ci: fix jenkins file

Should fix the problem with EarlyStopping callback.

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.3.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.ci/gpu.Dockerfile

@@ -0,0 +1,5 @@
+FROM nvcr.io/nvidia/pytorch:21.10-py3
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins

.ci/python310.Dockerfile

@@ -0,0 +1,5 @@
+FROM python:3.9
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins

.ci/python36.Dockerfile

@@ -0,0 +1,5 @@
+FROM python:3.6
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins

.ci/python37.Dockerfile

@@ -0,0 +1,5 @@
+FROM python:3.7
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins

.ci/python38.Dockerfile

@@ -0,0 +1,5 @@
+FROM python:3.8
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins

.ci/python39.Dockerfile

@@ -0,0 +1,5 @@
+FROM python:3.9
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins

.github/ISSUE_TEMPLATE/bug_report.md

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

.github/ISSUE_TEMPLATE/feature_request.md

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

.travis.yml

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

Jenkinsfile

@@ -0,0 +1,118 @@
+pipeline {
+  agent none
+  stages {
+    stage('Unit Tests') {
+          agent {
+            dockerfile {
+              filename 'python310.Dockerfile'
+              dir '.ci'
+            }
+
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh '~/.local/bin/pytest -v --junitxml=reports/result.xml --cov=prototorch/ --cov-report=xml:reports/coverage.xml'
+            cobertura coberturaReportFile: 'reports/coverage.xml'
+            junit 'reports/**/*.xml'
+          }
+    }
+
+    stage('CPU Examples') {
+      parallel {
+        stage('3.10') {
+          agent {
+            dockerfile {
+              filename 'python310.Dockerfile'
+              dir '.ci'
+            }
+
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh './tests/test_examples.sh examples'
+          }
+        }
+
+        stage('3.9') {
+          agent {
+            dockerfile {
+              filename 'python39.Dockerfile'
+              dir '.ci'
+            }
+
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh './tests/test_examples.sh examples'
+          }
+        }
+
+        stage('3.8') {
+          agent {
+            dockerfile {
+              filename 'python38.Dockerfile'
+              dir '.ci'
+            }
+
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh './tests/test_examples.sh examples'
+          }
+        }
+
+        stage('3.7') {
+          agent {
+            dockerfile {
+              filename 'python37.Dockerfile'
+              dir '.ci'
+            }
+
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh './tests/test_examples.sh examples'
+          }
+        }
+
+        stage('3.6') {
+          agent {
+            dockerfile {
+              filename 'python36.Dockerfile'
+              dir '.ci'
+            }
+
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh './tests/test_examples.sh examples'
+          }
+        }
+
+      }
+    }
+
+    stage('GPU Examples') {
+      agent {
+        dockerfile {
+          filename 'gpu.Dockerfile'
+          dir '.ci'
+          args '--gpus 1'
+        }
+
+      }
+      steps {
+        sh 'pip install -U pip --progress-bar off'
+        sh 'pip install .[all] --progress-bar off'
+        sh './tests/test_examples.sh examples --gpu'
+      }
+    }
+
+  }
+}

README.md

@@ -36,6 +36,7 @@ be available for use in your Python environment as `prototorch.models`.
 - Soft Learning Vector Quantization (SLVQ)
 - Robust Soft Learning Vector Quantization (RSLVQ)
 - Probabilistic Learning Vector Quantization (PLVQ)
+- Median-LVQ
 
 ### Other
 
@@ -51,7 +52,6 @@ be available for use in your Python environment as `prototorch.models`.
 
 ## Planned models
 
-- Median-LVQ
 - Generalized Tangent Learning Vector Quantization (GTLVQ)
 - Self-Incremental Learning Vector Quantization (SILVQ)
 

deprecated.travis.yml

@@ -0,0 +1,44 @@
+dist: bionic
+sudo: false
+language: python
+python:
+  - 3.9
+  - 3.8
+  - 3.7
+  - 3.6
+cache:
+  directories:
+  - "$HOME/.cache/pip"
+  - "./tests/artifacts"
+  - "$HOME/datasets"
+install:
+- pip install git+git://github.com/si-cim/prototorch@dev --progress-bar off
+- pip install .[all] --progress-bar off
+script:
+- coverage run -m pytest
+- ./tests/test_examples.sh examples/
+after_success:
+- bash <(curl -s https://codecov.io/bash)
+
+# Publish on PyPI
+jobs:
+  include:
+    - stage: build
+      python: 3.9
+      script: echo "Starting Pypi build"
+      deploy:
+        provider: pypi
+        username: __token__
+        distributions: "sdist bdist_wheel"
+        password:
+          secure: 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
+        on:
+          tags: true
+          skip_existing: true
+
+# The password is encrypted with:
+# `cd prototorch && travis encrypt your-pypi-api-token --add deploy.password`
+# See https://docs.travis-ci.com/user/deployment/pypi and
+# https://github.com/travis-ci/travis.rb#installation
+# for more details
+# Note: The encrypt command does not work well in ZSH.

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.2.0"
+release = "0.3.0"
 
 # -- General configuration ---------------------------------------------------
 

examples/cli/gmlvq.py

@@ -1,12 +1,11 @@
 """GMLVQ example using the MNIST dataset."""
 
-import torch
-from pytorch_lightning.utilities.cli import LightningCLI
-
 import prototorch as pt
+import torch
 from prototorch.models import ImageGMLVQ
 from prototorch.models.abstract import PrototypeModel
 from prototorch.models.data import MNISTDataModule
+from pytorch_lightning.utilities.cli import LightningCLI
 
 
 class ExperimentClass(ImageGMLVQ):

examples/glvq_spiral.py

@@ -66,7 +66,7 @@ if __name__ == "__main__":
         args,
         callbacks=[
             vis,
-            # es, # FIXME
+            es,
             pruning,
         ],
         terminate_on_nan=True,

examples/knn_iris.py

@@ -2,12 +2,11 @@
 
 import argparse
 
+import prototorch as pt
 import pytorch_lightning as pl
 import torch
 from sklearn.datasets import load_iris
 
-import prototorch as pt
-
 if __name__ == "__main__":
     # Command-line arguments
     parser = argparse.ArgumentParser()

examples/median_lvq_iris.py

@@ -0,0 +1,52 @@
+"""Median-LVQ example using the Iris dataset."""
+
+import argparse
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+
+if __name__ == "__main__":
+    # Command-line arguments
+    parser = argparse.ArgumentParser()
+    parser = pl.Trainer.add_argparse_args(parser)
+    args = parser.parse_args()
+
+    # Dataset
+    train_ds = pt.datasets.Iris(dims=[0, 2])
+
+    # Dataloaders
+    train_loader = torch.utils.data.DataLoader(
+        train_ds,
+        batch_size=len(train_ds),  # MedianLVQ cannot handle mini-batches
+    )
+
+    # Initialize the model
+    model = pt.models.MedianLVQ(
+        hparams=dict(distribution=(3, 2), lr=0.01),
+        prototypes_initializer=pt.initializers.SSCI(train_ds),
+    )
+
+    # Compute intermediate input and output sizes
+    model.example_input_array = torch.zeros(4, 2)
+
+    # Callbacks
+    vis = pt.models.VisGLVQ2D(data=train_ds)
+    es = pl.callbacks.EarlyStopping(
+        monitor="train_acc",
+        min_delta=0.01,
+        patience=5,
+        mode="max",
+        verbose=True,
+        check_on_train_epoch_end=True,
+    )
+
+    # Setup trainer
+    trainer = pl.Trainer.from_argparse_args(
+        args,
+        callbacks=[vis, es],
+        weights_summary="full",
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)

examples/warm_starting.py

@@ -37,7 +37,7 @@ if __name__ == "__main__":
 
     # Setup trainer for GNG
     trainer = pl.Trainer(
-        max_epochs=200,
+        max_epochs=100,
         callbacks=[es],
         weights_summary=None,
     )
@@ -71,11 +71,30 @@ if __name__ == "__main__":
 
     # Callbacks
     vis = pt.models.VisGLVQ2D(data=train_ds)
+    pruning = pt.models.PruneLoserPrototypes(
+        threshold=0.02,
+        idle_epochs=2,
+        prune_quota_per_epoch=5,
+        frequency=1,
+        verbose=True,
+    )
+    es = pl.callbacks.EarlyStopping(
+        monitor="train_loss",
+        min_delta=0.001,
+        patience=10,
+        mode="min",
+        verbose=True,
+        check_on_train_epoch_end=True,
+    )
 
     # Setup trainer
     trainer = pl.Trainer.from_argparse_args(
         args,
-        callbacks=[vis],
+        callbacks=[
+            vis,
+            pruning,
+            es,
+        ],
         weights_summary="full",
         accelerator="ddp",
     )

prototorch/models/__init__.py

@@ -1,7 +1,5 @@
 """`models` plugin for the `prototorch` package."""
 
-from importlib.metadata import PackageNotFoundError, version
-
 from .callbacks import PrototypeConvergence, PruneLoserPrototypes
 from .cbc import CBC, ImageCBC
 from .glvq import (
@@ -23,4 +21,4 @@ from .probabilistic import CELVQ, PLVQ, RSLVQ, SLVQ
 from .unsupervised import GrowingNeuralGas, HeskesSOM, KohonenSOM, NeuralGas
 from .vis import *
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"

prototorch/models/abstract.py

@@ -1,7 +1,5 @@
 """Abstract classes to be inherited by prototorch models."""
 
-from typing import Final, final
-
 import pytorch_lightning as pl
 import torch
 import torchmetrics
@@ -14,20 +12,8 @@ from ..core.pooling import stratified_min_pooling
 from ..nn.wrappers import LambdaLayer
 
 
-class ProtoTorchMixin(object):
-    pass
-
-
 class ProtoTorchBolt(pl.LightningModule):
     """All ProtoTorch models are ProtoTorch Bolts."""
-    def __repr__(self):
-        surep = super().__repr__()
-        indented = "".join([f"\t{line}\n" for line in surep.splitlines()])
-        wrapped = f"ProtoTorch Bolt(\n{indented})"
-        return wrapped
-
-
-class PrototypeModel(ProtoTorchBolt):
     def __init__(self, hparams, **kwargs):
         super().__init__()
 
@@ -42,6 +28,33 @@ class PrototypeModel(ProtoTorchBolt):
         self.lr_scheduler = kwargs.get("lr_scheduler", None)
         self.lr_scheduler_kwargs = kwargs.get("lr_scheduler_kwargs", dict())
 
+    def configure_optimizers(self):
+        optimizer = self.optimizer(self.parameters(), lr=self.hparams.lr)
+        if self.lr_scheduler is not None:
+            scheduler = self.lr_scheduler(optimizer,
+                                          **self.lr_scheduler_kwargs)
+            sch = {
+                "scheduler": scheduler,
+                "interval": "step",
+            }  # called after each training step
+            return [optimizer], [sch]
+        else:
+            return optimizer
+
+    def reconfigure_optimizers(self):
+        self.trainer.accelerator.setup_optimizers(self.trainer)
+
+    def __repr__(self):
+        surep = super().__repr__()
+        indented = "".join([f"\t{line}\n" for line in surep.splitlines()])
+        wrapped = f"ProtoTorch Bolt(\n{indented})"
+        return wrapped
+
+
+class PrototypeModel(ProtoTorchBolt):
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+
         distance_fn = kwargs.get("distance_fn", euclidean_distance)
         self.distance_layer = LambdaLayer(distance_fn)
 
@@ -58,23 +71,6 @@ class PrototypeModel(ProtoTorchBolt):
         """Only an alias for the prototypes."""
         return self.prototypes
 
-    def configure_optimizers(self):
-        optimizer = self.optimizer(self.parameters(), lr=self.hparams.lr)
-        if self.lr_scheduler is not None:
-            scheduler = self.lr_scheduler(optimizer,
-                                          **self.lr_scheduler_kwargs)
-            sch = {
-                "scheduler": scheduler,
-                "interval": "step",
-            }  # called after each training step
-            return [optimizer], [sch]
-        else:
-            return optimizer
-
-    @final
-    def reconfigure_optimizers(self):
-        self.trainer.accelerator_backend.setup_optimizers(self.trainer)
-
     def add_prototypes(self, *args, **kwargs):
         self.proto_layer.add_components(*args, **kwargs)
         self.reconfigure_optimizers()
@@ -97,7 +93,7 @@ class UnsupervisedPrototypeModel(PrototypeModel):
             )
 
     def compute_distances(self, x):
-        protos = self.proto_layer()
+        protos = self.proto_layer().type_as(x)
         distances = self.distance_layer(x, protos)
         return distances
 
@@ -137,14 +133,14 @@ class SupervisedPrototypeModel(PrototypeModel):
 
     def forward(self, x):
         distances = self.compute_distances(x)
-        plabels = self.proto_layer.labels
+        _, plabels = self.proto_layer()
         winning = stratified_min_pooling(distances, plabels)
         y_pred = torch.nn.functional.softmin(winning)
         return y_pred
 
     def predict_from_distances(self, distances):
         with torch.no_grad():
-            plabels = self.proto_layer.labels
+            _, plabels = self.proto_layer()
             y_pred = self.competition_layer(distances, plabels)
         return y_pred
 
@@ -167,11 +163,16 @@ class SupervisedPrototypeModel(PrototypeModel):
                  logger=True)
 
 
+class ProtoTorchMixin(object):
+    """All mixins are ProtoTorchMixins."""
+    pass
+
+
 class NonGradientMixin(ProtoTorchMixin):
     """Mixin for custom non-gradient optimization."""
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.automatic_optimization: Final = False
+        self.automatic_optimization = False
 
     def training_step(self, train_batch, batch_idx, optimizer_idx=None):
         raise NotImplementedError
@@ -179,7 +180,6 @@ class NonGradientMixin(ProtoTorchMixin):
 
 class ImagePrototypesMixin(ProtoTorchMixin):
     """Mixin for models with image prototypes."""
-    @final
     def on_train_batch_end(self, outputs, batch, batch_idx, dataloader_idx):
         """Constrain the components to the range [0, 1] by clamping after updates."""
         self.proto_layer.components.data.clamp_(0.0, 1.0)

prototorch/models/callbacks.py

@@ -55,7 +55,7 @@ class PruneLoserPrototypes(pl.Callback):
                 distribution = dict(zip(labels.tolist(), counts.tolist()))
                 if self.verbose:
                     print(f"Re-adding pruned prototypes...")
-                    print(f"{distribution=}")
+                    print(f"distribution={distribution}")
                 pl_module.add_prototypes(
                     distribution=distribution,
                     components_initializer=self.prototypes_initializer)
@@ -134,4 +134,4 @@ class GNGCallback(pl.Callback):
             pl_module.errors[
                 worst_neighbor] = errors[worst_neighbor] * self.reduction
 
-            trainer.accelerator_backend.setup_optimizers(trainer)
+            trainer.accelerator.setup_optimizers(trainer)

prototorch/models/cbc.py

@@ -48,7 +48,7 @@ class CBC(SiameseGLVQ):
         y_pred = self(x)
         num_classes = self.num_classes
         y_true = torch.nn.functional.one_hot(y.long(), num_classes=num_classes)
-        loss = self.loss(y_pred, y_true).mean(dim=0)
+        loss = self.loss(y_pred, y_true).mean()
         return y_pred, loss
 
     def training_step(self, batch, batch_idx, optimizer_idx=None):

prototorch/models/data.py

@@ -5,13 +5,12 @@ Mainly used for PytorchLightningCLI configurations.
 """
 from typing import Any, Optional, Type
 
+import prototorch as pt
 import pytorch_lightning as pl
 from torch.utils.data import DataLoader, Dataset, random_split
 from torchvision import transforms
 from torchvision.datasets import MNIST
 
-import prototorch as pt
-
 
 # MNIST
 class MNISTDataModule(pl.LightningDataModule):

prototorch/models/glvq.py

@@ -6,8 +6,8 @@ from torch.nn.parameter import Parameter
 from ..core.competitions import wtac
 from ..core.distances import lomega_distance, omega_distance, squared_euclidean_distance
 from ..core.initializers import EyeTransformInitializer
-from ..core.losses import glvq_loss, lvq1_loss, lvq21_loss
-from ..nn.activations import get_activation
+from ..core.losses import GLVQLoss, lvq1_loss, lvq21_loss
+from ..core.transforms import LinearTransform
 from ..nn.wrappers import LambdaLayer, LossLayer
 from .abstract import ImagePrototypesMixin, SupervisedPrototypeModel
 
@@ -18,15 +18,16 @@ class GLVQ(SupervisedPrototypeModel):
         super().__init__(hparams, **kwargs)
 
         # Default hparams
+        self.hparams.setdefault("margin", 0.0)
         self.hparams.setdefault("transfer_fn", "identity")
         self.hparams.setdefault("transfer_beta", 10.0)
 
-        # Layers
-        transfer_fn = get_activation(self.hparams.transfer_fn)
-        self.transfer_layer = LambdaLayer(transfer_fn)
-
         # Loss
-        self.loss = LossLayer(glvq_loss)
+        self.loss = GLVQLoss(
+            margin=self.hparams.margin,
+            transfer_fn=self.hparams.transfer_fn,
+            beta=self.hparams.transfer_beta,
+        )
 
     def initialize_prototype_win_ratios(self):
         self.register_buffer(
@@ -54,10 +55,8 @@ class GLVQ(SupervisedPrototypeModel):
     def shared_step(self, batch, batch_idx, optimizer_idx=None):
         x, y = batch
         out = self.compute_distances(x)
-        plabels = self.proto_layer.labels
-        mu = self.loss(out, y, prototype_labels=plabels)
-        batch_loss = self.transfer_layer(mu, beta=self.hparams.transfer_beta)
-        loss = batch_loss.sum(dim=0)
+        _, plabels = self.proto_layer()
+        loss = self.loss(out, y, plabels)
         return out, loss
 
     def training_step(self, batch, batch_idx, optimizer_idx=None):
@@ -113,7 +112,8 @@ class SiameseGLVQ(GLVQ):
         proto_opt = self.optimizer(self.proto_layer.parameters(),
                                    lr=self.hparams.proto_lr)
         # Only add a backbone optimizer if backbone has trainable parameters
-        if (bb_params := list(self.backbone.parameters())):
+        bb_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:
@@ -208,18 +208,22 @@ class SiameseGMLVQ(SiameseGLVQ):
         super().__init__(hparams, **kwargs)
 
         # Override the backbone
-        self.backbone = torch.nn.Linear(self.hparams.input_dim,
-                                        self.hparams.latent_dim,
-                                        bias=False)
+        omega_initializer = kwargs.get("omega_initializer",
+                                       EyeTransformInitializer())
+        self.backbone = LinearTransform(
+            self.hparams.input_dim,
+            self.hparams.output_dim,
+            initializer=omega_initializer,
+        )
 
     @property
     def omega_matrix(self):
-        return self.backbone.weight.detach().cpu()
+        return self.backbone.weights
 
     @property
     def lambda_matrix(self):
-        omega = self.backbone.weight  # (latent_dim, input_dim)
-        lam = omega.T @ omega
+        omega = self.backbone.weight  # (input_dim, latent_dim)
+        lam = omega @ omega.T
         return lam.detach().cpu()
 
 

prototorch/models/lvq.py

@@ -1,6 +1,8 @@
 """LVQ models that are optimized using non-gradient methods."""
 
 from ..core.losses import _get_dp_dm
+from ..nn.activations import get_activation
+from ..nn.wrappers import LambdaLayer
 from .abstract import NonGradientMixin
 from .glvq import GLVQ
 
@@ -8,9 +10,7 @@ from .glvq import GLVQ
 class LVQ1(NonGradientMixin, GLVQ):
     """Learning Vector Quantization 1."""
     def training_step(self, train_batch, batch_idx, optimizer_idx=None):
-        protos = self.proto_layer.components
-        plabels = self.proto_layer.labels
-
+        protos, plables = self.proto_layer()
         x, y = train_batch
         dis = self.compute_distances(x)
         # TODO Vectorized implementation
@@ -28,8 +28,8 @@ class LVQ1(NonGradientMixin, GLVQ):
             self.proto_layer.load_state_dict({"_components": updated_protos},
                                              strict=False)
 
-        print(f"{dis=}")
-        print(f"{y=}")
+        print(f"dis={dis}")
+        print(f"y={y}")
         # Logging
         self.log_acc(dis, y, tag="train_acc")
 
@@ -39,8 +39,7 @@ class LVQ1(NonGradientMixin, GLVQ):
 class LVQ21(NonGradientMixin, GLVQ):
     """Learning Vector Quantization 2.1."""
     def training_step(self, train_batch, batch_idx, optimizer_idx=None):
-        protos = self.proto_layer.components
-        plabels = self.proto_layer.labels
+        protos, plabels = self.proto_layer()
 
         x, y = train_batch
         dis = self.compute_distances(x)
@@ -66,4 +65,60 @@ class LVQ21(NonGradientMixin, GLVQ):
 
 
 class MedianLVQ(NonGradientMixin, GLVQ):
-    """Median LVQ"""
+    """Median LVQ
+
+    # TODO Avoid computing distances over and over
+
+    """
+    def __init__(self, hparams, verbose=True, **kwargs):
+        self.verbose = verbose
+        super().__init__(hparams, **kwargs)
+
+        self.transfer_layer = LambdaLayer(
+            get_activation(self.hparams.transfer_fn))
+
+    def _f(self, x, y, protos, plabels):
+        d = self.distance_layer(x, protos)
+        dp, dm = _get_dp_dm(d, y, plabels)
+        mu = (dp - dm) / (dp + dm)
+        invmu = -1.0 * mu
+        f = self.transfer_layer(invmu, beta=self.hparams.transfer_beta) + 1.0
+        return f
+
+    def expectation(self, x, y, protos, plabels):
+        f = self._f(x, y, protos, plabels)
+        gamma = f / f.sum()
+        return gamma
+
+    def lower_bound(self, x, y, protos, plabels, gamma):
+        f = self._f(x, y, protos, plabels)
+        lower_bound = (gamma * f.log()).sum()
+        return lower_bound
+
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
+        protos, plabels = self.proto_layer()
+
+        x, y = train_batch
+        dis = self.compute_distances(x)
+
+        for i, _ in enumerate(protos):
+            # Expectation step
+            gamma = self.expectation(x, y, protos, plabels)
+            lower_bound = self.lower_bound(x, y, protos, plabels, gamma)
+
+            # Maximization step
+            _protos = protos + 0
+            for k, xk in enumerate(x):
+                _protos[i] = xk
+                _lower_bound = self.lower_bound(x, y, _protos, plabels, gamma)
+                if _lower_bound > lower_bound:
+                    if self.verbose:
+                        print(f"Updating prototype {i} to data {k}...")
+                    self.proto_layer.load_state_dict({"_components": _protos},
+                                                     strict=False)
+                    break
+
+        # Logging
+        self.log_acc(dis, y, tag="train_acc")
+
+        return None

prototorch/models/probabilistic.py

@@ -20,11 +20,11 @@ class CELVQ(GLVQ):
     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.labels
+        _, plabels = self.proto_layer()
         winning = stratified_min_pooling(out, plabels)  # [None, num_classes]
         probs = -1.0 * winning
         batch_loss = self.loss(probs, y.long())
-        loss = batch_loss.sum(dim=0)
+        loss = batch_loss.sum()
         return out, loss
 
 
@@ -54,9 +54,9 @@ class ProbabilisticLVQ(GLVQ):
     def training_step(self, batch, batch_idx, optimizer_idx=None):
         x, y = batch
         out = self.forward(x)
-        plabels = self.proto_layer.labels
+        _, plabels = self.proto_layer()
         batch_loss = self.loss(out, y, plabels)
-        loss = batch_loss.sum(dim=0)
+        loss = batch_loss.sum()
         return loss
 
 
@@ -92,5 +92,5 @@ class PLVQ(ProbabilisticLVQ, SiameseGMLVQ):
     #     x, y = batch
     #     y_pred = self(x)
     #     batch_loss = self.loss(y_pred, y)
-    #     loss = batch_loss.sum(dim=0)
+    #     loss = batch_loss.sum()
     #     return loss

prototorch/models/unsupervised.py

@@ -53,7 +53,7 @@ class KohonenSOM(NonGradientMixin, UnsupervisedPrototypeModel):
         grid = self._grid.view(-1, 2)
         gd = squared_euclidean_distance(wp, grid)
         nh = torch.exp(-gd / self._sigma**2)
-        protos = self.proto_layer.components
+        protos = self.proto_layer()
         diff = x.unsqueeze(dim=1) - protos
         delta = self._lr * self.hparams.alpha * nh.unsqueeze(-1) * diff
         updated_protos = protos + delta.sum(dim=0)
@@ -132,7 +132,7 @@ class GrowingNeuralGas(NeuralGas):
         mask[torch.arange(len(mask)), winner] = 1.0
         dp = d * mask
 
-        self.errors += torch.sum(dp * dp, dim=0)
+        self.errors += torch.sum(dp * dp)
         self.errors *= self.hparams.step_reduction
 
         self.topology_layer(d)

prototorch/models/vis.py

@@ -251,8 +251,6 @@ class VisImgComp(Vis2DAbstract):
                                    size=self.embedding_data,
                                    replace=False)
             data = self.x_train[ind]
-            # print(f"{data.shape=}")
-            # print(f"{self.y_train[ind].shape=}")
             tb.add_embedding(data.view(len(ind), -1),
                              label_img=data,
                              global_step=None,

setup.py

@@ -22,7 +22,7 @@ with open("README.md", "r") as fh:
     long_description = fh.read()
 
 INSTALL_REQUIRES = [
-    "prototorch>=0.6.0",
+    "prototorch>=0.7.0",
     "pytorch_lightning>=1.3.5",
     "torchmetrics",
 ]
@@ -46,14 +46,14 @@ EXAMPLES = [
     "scikit-learn",
 ]
 TESTS = [
-    "codecov",
+    "pytest-cov",
     "pytest",
 ]
 ALL = CLI + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name=safe_name("prototorch_" + PLUGIN_NAME),
-    version="0.2.0",
+    version="0.3.0",
     description="Pre-packaged prototype-based "
     "machine learning models using ProtoTorch and PyTorch-Lightning.",
     long_description=long_description,
@@ -63,7 +63,7 @@ setup(
     url=PROJECT_URL,
     download_url=DOWNLOAD_URL,
     license="MIT",
-    python_requires=">=3.9",
+    python_requires=">=3.6",
     install_requires=INSTALL_REQUIRES,
     extras_require={
         "dev": DEV,
@@ -80,6 +80,9 @@ setup(
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.6",
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
         "Topic :: Software Development :: Libraries",

tests/test_examples.sh

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