build: bump version 1.0.0a2 → 1.0.0a3

.bumpversion.cfg

@@ -1,13 +1,15 @@
 [bumpversion]
-current_version = 0.7.1
+current_version = 1.0.0a3
 commit = True
 tag = True
-parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
-serialize = {major}.{minor}.{patch}
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)((?P<release>[a-zA-Z0-9_.-]+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}
+	{major}.{minor}.{patch}
 message = build: bump version {current_version} → {new_version}
 
-[bumpversion:file:pyproject.toml]
+[bumpversion:file:setup.py]
 
-[bumpversion:file:./src/prototorch/models/__init__.py]
+[bumpversion:file:./prototorch/models/__init__.py]
 
 [bumpversion:file:./docs/source/conf.py]

.github/workflows/examples.yml

@@ -6,16 +6,16 @@ name: examples
 on:
   push:
     paths:
-      - "examples/**.py"
+      - 'examples/**.py'
 jobs:
   cpu:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
       with:
-          python-version: "3.11"
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pythonapp.yml

@@ -6,42 +6,42 @@ name: tests
 on:
   push:
   pull_request:
-    branches: [master]
+    branches: [ master ]
 
 jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
       with:
-          python-version: "3.11"
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install .[all]
-      - uses: pre-commit/action@v3.0.0
+    - uses: pre-commit/action@v2.0.3
   compatibility:
     needs: style
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
         os: [ubuntu-latest, windows-latest]
         exclude:
+        - os: windows-latest
+          python-version: "3.7"
         - 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
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -56,18 +56,18 @@ jobs:
     needs: compatibility
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
       with:
-          python-version: "3.11"
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install .[all]
-          pip install build
+        pip install wheel
     - name: Build package
-        run: python -m build . -C verbose
+      run: python setup.py sdist bdist_wheel
     - name: Publish a Python distribution to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.pre-commit-config.yaml

@@ -2,52 +2,52 @@
 # See https://pre-commit.com/hooks.html for more hooks
 
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.2.0
   hooks:
   - id: trailing-whitespace
+    exclude: (^\.bumpversion\.cfg$|cli_messages\.py)
   - 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: v2.1.1
+- repo: https://github.com/myint/autoflake
+  rev: v1.4
   hooks:
   - id: autoflake
 
-  - repo: http://github.com/PyCQA/isort
-    rev: 5.12.0
+- repo: http://github.com/PyCQA/isort
+  rev: 5.10.1
   hooks:
   - id: isort
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.950
   hooks:
   - id: mypy
     files: prototorch
     additional_dependencies: [types-pkg_resources]
 
-  - repo: https://github.com/pre-commit/mirrors-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: v1.10.0
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.9.0
   hooks:
   - id: python-use-type-annotations
   - id: python-no-log-warn
   - id: python-check-blanket-noqa
 
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.7.0
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.32.1
   hooks:
   - id: pyupgrade
 
-  - repo: https://github.com/si-cim/gitlint
+- repo: https://github.com/si-cim/gitlint
   rev: v0.15.2-unofficial
   hooks:
   - id: gitlint

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.7.1"
+release = "1.0.0-a3"
 
 # -- General configuration ---------------------------------------------------
 

examples/cbc_iris.py

@@ -1,11 +1,12 @@
 """CBC example using the Iris dataset."""
+
 import argparse
 import warnings
 
 import prototorch as pt
 import pytorch_lightning as pl
-from lightning_fabric.utilities.seed import seed_everything
 from prototorch.models import CBC, VisCBC2D
+from pytorch_lightning.utilities.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -18,8 +19,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -53,10 +53,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/dynamic_pruning.py

@@ -7,13 +7,13 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -26,8 +26,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -84,10 +83,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             pruning,

examples/glvq_iris.py

@@ -7,8 +7,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.optim.lr_scheduler import ExponentialLR
 from torch.utils.data import DataLoader
@@ -21,8 +21,7 @@ if __name__ == "__main__":
     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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -56,10 +55,8 @@ if __name__ == "__main__":
     vis = VisGLVQ2D(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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/gmlvq_iris.py

@@ -6,8 +6,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.optim.lr_scheduler import ExponentialLR
 from torch.utils.data import DataLoader
@@ -22,8 +22,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -60,10 +59,8 @@ if __name__ == "__main__":
     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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],
@@ -74,5 +71,3 @@ if __name__ == "__main__":
 
     # Training loop
     trainer.fit(model, train_loader)
-
-    torch.save(model, "iris.pth")

examples/gmlvq_mnist.py

@@ -6,13 +6,13 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 from torchvision import transforms
@@ -26,8 +26,7 @@ if __name__ == "__main__":
     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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -97,10 +96,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             pruning,

examples/gmlvq_spiral.py

@@ -6,13 +6,13 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -25,8 +25,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -79,10 +78,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             es,

examples/gng_iris.py

@@ -7,8 +7,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -18,8 +18,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Reproducibility
@@ -52,10 +51,8 @@ if __name__ == "__main__":
     vis = VisNG2D(data=train_loader)
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/grlvq_iris.py

@@ -1,77 +0,0 @@
-"""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

@@ -6,13 +6,13 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 from torchvision import transforms
@@ -27,8 +27,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -101,10 +100,8 @@ if __name__ == "__main__":
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             pruning,

examples/gtlvq_moons.py

@@ -7,9 +7,9 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -19,8 +19,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Reproducibility
@@ -62,10 +61,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             es,

examples/knn_iris.py

@@ -18,8 +18,7 @@ warnings.filterwarnings("ignore", category=PossibleUserWarning)
 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -60,10 +59,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         max_epochs=1,
         callbacks=[
             vis,

examples/ksom_colors.py

@@ -7,10 +7,10 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader, TensorDataset
 
@@ -58,8 +58,7 @@ class Vis2DColorSOM(pl.Callback):
 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Reproducibility
@@ -105,10 +104,8 @@ if __name__ == "__main__":
     vis = Vis2DColorSOM(data=data)
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         max_epochs=500,
         callbacks=[
             vis,

examples/lgmlvq_moons.py

@@ -7,9 +7,9 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -19,8 +19,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Reproducibility
@@ -63,10 +62,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             es,

examples/lvqmln_iris.py

@@ -6,12 +6,12 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -39,8 +39,7 @@ class Backbone(torch.nn.Module):
 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -89,10 +88,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             pruning,

examples/median_lvq_iris.py

@@ -6,9 +6,9 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -20,8 +20,7 @@ if __name__ == "__main__":
     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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -54,10 +53,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             es,

examples/ng_iris.py

@@ -6,8 +6,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from sklearn.datasets import load_iris
 from sklearn.preprocessing import StandardScaler
@@ -23,8 +23,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Prepare and pre-process the dataset
@@ -61,10 +60,8 @@ if __name__ == "__main__":
     vis = VisNG2D(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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/rslvq_iris.py

@@ -6,8 +6,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -17,8 +17,7 @@ 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Reproducibility
@@ -55,10 +54,8 @@ if __name__ == "__main__":
     vis = VisGLVQ2D(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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/siamese_glvq_iris.py

@@ -6,8 +6,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -35,8 +35,7 @@ class Backbone(torch.nn.Module):
 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -51,7 +50,8 @@ if __name__ == "__main__":
     # Hyperparameters
     hparams = dict(
         distribution=[1, 2, 3],
-        lr=0.01,
+        proto_lr=0.01,
+        bb_lr=0.01,
     )
 
     # Initialize the backbone
@@ -69,10 +69,8 @@ if __name__ == "__main__":
     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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/siamese_gtlvq_iris.py

@@ -6,8 +6,8 @@ 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.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.utils.data import DataLoader
 
@@ -35,8 +35,7 @@ class Backbone(torch.nn.Module):
 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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Dataset
@@ -51,7 +50,8 @@ if __name__ == "__main__":
     # Hyperparameters
     hparams = dict(
         distribution=[1, 2, 3],
-        lr=0.01,
+        proto_lr=0.01,
+        bb_lr=0.01,
         input_dim=2,
         latent_dim=1,
     )
@@ -71,10 +71,8 @@ if __name__ == "__main__":
     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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
         ],

examples/warm_starting.py

@@ -6,7 +6,6 @@ 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,
@@ -15,6 +14,7 @@ from prototorch.models import (
     VisGLVQ2D,
 )
 from pytorch_lightning.callbacks import EarlyStopping
+from pytorch_lightning.utilities.seed import seed_everything
 from pytorch_lightning.utilities.warnings import PossibleUserWarning
 from torch.optim.lr_scheduler import ExponentialLR
 from torch.utils.data import DataLoader
@@ -27,8 +27,7 @@ if __name__ == "__main__":
     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)
+    parser = pl.Trainer.add_argparse_args(parser)
     args = parser.parse_args()
 
     # Prepare the data
@@ -55,9 +54,7 @@ if __name__ == "__main__":
 
     # Setup trainer for GNG
     trainer = pl.Trainer(
-        accelerator="cpu",
-        max_epochs=50 if args.fast_dev_run else
-        1000,  # 10 epochs fast dev run reproducible DIV error.
+        max_epochs=1000,
         callbacks=[
             es,
         ],
@@ -111,10 +108,8 @@ if __name__ == "__main__":
     )
 
     # 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,
+    trainer = pl.Trainer.from_argparse_args(
+        args,
         callbacks=[
             vis,
             pruning,

examples/y_architecture_example.py

@@ -0,0 +1,88 @@
+import prototorch as pt
+import pytorch_lightning as pl
+import torchmetrics
+from prototorch.core import SMCI
+from prototorch.y.callbacks import (
+    LogTorchmetricCallback,
+    PlotLambdaMatrixToTensorboard,
+    VisGMLVQ2D,
+)
+from prototorch.y.library.gmlvq import GMLVQ
+from pytorch_lightning.callbacks import EarlyStopping
+from torch.utils.data import DataLoader
+
+# ##############################################################################
+
+if __name__ == "__main__":
+
+    # ------------------------------------------------------------
+    # DATA
+    # ------------------------------------------------------------
+
+    # Dataset
+    train_ds = pt.datasets.Iris()
+
+    # Dataloader
+    train_loader = DataLoader(
+        train_ds,
+        batch_size=32,
+        num_workers=0,
+        shuffle=True,
+    )
+
+    # ------------------------------------------------------------
+    # HYPERPARAMETERS
+    # ------------------------------------------------------------
+
+    # Select Initializer
+    components_initializer = SMCI(train_ds)
+
+    # Define Hyperparameters
+    hyperparameters = GMLVQ.HyperParameters(
+        lr=dict(components_layer=0.1, _omega=0),
+        input_dim=4,
+        distribution=dict(
+            num_classes=3,
+            per_class=1,
+        ),
+        component_initializer=components_initializer,
+    )
+
+    # Create Model
+    model = GMLVQ(hyperparameters)
+
+    print(model)
+
+    # ------------------------------------------------------------
+    # TRAINING
+    # ------------------------------------------------------------
+
+    # Controlling Callbacks
+    stopping_criterion = LogTorchmetricCallback(
+        'recall',
+        torchmetrics.Recall,
+        num_classes=3,
+    )
+
+    es = EarlyStopping(
+        monitor=stopping_criterion.name,
+        mode="max",
+        patience=10,
+    )
+
+    # Visualization Callback
+    vis = VisGMLVQ2D(data=train_ds)
+
+    # Define trainer
+    trainer = pl.Trainer(
+        callbacks=[
+            vis,
+            stopping_criterion,
+            es,
+            PlotLambdaMatrixToTensorboard(),
+        ],
+        max_epochs=1000,
+    )
+
+    # Train
+    trainer.fit(model, train_loader)

prototorch/models/__init__.py

@@ -36,4 +36,4 @@ from .unsupervised import (
 )
 from .vis import *
 
-__version__ = "0.7.1"
+__version__ = "1.0.0-a3"

prototorch/models/abstract.py

@@ -22,7 +22,16 @@ from prototorch.nn.wrappers import LambdaLayer
 
 
 class ProtoTorchBolt(pl.LightningModule):
-    """All ProtoTorch models are ProtoTorch Bolts."""
+    """All ProtoTorch models are ProtoTorch Bolts.
+
+    hparams:
+        - lr: learning rate
+
+    kwargs:
+        - optimizer: optimizer class
+        - lr_scheduler: learning rate scheduler class
+        - lr_scheduler_kwargs: learning rate scheduler kwargs
+    """
 
     def __init__(self, hparams, **kwargs):
         super().__init__()
@@ -65,13 +74,18 @@ class ProtoTorchBolt(pl.LightningModule):
 
 
 class PrototypeModel(ProtoTorchBolt):
+    """Abstract Prototype Model
+
+    kwargs:
+        - distance_fn: distance function
+    """
     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, name="distance_fn")
+        self.distance_layer = LambdaLayer(distance_fn)
 
     @property
     def num_prototypes(self):
@@ -186,63 +200,20 @@ class SupervisedPrototypeModel(PrototypeModel):
 
     def log_acc(self, distances, targets, tag):
         preds = self.predict_from_distances(distances)
-        accuracy = torchmetrics.functional.accuracy(
-            preds.int(),
-            targets.int(),
-            "multiclass",
-            num_classes=self.num_classes,
-        )
+        accuracy = torchmetrics.functional.accuracy(preds.int(), targets.int())
+        # `.int()` because FloatTensors are assumed to be class probabilities
 
-        self.log(
-            tag,
+        self.log(tag,
                  accuracy,
                  on_step=False,
                  on_epoch=True,
                  prog_bar=True,
-            logger=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,
-        )
+        accuracy = torchmetrics.functional.accuracy(preds.int(), targets.int())
 
         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 = False
-
-    def training_step(self, train_batch, batch_idx):
-        raise NotImplementedError
-
-
-class ImagePrototypesMixin(ProtoTorchMixin):
-    """Mixin for models with image prototypes."""
-    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)
-
-    def get_prototype_grid(self, num_columns=2, return_channels_last=True):
-        from torchvision.utils import make_grid
-        grid = make_grid(self.components, nrow=num_columns)
-        if return_channels_last:
-            grid = grid.permute((1, 2, 0))
-        return grid.cpu()

prototorch/models/callbacks.py

@@ -40,8 +40,8 @@ class PruneLoserPrototypes(pl.Callback):
             return None
 
         ratios = pl_module.prototype_win_ratios.mean(dim=0)
-        to_prune = torch.arange(len(ratios))[ratios < self.threshold]
-        to_prune = to_prune.tolist()
+        to_prune_tensor = torch.arange(len(ratios))[ratios < self.threshold]
+        to_prune = to_prune_tensor.tolist()
         prune_labels = pl_module.prototype_labels[to_prune]
         if self.prune_quota_per_epoch > 0:
             to_prune = to_prune[:self.prune_quota_per_epoch]

prototorch/models/cbc.py

@@ -1,4 +1,5 @@
 import torch
+import torch.nn.functional as F
 import torchmetrics
 from prototorch.core.competitions import CBCC
 from prototorch.core.components import ReasoningComponents
@@ -7,12 +8,13 @@ from prototorch.core.losses import MarginLoss
 from prototorch.core.similarities import euclidean_similarity
 from prototorch.nn.wrappers import LambdaLayer
 
-from .abstract import ImagePrototypesMixin
 from .glvq import SiameseGLVQ
+from .mixins import ImagePrototypesMixin
 
 
 class CBC(SiameseGLVQ):
     """Classification-By-Components."""
+    proto_layer: ReasoningComponents
 
     def __init__(self, hparams, **kwargs):
         super().__init__(hparams, skip_proto_layer=True, **kwargs)
@@ -22,7 +24,7 @@ class CBC(SiameseGLVQ):
         reasonings_initializer = kwargs.get("reasonings_initializer",
                                             RandomReasoningsInitializer())
         self.components_layer = ReasoningComponents(
-            self.hparams.distribution,
+            self.hparams["distribution"],
             components_initializer=components_initializer,
             reasonings_initializer=reasonings_initializer,
         )
@@ -32,7 +34,7 @@ class CBC(SiameseGLVQ):
         # Namespace hook
         self.proto_layer = self.components_layer
 
-        self.loss = MarginLoss(self.hparams.margin)
+        self.loss = MarginLoss(self.hparams["margin"])
 
     def forward(self, x):
         components, reasonings = self.components_layer()
@@ -44,31 +46,25 @@ class CBC(SiameseGLVQ):
         probs = self.competition_layer(detections, reasonings)
         return probs
 
-    def shared_step(self, batch, batch_idx):
+    def shared_step(self, batch, batch_idx, optimizer_idx=None):
         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)
+        y_true = F.one_hot(y.long(), num_classes=num_classes)
         loss = self.loss(y_pred, y_true).mean()
         return y_pred, loss
 
-    def training_step(self, batch, batch_idx):
-        y_pred, train_loss = self.shared_step(batch, batch_idx)
+    def training_step(self, batch, batch_idx, optimizer_idx=None):
+        y_pred, train_loss = self.shared_step(batch, batch_idx, optimizer_idx)
         preds = torch.argmax(y_pred, dim=1)
-        accuracy = torchmetrics.functional.accuracy(
-            preds.int(),
-            batch[1].int(),
-            "multiclass",
-            num_classes=self.num_classes,
-        )
-        self.log(
-            "train_acc",
+        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,
-        )
+                 logger=True)
         return train_loss
 
     def predict(self, x):

prototorch/models/extras.py

@@ -39,7 +39,7 @@ def ltangent_distance(x, y, omegas):
     :param `torch.tensor` omegas: Three dimensional matrix
     :rtype: `torch.tensor`
     """
-    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
+    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

prototorch/models/glvq.py

@@ -17,8 +17,9 @@ from prototorch.core.transforms import LinearTransform
 from prototorch.nn.wrappers import LambdaLayer, LossLayer
 from torch.nn.parameter import Parameter
 
-from .abstract import ImagePrototypesMixin, SupervisedPrototypeModel
+from .abstract import SupervisedPrototypeModel
 from .extras import ltangent_distance, orthogonalization
+from .mixins import ImagePrototypesMixin
 
 
 class GLVQ(SupervisedPrototypeModel):
@@ -46,19 +47,24 @@ class GLVQ(SupervisedPrototypeModel):
     def initialize_prototype_win_ratios(self):
         self.register_buffer(
             "prototype_win_ratios",
-            torch.zeros(self.num_prototypes, device=self.device))
+            torch.zeros(self.num_prototypes, device=self.device),
+        )
 
     def on_train_epoch_start(self):
         self.initialize_prototype_win_ratios()
 
     def log_prototype_win_ratios(self, distances):
         batch_size = len(distances)
-        prototype_wc = torch.zeros(self.num_prototypes,
+        prototype_wc = torch.zeros(
+            self.num_prototypes,
             dtype=torch.long,
-                                   device=self.device)
-        wi, wc = torch.unique(distances.min(dim=-1).indices,
+            device=self.device,
+        )
+        wi, wc = torch.unique(
+            distances.min(dim=-1).indices,
             sorted=True,
-                              return_counts=True)
+            return_counts=True,
+        )
         prototype_wc[wi] = wc
         prototype_wr = prototype_wc / batch_size
         self.prototype_win_ratios = torch.vstack([
@@ -66,29 +72,27 @@ class GLVQ(SupervisedPrototypeModel):
             prototype_wr,
         ])
 
-    def shared_step(self, batch, batch_idx):
+    def shared_step(self, batch, batch_idx, optimizer_idx=None):
         x, y = batch
         out = self.compute_distances(x)
         _, plabels = self.proto_layer()
         loss = self.loss(out, y, plabels)
         return out, loss
 
-    def training_step(self, batch, batch_idx):
-        out, train_loss = self.shared_step(batch, batch_idx)
+    def training_step(self, batch, batch_idx, optimizer_idx=None):
+        out, train_loss = self.shared_step(batch, batch_idx, optimizer_idx)
         self.log_prototype_win_ratios(out)
         self.log("train_loss", train_loss)
         self.log_acc(out, batch[-1], tag="train_acc")
         return train_loss
 
     def validation_step(self, batch, batch_idx):
-        # `model.eval()` and `torch.no_grad()` handled by pl
         out, val_loss = self.shared_step(batch, batch_idx)
         self.log("val_loss", val_loss)
         self.log_acc(out, batch[-1], tag="val_acc")
         return val_loss
 
     def test_step(self, batch, batch_idx):
-        # `model.eval()` and `torch.no_grad()` handled by pl
         out, test_loss = self.shared_step(batch, batch_idx)
         self.log_acc(out, batch[-1], tag="test_acc")
         return test_loss
@@ -109,19 +113,43 @@ class SiameseGLVQ(GLVQ):
 
     """
 
-    def __init__(self,
+    def __init__(
+            self,
             hparams,
             backbone=torch.nn.Identity(),
             both_path_gradients=False,
-                 **kwargs):
+            **kwargs,
+    ):
         distance_fn = kwargs.pop("distance_fn", squared_euclidean_distance)
         super().__init__(hparams, distance_fn=distance_fn, **kwargs)
         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
+        bb_params = list(self.backbone.parameters())
+        if (bb_params):
+            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)
 
         bb_grad = any([el.requires_grad for el in self.backbone.parameters()])
@@ -185,12 +213,9 @@ class GRLVQ(SiameseGLVQ):
         self.register_parameter("_relevances", Parameter(relevances))
 
         # Override the backbone
-        self.backbone = LambdaLayer(self._apply_relevances,
+        self.backbone = LambdaLayer(lambda x: x @ torch.diag(self._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()
@@ -245,11 +270,19 @@ class GMLVQ(GLVQ):
         super().__init__(hparams, distance_fn=distance_fn, **kwargs)
 
         # Additional parameters
-        omega_initializer = kwargs.get("omega_initializer",
-                                       EyeLinearTransformInitializer())
-        omega = omega_initializer.generate(self.hparams["input_dim"],
-                                           self.hparams["latent_dim"])
+        omega_initializer = kwargs.get(
+            "omega_initializer",
+            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):

prototorch/models/knn.py

@@ -34,7 +34,7 @@ class KNN(SupervisedPrototypeModel):
             labels_initializer=LiteralLabelsInitializer(targets))
         self.competition_layer = KNNC(k=self.hparams.k)
 
-    def training_step(self, train_batch, batch_idx):
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
         return 1  # skip training step
 
     def on_train_batch_start(self, train_batch, batch_idx):

prototorch/models/lvq.py

@@ -1,20 +1,21 @@
 """LVQ models that are optimized using non-gradient methods."""
 
 import logging
+from collections import OrderedDict
 
 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
+from .mixins import NonGradientMixin
 
 
 class LVQ1(NonGradientMixin, GLVQ):
     """Learning Vector Quantization 1."""
 
-    def training_step(self, train_batch, batch_idx):
-        protos, plables = self.proto_layer()
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
+        protos, plabels = self.proto_layer()
         x, y = train_batch
         dis = self.compute_distances(x)
         # TODO Vectorized implementation
@@ -28,9 +29,11 @@ class LVQ1(NonGradientMixin, GLVQ):
             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)
+            updated_protos[w] = protos[w] + (self.hparams["lr"] * shift)
+            self.proto_layer.load_state_dict(
+                OrderedDict(_components=updated_protos),
+                strict=False,
+            )
 
         logging.debug(f"dis={dis}")
         logging.debug(f"y={y}")
@@ -43,7 +46,7 @@ class LVQ1(NonGradientMixin, GLVQ):
 class LVQ21(NonGradientMixin, GLVQ):
     """Learning Vector Quantization 2.1."""
 
-    def training_step(self, train_batch, batch_idx):
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
         protos, plabels = self.proto_layer()
 
         x, y = train_batch
@@ -58,10 +61,12 @@ class LVQ21(NonGradientMixin, GLVQ):
             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)
+            updated_protos[wp] = protos[wp] + (self.hparams["lr"] * shiftp)
+            updated_protos[wn] = protos[wn] + (self.hparams["lr"] * shiftn)
+            self.proto_layer.load_state_dict(
+                OrderedDict(_components=updated_protos),
+                strict=False,
+            )
 
         # Logging
         self.log_acc(dis, y, tag="train_acc")
@@ -80,14 +85,17 @@ class MedianLVQ(NonGradientMixin, GLVQ):
         super().__init__(hparams, **kwargs)
 
         self.transfer_layer = LambdaLayer(
-            get_activation(self.hparams.transfer_fn))
+            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)
+        dp, dm = _get_dp_dm(d, y, plabels, with_indices=False)
         mu = (dp - dm) / (dp + dm)
-        invmu = -1.0 * mu
-        f = self.transfer_layer(invmu, beta=self.hparams.transfer_beta) + 1.0
+        negative_mu = -1.0 * mu
+        f = self.transfer_layer(
+            negative_mu,
+            beta=self.hparams["transfer_beta"],
+        ) + 1.0
         return f
 
     def expectation(self, x, y, protos, plabels):
@@ -100,7 +108,7 @@ class MedianLVQ(NonGradientMixin, GLVQ):
         lower_bound = (gamma * f.log()).sum()
         return lower_bound
 
-    def training_step(self, train_batch, batch_idx):
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
         protos, plabels = self.proto_layer()
 
         x, y = train_batch
@@ -118,8 +126,10 @@ class MedianLVQ(NonGradientMixin, GLVQ):
                 _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)
+                    self.proto_layer.load_state_dict(
+                        OrderedDict(_components=_protos),
+                        strict=False,
+                    )
                     break
 
         # Logging

prototorch/models/mixins.py

@@ -0,0 +1,35 @@
+import pytorch_lightning as pl
+import torch
+from prototorch.core.components import Components
+
+
+class ProtoTorchMixin(pl.LightningModule):
+    """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 = False
+
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
+        raise NotImplementedError
+
+
+class ImagePrototypesMixin(ProtoTorchMixin):
+    """Mixin for models with image prototypes."""
+    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)
+
+    def get_prototype_grid(self, num_columns=2, return_channels_last=True):
+        from torchvision.utils import make_grid
+        grid = make_grid(self.components, nrow=num_columns)
+        if return_channels_last:
+            grid = grid.permute((1, 2, 0))
+        return grid.cpu()

prototorch/models/probabilistic.py

@@ -21,7 +21,7 @@ class CELVQ(GLVQ):
         # Loss
         self.loss = torch.nn.CrossEntropyLoss()
 
-    def shared_step(self, batch, batch_idx):
+    def shared_step(self, batch, batch_idx, optimizer_idx=None):
         x, y = batch
         out = self.compute_distances(x)  # [None, num_protos]
         _, plabels = self.proto_layer()
@@ -63,7 +63,7 @@ class ProbabilisticLVQ(GLVQ):
         prediction[confidence < self.rejection_confidence] = -1
         return prediction
 
-    def training_step(self, batch, batch_idx):
+    def training_step(self, batch, batch_idx, optimizer_idx=None):
         x, y = batch
         out = self.forward(x)
         _, plabels = self.proto_layer()
@@ -123,7 +123,7 @@ class PLVQ(ProbabilisticLVQ, SiameseGMLVQ):
         self.loss = torch.nn.KLDivLoss()
 
     # FIXME
-    # def training_step(self, batch, batch_idx):
+    # def training_step(self, batch, batch_idx, optimizer_idx=None):
     #     x, y = batch
     #     y_pred = self(x)
     #     batch_loss = self.loss(y_pred, y)

prototorch/models/unsupervised.py

@@ -6,9 +6,10 @@ from prototorch.core.competitions import wtac
 from prototorch.core.distances import squared_euclidean_distance
 from prototorch.core.losses import NeuralGasEnergy
 
-from .abstract import NonGradientMixin, UnsupervisedPrototypeModel
+from .abstract import UnsupervisedPrototypeModel
 from .callbacks import GNGCallback
 from .extras import ConnectionTopology
+from .mixins import NonGradientMixin
 
 
 class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
@@ -63,7 +64,7 @@ class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
             strict=False,
         )
 
-    def on_training_epoch_end(self, training_step_outputs):
+    def training_epoch_end(self, training_step_outputs):
         self._sigma = self.hparams.sigma * np.exp(
             -self.current_epoch / self.trainer.max_epochs)
 

prototorch/models/vis.py

@@ -1,5 +1,6 @@
 """Visualization Callbacks."""
 
+import os
 import warnings
 from typing import Sized
 
@@ -32,6 +33,10 @@ class Vis2DAbstract(pl.Callback):
                  tensorboard=False,
                  show_last_only=False,
                  pause_time=0.1,
+                 save=False,
+                 save_dir="./img",
+                 fig_size=(5, 4),
+                 dpi=500,
                  block=False):
         super().__init__()
 
@@ -75,8 +80,16 @@ class Vis2DAbstract(pl.Callback):
         self.tensorboard = tensorboard
         self.show_last_only = show_last_only
         self.pause_time = pause_time
+        self.save = save
+        self.save_dir = save_dir
+        self.fig_size = fig_size
+        self.dpi = dpi
         self.block = block
 
+        if save:
+            if not os.path.exists(save_dir):
+                os.makedirs(save_dir)
+
     def precheck(self, trainer):
         if self.show_last_only:
             if trainer.current_epoch != trainer.max_epochs - 1:
@@ -125,6 +138,11 @@ class Vis2DAbstract(pl.Callback):
     def log_and_display(self, trainer, pl_module):
         if self.tensorboard:
             self.add_to_tensorboard(trainer, pl_module)
+        if self.save:
+            plt.tight_layout()
+            self.fig.set_size_inches(*self.fig_size, forward=False)
+            plt.savefig(f"{self.save_dir}/{trainer.current_epoch}.png",
+                        dpi=self.dpi)
         if self.show:
             if not self.block:
                 plt.pause(self.pause_time)

prototorch/y/__init__.py

@@ -0,0 +1,23 @@
+from .architectures.base import BaseYArchitecture
+from .architectures.comparison import (
+    OmegaComparisonMixin,
+    SimpleComparisonMixin,
+)
+from .architectures.competition import WTACompetitionMixin
+from .architectures.components import SupervisedArchitecture
+from .architectures.loss import GLVQLossMixin
+from .architectures.optimization import (
+    MultipleLearningRateMixin,
+    SingleLearningRateMixin,
+)
+
+__all__ = [
+    'BaseYArchitecture',
+    "OmegaComparisonMixin",
+    "SimpleComparisonMixin",
+    "SingleLearningRateMixin",
+    "MultipleLearningRateMixin",
+    "SupervisedArchitecture",
+    "WTACompetitionMixin",
+    "GLVQLossMixin",
+]

prototorch/y/architectures/base.py

@@ -0,0 +1,212 @@
+"""
+Proto Y Architecture
+
+Network architecture for Component based Learning.
+"""
+from dataclasses import dataclass
+from typing import (
+    Callable,
+    Dict,
+    Set,
+    Type,
+)
+
+import pytorch_lightning as pl
+import torch
+from torchmetrics import Metric
+
+
+class BaseYArchitecture(pl.LightningModule):
+
+    @dataclass
+    class HyperParameters:
+        ...
+
+    # Fields
+    registered_metrics: Dict[Type[Metric], Metric] = {}
+    registered_metric_callbacks: Dict[Type[Metric], Set[Callable]] = {}
+
+    # Type Hints for Necessary Fields
+    components_layer: torch.nn.Module
+
+    def __init__(self, hparams) -> None:
+        super().__init__()
+
+        # Common Steps
+        self.init_components(hparams)
+        self.init_latent(hparams)
+        self.init_comparison(hparams)
+        self.init_competition(hparams)
+
+        # Train Steps
+        self.init_loss(hparams)
+
+        # Inference Steps
+        self.init_inference(hparams)
+
+    # external API
+    def get_competition(self, batch, components):
+        latent_batch, latent_components = self.latent(batch, components)
+        # TODO: => Latent Hook
+        comparison_tensor = self.comparison(latent_batch, latent_components)
+        # TODO: => Comparison Hook
+        return comparison_tensor
+
+    def forward(self, batch):
+        if isinstance(batch, torch.Tensor):
+            batch = (batch, None)
+        # TODO: manage different datatypes?
+        components = self.components_layer()
+        # TODO: => Component Hook
+        comparison_tensor = self.get_competition(batch, components)
+        # TODO: => Competition Hook
+        return self.inference(comparison_tensor, components)
+
+    def predict(self, batch):
+        """
+        Alias for forward
+        """
+        return self.forward(batch)
+
+    def forward_comparison(self, batch):
+        if isinstance(batch, torch.Tensor):
+            batch = (batch, None)
+        # TODO: manage different datatypes?
+        components = self.components_layer()
+        # TODO: => Component Hook
+        return self.get_competition(batch, components)
+
+    def loss_forward(self, batch):
+        # TODO: manage different datatypes?
+        components = self.components_layer()
+        # TODO: => Component Hook
+        comparison_tensor = self.get_competition(batch, components)
+        # TODO: => Competition Hook
+        return self.loss(comparison_tensor, batch, components)
+
+    # Empty Initialization
+    # TODO: Docs
+    def init_components(self, hparams: HyperParameters) -> None:
+        ...
+
+    def init_latent(self, hparams: HyperParameters) -> None:
+        ...
+
+    def init_comparison(self, hparams: HyperParameters) -> None:
+        ...
+
+    def init_competition(self, hparams: HyperParameters) -> None:
+        ...
+
+    def init_loss(self, hparams: HyperParameters) -> None:
+        ...
+
+    def init_inference(self, hparams: HyperParameters) -> None:
+        ...
+
+    # Empty Steps
+    # TODO: Type hints
+    def components(self):
+        """
+        This step has no input.
+
+        It returns the components.
+        """
+        raise NotImplementedError(
+            "The components step has no reasonable default.")
+
+    def latent(self, batch, components):
+        """
+        The latent step receives the data batch and the components.
+        It can transform both by an arbitrary function.
+
+        It returns the transformed batch and components, each of the same length as the original input.
+        """
+        return batch, components
+
+    def comparison(self, batch, components):
+        """
+        Takes a batch of size N and the component set of size M.
+
+        It returns an NxMxD tensor containing D (usually 1) pairwise comparison measures.
+        """
+        raise NotImplementedError(
+            "The comparison step has no reasonable default.")
+
+    def competition(self, comparison_measures, components):
+        """
+        Takes the tensor of comparison measures.
+
+        Assigns a competition vector to each class.
+        """
+        raise NotImplementedError(
+            "The competition step has no reasonable default.")
+
+    def loss(self, comparison_measures, batch, components):
+        """
+        Takes the tensor of competition measures.
+
+        Calculates a single loss value
+        """
+        raise NotImplementedError("The loss step has no reasonable default.")
+
+    def inference(self, comparison_measures, components):
+        """
+        Takes the tensor of competition measures.
+
+        Returns the inferred vector.
+        """
+        raise NotImplementedError(
+            "The inference step has no reasonable default.")
+
+    # Y Architecture Hooks
+
+    # internal API, called by models and callbacks
+    def register_torchmetric(
+        self,
+        name: Callable,
+        metric: Type[Metric],
+        **metric_kwargs,
+    ):
+        if metric not in self.registered_metrics:
+            self.registered_metrics[metric] = metric(**metric_kwargs)
+            self.registered_metric_callbacks[metric] = {name}
+        else:
+            self.registered_metric_callbacks[metric].add(name)
+
+    def update_metrics_step(self, batch):
+        # Prediction Metrics
+        preds = self(batch)
+
+        x, y = batch
+        for metric in self.registered_metrics:
+            instance = self.registered_metrics[metric].to(self.device)
+            instance(y, preds)
+
+    def update_metrics_epoch(self):
+        for metric in self.registered_metrics:
+            instance = self.registered_metrics[metric].to(self.device)
+            value = instance.compute()
+
+            for callback in self.registered_metric_callbacks[metric]:
+                callback(value, self)
+
+            instance.reset()
+
+    # Lightning Hooks
+
+    # Steps
+    def training_step(self, batch, batch_idx, optimizer_idx=None):
+        self.update_metrics_step([torch.clone(el) for el in batch])
+
+        return self.loss_forward(batch)
+
+    def validation_step(self, batch, batch_idx):
+        return self.loss_forward(batch)
+
+    def test_step(self, batch, batch_idx):
+        return self.loss_forward(batch)
+
+    # Other Hooks
+    def training_epoch_end(self, outs) -> None:
+        self.update_metrics_epoch()

prototorch/y/architectures/comparison.py

@@ -0,0 +1,112 @@
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Callable, Dict
+
+import torch
+from prototorch.core.distances import euclidean_distance
+from prototorch.core.initializers import (
+    AbstractLinearTransformInitializer,
+    EyeLinearTransformInitializer,
+)
+from prototorch.nn.wrappers import LambdaLayer
+from prototorch.y.architectures.base import BaseYArchitecture
+from torch import Tensor
+from torch.nn.parameter import Parameter
+
+
+class SimpleComparisonMixin(BaseYArchitecture):
+    """
+    Simple Comparison
+
+    A comparison layer that only uses the positions of the components and the batch for dissimilarity computation.
+    """
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(BaseYArchitecture.HyperParameters):
+        """
+        comparison_fn: The comparison / dissimilarity function to use. Default: euclidean_distance.
+        comparison_args: Keyword arguments for the comparison function. Default: {}.
+        """
+        comparison_fn: Callable = euclidean_distance
+        comparison_args: dict = field(default_factory=lambda: dict())
+
+        comparison_parameters: dict = field(default_factory=lambda: dict())
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def init_comparison(self, hparams: HyperParameters):
+        self.comparison_layer = LambdaLayer(
+            fn=hparams.comparison_fn,
+            **hparams.comparison_args,
+        )
+
+        self.comparison_kwargs: dict[str, Tensor] = dict()
+
+    def comparison(self, batch, components):
+        comp_tensor, _ = components
+        batch_tensor, _ = batch
+
+        comp_tensor = comp_tensor.unsqueeze(1)
+
+        distances = self.comparison_layer(
+            batch_tensor,
+            comp_tensor,
+            **self.comparison_kwargs,
+        )
+
+        return distances
+
+
+class OmegaComparisonMixin(SimpleComparisonMixin):
+    """
+    Omega Comparison
+
+    A comparison layer that uses the positions of the components and the batch for dissimilarity computation.
+    """
+
+    _omega: torch.Tensor
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(SimpleComparisonMixin.HyperParameters):
+        """
+        input_dim: Necessary Field: The dimensionality of the input.
+        latent_dim: The dimensionality of the latent space. Default: 2.
+        omega_initializer: The initializer to use for the omega matrix. Default: EyeLinearTransformInitializer.
+        """
+        input_dim: int | None = None
+        latent_dim: int = 2
+        omega_initializer: type[
+            AbstractLinearTransformInitializer] = EyeLinearTransformInitializer
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def init_comparison(self, hparams: HyperParameters) -> None:
+        super().init_comparison(hparams)
+
+        # Initialize the omega matrix
+        if hparams.input_dim is None:
+            raise ValueError("input_dim must be specified.")
+        else:
+            omega = hparams.omega_initializer().generate(
+                hparams.input_dim,
+                hparams.latent_dim,
+            )
+            self.register_parameter("_omega", Parameter(omega))
+            self.comparison_kwargs = dict(omega=self._omega)
+
+    # Properties
+    # ----------------------------------------------------------------------------------------------------
+    @property
+    def omega_matrix(self):
+        return self._omega.detach().cpu()
+
+    @property
+    def lambda_matrix(self):
+        omega = self._omega.detach()
+        lam = omega @ omega.T
+        return lam.detach().cpu()

prototorch/y/architectures/competition.py

@@ -0,0 +1,29 @@
+from dataclasses import dataclass
+
+from prototorch.core.competitions import WTAC
+from prototorch.y.architectures.base import BaseYArchitecture
+
+
+class WTACompetitionMixin(BaseYArchitecture):
+    """
+    Winner Take All Competition
+
+    A competition layer that uses the winner-take-all strategy.
+    """
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(BaseYArchitecture.HyperParameters):
+        """
+        No hyperparameters.
+        """
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def init_inference(self, hparams: HyperParameters):
+        self.competition_layer = WTAC()
+
+    def inference(self, comparison_measures, components):
+        comp_labels = components[1]
+        return self.competition_layer(comparison_measures, comp_labels)

prototorch/y/architectures/components.py

@@ -0,0 +1,53 @@
+from dataclasses import dataclass
+
+from prototorch.core.components import LabeledComponents
+from prototorch.core.initializers import (
+    AbstractComponentsInitializer,
+    LabelsInitializer,
+)
+from prototorch.y import BaseYArchitecture
+
+
+class SupervisedArchitecture(BaseYArchitecture):
+    """
+    Supervised Architecture
+
+    An architecture that uses labeled Components as component Layer.
+    """
+    components_layer: LabeledComponents
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters:
+        """
+        distribution: A valid prototype distribution. No default possible.
+        components_initializer: An implementation of AbstractComponentsInitializer. No default possible.
+        """
+        distribution: "dict[str, int]"
+        component_initializer: AbstractComponentsInitializer
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def init_components(self, hparams: HyperParameters):
+        self.components_layer = LabeledComponents(
+            distribution=hparams.distribution,
+            components_initializer=hparams.component_initializer,
+            labels_initializer=LabelsInitializer(),
+        )
+
+    # Properties
+    # ----------------------------------------------------------------------------------------------------
+    @property
+    def prototypes(self):
+        """
+        Returns the position of the prototypes.
+        """
+        return self.components_layer.components.detach().cpu()
+
+    @property
+    def prototype_labels(self):
+        """
+        Returns the labels of the prototypes.
+        """
+        return self.components_layer.labels.detach().cpu()

prototorch/y/architectures/loss.py

@@ -0,0 +1,42 @@
+from dataclasses import dataclass, field
+
+from prototorch.core.losses import GLVQLoss
+from prototorch.y.architectures.base import BaseYArchitecture
+
+
+class GLVQLossMixin(BaseYArchitecture):
+    """
+    GLVQ Loss
+
+    A loss layer that uses the Generalized Learning Vector Quantization (GLVQ) loss.
+    """
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(BaseYArchitecture.HyperParameters):
+        """
+        margin: The margin of the GLVQ loss. Default: 0.0.
+        transfer_fn: Transfer function to use. Default: sigmoid_beta.
+        transfer_args: Keyword arguments for the transfer function. Default: {beta: 10.0}.
+        """
+        margin: float = 0.0
+
+        transfer_fn: str = "sigmoid_beta"
+        transfer_args: dict = field(default_factory=lambda: dict(beta=10.0))
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def init_loss(self, hparams: HyperParameters):
+        self.loss_layer = GLVQLoss(
+            margin=hparams.margin,
+            transfer_fn=hparams.transfer_fn,
+            **hparams.transfer_args,
+        )
+
+    def loss(self, comparison_measures, batch, components):
+        target = batch[1]
+        comp_labels = components[1]
+        loss = self.loss_layer(comparison_measures, target, comp_labels)
+        self.log('loss', loss)
+        return loss

prototorch/y/architectures/optimization.py

@@ -0,0 +1,86 @@
+from dataclasses import dataclass, field
+from typing import Type
+
+import torch
+from prototorch.y import BaseYArchitecture
+from torch.nn.parameter import Parameter
+
+
+class SingleLearningRateMixin(BaseYArchitecture):
+    """
+    Single Learning Rate
+
+    All parameters are updated with a single learning rate.
+    """
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(BaseYArchitecture.HyperParameters):
+        """
+        lr: The learning rate. Default: 0.1.
+        optimizer: The optimizer to use. Default: torch.optim.Adam.
+        """
+        lr: float = 0.1
+        optimizer: Type[torch.optim.Optimizer] = torch.optim.Adam
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def __init__(self, hparams: HyperParameters) -> None:
+        super().__init__(hparams)
+        self.lr = hparams.lr
+        self.optimizer = hparams.optimizer
+
+    # Hooks
+    # ----------------------------------------------------------------------------------------------------
+    def configure_optimizers(self):
+        return self.optimizer(self.parameters(), lr=self.lr)  # type: ignore
+
+
+class MultipleLearningRateMixin(BaseYArchitecture):
+    """
+    Multiple Learning Rates
+
+    Define Different Learning Rates for different parameters.
+    """
+
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(BaseYArchitecture.HyperParameters):
+        """
+        lr: The learning rate. Default: 0.1.
+        optimizer: The optimizer to use. Default: torch.optim.Adam.
+        """
+        lr: dict = field(default_factory=lambda: dict())
+        optimizer: Type[torch.optim.Optimizer] = torch.optim.Adam
+
+    # Steps
+    # ----------------------------------------------------------------------------------------------------
+    def __init__(self, hparams: HyperParameters) -> None:
+        super().__init__(hparams)
+        self.lr = hparams.lr
+        self.optimizer = hparams.optimizer
+
+    # Hooks
+    # ----------------------------------------------------------------------------------------------------
+    def configure_optimizers(self):
+        optimizers = []
+        for name, lr in self.lr.items():
+            if not hasattr(self, name):
+                raise ValueError(f"{name} is not a parameter of {self}")
+            else:
+                model_part = getattr(self, name)
+                if isinstance(model_part, Parameter):
+                    optimizers.append(
+                        self.optimizer(
+                            [model_part],
+                            lr=lr,  # type: ignore
+                        ))
+                elif hasattr(model_part, "parameters"):
+                    optimizers.append(
+                        self.optimizer(
+                            model_part.parameters(),
+                            lr=lr,  # type: ignore
+                        ))
+        return optimizers

prototorch/y/callbacks.py

@@ -0,0 +1,218 @@
+import warnings
+from typing import Optional, Type
+
+import numpy as np
+import pytorch_lightning as pl
+import torch
+import torchmetrics
+from matplotlib import pyplot as plt
+from prototorch.models.vis import Vis2DAbstract
+from prototorch.utils.utils import mesh2d
+from prototorch.y.architectures.base import BaseYArchitecture
+from prototorch.y.library.gmlvq import GMLVQ
+from pytorch_lightning.loggers import TensorBoardLogger
+
+DIVERGING_COLOR_MAPS = [
+    'PiYG',
+    'PRGn',
+    'BrBG',
+    'PuOr',
+    'RdGy',
+    'RdBu',
+    'RdYlBu',
+    'RdYlGn',
+    'Spectral',
+    'coolwarm',
+    'bwr',
+    'seismic',
+]
+
+
+class LogTorchmetricCallback(pl.Callback):
+
+    def __init__(
+        self,
+        name,
+        metric: Type[torchmetrics.Metric],
+        on="prediction",
+        **metric_kwargs,
+    ) -> None:
+        self.name = name
+        self.metric = metric
+        self.metric_kwargs = metric_kwargs
+        self.on = on
+
+    def setup(
+        self,
+        trainer: pl.Trainer,
+        pl_module: BaseYArchitecture,
+        stage: Optional[str] = None,
+    ) -> None:
+        if self.on == "prediction":
+            pl_module.register_torchmetric(
+                self,
+                self.metric,
+                **self.metric_kwargs,
+            )
+        else:
+            raise ValueError(f"{self.on} is no valid metric hook")
+
+    def __call__(self, value, pl_module: BaseYArchitecture):
+        pl_module.log(self.name, value)
+
+
+class LogConfusionMatrix(LogTorchmetricCallback):
+
+    def __init__(
+        self,
+        num_classes,
+        name="confusion",
+        on='prediction',
+        **kwargs,
+    ):
+        super().__init__(
+            name,
+            torchmetrics.ConfusionMatrix,
+            on=on,
+            num_classes=num_classes,
+            **kwargs,
+        )
+
+    def __call__(self, value, pl_module: BaseYArchitecture):
+        fig, ax = plt.subplots()
+        ax.imshow(value.detach().cpu().numpy())
+
+        # Show all ticks and label them with the respective list entries
+        # ax.set_xticks(np.arange(len(farmers)), labels=farmers)
+        # ax.set_yticks(np.arange(len(vegetables)), labels=vegetables)
+
+        # Rotate the tick labels and set their alignment.
+        plt.setp(
+            ax.get_xticklabels(),
+            rotation=45,
+            ha="right",
+            rotation_mode="anchor",
+        )
+
+        # Loop over data dimensions and create text annotations.
+        for i in range(len(value)):
+            for j in range(len(value)):
+                text = ax.text(
+                    j,
+                    i,
+                    value[i, j].item(),
+                    ha="center",
+                    va="center",
+                    color="w",
+                )
+
+        ax.set_title(self.name)
+        fig.tight_layout()
+
+        pl_module.logger.experiment.add_figure(
+            tag=self.name,
+            figure=fig,
+            close=True,
+            global_step=pl_module.global_step,
+        )
+
+
+class VisGLVQ2D(Vis2DAbstract):
+
+    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()
+        self.plot_protos(ax, protos, plabels)
+        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.components_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)
+
+
+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 PlotLambdaMatrixToTensorboard(pl.Callback):
+
+    def __init__(self, cmap='seismic') -> None:
+        super().__init__()
+        self.cmap = cmap
+
+        if self.cmap not in DIVERGING_COLOR_MAPS and type(self.cmap) is str:
+            warnings.warn(
+                f"{self.cmap} is not a diverging color map. We recommend to use one of the following: {DIVERGING_COLOR_MAPS}"
+            )
+
+    def on_train_start(self, trainer, pl_module: GMLVQ):
+        self.plot_lambda(trainer, pl_module)
+
+    def on_train_epoch_end(self, trainer, pl_module: GMLVQ):
+        self.plot_lambda(trainer, pl_module)
+
+    def plot_lambda(self, trainer, pl_module: GMLVQ):
+
+        self.fig, self.ax = plt.subplots(1, 1)
+
+        # plot lambda matrix
+        l_matrix = pl_module.lambda_matrix
+
+        # normalize lambda matrix
+        l_matrix = l_matrix / torch.max(torch.abs(l_matrix))
+
+        # plot lambda matrix
+        self.ax.imshow(l_matrix.detach().numpy(), self.cmap, vmin=-1, vmax=1)
+
+        self.fig.colorbar(self.ax.images[-1])
+
+        # add title
+        self.ax.set_title('Lambda Matrix')
+
+        # add to tensorboard
+        if isinstance(trainer.logger, TensorBoardLogger):
+            trainer.logger.experiment.add_figure(
+                f"lambda_matrix",
+                self.fig,
+                trainer.global_step,
+            )
+        else:
+            warnings.warn(
+                f"{self.__class__.__name__} is not compatible with {trainer.logger.__class__.__name__} as logger. Use TensorBoardLogger instead."
+            )

prototorch/y/library/__init__.py

@@ -0,0 +1,5 @@
+from .glvq import GLVQ
+
+__all__ = [
+    "GLVQ",
+]

prototorch/y/library/glvq.py

@@ -0,0 +1,35 @@
+from dataclasses import dataclass
+
+from prototorch.y import (
+    SimpleComparisonMixin,
+    SingleLearningRateMixin,
+    SupervisedArchitecture,
+    WTACompetitionMixin,
+)
+from prototorch.y.architectures.loss import GLVQLossMixin
+
+
+class GLVQ(
+        SupervisedArchitecture,
+        SimpleComparisonMixin,
+        GLVQLossMixin,
+        WTACompetitionMixin,
+        SingleLearningRateMixin,
+):
+    """
+    Generalized Learning Vector Quantization (GLVQ)
+
+    A GLVQ architecture that uses the winner-take-all strategy and the GLVQ loss.
+    """
+
+    @dataclass
+    class HyperParameters(
+            SimpleComparisonMixin.HyperParameters,
+            SingleLearningRateMixin.HyperParameters,
+            GLVQLossMixin.HyperParameters,
+            WTACompetitionMixin.HyperParameters,
+            SupervisedArchitecture.HyperParameters,
+    ):
+        """
+        No hyperparameters.
+        """

prototorch/y/library/gmlvq.py

@@ -0,0 +1,50 @@
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Callable
+
+import torch
+from prototorch.core.distances import omega_distance
+from prototorch.y import (
+    GLVQLossMixin,
+    MultipleLearningRateMixin,
+    OmegaComparisonMixin,
+    SupervisedArchitecture,
+    WTACompetitionMixin,
+)
+
+
+class GMLVQ(
+        SupervisedArchitecture,
+        OmegaComparisonMixin,
+        GLVQLossMixin,
+        WTACompetitionMixin,
+        MultipleLearningRateMixin,
+):
+    """
+    Generalized Matrix Learning Vector Quantization (GMLVQ)
+
+    A GMLVQ architecture that uses the winner-take-all strategy and the GLVQ loss.
+    """
+    # HyperParameters
+    # ----------------------------------------------------------------------------------------------------
+    @dataclass
+    class HyperParameters(
+            MultipleLearningRateMixin.HyperParameters,
+            OmegaComparisonMixin.HyperParameters,
+            GLVQLossMixin.HyperParameters,
+            WTACompetitionMixin.HyperParameters,
+            SupervisedArchitecture.HyperParameters,
+    ):
+        """
+        comparison_fn: The comparison / dissimilarity function to use. Override Default: omega_distance.
+        comparison_args: Keyword arguments for the comparison function. Override Default: {}.
+        """
+        comparison_fn: Callable = omega_distance
+        comparison_args: dict = field(default_factory=lambda: dict())
+        optimizer: type[torch.optim.Optimizer] = torch.optim.Adam
+
+        lr: dict = field(default_factory=lambda: dict(
+            components_layer=0.1,
+            _omega=0.5,
+        ))

pyproject.toml

@@ -1,90 +0,0 @@
-
-[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

@@ -0,0 +1,23 @@
+[yapf]
+based_on_style = pep8
+spaces_before_comment = 2
+split_before_logical_operator = true
+
+[pylint]
+disable =
+	too-many-arguments,
+	too-few-public-methods,
+	fixme,
+
+
+[pycodestyle]
+max-line-length = 79
+
+[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

setup.py

@@ -0,0 +1,99 @@
+"""
+
+ ######
+ #     # #####   ####  #####  ####  #####  ####  #####   ####  #    #
+ #     # #    # #    #   #   #    #   #   #    # #    # #    # #    #
+ ######  #    # #    #   #   #    #   #   #    # #    # #      ######
+ #       #####  #    #   #   #    #   #   #    # #####  #      #    #
+ #       #   #  #    #   #   #    #   #   #    # #   #  #    # #    #
+ #       #    #  ####    #    ####    #    ####  #    #  ####  #    #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>=0.7.3",
+    "pytorch_lightning>=1.6.0",
+    "torchmetrics",
+    "protobuf<3.20.0",
+]
+CLI = [
+    "jsonargparse",
+]
+DEV = [
+    "bumpversion",
+    "pre-commit",
+]
+DOCS = [
+    "recommonmark",
+    "sphinx",
+    "nbsphinx",
+    "ipykernel",
+    "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="1.0.0-a3",
+    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=">=3.7",
+    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",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.7",
+        "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,
+)

tests/test_models.py

@@ -1,193 +1,195 @@
 """prototorch.models test suite."""
 
-import prototorch.models
+import prototorch as pt
+import pytest
+import torch
 
 
 def test_glvq_model_build():
-    model = prototorch.models.GLVQ(
+    model = pt.models.GLVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_glvq1_model_build():
-    model = prototorch.models.GLVQ1(
+    model = pt.models.GLVQ1(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_glvq21_model_build():
-    model = prototorch.models.GLVQ1(
+    model = pt.models.GLVQ1(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_gmlvq_model_build():
-    model = prototorch.models.GMLVQ(
+    model = pt.models.GMLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 2,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_grlvq_model_build():
-    model = prototorch.models.GRLVQ(
+    model = pt.models.GRLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_gtlvq_model_build():
-    model = prototorch.models.GTLVQ(
+    model = pt.models.GTLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 4,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_lgmlvq_model_build():
-    model = prototorch.models.LGMLVQ(
+    model = pt.models.LGMLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 4,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_image_glvq_model_build():
-    model = prototorch.models.ImageGLVQ(
+    model = pt.models.ImageGLVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(16),
+        prototypes_initializer=pt.initializers.RNCI(16),
     )
 
 
 def test_image_gmlvq_model_build():
-    model = prototorch.models.ImageGMLVQ(
+    model = pt.models.ImageGMLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 16,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(16),
+        prototypes_initializer=pt.initializers.RNCI(16),
     )
 
 
 def test_image_gtlvq_model_build():
-    model = prototorch.models.ImageGMLVQ(
+    model = pt.models.ImageGMLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 16,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(16),
+        prototypes_initializer=pt.initializers.RNCI(16),
     )
 
 
 def test_siamese_glvq_model_build():
-    model = prototorch.models.SiameseGLVQ(
+    model = pt.models.SiameseGLVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(4),
+        prototypes_initializer=pt.initializers.RNCI(4),
     )
 
 
 def test_siamese_gmlvq_model_build():
-    model = prototorch.models.SiameseGMLVQ(
+    model = pt.models.SiameseGMLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 4,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(4),
+        prototypes_initializer=pt.initializers.RNCI(4),
     )
 
 
 def test_siamese_gtlvq_model_build():
-    model = prototorch.models.SiameseGTLVQ(
+    model = pt.models.SiameseGTLVQ(
         {
             "distribution": (3, 2),
             "input_dim": 4,
             "latent_dim": 2,
         },
-        prototypes_initializer=prototorch.initializers.RNCI(4),
+        prototypes_initializer=pt.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)
+    train_ds = pt.datasets.Iris(dims=[0, 2])
+    model = pt.models.KNN(dict(k=3), data=train_ds)
 
 
 def test_lvq1_model_build():
-    model = prototorch.models.LVQ1(
+    model = pt.models.LVQ1(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_lvq21_model_build():
-    model = prototorch.models.LVQ21(
+    model = pt.models.LVQ21(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_median_lvq_model_build():
-    model = prototorch.models.MedianLVQ(
+    model = pt.models.MedianLVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_celvq_model_build():
-    model = prototorch.models.CELVQ(
+    model = pt.models.CELVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_rslvq_model_build():
-    model = prototorch.models.RSLVQ(
+    model = pt.models.RSLVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_slvq_model_build():
-    model = prototorch.models.SLVQ(
+    model = pt.models.SLVQ(
         {"distribution": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_growing_neural_gas_model_build():
-    model = prototorch.models.GrowingNeuralGas(
+    model = pt.models.GrowingNeuralGas(
         {"num_prototypes": 5},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_kohonen_som_model_build():
-    model = prototorch.models.KohonenSOM(
+    model = pt.models.KohonenSOM(
         {"shape": (3, 2)},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )
 
 
 def test_neural_gas_model_build():
-    model = prototorch.models.NeuralGas(
+    model = pt.models.NeuralGas(
         {"num_prototypes": 5},
-        prototypes_initializer=prototorch.initializers.RNCI(2),
+        prototypes_initializer=pt.initializers.RNCI(2),
     )