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Merge pull request #4 from si-cim/dev

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Dev
This commit is contained in:
Jensun Ravichandran
2021-05-07 16:33:31 +02:00
committed by GitHub
parent c50f139559 dd75fbfff8
commit 84257bfb0d
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52
README.md
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@@ -5,9 +5,15 @@ PyTorch-Lightning.
## Installation
To install this plugin, simple install
[ProtoTorch](https://github.com/si-cim/prototorch) first by following the
installation instructions there and then install this plugin by doing:
To install this plugin, first install
[ProtoTorch](https://github.com/si-cim/prototorch) with:
```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
@@ -28,9 +34,14 @@ following:
```sh
export WORKON_HOME=~/pyenvs
mkdir -p $WORKON_HOME
source /usr/local/bin/virtualenvwrapper.sh # might be different
# source ~/.local/bin/virtualenvwrapper.sh
source /usr/local/bin/virtualenvwrapper.sh # location may vary
mkvirtualenv pt
```
Once you have a virtual environment setup, you can start install the `models`
plugin with:
```sh
workon pt
git clone git@github.com:si-cim/prototorch_models.git
cd prototorch_models
@@ -43,18 +54,31 @@ To assist in the development process, you may also find it useful to install
## Available models
- GLVQ
- Generalized Learning Vector Quantization (GLVQ)
- Generalized Matrix Learning Vector Quantization (GMLVQ)
- Limited-Rank Matrix Learning Vector Quantization (LiRaMLVQ)
- Siamese GLVQ
- Neural Gas
- Neural Gas (NG)
## Work in Progress
- CBC
- Classification-By-Components Network (CBC)
- Learning Vector Quantization Multi-Layer Network (LVQMLN)
## Planned models
- GMLVQ
- Local-Matrix GMLVQ
- Limited-Rank GMLVQ
- GTLVQ
- RSLVQ
- PLVQ
- LVQMLN
- Generalized Tangent Learning Vector Quantization (GTLVQ)
- 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
### How do I update the plugin?
If you have already cloned and installed `prototorch` and the
`prototorch_models` plugin with the `-e` flag via `pip`, all you have to do is
navigate to those folders from your terminal and do `git pull` to update.

129
examples/cbc_circle.py
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@@ -1,129 +0,0 @@
"""CBC example using the Iris dataset."""
import numpy as np
import pytorch_lightning as pl
import torch
from matplotlib import pyplot as plt
from sklearn.datasets import make_circles
from torch.utils.data import DataLoader
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.callbacks.visualization import VisPointProtos
from prototorch.models.cbc import CBC, euclidean_similarity
from prototorch.models.glvq import GLVQ
class VisualizationCallback(pl.Callback):
def __init__(
self,
x_train,
y_train,
prototype_model=True,
title="Prototype Visualization",
cmap="viridis",
):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
self.prototype_model = prototype_model
def on_epoch_end(self, trainer, pl_module):
if self.prototype_model:
protos = pl_module.prototypes
color = pl_module.prototype_labels
else:
protos = pl_module.components
color = "k"
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.set_xlabel("Data dimension 1")
ax.set_ylabel("Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
c=color,
cmap=self.cmap,
edgecolor="k",
marker="D",
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
plt.pause(0.1)
if __name__ == "__main__":
# Dataset
x_train, y_train = make_circles(n_samples=300,
shuffle=True,
noise=0.05,
random_state=None,
factor=0.5)
train_ds = NumpyDataset(x_train, y_train)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
# Hyperparameters
hparams = dict(
input_dim=x_train.shape[1],
nclasses=len(np.unique(y_train)),
prototypes_per_class=5,
prototype_initializer="randn",
lr=0.01,
)
# Initialize the model
model = CBC(
hparams,
data=[x_train, y_train],
similarity=euclidean_similarity,
)
model = GLVQ(hparams, data=[x_train, y_train])
# Fix the component locations
# model.proto_layer.requires_grad_(False)
# import sys
# sys.exit()
# Model summary
print(model)
# Callbacks
dvis = VisPointProtos(
data=(x_train, y_train),
save=True,
snap=False,
voronoi=True,
resolution=50,
pause_time=0.1,
make_gif=True,
)
# Setup trainer
trainer = pl.Trainer(
max_epochs=10,
callbacks=[
dvis,
],
)
# Training loop
trainer.fit(model, train_loader)

99
examples/cbc_iris.py
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@@ -1,112 +1,45 @@
"""CBC example using the Iris dataset."""
import numpy as np
import prototorch as pt
import pytorch_lightning as pl
import torch
from matplotlib import pyplot as plt
from sklearn.datasets import load_iris
from torch.utils.data import DataLoader
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.cbc import CBC
class VisualizationCallback(pl.Callback):
def __init__(self,
x_train,
y_train,
title="Prototype Visualization",
cmap="viridis"):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
def on_epoch_end(self, trainer, pl_module):
# protos = pl_module.prototypes
protos = pl_module.components
# plabels = pl_module.prototype_labels
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.set_xlabel("Data dimension 1")
ax.set_ylabel("Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
# c=plabels,
c="k",
cmap=self.cmap,
edgecolor="k",
marker="D",
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
plt.pause(0.1)
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 = NumpyDataset(x_train, y_train)
train_ds = pt.datasets.NumpyDataset(x_train, y_train)
# Reproducibility
pl.utilities.seed.seed_everything(seed=2)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
train_loader = torch.utils.data.DataLoader(train_ds,
num_workers=0,
batch_size=150)
# Hyperparameters
hparams = dict(
input_dim=x_train.shape[1],
nclasses=3,
prototypes_per_class=3,
prototype_initializer="stratified_mean",
num_components=5,
component_initializer=pt.components.SSI(train_ds, noise=0.01),
lr=0.01,
)
# Initialize the model
model = CBC(hparams, data=[x_train, y_train])
# Fix the component locations
# model.proto_layer.requires_grad_(False)
# Pure-positive reasonings
ncomps = 3
nclasses = 3
rmat = torch.stack(
[0.9 * torch.eye(ncomps),
torch.zeros(ncomps, nclasses)], dim=0)
# model.reasoning_layer.load_state_dict({"reasoning_probabilities": rmat},
# strict=True)
print(model.reasoning_layer.reasoning_probabilities)
# import sys
# sys.exit()
# Model summary
print(model)
model = pt.models.CBC(hparams)
# Callbacks
vis = VisualizationCallback(x_train, y_train)
dvis = pt.models.VisCBC2D(data=(x_train, y_train),
title="CBC Iris Example")
# Setup trainer
trainer = pl.Trainer(
max_epochs=100,
max_epochs=200,
callbacks=[
vis,
dvis,
],
)

128
examples/cbc_mnist.py
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@@ -1,128 +0,0 @@
"""CBC example using the MNIST dataset.
This script also shows how to use Tensorboard for visualizing the prototypes.
"""
import argparse
import pytorch_lightning as pl
import torchvision
from torch.utils.data import DataLoader
from torchvision import transforms
from torchvision.datasets import MNIST
from prototorch.models.cbc import CBC, ImageCBC, euclidean_similarity
class VisualizationCallback(pl.Callback):
def __init__(self, to_shape=(-1, 1, 28, 28), nrow=2):
super().__init__()
self.to_shape = to_shape
self.nrow = nrow
def on_epoch_end(self, trainer, pl_module: ImageCBC):
tb = pl_module.logger.experiment
# components
components = pl_module.components
components_img = components.reshape(self.to_shape)
grid = torchvision.utils.make_grid(components_img, nrow=self.nrow)
tb.add_image(
tag="MNIST Components",
img_tensor=grid,
global_step=trainer.current_epoch,
dataformats="CHW",
)
# Reasonings
reasonings = pl_module.reasonings
tb.add_images(
tag="MNIST Reasoning",
img_tensor=reasonings,
global_step=trainer.current_epoch,
dataformats="NCHW",
)
if __name__ == "__main__":
# Arguments
parser = argparse.ArgumentParser()
parser.add_argument("--epochs",
type=int,
default=10,
help="Epochs to train.")
parser.add_argument("--lr",
type=float,
default=0.001,
help="Learning rate.")
parser.add_argument("--batch_size",
type=int,
default=256,
help="Batch size.")
parser.add_argument("--gpus",
type=int,
default=0,
help="Number of GPUs to use.")
parser.add_argument("--ppc",
type=int,
default=1,
help="Prototypes-Per-Class.")
args = parser.parse_args()
# Dataset
mnist_train = MNIST(
"./datasets",
train=True,
download=True,
transform=transforms.Compose([
transforms.ToTensor(),
transforms.Normalize((0.1307, ), (0.3081, ))
]),
)
mnist_test = MNIST(
"./datasets",
train=False,
download=True,
transform=transforms.Compose([
transforms.ToTensor(),
transforms.Normalize((0.1307, ), (0.3081, ))
]),
)
# Dataloaders
train_loader = DataLoader(mnist_train, batch_size=32)
test_loader = DataLoader(mnist_test, batch_size=32)
# Grab the full dataset to warm-start prototypes
x, y = next(iter(DataLoader(mnist_train, batch_size=len(mnist_train))))
x = x.view(len(mnist_train), -1)
# Hyperparameters
hparams = dict(
input_dim=28 * 28,
nclasses=10,
prototypes_per_class=args.ppc,
prototype_initializer="randn",
lr=0.01,
similarity=euclidean_similarity,
)
# Initialize the model
model = CBC(hparams, data=[x, y])
# Model summary
print(model)
# Callbacks
vis = VisualizationCallback(to_shape=(-1, 1, 28, 28), nrow=args.ppc)
# Setup trainer
trainer = pl.Trainer(
gpus=args.gpus, # change to use GPUs for training
max_epochs=args.epochs,
callbacks=[vis],
track_grad_norm=2,
# accelerator="ddp_cpu", # DEBUG-ONLY
# num_processes=2, # DEBUG-ONLY
)
# Training loop
trainer.fit(model, train_loader, test_loader)

135
examples/cbc_spiral.py
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@@ -1,135 +0,0 @@
"""CBC example using the Iris dataset."""
import numpy as np
import pytorch_lightning as pl
import torch
from matplotlib import pyplot as plt
from torch.utils.data import DataLoader
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.cbc import CBC
class VisualizationCallback(pl.Callback):
def __init__(
self,
x_train,
y_train,
prototype_model=True,
title="Prototype Visualization",
cmap="viridis",
):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
self.prototype_model = prototype_model
def on_epoch_end(self, trainer, pl_module):
if self.prototype_model:
protos = pl_module.prototypes
color = pl_module.prototype_labels
else:
protos = pl_module.components
color = "k"
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.set_xlabel("Data dimension 1")
ax.set_ylabel("Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
c=color,
cmap=self.cmap,
edgecolor="k",
marker="D",
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
plt.pause(0.1)
def make_spirals(n_samples=500, noise=0.3):
def get_samples(n, delta_t):
points = []
for i in range(n):
r = i / n_samples * 5
t = 1.75 * i / n * 2 * np.pi + delta_t
x = r * np.sin(t) + np.random.rand(1) * noise
y = r * np.cos(t) + np.random.rand(1) * noise
points.append([x, y])
return points
n = n_samples // 2
positive = get_samples(n=n, delta_t=0)
negative = get_samples(n=n, delta_t=np.pi)
x = np.concatenate(
[np.array(positive).reshape(n, -1),
np.array(negative).reshape(n, -1)],
axis=0)
y = np.concatenate([np.zeros(n), np.ones(n)])
return x, y
if __name__ == "__main__":
# Dataset
x_train, y_train = make_spirals(n_samples=1000, noise=0.3)
train_ds = NumpyDataset(x_train, y_train)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
# Hyperparameters
hparams = dict(
input_dim=x_train.shape[1],
nclasses=2,
prototypes_per_class=40,
prototype_initializer="stratified_random",
lr=0.05,
)
# Initialize the model
model_class = CBC
model = model_class(hparams, data=[x_train, y_train])
# Pure-positive reasonings
new_reasoning = torch.zeros_like(
model.reasoning_layer.reasoning_probabilities)
for i, label in enumerate(model.proto_layer.prototype_labels):
new_reasoning[0][0][i][int(label)] = 1.0
model.reasoning_layer.reasoning_probabilities.data = new_reasoning
# Model summary
print(model)
# Callbacks
vis = VisualizationCallback(x_train,
y_train,
prototype_model=hasattr(model, "prototypes"))
# Setup trainer
trainer = pl.Trainer(
max_epochs=500,
callbacks=[
vis,
],
)
# Training loop
trainer.fit(model, train_loader)

146
examples/cbc_spiral_with_glvq_start.py
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@@ -1,146 +0,0 @@
"""CBC example using the spirals dataset.
This example shows how to jump start a model by transferring weights from
another more stable model.
"""
import numpy as np
import pytorch_lightning as pl
import torch
from matplotlib import pyplot as plt
from torch.utils.data import DataLoader
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.cbc import CBC
from prototorch.models.glvq import GLVQ
class VisualizationCallback(pl.Callback):
def __init__(
self,
x_train,
y_train,
prototype_model=True,
title="Prototype Visualization",
cmap="viridis",
):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
self.prototype_model = prototype_model
def on_epoch_end(self, trainer, pl_module):
if self.prototype_model:
protos = pl_module.prototypes
color = pl_module.prototype_labels
else:
protos = pl_module.components
color = "k"
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.set_xlabel("Data dimension 1")
ax.set_ylabel("Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
c=color,
cmap=self.cmap,
edgecolor="k",
marker="D",
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
plt.pause(0.1)
def make_spirals(n_samples=500, noise=0.3):
def get_samples(n, delta_t):
points = []
for i in range(n):
r = i / n_samples * 5
t = 1.75 * i / n * 2 * np.pi + delta_t
x = r * np.sin(t) + np.random.rand(1) * noise
y = r * np.cos(t) + np.random.rand(1) * noise
points.append([x, y])
return points
n = n_samples // 2
positive = get_samples(n=n, delta_t=0)
negative = get_samples(n=n, delta_t=np.pi)
x = np.concatenate(
[np.array(positive).reshape(n, -1),
np.array(negative).reshape(n, -1)],
axis=0)
y = np.concatenate([np.zeros(n), np.ones(n)])
return x, y
def train(model, x_train, y_train, train_loader, epochs=100):
# Callbacks
vis = VisualizationCallback(x_train,
y_train,
prototype_model=hasattr(model, "prototypes"))
# Setup trainer
trainer = pl.Trainer(
max_epochs=epochs,
callbacks=[
vis,
],
)
# Training loop
trainer.fit(model, train_loader)
if __name__ == "__main__":
# Dataset
x_train, y_train = make_spirals(n_samples=1000, noise=0.3)
train_ds = NumpyDataset(x_train, y_train)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
# Hyperparameters
hparams = dict(
input_dim=x_train.shape[1],
nclasses=2,
prototypes_per_class=40,
prototype_initializer="stratified_random",
lr=0.05,
)
# Initialize the model
glvq_model = GLVQ(hparams, data=[x_train, y_train])
cbc_model = CBC(hparams, data=[x_train, y_train])
# Train GLVQ
train(glvq_model, x_train, y_train, train_loader, epochs=10)
# Transfer Prototypes
cbc_model.proto_layer.load_state_dict(glvq_model.proto_layer.state_dict())
# Pure-positive reasonings
new_reasoning = torch.zeros_like(
cbc_model.reasoning_layer.reasoning_probabilities)
for i, label in enumerate(cbc_model.proto_layer.prototype_labels):
new_reasoning[0][0][i][int(label)] = 1.0
new_reasoning[1][0][i][1 - int(label)] = 1.0
cbc_model.reasoning_layer.reasoning_probabilities.data = new_reasoning
# Train CBC
train(cbc_model, x_train, y_train, train_loader, epochs=50)

133
examples/glvq_iris.py
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@@ -1,131 +1,40 @@
"""GLVQ example using the Iris dataset."""
import argparse
import numpy as np
import prototorch as pt
import pytorch_lightning as pl
import torch
from matplotlib import pyplot as plt
from sklearn.datasets import load_iris
from torch.utils.data import DataLoader
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.glvq import GLVQ
class GLVQIris(GLVQ):
@staticmethod
def add_model_specific_args(parent_parser):
parser = argparse.ArgumentParser(parents=[parent_parser],
add_help=False)
parser.add_argument("--epochs", type=int, default=1)
parser.add_argument("--lr", type=float, default=1e-1)
parser.add_argument("--batch_size", type=int, default=150)
parser.add_argument("--input_dim", type=int, default=2)
parser.add_argument("--nclasses", type=int, default=3)
parser.add_argument("--prototypes_per_class", type=int, default=3)
parser.add_argument("--prototype_initializer",
type=str,
default="stratified_mean")
return parser
class VisualizationCallback(pl.Callback):
def __init__(self,
x_train,
y_train,
title="Prototype Visualization",
cmap="viridis"):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
def on_epoch_end(self, trainer, pl_module):
protos = pl_module.prototypes
plabels = pl_module.prototype_labels
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.set_xlabel("Data dimension 1")
ax.set_ylabel("Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
c=plabels,
cmap=self.cmap,
edgecolor="k",
marker="D",
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
plt.pause(0.1)
if __name__ == "__main__":
# For best-practices when using `argparse` with `pytorch_lightning`, see
# https://pytorch-lightning.readthedocs.io/en/stable/common/hyperparameters.html
parser = argparse.ArgumentParser()
# 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 = NumpyDataset(x_train, y_train)
train_ds = pt.datasets.NumpyDataset(x_train, y_train)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
train_loader = torch.utils.data.DataLoader(train_ds,
num_workers=0,
batch_size=150)
# Add model specific args
parser = GLVQIris.add_model_specific_args(parser)
# Callbacks
vis = VisualizationCallback(x_train, y_train)
# Automatically add trainer-specific-args like `--gpus`, `--num_nodes` etc.
parser = pl.Trainer.add_argparse_args(parser)
# Setup trainer
trainer = pl.Trainer.from_argparse_args(
parser,
max_epochs=10,
callbacks=[
vis,
], # comment this line out to disable the visualization
# Hyperparameters
hparams = dict(
nclasses=3,
prototypes_per_class=2,
prototype_initializer=pt.components.SMI(train_ds),
lr=0.01,
)
# trainer.tune(model)
# Initialize the model
args = parser.parse_args()
model = GLVQIris(args, data=[x_train, y_train])
model = pt.models.GLVQ(hparams)
# Model summary
print(model)
# Callbacks
vis = pt.models.VisGLVQ2D(data=(x_train, y_train))
# Setup trainer
trainer = pl.Trainer(
max_epochs=50,
callbacks=[vis],
)
# Training loop
trainer.fit(model, train_loader)
# Save the model manually (use `pl.callbacks.ModelCheckpoint` to automate)
ckpt = "glvq_iris.ckpt"
trainer.save_checkpoint(ckpt)
# Load the checkpoint
new_model = GLVQIris.load_from_checkpoint(checkpoint_path=ckpt)
print(new_model)
# Continue training
trainer.fit(new_model, train_loader) # TODO See why this fails!

40
examples/glvq_iris_v1.py
View File

@@ -1,40 +0,0 @@
"""GLVQ example using the Iris dataset."""
import pytorch_lightning as pl
import torch
from prototorch.components import initializers as cinit
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.callbacks.visualization import VisGLVQ2D
from prototorch.models.glvq import GLVQ
from sklearn.datasets import load_iris
from torch.utils.data import DataLoader
if __name__ == "__main__":
# Dataset
x_train, y_train = load_iris(return_X_y=True)
x_train = x_train[:, [0, 2]]
train_ds = NumpyDataset(x_train, y_train)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
# Hyperparameters
hparams = dict(
nclasses=3,
prototypes_per_class=2,
prototype_initializer=cinit.StratifiedMeanInitializer(
torch.Tensor(x_train), torch.Tensor(y_train)),
lr=0.01,
)
# Initialize the model
model = GLVQ(hparams, data=[x_train, y_train])
# Setup trainer
trainer = pl.Trainer(
max_epochs=50,
callbacks=[VisGLVQ2D(x_train, y_train)],
)
# Training loop
trainer.fit(model, train_loader)

118
examples/glvq_mnist.py
View File

@@ -1,118 +0,0 @@
"""GLVQ example using the MNIST dataset.
This script also shows how to use Tensorboard for visualizing the prototypes.
"""
import argparse
import pytorch_lightning as pl
import torchvision
from torch.utils.data import DataLoader
from torchvision import transforms
from torchvision.datasets import MNIST
from prototorch.models.glvq import ImageGLVQ
class VisualizationCallback(pl.Callback):
def __init__(self, to_shape=(-1, 1, 28, 28), nrow=2):
super().__init__()
self.to_shape = to_shape
self.nrow = nrow
def on_epoch_end(self, trainer, pl_module):
protos = pl_module.proto_layer.prototypes.detach().cpu()
protos_img = protos.reshape(self.to_shape)
grid = torchvision.utils.make_grid(protos_img, nrow=self.nrow)
# grid = grid.permute((1, 2, 0))
tb = pl_module.logger.experiment
tb.add_image(
tag="MNIST Prototypes",
img_tensor=grid,
global_step=trainer.current_epoch,
dataformats="CHW",
)
if __name__ == "__main__":
# Arguments
parser = argparse.ArgumentParser()
parser.add_argument("--epochs",
type=int,
default=10,
help="Epochs to train.")
parser.add_argument("--lr",
type=float,
default=0.001,
help="Learning rate.")
parser.add_argument("--batch_size",
type=int,
default=256,
help="Batch size.")
parser.add_argument("--gpus",
type=int,
default=0,
help="Number of GPUs to use.")
parser.add_argument("--ppc",
type=int,
default=1,
help="Prototypes-Per-Class.")
args = parser.parse_args()
# Dataset
mnist_train = MNIST(
"./datasets",
train=True,
download=True,
transform=transforms.Compose([
transforms.ToTensor(),
transforms.Normalize((0.1307, ), (0.3081, ))
]),
)
mnist_test = MNIST(
"./datasets",
train=False,
download=True,
transform=transforms.Compose([
transforms.ToTensor(),
transforms.Normalize((0.1307, ), (0.3081, ))
]),
)
# Dataloaders
train_loader = DataLoader(mnist_train, batch_size=1024)
test_loader = DataLoader(mnist_test, batch_size=1024)
# Grab the full dataset to warm-start prototypes
x, y = next(iter(DataLoader(mnist_train, batch_size=len(mnist_train))))
x = x.view(len(mnist_train), -1)
# Hyperparameters
hparams = dict(
input_dim=28 * 28,
nclasses=10,
prototypes_per_class=1,
prototype_initializer="stratified_mean",
lr=args.lr,
)
# Initialize the model
model = ImageGLVQ(hparams, data=[x, y])
# Model summary
print(model)
# Callbacks
vis = VisualizationCallback(to_shape=(-1, 1, 28, 28), nrow=args.ppc)
# Setup trainer
trainer = pl.Trainer(
gpus=args.gpus, # change to use GPUs for training
max_epochs=args.epochs,
callbacks=[vis],
# accelerator="ddp_cpu", # DEBUG-ONLY
# num_processes=2, # DEBUG-ONLY
)
# Training loop
trainer.fit(model, train_loader, test_loader)

51
examples/glvq_spiral.py Normal file
View File

@@ -0,0 +1,51 @@
"""GLVQ example using the spiral dataset."""
import prototorch as pt
import pytorch_lightning as pl
import torch
class StopOnNaN(pl.Callback):
def __init__(self, param):
super().__init__()
self.param = param
def on_epoch_end(self, trainer, pl_module, logs={}):
if torch.isnan(self.param).any():
raise ValueError("NaN encountered. Stopping.")
if __name__ == "__main__":
# Dataset
train_ds = pt.datasets.Spiral(n_samples=600, noise=0.6)
# Dataloaders
train_loader = torch.utils.data.DataLoader(train_ds,
num_workers=0,
batch_size=256)
# Hyperparameters
hparams = dict(
nclasses=2,
prototypes_per_class=20,
prototype_initializer=pt.components.SSI(train_ds, noise=1e-7),
transfer_function="sigmoid_beta",
transfer_beta=10.0,
lr=0.01,
)
# Initialize the model
model = pt.models.GLVQ(hparams)
# Callbacks
vis = pt.models.VisGLVQ2D(train_ds, show_last_only=True, block=True)
snan = StopOnNaN(model.proto_layer.components)
# Setup trainer
trainer = pl.Trainer(
max_epochs=200,
callbacks=[vis, snan],
)
# Training loop
trainer.fit(model, train_loader)

37
examples/gmlvq_iris.py Normal file
View File

@@ -0,0 +1,37 @@
"""GMLVQ example using all four dimensions of 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)
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=1,
input_dim=x_train.shape[1],
latent_dim=x_train.shape[1],
prototype_initializer=pt.components.SMI(train_ds),
lr=0.01,
)
# Initialize the model
model = pt.models.GMLVQ(hparams)
# Setup trainer
trainer = pl.Trainer(max_epochs=100)
# Training loop
trainer.fit(model, train_loader)
# Display the Lambda matrix
model.show_lambda()

45
examples/liramlvq_tecator.py Normal file
View File

@@ -0,0 +1,45 @@
"""Limited Rank Matrix LVQ example using the Tecator dataset."""
import prototorch as pt
import pytorch_lightning as pl
import torch
if __name__ == "__main__":
# Dataset
train_ds = pt.datasets.Tecator(root="~/datasets/", train=True)
# Reproducibility
pl.utilities.seed.seed_everything(seed=42)
# Dataloaders
train_loader = torch.utils.data.DataLoader(train_ds,
num_workers=0,
batch_size=32)
# Hyperparameters
hparams = dict(
nclasses=2,
prototypes_per_class=2,
input_dim=100,
latent_dim=2,
prototype_initializer=pt.components.SMI(train_ds),
lr=0.001,
)
# Initialize the model
model = pt.models.GMLVQ(hparams)
# Model summary
print(model)
# Callbacks
vis = pt.models.VisSiameseGLVQ2D(train_ds, border=0.1)
# Namespace hook for the visualization to work
model.backbone = model.omega_layer
# Setup trainer
trainer = pl.Trainer(max_epochs=200, callbacks=[vis])
# Training loop
trainer.fit(model, train_loader)

37
examples/ng_iris.py
View File

@@ -1,51 +1,40 @@
"""Neural Gas example using the Iris dataset."""
import numpy as np
import prototorch as pt
import pytorch_lightning as pl
from matplotlib import pyplot as plt
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.callbacks.visualization import VisNG2D
from prototorch.models.neural_gas import NeuralGas
from sklearn.datasets import load_iris
from sklearn.preprocessing import StandardScaler
from torch.utils.data import DataLoader
import torch
if __name__ == "__main__":
# Dataset
# Prepare and pre-process the dataset
from sklearn.datasets import load_iris
from sklearn.preprocessing import StandardScaler
x_train, y_train = load_iris(return_X_y=True)
x_train = x_train[:, [0, 2]]
scaler = StandardScaler()
scaler.fit(x_train)
x_train = scaler.transform(x_train)
train_ds = NumpyDataset(x_train, y_train)
train_ds = pt.datasets.NumpyDataset(x_train, y_train)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
train_loader = torch.utils.data.DataLoader(train_ds,
num_workers=0,
batch_size=150)
# Hyperparameters
hparams = dict(
input_dim=x_train.shape[1],
num_prototypes=30,
lr=0.01,
)
hparams = dict(num_prototypes=30, lr=0.03)
# Initialize the model
model = NeuralGas(hparams)
model = pt.models.NeuralGas(hparams)
# Model summary
print(model)
# Callbacks
vis = VisNG2D(x_train, y_train)
vis = pt.models.VisNG2D(data=train_ds)
# Setup trainer
trainer = pl.Trainer(
max_epochs=100,
callbacks=[
vis,
],
)
trainer = pl.Trainer(max_epochs=200, callbacks=[vis])
# Training loop
trainer.fit(model, train_loader)

35
examples/siamese_glvq_iris.py
View File

@@ -1,17 +1,12 @@
"""Siamese GLVQ example using all four dimensions of the Iris dataset."""
import prototorch as pt
import pytorch_lightning as pl
import torch
from prototorch.components import (StratifiedMeanInitializer,
StratifiedSelectionInitializer)
from prototorch.datasets.abstract import NumpyDataset
from prototorch.models.callbacks.visualization import VisSiameseGLVQ2D
from prototorch.models.glvq import SiameseGLVQ
from sklearn.datasets import load_iris
from torch.utils.data import DataLoader
class Backbone(torch.nn.Module):
"""Two fully connected layers with ReLU activation."""
def __init__(self, input_size=4, hidden_size=10, latent_size=2):
super().__init__()
self.input_size = input_size
@@ -22,28 +17,36 @@ class Backbone(torch.nn.Module):
self.relu = torch.nn.ReLU()
def forward(self, x):
return self.relu(self.dense2(self.relu(self.dense1(x))))
x = self.relu(self.dense1(x))
out = self.relu(self.dense2(x))
return out
if __name__ == "__main__":
# Dataset
from sklearn.datasets import load_iris
x_train, y_train = load_iris(return_X_y=True)
train_ds = NumpyDataset(x_train, y_train)
train_ds = pt.datasets.NumpyDataset(x_train, y_train)
# Reproducibility
pl.utilities.seed.seed_everything(seed=2)
# Dataloaders
train_loader = DataLoader(train_ds, num_workers=0, batch_size=150)
train_loader = torch.utils.data.DataLoader(train_ds,
num_workers=0,
batch_size=150)
# Hyperparameters
hparams = dict(
nclasses=3,
prototypes_per_class=1,
prototype_initializer=StratifiedMeanInitializer(
torch.Tensor(x_train), torch.Tensor(y_train)),
lr=0.01,
prototypes_per_class=2,
prototype_initializer=pt.components.SMI((x_train, y_train)),
proto_lr=0.001,
bb_lr=0.001,
)
# Initialize the model
model = SiameseGLVQ(
model = pt.models.SiameseGLVQ(
hparams,
backbone_module=Backbone,
)
@@ -52,7 +55,7 @@ if __name__ == "__main__":
print(model)
# Callbacks
vis = VisSiameseGLVQ2D(x_train, y_train)
vis = pt.models.VisSiameseGLVQ2D(data=(x_train, y_train), border=0.1)
# Setup trainer
trainer = pl.Trainer(max_epochs=100, callbacks=[vis])

5
prototorch/models/__init__.py
View File

@@ -1,5 +1,10 @@
from importlib.metadata import PackageNotFoundError, version
from .cbc import CBC
from .glvq import GLVQ, GMLVQ, GRLVQ, LVQMLN, ImageGLVQ, SiameseGLVQ
from .neural_gas import NeuralGas
from .vis import *
VERSION_FALLBACK = "uninstalled_version"
try:
__version__ = version(__name__.replace(".", "-"))

23
prototorch/models/abstract.py Normal file
View File

@@ -0,0 +1,23 @@
import pytorch_lightning as pl
import torch
from torch.optim.lr_scheduler import ExponentialLR
class AbstractLightningModel(pl.LightningModule):
def configure_optimizers(self):
optimizer = torch.optim.Adam(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 AbstractPrototypeModel(AbstractLightningModel):
@property
def prototypes(self):
return self.proto_layer.components.detach().cpu()

17
prototorch/models/cbc.py
View File

@@ -1,10 +1,9 @@
import pytorch_lightning as pl
import torch
import torchmetrics
from prototorch.components.components import Components
from prototorch.functions.distances import euclidean_distance
from prototorch.functions.similarities import cosine_similarity
from prototorch.modules.prototypes import Prototypes1D
def rescaled_cosine_similarity(x, y):
@@ -93,12 +92,8 @@ class CBC(pl.LightningModule):
super().__init__()
self.save_hyperparameters(hparams)
self.margin = margin
self.proto_layer = Prototypes1D(
input_dim=self.hparams.input_dim,
nclasses=self.hparams.nclasses,
prototypes_per_class=self.hparams.prototypes_per_class,
prototype_initializer=self.hparams.prototype_initializer,
**kwargs)
self.component_layer = Components(self.hparams.num_components,
self.hparams.component_initializer)
# self.similarity = CosineSimilarity()
self.similarity = similarity
self.backbone = backbone_class()
@@ -110,7 +105,7 @@ class CBC(pl.LightningModule):
@property
def components(self):
return self.proto_layer.prototypes.detach().cpu()
return self.component_layer.components.detach().cpu()
@property
def reasonings(self):
@@ -126,7 +121,7 @@ class CBC(pl.LightningModule):
def forward(self, x):
self.sync_backbones()
protos, _ = self.proto_layer()
protos = self.component_layer()
latent_x = self.backbone(x)
latent_protos = self.backbone_dependent(protos)
@@ -167,4 +162,4 @@ class ImageCBC(CBC):
"""
def on_train_batch_end(self, outputs, batch, batch_idx, dataloader_idx):
# super().on_train_batch_end(outputs, batch, batch_idx, dataloader_idx)
self.proto_layer.prototypes.data.clamp_(0.0, 1.0)
self.component_layer.prototypes.data.clamp_(0.0, 1.0)

216
prototorch/models/glvq.py
View File

@@ -1,11 +1,11 @@
import pytorch_lightning as pl
import torch
import torchmetrics
from prototorch.components import LabeledComponents
from prototorch.functions.activations import get_activation
from prototorch.functions.competitions import wtac
from prototorch.functions.distances import euclidean_distance
from prototorch.functions.distances import (euclidean_distance, omega_distance,
squared_euclidean_distance)
from prototorch.functions.losses import glvq_loss
from prototorch.modules.prototypes import Prototypes1D
from .abstract import AbstractPrototypeModel
@@ -19,50 +19,53 @@ class GLVQ(AbstractPrototypeModel):
# 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),
initializer=self.hparams.prototype_initializer)
self.transfer_function = get_activation(self.hparams.transfer_function)
self.train_acc = torchmetrics.Accuracy()
@property
def prototype_labels(self):
return self.proto_layer.component_labels.detach().numpy()
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 training_step(self, train_batch, batch_idx):
def training_step(self, train_batch, batch_idx, optimizer_idx=None):
x, y = train_batch
x = x.view(x.size(0), -1)
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)
loss = mu.sum(dim=0)
self.log("train_loss", loss)
batch_loss = self.transfer_function(mu,
beta=self.hparams.transfer_beta)
loss = batch_loss.sum(dim=0)
# Compute training accuracy
with torch.no_grad():
preds = wtac(dis, plabels)
# self.train_acc.update(preds.int(), y.int())
self.train_acc(
preds.int(),
y.int()) # FloatTensors are assumed to be class probabilities
self.log(
"acc",
self.train_acc(preds.int(), y.int())
# `.int()` because FloatTensors are assumed to be class probabilities
# Logging
self.log("train_loss", loss)
self.log("acc",
self.train_acc,
on_step=False,
on_epoch=True,
prog_bar=True,
logger=True,
)
return loss
logger=True)
# def training_epoch_end(self, outs):
# # Calling `self.train_acc.compute()` is
# # automatically done by setting `on_epoch=True` when logging in `self.training_step(...)`
# self.log("train_acc_epoch", self.train_acc.compute())
return loss
def predict(self, x):
# model.eval() # ?!
@@ -76,8 +79,9 @@ class GLVQ(AbstractPrototypeModel):
class ImageGLVQ(GLVQ):
"""GLVQ for training on image data.
GLVQ model that constrains the prototypes to the range [0, 1] by
clamping after updates.
GLVQ model that constrains the prototypes to the range [0, 1] by clamping
after updates.
"""
def on_train_batch_end(self, outputs, batch, batch_idx, dataloader_idx):
self.proto_layer.components.data.clamp_(0.0, 1.0)
@@ -89,6 +93,155 @@ class SiameseGLVQ(GLVQ):
GLVQ model that applies an arbitrary transformation on the inputs and the
prototypes before computing the distances between them. The weights in the
transformation pipeline are only learned from the inputs.
"""
def __init__(self,
hparams,
backbone_module=torch.nn.Identity,
backbone_params={},
sync=True,
**kwargs):
super().__init__(hparams, **kwargs)
self.backbone = backbone_module(**backbone_params)
self.backbone_dependent = backbone_module(
**backbone_params).requires_grad_(False)
self.sync = sync
def sync_backbones(self):
master_state = self.backbone.state_dict()
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)
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)
return proto_opt, bb_opt
else:
return proto_opt
def forward(self, x):
if self.sync:
self.sync_backbones()
protos, _ = self.proto_layer()
latent_x = self.backbone(x)
latent_protos = self.backbone_dependent(protos)
dis = euclidean_distance(latent_x, latent_protos)
return dis
def predict_latent(self, x):
"""Predict `x` assuming it is already embedded in the latent space.
Only the prototypes are embedded in the latent space using the
backbone.
"""
# model.eval() # ?!
with torch.no_grad():
protos, plabels = self.proto_layer()
latent_protos = self.backbone_dependent(protos)
d = euclidean_distance(x, latent_protos)
y_pred = wtac(d, plabels)
return y_pred.numpy()
class GRLVQ(GLVQ):
"""Generalized Relevance Learning Vector Quantization."""
def __init__(self, hparams, **kwargs):
super().__init__(hparams, **kwargs)
self.relevances = torch.nn.parameter.Parameter(
torch.ones(self.hparams.input_dim))
def forward(self, x):
protos, _ = self.proto_layer()
dis = omega_distance(x, protos, torch.diag(self.relevances))
return dis
def backbone(self, x):
return x @ torch.diag(self.relevances)
@property
def relevance_profile(self):
return self.relevances.detach().cpu()
def predict_latent(self, x):
"""Predict `x` assuming it is already embedded in the latent space.
Only the prototypes are embedded in the latent space using the
backbone.
"""
# model.eval() # ?!
with torch.no_grad():
protos, plabels = self.proto_layer()
latent_protos = protos @ torch.diag(self.relevances)
d = squared_euclidean_distance(x, latent_protos)
y_pred = wtac(d, plabels)
return y_pred.numpy()
class GMLVQ(GLVQ):
"""Generalized Matrix Learning Vector Quantization."""
def __init__(self, hparams, **kwargs):
super().__init__(hparams, **kwargs)
self.omega_layer = torch.nn.Linear(self.hparams.input_dim,
self.hparams.latent_dim,
bias=False)
@property
def omega_matrix(self):
return self.omega_layer.weight.detach().cpu()
@property
def lambda_matrix(self):
omega = self.omega_layer.weight
lam = omega @ omega.T
return lam.detach().cpu()
def show_lambda(self):
import matplotlib.pyplot as plt
title = "Lambda matrix"
plt.figure(title)
plt.title(title)
plt.imshow(self.lambda_matrix, cmap="gray")
plt.axis("off")
plt.colorbar()
plt.show(block=True)
def forward(self, x):
protos, _ = self.proto_layer()
latent_x = self.omega_layer(x)
latent_protos = self.omega_layer(protos)
dis = squared_euclidean_distance(latent_x, latent_protos)
return dis
def predict_latent(self, x):
"""Predict `x` assuming it is already embedded in the latent space.
Only the prototypes are embedded in the latent space using the
backbone.
"""
# model.eval() # ?!
with torch.no_grad():
protos, plabels = self.proto_layer()
latent_protos = self.omega_layer(protos)
d = squared_euclidean_distance(x, latent_protos)
y_pred = wtac(d, plabels)
return y_pred.numpy()
class LVQMLN(GLVQ):
"""Learning Vector Quantization Multi-Layer Network.
GLVQ model that applies an arbitrary transformation on the inputs, BUT NOT
on the prototypes before computing the distances between them. This of
course, means that the prototypes no longer live the input space, but
rather in the embedding space.
"""
def __init__(self,
hparams,
@@ -97,28 +250,17 @@ class SiameseGLVQ(GLVQ):
**kwargs):
super().__init__(hparams, **kwargs)
self.backbone = backbone_module(**backbone_params)
self.backbone_dependent = backbone_module(
**backbone_params).requires_grad_(False)
def sync_backbones(self):
master_state = self.backbone.state_dict()
self.backbone_dependent.load_state_dict(master_state, strict=True)
def forward(self, x):
self.sync_backbones()
protos, _ = self.proto_layer()
latent_protos, _ = self.proto_layer()
latent_x = self.backbone(x)
latent_protos = self.backbone_dependent(protos)
dis = euclidean_distance(latent_x, latent_protos)
return dis
def predict_latent(self, x):
# model.eval() # ?!
"""Predict `x` assuming it is already embedded in the latent space."""
with torch.no_grad():
protos, plabels = self.proto_layer()
latent_protos = self.backbone_dependent(protos)
latent_protos, plabels = self.proto_layer()
d = euclidean_distance(x, latent_protos)
y_pred = wtac(d, plabels)
return y_pred.numpy()

2
prototorch/models/neural_gas.py
View File

@@ -1,9 +1,7 @@
import pytorch_lightning as pl
import torch
from prototorch.components import Components
from prototorch.components import initializers as cinit
from prototorch.functions.distances import euclidean_distance
from prototorch.modules import Prototypes1D
from prototorch.modules.losses import NeuralGasEnergy
from .abstract import AbstractPrototypeModel

184
prototorch/models/callbacks/visualization.py → prototorch/models/vis.py
View File

@@ -9,6 +9,7 @@ from prototorch.utils.celluloid import Camera
from prototorch.utils.colors import color_scheme
from prototorch.utils.utils import (gif_from_dir, make_directory,
prettify_string)
from torch.utils.data import DataLoader, Dataset
class VisWeights(pl.Callback):
@@ -261,29 +262,82 @@ class VisPointProtos(VisWeights):
self._show_and_save(epoch)
class VisGLVQ2D(pl.Callback):
class Vis2DAbstract(pl.Callback):
def __init__(self,
x_train,
y_train,
data,
title="Prototype Visualization",
cmap="viridis"):
cmap="viridis",
border=1,
resolution=50,
tensorboard=False,
show_last_only=False,
pause_time=0.1,
block=False):
super().__init__()
self.x_train = x_train
self.y_train = y_train
if isinstance(data, Dataset):
x, y = next(iter(DataLoader(data, batch_size=len(data))))
x = x.view(len(data), -1) # flatten
else:
x, y = data
self.x_train = x
self.y_train = y
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
self.border = border
self.resolution = resolution
self.tensorboard = tensorboard
self.show_last_only = show_last_only
self.pause_time = pause_time
self.block = block
def on_epoch_end(self, trainer, pl_module):
protos = pl_module.prototypes
plabels = pl_module.prototype_labels
x_train, y_train = self.x_train, self.y_train
def setup_ax(self, xlabel=None, ylabel=None):
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.axis("off")
if xlabel:
ax.set_xlabel("Data dimension 1")
if ylabel:
ax.set_ylabel("Data dimension 2")
return ax
def get_mesh_input(self, x):
x_min, x_max = x[:, 0].min() - self.border, x[:, 0].max() + self.border
y_min, y_max = x[:, 1].min() - self.border, x[:, 1].max() + self.border
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / self.resolution),
np.arange(y_min, y_max, 1 / self.resolution))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
return mesh_input, xx, yy
def add_to_tensorboard(self, trainer, pl_module):
tb = pl_module.logger.experiment
tb.add_figure(tag=f"{self.title}",
figure=self.fig,
global_step=trainer.current_epoch,
close=False)
def log_and_display(self, trainer, pl_module):
if self.tensorboard:
self.add_to_tensorboard(trainer, pl_module)
if not self.block:
plt.pause(self.pause_time)
else:
plt.show(block=True)
class VisGLVQ2D(Vis2DAbstract):
def on_epoch_end(self, trainer, pl_module):
if self.show_last_only:
if trainer.current_epoch != trainer.max_epochs - 1:
return
protos = pl_module.prototypes
plabels = pl_module.prototype_labels
x_train, y_train = self.x_train, self.y_train
ax = self.setup_ax(xlabel="Data dimension 1",
ylabel="Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
@@ -295,43 +349,25 @@ class VisGLVQ2D(pl.Callback):
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
mesh_input, xx, yy = self.get_mesh_input(x)
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
plt.pause(0.1)
# ax.set_xlim(left=x_min + 0, right=x_max - 0)
# ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
self.log_and_display(trainer, pl_module)
class VisSiameseGLVQ2D(pl.Callback):
def __init__(self,
x_train,
y_train,
title="Prototype Visualization",
cmap="viridis"):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
class VisSiameseGLVQ2D(Vis2DAbstract):
def on_epoch_end(self, trainer, pl_module):
protos = pl_module.prototypes
plabels = pl_module.prototype_labels
x_train, y_train = self.x_train, self.y_train
x_train = pl_module.backbone(torch.Tensor(x_train)).detach()
protos = pl_module.backbone(torch.Tensor(protos)).detach()
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.axis("off")
ax = self.setup_ax()
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
@@ -343,54 +379,54 @@ class VisSiameseGLVQ2D(pl.Callback):
s=50,
)
x = np.vstack((x_train, protos))
x_min, x_max = x[:, 0].min() - 1, x[:, 0].max() + 1
y_min, y_max = x[:, 1].min() - 1, x[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, 1 / 50),
np.arange(y_min, y_max, 1 / 50))
mesh_input = np.c_[xx.ravel(), yy.ravel()]
mesh_input, xx, yy = self.get_mesh_input(x)
y_pred = pl_module.predict_latent(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
ax.set_xlim(left=x_min + 0, right=x_max - 0)
ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
tb = pl_module.logger.experiment
tb.add_figure(
tag=f"{self.title}",
figure=self.fig,
global_step=trainer.current_epoch,
close=False,
)
plt.pause(0.1)
# ax.set_xlim(left=x_min + 0, right=x_max - 0)
# ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
self.log_and_display(trainer, pl_module)
class VisNG2D(pl.Callback):
def __init__(self,
x_train,
y_train,
title="Neural Gas Visualization",
cmap="viridis"):
super().__init__()
self.x_train = x_train
self.y_train = y_train
self.title = title
self.fig = plt.figure(self.title)
self.cmap = cmap
class VisCBC2D(Vis2DAbstract):
def on_epoch_end(self, trainer, pl_module):
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")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
c="w",
cmap=self.cmap,
edgecolor="k",
marker="D",
s=50,
)
x = np.vstack((x_train, protos))
mesh_input, xx, yy = self.get_mesh_input(x)
y_pred = pl_module.predict(torch.Tensor(mesh_input))
y_pred = y_pred.reshape(xx.shape)
ax.contourf(xx, yy, y_pred, cmap=self.cmap, alpha=0.35)
# ax.set_xlim(left=x_min + 0, right=x_max - 0)
# ax.set_ylim(bottom=y_min + 0, top=y_max - 0)
self.log_and_display(trainer, pl_module)
class VisNG2D(Vis2DAbstract):
def on_epoch_end(self, trainer, pl_module):
x_train, y_train = self.x_train, self.y_train
protos = pl_module.prototypes
cmat = pl_module.topology_layer.cmat.cpu().numpy()
# Visualize the data and the prototypes
ax = self.fig.gca()
ax.cla()
ax.set_title(self.title)
ax.set_xlabel("Data dimension 1")
ax.set_ylabel("Data dimension 2")
ax.scatter(self.x_train[:, 0],
self.x_train[:, 1],
c=self.y_train,
edgecolor="k")
ax = self.setup_ax(xlabel="Data dimension 1",
ylabel="Data dimension 2")
ax.scatter(x_train[:, 0], x_train[:, 1], c=y_train, edgecolor="k")
ax.scatter(
protos[:, 0],
protos[:, 1],
@@ -410,4 +446,4 @@ class VisNG2D(pl.Callback):
"k-",
)
plt.pause(0.01)
self.log_and_display(trainer, pl_module)