build: bump version 1.0.0a3 → 1.0.0a4

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0a2
+current_version = 1.0.0a4
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)((?P<release>[a-zA-Z0-9_.-]+))?

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "1.0.0-a2"
+release = "1.0.0-a4"
 
 # -- General configuration ---------------------------------------------------
 

examples/y_architecture_example.py

@@ -13,8 +13,8 @@ from torch.utils.data import DataLoader
 
 # ##############################################################################
 
-if __name__ == "__main__":
 
+def main():
     # ------------------------------------------------------------
     # DATA
     # ------------------------------------------------------------
@@ -51,7 +51,7 @@ if __name__ == "__main__":
     # Create Model
     model = GMLVQ(hyperparameters)
 
-    print(model)
+    print(model.hparams)
 
     # ------------------------------------------------------------
     # TRAINING
@@ -74,15 +74,27 @@ if __name__ == "__main__":
     vis = VisGMLVQ2D(data=train_ds)
 
     # Define trainer
-    trainer = pl.Trainer(
+    trainer = pl.Trainer(callbacks=[
-        callbacks=[
+        vis,
-            vis,
+        stopping_criterion,
-            stopping_criterion,
+        es,
-            es,
+        PlotLambdaMatrixToTensorboard(),
-            PlotLambdaMatrixToTensorboard(),
+    ], )
-        ],
-        max_epochs=1000,
-    )
 
     # Train
     trainer.fit(model, train_loader)
+
+    # Manual save
+    trainer.save_checkpoint("./y_arch.ckpt")
+
+    # Load saved model
+    new_model = GMLVQ.load_from_checkpoint(
+        checkpoint_path="./y_arch.ckpt",
+        strict=True,
+    )
+
+    print(new_model.hparams)
+
+
+if __name__ == "__main__":
+    main()

prototorch/models/__init__.py

@@ -36,4 +36,4 @@ from .unsupervised import (
 )
 from .vis import *
 
-__version__ = "1.0.0-a2"
+__version__ = "1.0.0-a4"

prototorch/y/architectures/base.py

@@ -3,17 +3,14 @@ Proto Y Architecture
 
 Network architecture for Component based Learning.
 """
+from __future__ import annotations
+
 from dataclasses import dataclass
-from typing import (
+from typing import Any, Callable
-    Dict,
-    Set,
-    Type,
-)
 
 import pytorch_lightning as pl
 import torch
 from torchmetrics import Metric
-from torchmetrics.classification.accuracy import Accuracy
 
 
 class BaseYArchitecture(pl.LightningModule):
@@ -22,12 +19,25 @@ class BaseYArchitecture(pl.LightningModule):
     class HyperParameters:
         ...
 
-    registered_metrics: Dict[Type[Metric], Metric] = {}
+    # Fields
-    registered_metric_names: Dict[Type[Metric], Set[str]] = {}
+    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:
+        if type(hparams) is dict:
+            self.save_hyperparameters(hparams)
+            # TODO: => Move into Component Child
+            del hparams["initialized_proto_shape"]
+            hparams = self.HyperParameters(**hparams)
+        else:
+            self.save_hyperparameters(
+                hparams.__dict__,
+                ignore=["component_initializer"],
+            )
+
         super().__init__()
 
         # Common Steps
@@ -42,22 +52,6 @@ class BaseYArchitecture(pl.LightningModule):
         # Inference Steps
         self.init_inference(hparams)
 
-        # Initialize Model Metrics
-        self.init_model_metrics()
-
-    # internal API, called by models and callbacks
-    def register_torchmetric(
-        self,
-        name: str,
-        metric: Type[Metric],
-        **metric_kwargs,
-    ):
-        if metric not in self.registered_metrics:
-            self.registered_metrics[metric] = metric(**metric_kwargs)
-            self.registered_metric_names[metric] = {name}
-        else:
-            self.registered_metric_names[metric].add(name)
-
     # external API
     def get_competition(self, batch, components):
         latent_batch, latent_components = self.latent(batch, components)
@@ -99,7 +93,6 @@ class BaseYArchitecture(pl.LightningModule):
         return self.loss(comparison_tensor, batch, components)
 
     # Empty Initialization
-    # TODO: Type hints
     # TODO: Docs
     def init_components(self, hparams: HyperParameters) -> None:
         ...
@@ -119,9 +112,6 @@ class BaseYArchitecture(pl.LightningModule):
     def init_inference(self, hparams: HyperParameters) -> None:
         ...
 
-    def init_model_metrics(self) -> None:
-        self.register_torchmetric('accuracy', Accuracy)
-
     # Empty Steps
     # TODO: Type hints
     def components(self):
@@ -177,11 +167,26 @@ class BaseYArchitecture(pl.LightningModule):
         raise NotImplementedError(
             "The inference step has no reasonable default.")
 
-    def update_metrics_step(self, batch):
+    # Y Architecture Hooks
-        x, y = batch
 
+    # 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(x)
+        preds = self(batch)
+
+        x, y = batch
         for metric in self.registered_metrics:
             instance = self.registered_metrics[metric].to(self.device)
             instance(y, preds)
@@ -191,22 +196,31 @@ class BaseYArchitecture(pl.LightningModule):
             instance = self.registered_metrics[metric].to(self.device)
             value = instance.compute()
 
-            for name in self.registered_metric_names[metric]:
+            for callback in self.registered_metric_callbacks[metric]:
-                self.log(name, value)
+                callback(value, self)
 
             instance.reset()
 
     # Lightning Hooks
+
+    # Steps
     def training_step(self, batch, batch_idx, optimizer_idx=None):
-        self.update_metrics_step(batch)
+        self.update_metrics_step([torch.clone(el) for el in batch])
 
         return self.loss_forward(batch)
 
-    def training_epoch_end(self, outs) -> None:
-        self.update_metrics_epoch()
-
     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()
+
+    def on_save_checkpoint(self, checkpoint: dict[str, Any]) -> None:
+        checkpoint["hyper_parameters"] = {
+            'hparams': checkpoint["hyper_parameters"]
+        }
+        return super().on_save_checkpoint(checkpoint)

prototorch/y/architectures/components.py

@@ -4,6 +4,7 @@ from prototorch.core.components import LabeledComponents
 from prototorch.core.initializers import (
     AbstractComponentsInitializer,
     LabelsInitializer,
+    ZerosCompInitializer,
 )
 from prototorch.y import BaseYArchitecture
 
@@ -30,11 +31,21 @@ class SupervisedArchitecture(BaseYArchitecture):
     # Steps
     # ----------------------------------------------------------------------------------------------------
     def init_components(self, hparams: HyperParameters):
-        self.components_layer = LabeledComponents(
+        if hparams.component_initializer is not None:
-            distribution=hparams.distribution,
+            self.components_layer = LabeledComponents(
-            components_initializer=hparams.component_initializer,
+                distribution=hparams.distribution,
-            labels_initializer=LabelsInitializer(),
+                components_initializer=hparams.component_initializer,
-        )
+                labels_initializer=LabelsInitializer(),
+            )
+            proto_shape = self.components_layer.components.shape[1:]
+            self.hparams["initialized_proto_shape"] = proto_shape
+        else:
+            # when restoring a checkpointed model
+            self.components_layer = LabeledComponents(
+                distribution=hparams.distribution,
+                components_initializer=ZerosCompInitializer(
+                    self.hparams["initialized_proto_shape"]),
+            )
 
     # Properties
     # ----------------------------------------------------------------------------------------------------

prototorch/y/architectures/optimization.py

@@ -24,17 +24,11 @@ class SingleLearningRateMixin(BaseYArchitecture):
         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
+        return self.hparams.optimizer(self.parameters(),
+                                      lr=self.hparams.lr)  # type: ignore
 
 
 class MultipleLearningRateMixin(BaseYArchitecture):
@@ -55,31 +49,24 @@ class MultipleLearningRateMixin(BaseYArchitecture):
         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():
+        for name, lr in self.hparams.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(
+                        self.hparams.optimizer(
                             [model_part],
                             lr=lr,  # type: ignore
                         ))
                 elif hasattr(model_part, "parameters"):
                     optimizers.append(
-                        self.optimizer(
+                        self.hparams.optimizer(
                             model_part.parameters(),
                             lr=lr,  # type: ignore
                         ))

prototorch/y/callbacks.py

@@ -13,8 +13,18 @@ from prototorch.y.library.gmlvq import GMLVQ
 from pytorch_lightning.loggers import TensorBoardLogger
 
 DIVERGING_COLOR_MAPS = [
-    'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', 'RdYlBu', 'RdYlGn',
+    'PiYG',
-    'Spectral', 'coolwarm', 'bwr', 'seismic'
+    'PRGn',
+    'BrBG',
+    'PuOr',
+    'RdGy',
+    'RdBu',
+    'RdYlBu',
+    'RdYlGn',
+    'Spectral',
+    'coolwarm',
+    'bwr',
+    'seismic',
 ]
 
 
@@ -40,13 +50,72 @@ class LogTorchmetricCallback(pl.Callback):
     ) -> None:
         if self.on == "prediction":
             pl_module.register_torchmetric(
-                self.name,
+                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):
 

prototorch/y/library/__init__.py

@@ -1,5 +1,7 @@
 from .glvq import GLVQ
+from .gmlvq import GMLVQ
 
 __all__ = [
     "GLVQ",
+    "GMLVQ",
 ]

setup.py

@@ -55,7 +55,7 @@ ALL = CLI + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name=safe_name("prototorch_" + PLUGIN_NAME),
-    version="1.0.0-a2",
+    version="1.0.0-a4",
     description="Pre-packaged prototype-based "
     "machine learning models using ProtoTorch and PyTorch-Lightning.",
     long_description=long_description,