Bump version: 0.1.5 → 0.1.6

Merge branch 'dev' into main

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.0
+current_version = 0.1.6
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.travis.yml

@@ -17,5 +17,5 @@ deploy:
   password:
     secure: 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
   on:
-  tags: true
-  skip_existing: true
+    tags: true
+    skip_existing: true

README.md

@@ -1,5 +1,8 @@
 # ProtoTorch Models
 
+[![Build Status](https://travis-ci.org/si-cim/prototorch_models.svg?branch=main)](https://travis-ci.org/si-cim/prototorch_models)
+[![PyPI](https://img.shields.io/pypi/v/prototorch_models)](https://pypi.org/project/prototorch_models/)
+
 Pre-packaged prototype-based machine learning models using ProtoTorch and
 PyTorch-Lightning.
 

examples/lvq_iris.py

@@ -0,0 +1,42 @@
+"""Classical LVQ using GLVQ example on the Iris dataset."""
+
+import prototorch as pt
+import pytorch_lightning as pl
+import torch
+
+if __name__ == "__main__":
+    # Dataset
+    from sklearn.datasets import load_iris
+    x_train, y_train = load_iris(return_X_y=True)
+    x_train = x_train[:, [0, 2]]
+    train_ds = pt.datasets.NumpyDataset(x_train, y_train)
+
+    # Dataloaders
+    train_loader = torch.utils.data.DataLoader(train_ds,
+                                               num_workers=0,
+                                               batch_size=150)
+
+    # Hyperparameters
+    hparams = dict(
+        nclasses=3,
+        prototypes_per_class=2,
+        prototype_initializer=pt.components.SMI(train_ds),
+        #prototype_initializer=pt.components.Random(2),
+        lr=0.005,
+    )
+
+    # Initialize the model
+    model = pt.models.LVQ1(hparams)
+    #model = pt.models.LVQ21(hparams)
+
+    # Callbacks
+    vis = pt.models.VisGLVQ2D(data=(x_train, y_train))
+
+    # Setup trainer
+    trainer = pl.Trainer(
+        max_epochs=200,
+        callbacks=[vis],
+    )
+
+    # Training loop
+    trainer.fit(model, train_loader)

prototorch/models/__init__.py

@@ -1,8 +1,8 @@
 from importlib.metadata import PackageNotFoundError, version
 
 from .cbc import CBC
-from .glvq import GLVQ, GMLVQ, GRLVQ, LVQMLN, ImageGLVQ, SiameseGLVQ
+from .glvq import GLVQ, GMLVQ, GRLVQ, LVQMLN, ImageGLVQ, SiameseGLVQ, LVQ1, LVQ21
 from .neural_gas import NeuralGas
 from .vis import *
 
-__version__ = "0.1.0"
+__version__ = "0.1.6"

prototorch/models/glvq.py

@@ -5,10 +5,12 @@ from prototorch.functions.activations import get_activation
 from prototorch.functions.competitions import wtac
 from prototorch.functions.distances import (euclidean_distance, omega_distance,
                                             squared_euclidean_distance)
-from prototorch.functions.losses import glvq_loss
+from prototorch.functions.losses import glvq_loss, lvq1_loss, lvq21_loss
 
 from .abstract import AbstractPrototypeModel
 
+from torch.optim.lr_scheduler import ExponentialLR
+
 
 class GLVQ(AbstractPrototypeModel):
     """Generalized Learning Vector Quantization."""
@@ -30,6 +32,8 @@ class GLVQ(AbstractPrototypeModel):
         self.transfer_function = get_activation(self.hparams.transfer_function)
         self.train_acc = torchmetrics.Accuracy()
 
+        self.loss = glvq_loss
+
     @property
     def prototype_labels(self):
         return self.proto_layer.component_labels.detach().cpu()
@@ -44,7 +48,7 @@ class GLVQ(AbstractPrototypeModel):
         x = x.view(x.size(0), -1)  # flatten
         dis = self(x)
         plabels = self.proto_layer.component_labels
-        mu = glvq_loss(dis, y, prototype_labels=plabels)
+        mu = self.loss(dis, y, prototype_labels=plabels)
         batch_loss = self.transfer_function(mu,
                                             beta=self.hparams.transfer_beta)
         loss = batch_loss.sum(dim=0)
@@ -76,6 +80,42 @@ class GLVQ(AbstractPrototypeModel):
         return y_pred.numpy()
 
 
+class LVQ1(GLVQ):
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+        self.loss = lvq1_loss
+
+    def configure_optimizers(self):
+        optimizer = torch.optim.SGD(self.parameters(), lr=self.hparams.lr)
+        scheduler = ExponentialLR(optimizer,
+                                  gamma=0.99,
+                                  last_epoch=-1,
+                                  verbose=False)
+        sch = {
+            "scheduler": scheduler,
+            "interval": "step",
+        }  # called after each training step
+        return [optimizer], [sch]
+
+
+class LVQ21(GLVQ):
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+        self.loss = lvq21_loss
+
+    def configure_optimizers(self):
+        optimizer = torch.optim.SGD(self.parameters(), lr=self.hparams.lr)
+        scheduler = ExponentialLR(optimizer,
+                                  gamma=0.99,
+                                  last_epoch=-1,
+                                  verbose=False)
+        sch = {
+            "scheduler": scheduler,
+            "interval": "step",
+        }  # called after each training step
+        return [optimizer], [sch]
+
+
 class ImageGLVQ(GLVQ):
     """GLVQ for training on image data.
 

setup.py

@@ -19,7 +19,7 @@ DOWNLOAD_URL = "https://github.com/si-cim/prototorch_models.git"
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-INSTALL_REQUIRES = ["prototorch", "pytorch_lightning", "torchmetrics"]
+INSTALL_REQUIRES = ["prototorch>=0.4.1", "pytorch_lightning", "torchmetrics"]
 DEV = ["bumpversion"]
 EXAMPLES = ["matplotlib", "scikit-learn"]
 TESTS = ["codecov", "pytest"]
@@ -27,10 +27,11 @@ ALL = DEV + EXAMPLES + TESTS
 
 setup(
     name=safe_name("prototorch_" + PLUGIN_NAME),
-    version="0.1.0",
+    version="0.1.6",
     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,

tests/test_dummy.py

@@ -0,0 +1,6 @@
+import unittest
+
+
+class TestDummy(unittest.TestCase):
+    def test_one(self):
+        self.assertEqual(True, True)