Bump version: 0.1.6 → 0.1.7

Merge branch 'dev' into main

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.0
+current_version = 0.1.7
 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

@@ -1,28 +1,25 @@
 # 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.
 
 ## Installation
 
-To install this plugin, first install
-[ProtoTorch](https://github.com/si-cim/prototorch) with:
+To install this plugin, simply run the following command:
 
 ```sh
-git clone https://github.com/si-cim/prototorch.git && cd prototorch
-pip install -e .
-```
-
-and then install the plugin itself with:
-
-```sh
-git clone https://github.com/si-cim/prototorch_models.git && cd prototorch_models
-pip install -e .
+pip install prototorch_models
 ```
 
 The plugin should then be available for use in your Python environment as
 `prototorch.models`.
 
+*Note: Installing the models plugin should automatically install a suitable
+version of * [ProtoTorch](https://github.com/si-cim/prototorch).
+
 ## Development setup
 
 It is recommended that you use a virtual environment for development. If you do
@@ -54,17 +51,20 @@ To assist in the development process, you may also find it useful to install
 
 ## Available models
 
+- K-Nearest Neighbors (KNN)
+- Learning Vector Quantization 1 (LVQ1)
 - Generalized Learning Vector Quantization (GLVQ)
 - Generalized Relevance Learning Vector Quantization (GRLVQ)
 - Generalized Matrix Learning Vector Quantization (GMLVQ)
 - Limited-Rank Matrix Learning Vector Quantization (LiRaMLVQ)
+- Learning Vector Quantization Multi-Layer Network (LVQMLN)
 - Siamese GLVQ
 - Neural Gas (NG)
 
 ## Work in Progress
 
 - Classification-By-Components Network (CBC)
-- Learning Vector Quantization Multi-Layer Network (LVQMLN)
+- Learning Vector Quantization 2.1 (LVQ2.1)
 
 ## Planned models
 
@@ -73,8 +73,6 @@ To assist in the development process, you may also find it useful to install
 - Robust Soft Learning Vector Quantization (RSLVQ)
 - Probabilistic Learning Vector Quantization (PLVQ)
 - Self-Incremental Learning Vector Quantization (SILVQ)
-- K-Nearest Neighbors (KNN)
-- Learning Vector Quantization 1 (LVQ1)
 
 ## FAQ
 

examples/glvq_iris.py

@@ -17,15 +17,16 @@ if __name__ == "__main__":
                                                batch_size=150)
 
     # Hyperparameters
+    nclasses = 3
+    prototypes_per_class = 2
     hparams = dict(
-        nclasses=3,
-        prototypes_per_class=2,
+        distribution=(nclasses, prototypes_per_class),
         prototype_initializer=pt.components.SMI(train_ds),
         lr=0.01,
     )
 
     # Initialize the model
-    model = pt.models.GLVQ(hparams)
+    model = pt.models.GLVQ(hparams, optimizer=torch.optim.Adam)
 
     # Callbacks
     vis = pt.models.VisGLVQ2D(data=(x_train, y_train))

examples/glvq_spiral.py

@@ -25,10 +25,11 @@ if __name__ == "__main__":
                                                batch_size=256)
 
     # Hyperparameters
+    nclasses = 2
+    prototypes_per_class = 20
     hparams = dict(
-        nclasses=2,
-        prototypes_per_class=20,
-        prototype_initializer=pt.components.SSI(train_ds, noise=1e-7),
+        distribution=(nclasses, prototypes_per_class),
+        prototype_initializer=pt.components.SSI(train_ds, noise=1e-1),
         transfer_function="sigmoid_beta",
         transfer_beta=10.0,
         lr=0.01,

examples/gmlvq_iris.py

@@ -15,9 +15,10 @@ if __name__ == "__main__":
                                                num_workers=0,
                                                batch_size=150)
     # Hyperparameters
+    nclasses = 3
+    prototypes_per_class = 1
     hparams = dict(
-        nclasses=3,
-        prototypes_per_class=1,
+        distribution=(nclasses, prototypes_per_class),
         input_dim=x_train.shape[1],
         latent_dim=x_train.shape[1],
         prototype_initializer=pt.components.SMI(train_ds),

examples/knn_iris.py

@@ -0,0 +1,37 @@
+"""k-NN example using 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(k=20)
+
+    # Initialize the model
+    model = pt.models.KNN(hparams, data=train_ds)
+
+    # Callbacks
+    vis = pt.models.VisGLVQ2D(data=(x_train, y_train))
+
+    # Setup trainer
+    trainer = pl.Trainer(max_epochs=1, callbacks=[vis])
+
+    # Training loop
+    # This is only for visualization. k-NN has no training phase.
+    trainer.fit(model, train_loader)
+
+    # Recall
+    y_pred = model.predict(torch.tensor(x_train))
+    print(y_pred)

examples/liramlvq_tecator.py

@@ -17,9 +17,10 @@ if __name__ == "__main__":
                                                batch_size=32)
 
     # Hyperparameters
+    nclasses = 2
+    prototypes_per_class = 2
     hparams = dict(
-        nclasses=2,
-        prototypes_per_class=2,
+        distribution=(nclasses, prototypes_per_class),
         input_dim=100,
         latent_dim=2,
         prototype_initializer=pt.components.SMI(train_ds),

examples/siamese_glvq_iris.py

@@ -24,9 +24,7 @@ class Backbone(torch.nn.Module):
 
 if __name__ == "__main__":
     # Dataset
-    from sklearn.datasets import load_iris
-    x_train, y_train = load_iris(return_X_y=True)
-    train_ds = pt.datasets.NumpyDataset(x_train, y_train)
+    train_ds = pt.datasets.Iris()
 
     # Reproducibility
     pl.utilities.seed.seed_everything(seed=2)
@@ -38,11 +36,10 @@ if __name__ == "__main__":
 
     # Hyperparameters
     hparams = dict(
-        nclasses=3,
-        prototypes_per_class=2,
-        prototype_initializer=pt.components.SMI((x_train, y_train)),
-        proto_lr=0.001,
-        bb_lr=0.001,
+        distribution=[1, 2, 3],
+        prototype_initializer=pt.components.SMI(train_ds),
+        proto_lr=0.01,
+        bb_lr=0.01,
     )
 
     # Initialize the model
@@ -55,7 +52,7 @@ if __name__ == "__main__":
     print(model)
 
     # Callbacks
-    vis = pt.models.VisSiameseGLVQ2D(data=(x_train, y_train), border=0.1)
+    vis = pt.models.VisSiameseGLVQ2D(data=train_ds, border=0.1)
 
     # Setup trainer
     trainer = pl.Trainer(max_epochs=100, callbacks=[vis])

prototorch/models/__init__.py

@@ -1,8 +1,10 @@
 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, LVQ1, LVQ21, LVQMLN, ImageGLVQ,
+                   SiameseGLVQ)
+from .knn import KNN
 from .neural_gas import NeuralGas
 from .vis import *
 
-__version__ = "0.1.0"
+__version__ = "0.1.7"

prototorch/models/abstract.py

@@ -3,9 +3,13 @@ import torch
 from torch.optim.lr_scheduler import ExponentialLR
 
 
-class AbstractLightningModel(pl.LightningModule):
+class AbstractPrototypeModel(pl.LightningModule):
+    @property
+    def prototypes(self):
+        return self.proto_layer.components.detach().cpu()
+
     def configure_optimizers(self):
-        optimizer = torch.optim.Adam(self.parameters(), lr=self.hparams.lr)
+        optimizer = self.optimizer(self.parameters(), lr=self.hparams.lr)
         scheduler = ExponentialLR(optimizer,
                                   gamma=0.99,
                                   last_epoch=-1,
@@ -15,9 +19,3 @@ class AbstractLightningModel(pl.LightningModule):
             "interval": "step",
         }  # called after each training step
         return [optimizer], [sch]
-
-
-class AbstractPrototypeModel(AbstractLightningModel):
-    @property
-    def prototypes(self):
-        return self.proto_layer.components.detach().cpu()

prototorch/models/glvq.py

@@ -5,7 +5,7 @@ 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
 
@@ -17,19 +17,22 @@ class GLVQ(AbstractPrototypeModel):
 
         self.save_hyperparameters(hparams)
 
+        self.optimizer = kwargs.get("optimizer", torch.optim.Adam)
+
         # Default Values
         self.hparams.setdefault("distance", euclidean_distance)
-        self.hparams.setdefault("optimizer", torch.optim.Adam)
         self.hparams.setdefault("transfer_function", "identity")
         self.hparams.setdefault("transfer_beta", 10.0)
 
         self.proto_layer = LabeledComponents(
-            labels=(self.hparams.nclasses, self.hparams.prototypes_per_class),
+            distribution=self.hparams.distribution,
             initializer=self.hparams.prototype_initializer)
 
         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 +47,7 @@ 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 +79,22 @@ class GLVQ(AbstractPrototypeModel):
         return y_pred.numpy()
 
 
+class LVQ1(GLVQ):
+    """Learning Vector Quantization 1."""
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+        self.loss = lvq1_loss
+        self.optimizer = torch.optim.SGD
+
+
+class LVQ21(GLVQ):
+    """Learning Vector Quantization 2.1."""
+    def __init__(self, hparams, **kwargs):
+        super().__init__(hparams, **kwargs)
+        self.loss = lvq21_loss
+        self.optimizer = torch.optim.SGD
+
+
 class ImageGLVQ(GLVQ):
     """GLVQ for training on image data.
 
@@ -112,13 +131,13 @@ class SiameseGLVQ(GLVQ):
         self.backbone_dependent.load_state_dict(master_state, strict=True)
 
     def configure_optimizers(self):
-        optim = self.hparams.optimizer
-        proto_opt = optim(self.proto_layer.parameters(),
-                          lr=self.hparams.proto_lr)
+        proto_opt = self.optimizer(self.proto_layer.parameters(),
+                                   lr=self.hparams.proto_lr)
         if list(self.backbone.parameters()):
             # only add an optimizer is the backbone has trainable parameters
             # otherwise, the next line fails
-            bb_opt = optim(self.backbone.parameters(), lr=self.hparams.bb_lr)
+            bb_opt = self.optimizer(self.backbone.parameters(),
+                                    lr=self.hparams.bb_lr)
             return proto_opt, bb_opt
         else:
             return proto_opt

prototorch/models/knn.py

@@ -0,0 +1,62 @@
+"""The popular K-Nearest-Neighbors classification algorithm."""
+
+import warnings
+
+import torch
+import torchmetrics
+from prototorch.components import LabeledComponents
+from prototorch.components.initializers import parse_init_arg
+from prototorch.functions.competitions import knnc
+from prototorch.functions.distances import euclidean_distance
+
+from .abstract import AbstractPrototypeModel
+
+
+class KNN(AbstractPrototypeModel):
+    """K-Nearest-Neighbors classification algorithm."""
+    def __init__(self, hparams, **kwargs):
+        super().__init__()
+
+        self.save_hyperparameters(hparams)
+
+        # Default Values
+        self.hparams.setdefault("k", 1)
+        self.hparams.setdefault("distance", euclidean_distance)
+
+        data = kwargs.get("data")
+        x_train, y_train = parse_init_arg(data)
+
+        self.proto_layer = LabeledComponents(initialized_components=(x_train,
+                                                                     y_train))
+
+        self.train_acc = torchmetrics.Accuracy()
+
+    @property
+    def prototype_labels(self):
+        return self.proto_layer.component_labels.detach().cpu()
+
+    def forward(self, x):
+        protos, _ = self.proto_layer()
+        dis = self.hparams.distance(x, protos)
+        return dis
+
+    def predict(self, x):
+        # model.eval()  # ?!
+        with torch.no_grad():
+            d = self(x)
+            plabels = self.proto_layer.component_labels
+            y_pred = knnc(d, plabels, k=self.hparams.k)
+        return y_pred.numpy()
+
+    def training_step(self, train_batch, batch_idx, optimizer_idx=None):
+        return 1
+
+    def on_train_batch_start(self,
+                             train_batch,
+                             batch_idx,
+                             dataloader_idx=None):
+        warnings.warn("k-NN has no training, skipping!")
+        return -1
+
+    def configure_optimizers(self):
+        return None

prototorch/models/neural_gas.py

@@ -1,6 +1,7 @@
 import torch
 from prototorch.components import Components
 from prototorch.components import initializers as cinit
+from prototorch.components.initializers import ZerosInitializer
 from prototorch.functions.distances import euclidean_distance
 from prototorch.modules.losses import NeuralGasEnergy
 
@@ -41,12 +42,14 @@ class NeuralGas(AbstractPrototypeModel):
 
         self.save_hyperparameters(hparams)
 
+        self.optimizer = kwargs.get("optimizer", torch.optim.Adam)
+
         # Default Values
         self.hparams.setdefault("input_dim", 2)
         self.hparams.setdefault("agelimit", 10)
         self.hparams.setdefault("lm", 1)
         self.hparams.setdefault("prototype_initializer",
-                                cinit.ZerosInitializer(self.hparams.input_dim))
+                                ZerosInitializer(self.hparams.input_dim))
 
         self.proto_layer = Components(
             self.hparams.num_prototypes,

prototorch/models/vis.py

@@ -298,7 +298,8 @@ class Vis2DAbstract(pl.Callback):
     def precheck(self, trainer):
         if self.show_last_only:
             if trainer.current_epoch != trainer.max_epochs - 1:
-                return
+                return False
+        return True
 
     def setup_ax(self, xlabel=None, ylabel=None):
         ax = self.fig.gca()
@@ -362,7 +363,8 @@ class Vis2DAbstract(pl.Callback):
 
 class VisGLVQ2D(Vis2DAbstract):
     def on_epoch_end(self, trainer, pl_module):
-        self.precheck(trainer)
+        if not self.precheck(trainer):
+            return True
 
         protos = pl_module.prototypes
         plabels = pl_module.prototype_labels
@@ -386,7 +388,8 @@ class VisSiameseGLVQ2D(Vis2DAbstract):
         self.map_protos = map_protos
 
     def on_epoch_end(self, trainer, pl_module):
-        self.precheck(trainer)
+        if not self.precheck(trainer):
+            return True
 
         protos = pl_module.prototypes
         plabels = pl_module.prototype_labels
@@ -411,14 +414,15 @@ class VisSiameseGLVQ2D(Vis2DAbstract):
 
 class VisCBC2D(Vis2DAbstract):
     def on_epoch_end(self, trainer, pl_module):
-        self.precheck(trainer)
+        if not self.precheck(trainer):
+            return True
 
         x_train, y_train = self.x_train, self.y_train
         protos = pl_module.components
         ax = self.setup_ax(xlabel="Data dimension 1",
                            ylabel="Data dimension 2")
         self.plot_data(ax, x_train, y_train)
-        self.plot_protos(ax, protos, plabels)
+        self.plot_protos(ax, protos, "w")
         x = np.vstack((x_train, protos))
         mesh_input, xx, yy = self.get_mesh_input(x)
         y_pred = pl_module.predict(torch.Tensor(mesh_input))
@@ -431,7 +435,8 @@ class VisCBC2D(Vis2DAbstract):
 
 class VisNG2D(Vis2DAbstract):
     def on_epoch_end(self, trainer, pl_module):
-        self.precheck(trainer)
+        if not self.precheck(trainer):
+            return True
 
         x_train, y_train = self.x_train, self.y_train
         protos = pl_module.prototypes

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>=0.4.4", "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="0.1.7",
     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)