
-        self.log_and_display(trainer, pl_module)
+
+class VisGMLVQ2D(Vis2DAbstract):
+
+    def __init__(self, *args, ev_proj=True, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.ev_proj = ev_proj
+
+    def visualize(self, pl_module):
+        protos = pl_module.prototypes
+        plabels = pl_module.prototype_labels
+        x_train, y_train = self.x_train, self.y_train
+        device = pl_module.device
+        omega = pl_module._omega.detach()
+        lam = omega @ omega.T
+        u, _, _ = torch.pca_lowrank(lam, q=2)
+        with torch.no_grad():
+            x_train = torch.Tensor(x_train).to(device)
+            x_train = x_train @ u
+            x_train = x_train.cpu().detach()
+        if self.show_protos:
+            with torch.no_grad():
+                protos = torch.Tensor(protos).to(device)
+                protos = protos @ u
+                protos = protos.cpu().detach()
+        ax = self.setup_ax()
+        self.plot_data(ax, x_train, y_train)
+        if self.show_protos:
+            self.plot_protos(ax, protos, plabels)
 
 
 class VisCBC2D(Vis2DAbstract):
-    def on_epoch_end(self, trainer, pl_module):
-        if not self.precheck(trainer):
-            return True
 
+    def visualize(self, pl_module):
         x_train, y_train = self.x_train, self.y_train
         protos = pl_module.components
-        ax = self.setup_ax(xlabel="Data dimension 1",
-                           ylabel="Data dimension 2")
+        ax = self.setup_ax()
         self.plot_data(ax, x_train, y_train)
         self.plot_protos(ax, protos, "w")
         x = np.vstack((x_train, protos))
@@ -198,20 +245,15 @@ class VisCBC2D(Vis2DAbstract):
 
         ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
 
-        self.log_and_display(trainer, pl_module)
-
 
 class VisNG2D(Vis2DAbstract):
-    def on_epoch_end(self, trainer, pl_module):
-        if not self.precheck(trainer):
-            return True
 
+    def visualize(self, pl_module):
         x_train, y_train = self.x_train, self.y_train
         protos = pl_module.prototypes
         cmat = pl_module.topology_layer.cmat.cpu().numpy()
 
-        ax = self.setup_ax(xlabel="Data dimension 1",
-                           ylabel="Data dimension 2")
+        ax = self.setup_ax()
         self.plot_data(ax, x_train, y_train)
         self.plot_protos(ax, protos, "w")
 
@@ -225,10 +267,27 @@ class VisNG2D(Vis2DAbstract):
                         "k-",
                     )
 
-        self.log_and_display(trainer, pl_module)
+
+class VisSpectralProtos(Vis2DAbstract):
+
+    def visualize(self, pl_module):
+        protos = pl_module.prototypes
+        plabels = pl_module.prototype_labels
+        ax = self.setup_ax()
+        colors = get_colors(vmax=max(plabels), vmin=min(plabels))
+        for p, pl in zip(protos, plabels):
+            ax.plot(p, c=colors[int(pl)])
+        if self.legend_labels:
+            handles = get_legend_handles(
+                colors,
+                self.legend_labels,
+                marker="lines",
+            )
+            ax.legend(handles=handles)
 
 
 class VisImgComp(Vis2DAbstract):
+
     def __init__(self,
                  *args,
                  random_data=0,
@@ -244,32 +303,45 @@ class VisImgComp(Vis2DAbstract):
         self.add_embedding = add_embedding
         self.embedding_data = embedding_data
 
-    def on_train_start(self, trainer, pl_module):
-        tb = pl_module.logger.experiment
-        if self.add_embedding:
-            ind = np.random.choice(len(self.x_train),
-                                   size=self.embedding_data,
-                                   replace=False)
-            data = self.x_train[ind]
-            # print(f"{data.shape=}")
-            # print(f"{self.y_train[ind].shape=}")
-            tb.add_embedding(data.view(len(ind), -1),
-                             label_img=data,
-                             global_step=None,
-                             tag="Data Embedding",
-                             metadata=self.y_train[ind],
-                             metadata_header=None)
+    def on_train_start(self, _, pl_module):
+        if isinstance(pl_module.logger, TensorBoardLogger):
+            tb = pl_module.logger.experiment
 
-        if self.random_data:
-            ind = np.random.choice(len(self.x_train),
-                                   size=self.random_data,
-                                   replace=False)
-            data = self.x_train[ind]
-            grid = torchvision.utils.make_grid(data, nrow=self.num_columns)
-            tb.add_image(tag="Data",
-                         img_tensor=grid,
-                         global_step=None,
-                         dataformats=self.dataformats)
+            # Add embedding
+            if self.add_embedding:
+                if self.x_train is not None and self.y_train is not None:
+                    ind = np.random.choice(len(self.x_train),
+                                           size=self.embedding_data,
+                                           replace=False)
+                    data = self.x_train[ind]
+                    tb.add_embedding(data.view(len(ind), -1),
+                                     label_img=data,
+                                     global_step=None,
+                                     tag="Data Embedding",
+                                     metadata=self.y_train[ind],
+                                     metadata_header=None)
+                else:
+                    raise ValueError("No data for add embedding flag")
+
+            # Random Data
+            if self.random_data:
+                if self.x_train is not None:
+                    ind = np.random.choice(len(self.x_train),
+                                           size=self.random_data,
+                                           replace=False)
+                    data = self.x_train[ind]
+                    grid = torchvision.utils.make_grid(data,
+                                                       nrow=self.num_columns)
+                    tb.add_image(tag="Data",
+                                 img_tensor=grid,
+                                 global_step=None,
+                                 dataformats=self.dataformats)
+                else:
+                    raise ValueError("No data for random data flag")
+
+        else:
+            warnings.warn(
+                f"TensorBoardLogger is required, got {type(pl_module.logger)}")
 
     def add_to_tensorboard(self, trainer, pl_module):
         tb = pl_module.logger.experiment
@@ -283,14 +355,9 @@ class VisImgComp(Vis2DAbstract):
             dataformats=self.dataformats,
         )
 
-    def on_epoch_end(self, trainer, pl_module):
-        if not self.precheck(trainer):
-            return True
-
+    def visualize(self, pl_module):
         if self.show:
             components = pl_module.components
             grid = torchvision.utils.make_grid(components,
                                                nrow=self.num_columns)
             plt.imshow(grid.permute((1, 2, 0)).cpu(), cmap=self.cmap)
-
-        self.log_and_display(trainer, pl_module)

tests/test_.py

@@ -1,14 +0,0 @@
-"""prototorch.models test suite."""
-
-import unittest
-
-
-class TestDummy(unittest.TestCase):
-    def setUp(self):
-        pass
-
-    def test_dummy(self):
-        pass
-
-    def tearDown(self):
-        pass

tests/test_examples.sh

@@ -1,11 +1,27 @@
 #! /bin/bash
 
+
+# Read Flags
+gpu=0
+while [ -n "$1" ]; do
+	case "$1" in
+	    --gpu) gpu=1;;
+	    -g) gpu=1;;
+        *) path=$1;;
+	esac
+	shift
+done
+
+python --version
+echo "Using GPU: " $gpu
+
+# Loop
 failed=0
 
-for example in $(find $1 -maxdepth 1 -name "*.py")
+for example in $(find $path -maxdepth 1 -name "*.py")
 do
     echo  -n "$x" $example '... '
-    export DISPLAY= && python $example --fast_dev_run 1 &> run_log.txt
+    export DISPLAY= && python $example --fast_dev_run 1 --gpus $gpu &> run_log.txt
     if [[ $? -ne 0 ]]; then
         echo "FAILED!!"
         cat run_log.txt

tests/test_models.py

@@ -0,0 +1,193 @@
+"""prototorch.models test suite."""
+
+import prototorch.models
+
+
+def test_glvq_model_build():
+    model = prototorch.models.GLVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_glvq1_model_build():
+    model = prototorch.models.GLVQ1(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_glvq21_model_build():
+    model = prototorch.models.GLVQ1(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_gmlvq_model_build():
+    model = prototorch.models.GMLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 2,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_grlvq_model_build():
+    model = prototorch.models.GRLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_gtlvq_model_build():
+    model = prototorch.models.GTLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 4,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_lgmlvq_model_build():
+    model = prototorch.models.LGMLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 4,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_image_glvq_model_build():
+    model = prototorch.models.ImageGLVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(16),
+    )
+
+
+def test_image_gmlvq_model_build():
+    model = prototorch.models.ImageGMLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 16,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(16),
+    )
+
+
+def test_image_gtlvq_model_build():
+    model = prototorch.models.ImageGMLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 16,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(16),
+    )
+
+
+def test_siamese_glvq_model_build():
+    model = prototorch.models.SiameseGLVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(4),
+    )
+
+
+def test_siamese_gmlvq_model_build():
+    model = prototorch.models.SiameseGMLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 4,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(4),
+    )
+
+
+def test_siamese_gtlvq_model_build():
+    model = prototorch.models.SiameseGTLVQ(
+        {
+            "distribution": (3, 2),
+            "input_dim": 4,
+            "latent_dim": 2,
+        },
+        prototypes_initializer=prototorch.initializers.RNCI(4),
+    )
+
+
+def test_knn_model_build():
+    train_ds = prototorch.datasets.Iris(dims=[0, 2])
+    model = prototorch.models.KNN(dict(k=3), data=train_ds)
+
+
+def test_lvq1_model_build():
+    model = prototorch.models.LVQ1(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_lvq21_model_build():
+    model = prototorch.models.LVQ21(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_median_lvq_model_build():
+    model = prototorch.models.MedianLVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_celvq_model_build():
+    model = prototorch.models.CELVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_rslvq_model_build():
+    model = prototorch.models.RSLVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_slvq_model_build():
+    model = prototorch.models.SLVQ(
+        {"distribution": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_growing_neural_gas_model_build():
+    model = prototorch.models.GrowingNeuralGas(
+        {"num_prototypes": 5},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_kohonen_som_model_build():
+    model = prototorch.models.KohonenSOM(
+        {"shape": (3, 2)},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )
+
+
+def test_neural_gas_model_build():
+    model = prototorch.models.NeuralGas(
+        {"num_prototypes": 5},
+        prototypes_initializer=prototorch.initializers.RNCI(2),
+    )