Merge branch 'dev' of github.com:si-cim/prototorch_models into dev

examples/cli/gmlvq.py

@@ -1,12 +1,11 @@
 """GLVQ example using the MNIST dataset."""
 
 from prototorch.models import ImageGLVQ
+from prototorch.models.data import train_on_mnist
 from pytorch_lightning.utilities.cli import LightningCLI
 
-from mnist import TrainOnMNIST
 
-
+class GLVQMNIST(train_on_mnist(batch_size=64), ImageGLVQ):
-class GLVQMNIST(TrainOnMNIST, ImageGLVQ):
     """Model Definition."""
 
 

examples/probabilistic.py

@@ -33,11 +33,12 @@ if __name__ == "__main__":
     )
 
     # Initialize the model
-    model = pt.models.probabilistic.RSLVQ(
+    model = pt.models.probabilistic.LikelihoodRatioLVQ(
+        #model = pt.models.probabilistic.RSLVQ(
         hparams,
         optimizer=torch.optim.Adam,
-        prototype_initializer=pt.components.SSI(train_ds, noise=2),
+        #prototype_initializer=pt.components.SSI(train_ds, noise=2),
-        #prototype_initializer=pt.components.UniformInitializer(2),
+        prototype_initializer=pt.components.UniformInitializer(2),
     )
 
     # Callbacks

prototorch/models/data.py

@@ -10,15 +10,12 @@ class MNISTDataModule(pl.LightningDataModule):
         super().__init__()
         self.batch_size = batch_size
 
-    # When doing distributed training, Datamodules have two optional arguments for
+    # Download mnist dataset as side-effect, only called on the first cpu
-    # granular control over download/prepare/splitting data:
-
-    # OPTIONAL, called only on 1 GPU/machine
     def prepare_data(self):
         MNIST("~/datasets", train=True, download=True)
         MNIST("~/datasets", train=False, download=True)
 
-    # OPTIONAL, called for every GPU/machine (assigning state is OK)
+    # called for every GPU/machine (assigning state is OK)
     def setup(self, stage=None):
         # Transforms
         transform = transforms.Compose([
@@ -28,13 +25,17 @@ class MNISTDataModule(pl.LightningDataModule):
         if stage in (None, "fit"):
             mnist_train = MNIST("~/datasets", train=True, transform=transform)
             self.mnist_train, self.mnist_val = random_split(
-                mnist_train, [55000, 5000])
+                mnist_train,
+                [55000, 5000],
+            )
         if stage == (None, "test"):
-            self.mnist_test = MNIST("~/datasets",
+            self.mnist_test = MNIST(
-                                    train=False,
+                "~/datasets",
-                                    transform=transform)
+                train=False,
+                transform=transform,
+            )
 
-    # Return the dataloader for each split
+    # Dataloaders
     def train_dataloader(self):
         mnist_train = DataLoader(self.mnist_train, batch_size=self.batch_size)
         return mnist_train
@@ -48,8 +49,11 @@ class MNISTDataModule(pl.LightningDataModule):
         return mnist_test
 
 
-class TrainOnMNIST(pl.LightningModule):
+def train_on_mnist(batch_size=256) -> type:
-    datamodule = MNISTDataModule(batch_size=256)
+    class DataClass(pl.LightningModule):
+        datamodule = MNISTDataModule(batch_size=batch_size)
 
-    def prototype_initializer(self, **kwargs):
+        def prototype_initializer(self, **kwargs):
-        return pt.components.Zeros((28, 28, 1))
+            return pt.components.Zeros((28, 28, 1))
+
+    return DataClass

prototorch/models/probabilistic.py

@@ -1,100 +1,26 @@
 """Probabilistic GLVQ methods"""
 
 import torch
+from prototorch.functions.competitions import stratified_sum
+from prototorch.functions.losses import (log_likelihood_ratio_loss,
+                                         robust_soft_loss)
+from prototorch.functions.transform import gaussian
 
 from .glvq import GLVQ
 
 
-# HELPER
+class ProbabilisticLVQ(GLVQ):
-# TODO: Refactor into general files, if useful
+    def __init__(self, hparams, rejection_confidence=1.0, **kwargs):
-def probability(distance, variance):
-    return torch.exp(-(distance * distance) / (2 * variance))
-
-
-def grouped_sum(value: torch.Tensor,
-                labels: torch.LongTensor) -> (torch.Tensor, torch.LongTensor):
-    """Group-wise average for (sparse) grouped tensors
-
-    Args:
-        value (torch.Tensor): values to average (# samples, latent dimension)
-        labels (torch.LongTensor): labels for embedding parameters (# samples,)
-
-    Returns:
-        result (torch.Tensor): (# unique labels, latent dimension)
-        new_labels (torch.LongTensor): (# unique labels,)
-
-    Examples:
-        >>> samples = torch.Tensor([
-                             [0.15, 0.15, 0.15],    #-> group / class 1
-                             [0.2,  0.2,  0.2 ],    #-> group / class 3
-                             [0.4,  0.4,  0.4 ],    #-> group / class 3
-                             [0.0,  0.0,  0.0 ]     #-> group / class 0
-                      ])
-        >>> labels = torch.LongTensor([1, 5, 5, 0])
-        >>> result, new_labels = groupby_mean(samples, labels)
-
-        >>> result
-        tensor([[0.0000, 0.0000, 0.0000],
-                [0.1500, 0.1500, 0.1500],
-                [0.3000, 0.3000, 0.3000]])
-
-        >>> new_labels
-        tensor([0, 1, 5])
-    """
-    uniques = labels.unique(sorted=True).tolist()
-    labels = labels.tolist()
-
-    key_val = {key: val for key, val in zip(uniques, range(len(uniques)))}
-    labels = torch.LongTensor(list(map(key_val.get, labels)))
-
-    labels = labels.view(labels.size(0), 1).expand(-1, value.size(1))
-
-    unique_labels = labels.unique(dim=0)
-    result = torch.zeros_like(unique_labels, dtype=torch.float).scatter_add_(
-        0, labels, value)
-    return result.T
-
-
-def likelihood_loss(probabilities, target, prototype_labels):
-    uniques = prototype_labels.unique(sorted=True).tolist()
-    labels = target.tolist()
-
-    key_val = {key: val for key, val in zip(uniques, range(len(uniques)))}
-    target_indices = torch.LongTensor(list(map(key_val.get, labels)))
-
-    whole_probability = probabilities.sum(dim=1)
-    correct_probability = probabilities[torch.arange(len(probabilities)),
-                                        target_indices]
-    wrong_probability = whole_probability - correct_probability
-
-    likelihood = correct_probability / wrong_probability
-    log_likelihood = torch.log(likelihood)
-    return log_likelihood
-
-
-def robust_soft_loss(probabilities, target, prototype_labels):
-    uniques = prototype_labels.unique(sorted=True).tolist()
-    labels = target.tolist()
-
-    key_val = {key: val for key, val in zip(uniques, range(len(uniques)))}
-    target_indices = torch.LongTensor(list(map(key_val.get, labels)))
-
-    whole_probability = probabilities.sum(dim=1)
-    correct_probability = probabilities[torch.arange(len(probabilities)),
-                                        target_indices]
-
-    likelihood = correct_probability / whole_probability
-    log_likelihood = torch.log(likelihood)
-    return log_likelihood
-
-
-class LikelihoodRatioLVQ(GLVQ):
-    """Learning Vector Quantization based on Likelihood Ratios
-    """
-    def __init__(self, hparams, **kwargs):
         super().__init__(hparams, **kwargs)
 
-        self.conditional_distribution = probability
+        self.conditional_distribution = gaussian
+        self.rejection_confidence = rejection_confidence
+
+    def predict(self, x):
+        probabilities = self.forward(x)
+        confidence, prediction = torch.max(probabilities, dim=1)
+        prediction[confidence < self.rejection_confidence] = -1
+        return prediction
 
     def forward(self, x):
         distances = self._forward(x)
@@ -104,7 +30,7 @@ class LikelihoodRatioLVQ(GLVQ):
         posterior = conditional * prior
 
         plabels = torch.LongTensor(self.proto_layer.component_labels)
-        y_pred = grouped_sum(posterior.T, plabels)
+        y_pred = stratified_sum(posterior.T, plabels)
 
         return y_pred
 
@@ -112,52 +38,26 @@ class LikelihoodRatioLVQ(GLVQ):
         X, y = batch
         out = self.forward(X)
         plabels = self.proto_layer.component_labels
-        batch_loss = -likelihood_loss(out, y, prototype_labels=plabels)
+        batch_loss = -self.loss_fn(out, y, plabels)
         loss = batch_loss.sum(dim=0)
 
         return loss
 
-    def predict(self, x):
-        probabilities = self.forward(x)
-        confidence, prediction = torch.max(probabilities, dim=1)
-        prediction[confidence < 0.1] = -1
-        return prediction
 
-
+class LikelihoodRatioLVQ(ProbabilisticLVQ):
-class RSLVQ(GLVQ):
     """Learning Vector Quantization based on Likelihood Ratios
     """
-    def __init__(self, hparams, **kwargs):
+    def __init__(self, *args, **kwargs):
-        super().__init__(hparams, **kwargs)
+        super().__init__(*args, **kwargs)
-
+        self.loss_fn = log_likelihood_ratio_loss
-        self.conditional_distribution = probability
-
-    def forward(self, x):
-        distances = self._forward(x)
-        conditional = self.conditional_distribution(distances,
-                                                    self.hparams.variance)
-        prior = 1.0 / torch.Tensor(self.proto_layer.distribution).sum().item()
-        posterior = conditional * prior
-
-        plabels = torch.LongTensor(self.proto_layer.component_labels)
-        y_pred = grouped_sum(posterior.T, plabels)
-
-        return y_pred
-
-    def training_step(self, batch, batch_idx, optimizer_idx=None):
-        X, y = batch
-        out = self.forward(X)
-        plabels = self.proto_layer.component_labels
-        batch_loss = -robust_soft_loss(out, y, prototype_labels=plabels)
-        loss = batch_loss.sum(dim=0)
-
-        return loss
-
-    def predict(self, x):
-        probabilities = self.forward(x)
-        confidence, prediction = torch.max(probabilities, dim=1)
-        #prediction[confidence < 0.1] = -1
-        return prediction
 
 
-__all__ = ["LikelihoodRatioLVQ", "probability", "grouped_sum"]
+class RSLVQ(ProbabilisticLVQ):
+    """Learning Vector Quantization based on Likelihood Ratios
+    """
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.loss_fn = robust_soft_loss
+
+
+__all__ = ["LikelihoodRatioLVQ", "RSLVQ"]