Merge branch 'master' into kernel_distances
This commit is contained in:
commit
09c80e2d54
@ -1,20 +1,11 @@
|
|||||||
[bumpversion]
|
[bumpversion]
|
||||||
current_version = 0.3.0-dev0
|
current_version = 0.4.2
|
||||||
commit = True
|
commit = True
|
||||||
tag = True
|
tag = True
|
||||||
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
|
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
|
||||||
serialize =
|
serialize =
|
||||||
{major}.{minor}.{patch}-{release}{build}
|
|
||||||
{major}.{minor}.{patch}
|
{major}.{minor}.{patch}
|
||||||
|
|
||||||
[bumpversion:part:release]
|
|
||||||
optional_value = prod
|
|
||||||
first_value = dev
|
|
||||||
values =
|
|
||||||
dev
|
|
||||||
rc
|
|
||||||
prod
|
|
||||||
|
|
||||||
[bumpversion:file:setup.py]
|
[bumpversion:file:setup.py]
|
||||||
|
|
||||||
[bumpversion:file:./prototorch/__init__.py]
|
[bumpversion:file:./prototorch/__init__.py]
|
||||||
|
31
.github/ISSUE_TEMPLATE/bug_report.md
vendored
Normal file
31
.github/ISSUE_TEMPLATE/bug_report.md
vendored
Normal file
@ -0,0 +1,31 @@
|
|||||||
|
---
|
||||||
|
name: Bug report
|
||||||
|
about: Create a report to help us improve
|
||||||
|
title: ''
|
||||||
|
labels: ''
|
||||||
|
assignees: ''
|
||||||
|
|
||||||
|
---
|
||||||
|
|
||||||
|
**Describe the bug**
|
||||||
|
A clear and concise description of what the bug is.
|
||||||
|
|
||||||
|
**To Reproduce**
|
||||||
|
Steps to reproduce the behavior:
|
||||||
|
1. Install Prototorch by running '...'
|
||||||
|
2. Run script '...'
|
||||||
|
3. See errors
|
||||||
|
|
||||||
|
**Expected behavior**
|
||||||
|
A clear and concise description of what you expected to happen.
|
||||||
|
|
||||||
|
**Screenshots**
|
||||||
|
If applicable, add screenshots to help explain your problem.
|
||||||
|
|
||||||
|
**Desktop (please complete the following information):**
|
||||||
|
- OS: [e.g. Ubuntu 20.10]
|
||||||
|
- Prototorch Version: [e.g. v0.4.0]
|
||||||
|
- Python Version: [e.g. 3.9.5]
|
||||||
|
|
||||||
|
**Additional context**
|
||||||
|
Add any other context about the problem here.
|
20
.github/ISSUE_TEMPLATE/feature_request.md
vendored
Normal file
20
.github/ISSUE_TEMPLATE/feature_request.md
vendored
Normal file
@ -0,0 +1,20 @@
|
|||||||
|
---
|
||||||
|
name: Feature request
|
||||||
|
about: Suggest an idea for this project
|
||||||
|
title: ''
|
||||||
|
labels: ''
|
||||||
|
assignees: ''
|
||||||
|
|
||||||
|
---
|
||||||
|
|
||||||
|
**Is your feature request related to a problem? Please describe.**
|
||||||
|
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
|
||||||
|
|
||||||
|
**Describe the solution you'd like**
|
||||||
|
A clear and concise description of what you want to happen.
|
||||||
|
|
||||||
|
**Describe alternatives you've considered**
|
||||||
|
A clear and concise description of any alternative solutions or features you've considered.
|
||||||
|
|
||||||
|
**Additional context**
|
||||||
|
Add any other context or screenshots about the feature request here.
|
5
.github/workflows/pythonapp.yml
vendored
5
.github/workflows/pythonapp.yml
vendored
@ -23,10 +23,7 @@ jobs:
|
|||||||
- name: Install dependencies
|
- name: Install dependencies
|
||||||
run: |
|
run: |
|
||||||
python -m pip install --upgrade pip
|
python -m pip install --upgrade pip
|
||||||
pip install .
|
pip install .[all]
|
||||||
- name: Install extras
|
|
||||||
run: |
|
|
||||||
pip install -r requirements.txt
|
|
||||||
- name: Lint with flake8
|
- name: Lint with flake8
|
||||||
run: |
|
run: |
|
||||||
pip install flake8
|
pip install flake8
|
||||||
|
@ -5,10 +5,8 @@ python: 3.8
|
|||||||
cache:
|
cache:
|
||||||
directories:
|
directories:
|
||||||
- "./tests/artifacts"
|
- "./tests/artifacts"
|
||||||
# - "$HOME/.prototorch/datasets"
|
|
||||||
install:
|
install:
|
||||||
- pip install . --progress-bar off
|
- pip install .[all] --progress-bar off
|
||||||
- pip install -r requirements.txt
|
|
||||||
|
|
||||||
# Generate code coverage report
|
# Generate code coverage report
|
||||||
script:
|
script:
|
||||||
@ -25,8 +23,8 @@ deploy:
|
|||||||
password:
|
password:
|
||||||
secure: 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
|
secure: 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
|
||||||
on:
|
on:
|
||||||
tags: true
|
tags: true
|
||||||
skip_existing: true
|
skip_existing: true
|
||||||
|
|
||||||
# The password is encrypted with:
|
# The password is encrypted with:
|
||||||
# `cd prototorch && travis encrypt your-pypi-api-token --add deploy.password`
|
# `cd prototorch && travis encrypt your-pypi-api-token --add deploy.password`
|
||||||
|
@ -31,15 +31,15 @@ To also install the extras, use
|
|||||||
pip install -U prototorch[all]
|
pip install -U prototorch[all]
|
||||||
```
|
```
|
||||||
|
|
||||||
*Note: If you're using [ZSH](https://www.zsh.org/), the square brackets `[ ]`
|
*Note: If you're using [ZSH](https://www.zsh.org/) (which is also the default
|
||||||
have to be escaped like so: `\[\]`, making the install command `pip install -U
|
shell on MacOS now), the square brackets `[ ]` have to be escaped like so:
|
||||||
prototorch\[all\]`.*
|
`\[\]`, making the install command `pip install -U prototorch\[all\]`.*
|
||||||
|
|
||||||
To install the bleeding-edge features and improvements:
|
To install the bleeding-edge features and improvements:
|
||||||
```bash
|
```bash
|
||||||
git clone https://github.com/si-cim/prototorch.git
|
git clone https://github.com/si-cim/prototorch.git
|
||||||
git checkout dev
|
|
||||||
cd prototorch
|
cd prototorch
|
||||||
|
git checkout dev
|
||||||
pip install -e .[all]
|
pip install -e .[all]
|
||||||
```
|
```
|
||||||
|
|
||||||
|
@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
|
|||||||
|
|
||||||
# The full version, including alpha/beta/rc tags
|
# The full version, including alpha/beta/rc tags
|
||||||
#
|
#
|
||||||
release = "0.3.0-dev0"
|
release = "0.4.2"
|
||||||
|
|
||||||
# -- General configuration ---------------------------------------------------
|
# -- General configuration ---------------------------------------------------
|
||||||
|
|
||||||
|
@ -1,6 +1,9 @@
|
|||||||
#
|
"""This example script shows the usage of the new components architecture.
|
||||||
|
|
||||||
|
Serialization/deserialization also works as expected.
|
||||||
|
"""
|
||||||
|
|
||||||
# DATASET
|
# DATASET
|
||||||
#
|
|
||||||
import torch
|
import torch
|
||||||
from sklearn.datasets import load_iris
|
from sklearn.datasets import load_iris
|
||||||
from sklearn.preprocessing import StandardScaler
|
from sklearn.preprocessing import StandardScaler
|
||||||
@ -15,9 +18,7 @@ x_train = torch.Tensor(x_train)
|
|||||||
y_train = torch.Tensor(y_train)
|
y_train = torch.Tensor(y_train)
|
||||||
num_classes = len(torch.unique(y_train))
|
num_classes = len(torch.unique(y_train))
|
||||||
|
|
||||||
#
|
|
||||||
# CREATE NEW COMPONENTS
|
# CREATE NEW COMPONENTS
|
||||||
#
|
|
||||||
from prototorch.components import *
|
from prototorch.components import *
|
||||||
from prototorch.components.initializers import *
|
from prototorch.components.initializers import *
|
||||||
|
|
||||||
@ -32,9 +33,7 @@ components = ReasoningComponents(
|
|||||||
(3, 6), StratifiedSelectionInitializer(x_train, y_train))
|
(3, 6), StratifiedSelectionInitializer(x_train, y_train))
|
||||||
print(components())
|
print(components())
|
||||||
|
|
||||||
#
|
|
||||||
# TEST SERIALIZATION
|
# TEST SERIALIZATION
|
||||||
#
|
|
||||||
import io
|
import io
|
||||||
|
|
||||||
save = io.BytesIO()
|
save = io.BytesIO()
|
||||||
@ -52,8 +51,8 @@ serialized_prototypes = torch.load(save)
|
|||||||
|
|
||||||
assert torch.all(prototypes.components == serialized_prototypes.components
|
assert torch.all(prototypes.components == serialized_prototypes.components
|
||||||
), "Serialization of Components failed."
|
), "Serialization of Components failed."
|
||||||
assert torch.all(prototypes.labels == serialized_prototypes.labels
|
assert torch.all(prototypes.component_labels == serialized_prototypes.
|
||||||
), "Serialization of Components failed."
|
component_labels), "Serialization of Components failed."
|
||||||
|
|
||||||
save = io.BytesIO()
|
save = io.BytesIO()
|
||||||
torch.save(components, save)
|
torch.save(components, save)
|
||||||
|
@ -1,9 +1,7 @@
|
|||||||
"""ProtoTorch package."""
|
"""ProtoTorch package."""
|
||||||
|
|
||||||
# #############################################
|
|
||||||
# Core Setup
|
# Core Setup
|
||||||
# #############################################
|
__version__ = "0.4.2"
|
||||||
__version__ = "0.3.0-dev0"
|
|
||||||
|
|
||||||
__all_core__ = [
|
__all_core__ = [
|
||||||
"datasets",
|
"datasets",
|
||||||
@ -11,9 +9,9 @@ __all_core__ = [
|
|||||||
"modules",
|
"modules",
|
||||||
]
|
]
|
||||||
|
|
||||||
# #############################################
|
from .datasets import *
|
||||||
|
|
||||||
# Plugin Loader
|
# Plugin Loader
|
||||||
# #############################################
|
|
||||||
import pkgutil
|
import pkgutil
|
||||||
|
|
||||||
import pkg_resources
|
import pkg_resources
|
||||||
|
@ -1,11 +1,2 @@
|
|||||||
from prototorch.components.components import (
|
from prototorch.components.components import *
|
||||||
Components,
|
from prototorch.components.initializers import *
|
||||||
LabeledComponents,
|
|
||||||
ReasoningComponents,
|
|
||||||
)
|
|
||||||
|
|
||||||
__all__ = [
|
|
||||||
"Components",
|
|
||||||
"LabeledComponents",
|
|
||||||
"ReasoningComponents",
|
|
||||||
]
|
|
||||||
|
@ -1,48 +1,52 @@
|
|||||||
"""ProtoTorch components modules."""
|
"""ProtoTorch components modules."""
|
||||||
|
|
||||||
import warnings
|
import warnings
|
||||||
|
from typing import Tuple
|
||||||
|
|
||||||
import torch
|
import torch
|
||||||
|
from prototorch.components.initializers import (ClassAwareInitializer,
|
||||||
|
ComponentsInitializer,
|
||||||
|
EqualLabelsInitializer,
|
||||||
|
UnequalLabelsInitializer,
|
||||||
|
ZeroReasoningsInitializer)
|
||||||
|
from prototorch.functions.initializers import get_initializer
|
||||||
from torch.nn.parameter import Parameter
|
from torch.nn.parameter import Parameter
|
||||||
|
|
||||||
from prototorch.components.initializers import (
|
|
||||||
EqualLabelInitializer,
|
|
||||||
ZeroReasoningsInitializer,
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
class Components(torch.nn.Module):
|
class Components(torch.nn.Module):
|
||||||
"""
|
"""Components is a set of learnable Tensors."""
|
||||||
Components is a set of learnable Tensors.
|
def __init__(self,
|
||||||
"""
|
number_of_components=None,
|
||||||
def __init__(
|
initializer=None,
|
||||||
self,
|
*,
|
||||||
number_of_components=None,
|
initialized_components=None,
|
||||||
initializer=None,
|
dtype=torch.float32):
|
||||||
*,
|
|
||||||
initialized_components=None,
|
|
||||||
dtype=torch.float32,
|
|
||||||
):
|
|
||||||
super().__init__()
|
super().__init__()
|
||||||
|
|
||||||
# Ignore all initialization settings if initialized_components is given.
|
# Ignore all initialization settings if initialized_components is given.
|
||||||
if initialized_components is not None:
|
if initialized_components is not None:
|
||||||
self._components = Parameter(initialized_components)
|
self._components = Parameter(initialized_components)
|
||||||
if number_of_components is not None or initializer is not None:
|
if number_of_components is not None or initializer is not None:
|
||||||
warnings.warn(
|
wmsg = "Arguments ignored while initializing Components"
|
||||||
"Arguments ignored while initializing Components")
|
warnings.warn(wmsg)
|
||||||
else:
|
else:
|
||||||
self._initialize_components(number_of_components, initializer)
|
self._initialize_components(number_of_components, initializer)
|
||||||
|
|
||||||
|
def _precheck_initializer(self, initializer):
|
||||||
|
if not isinstance(initializer, ComponentsInitializer):
|
||||||
|
emsg = f"`initializer` has to be some subtype of " \
|
||||||
|
f"{ComponentsInitializer}. " \
|
||||||
|
f"You have provided: {initializer=} instead."
|
||||||
|
raise TypeError(emsg)
|
||||||
|
|
||||||
def _initialize_components(self, number_of_components, initializer):
|
def _initialize_components(self, number_of_components, initializer):
|
||||||
|
self._precheck_initializer(initializer)
|
||||||
self._components = Parameter(
|
self._components = Parameter(
|
||||||
initializer.generate(number_of_components))
|
initializer.generate(number_of_components))
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def components(self):
|
def components(self):
|
||||||
"""
|
"""Tensor containing the component tensors."""
|
||||||
Tensor containing the component tensors.
|
|
||||||
"""
|
|
||||||
return self._components.detach().cpu()
|
return self._components.detach().cpu()
|
||||||
|
|
||||||
def forward(self):
|
def forward(self):
|
||||||
@ -53,12 +57,12 @@ class Components(torch.nn.Module):
|
|||||||
|
|
||||||
|
|
||||||
class LabeledComponents(Components):
|
class LabeledComponents(Components):
|
||||||
"""
|
"""LabeledComponents generate a set of components and a set of labels.
|
||||||
LabeledComponents generate a set of components and a set of labels.
|
|
||||||
Every Component has a label assigned.
|
Every Component has a label assigned.
|
||||||
"""
|
"""
|
||||||
def __init__(self,
|
def __init__(self,
|
||||||
labels=None,
|
distribution=None,
|
||||||
initializer=None,
|
initializer=None,
|
||||||
*,
|
*,
|
||||||
initialized_components=None):
|
initialized_components=None):
|
||||||
@ -66,22 +70,32 @@ class LabeledComponents(Components):
|
|||||||
super().__init__(initialized_components=initialized_components[0])
|
super().__init__(initialized_components=initialized_components[0])
|
||||||
self._labels = initialized_components[1]
|
self._labels = initialized_components[1]
|
||||||
else:
|
else:
|
||||||
self._initialize_labels(labels, initializer)
|
self._initialize_labels(distribution)
|
||||||
super().__init__(number_of_components=len(self._labels),
|
super().__init__(number_of_components=len(self._labels),
|
||||||
initializer=initializer)
|
initializer=initializer)
|
||||||
|
|
||||||
def _initialize_labels(self, labels, initializer):
|
def _initialize_components(self, number_of_components, initializer):
|
||||||
if type(labels) == tuple:
|
if isinstance(initializer, ClassAwareInitializer):
|
||||||
num_classes, prototypes_per_class = labels
|
self._precheck_initializer(initializer)
|
||||||
labels = EqualLabelInitializer(num_classes, prototypes_per_class)
|
self._components = Parameter(
|
||||||
|
initializer.generate(number_of_components, self.distribution))
|
||||||
|
else:
|
||||||
|
super()._initialize_components(self, number_of_components,
|
||||||
|
initializer)
|
||||||
|
|
||||||
|
def _initialize_labels(self, distribution):
|
||||||
|
if type(distribution) == tuple:
|
||||||
|
num_classes, prototypes_per_class = distribution
|
||||||
|
labels = EqualLabelsInitializer(num_classes, prototypes_per_class)
|
||||||
|
elif type(distribution) == list:
|
||||||
|
labels = UnequalLabelsInitializer(distribution)
|
||||||
|
|
||||||
|
self.distribution = labels.distribution
|
||||||
self._labels = labels.generate()
|
self._labels = labels.generate()
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def labels(self):
|
def component_labels(self):
|
||||||
"""
|
"""Tensor containing the component tensors."""
|
||||||
Tensor containing the component tensors.
|
|
||||||
"""
|
|
||||||
return self._labels.detach().cpu()
|
return self._labels.detach().cpu()
|
||||||
|
|
||||||
def forward(self):
|
def forward(self):
|
||||||
@ -89,16 +103,19 @@ class LabeledComponents(Components):
|
|||||||
|
|
||||||
|
|
||||||
class ReasoningComponents(Components):
|
class ReasoningComponents(Components):
|
||||||
"""
|
"""ReasoningComponents generate a set of components and a set of reasoning matrices.
|
||||||
ReasoningComponents generate a set of components and a set of reasoning matrices.
|
|
||||||
Every Component has a reasoning matrix assigned.
|
Every Component has a reasoning matrix assigned.
|
||||||
|
|
||||||
A reasoning matrix is a Nx2 matrix, where N is the number of Classes.
|
A reasoning matrix is a Nx2 matrix, where N is the number of Classes. The
|
||||||
The first element is called positive reasoning :math:`p`, the second negative reasoning :math:`n`.
|
first element is called positive reasoning :math:`p`, the second negative
|
||||||
A components can reason in favour (positive) of a class, against (negative) a class or not at all (neutral).
|
reasoning :math:`n`. A components can reason in favour (positive) of a
|
||||||
|
class, against (negative) a class or not at all (neutral).
|
||||||
|
|
||||||
|
It holds that :math:`0 \leq n \leq 1`, :math:`0 \leq p \leq 1` and :math:`0
|
||||||
|
\leq n+p \leq 1`. Therefore :math:`n` and :math:`p` are two elements of a
|
||||||
|
three element probability distribution.
|
||||||
|
|
||||||
It holds that :math:`0 \leq n \leq 1`, :math:`0 \leq p \leq 1` and :math:`0 \leq n+p \leq 1`.
|
|
||||||
Therefore :math:`n` and :math:`p` are two elements of a three element probability distribution.
|
|
||||||
"""
|
"""
|
||||||
def __init__(self,
|
def __init__(self,
|
||||||
reasonings=None,
|
reasonings=None,
|
||||||
@ -123,10 +140,10 @@ class ReasoningComponents(Components):
|
|||||||
|
|
||||||
@property
|
@property
|
||||||
def reasonings(self):
|
def reasonings(self):
|
||||||
"""
|
"""Returns Reasoning Matrix.
|
||||||
Returns Reasoning Matrix.
|
|
||||||
|
|
||||||
Dimension NxCx2
|
Dimension NxCx2
|
||||||
|
|
||||||
"""
|
"""
|
||||||
return self._reasonings.detach().cpu()
|
return self._reasonings.detach().cpu()
|
||||||
|
|
||||||
|
@ -1,12 +1,33 @@
|
|||||||
|
"""ProtoTroch Initializers."""
|
||||||
|
import warnings
|
||||||
from collections.abc import Iterable
|
from collections.abc import Iterable
|
||||||
|
from itertools import chain
|
||||||
|
|
||||||
import torch
|
import torch
|
||||||
|
from torch.utils.data import DataLoader, Dataset
|
||||||
|
|
||||||
|
|
||||||
|
def parse_init_arg(arg):
|
||||||
|
if isinstance(arg, Dataset):
|
||||||
|
data, labels = next(iter(DataLoader(arg, batch_size=len(arg))))
|
||||||
|
# data = data.view(len(arg), -1) # flatten
|
||||||
|
else:
|
||||||
|
data, labels = arg
|
||||||
|
if not isinstance(data, torch.Tensor):
|
||||||
|
wmsg = f"Converting data to {torch.Tensor}."
|
||||||
|
warnings.warn(wmsg)
|
||||||
|
data = torch.Tensor(data)
|
||||||
|
if not isinstance(labels, torch.Tensor):
|
||||||
|
wmsg = f"Converting labels to {torch.Tensor}."
|
||||||
|
warnings.warn(wmsg)
|
||||||
|
labels = torch.Tensor(labels)
|
||||||
|
return data, labels
|
||||||
|
|
||||||
|
|
||||||
# Components
|
# Components
|
||||||
class ComponentsInitializer:
|
class ComponentsInitializer(object):
|
||||||
def generate(self, number_of_components):
|
def generate(self, number_of_components):
|
||||||
pass
|
raise NotImplementedError("Subclasses should implement this!")
|
||||||
|
|
||||||
|
|
||||||
class DimensionAwareInitializer(ComponentsInitializer):
|
class DimensionAwareInitializer(ComponentsInitializer):
|
||||||
@ -39,7 +60,7 @@ class UniformInitializer(DimensionAwareInitializer):
|
|||||||
|
|
||||||
def generate(self, length):
|
def generate(self, length):
|
||||||
gen_dims = (length, ) + self.components_dims
|
gen_dims = (length, ) + self.components_dims
|
||||||
return torch.FloatTensor(gen_dims).uniform_(self.min, self.max)
|
return torch.ones(gen_dims).uniform_(self.min, self.max)
|
||||||
|
|
||||||
|
|
||||||
class PositionAwareInitializer(ComponentsInitializer):
|
class PositionAwareInitializer(ComponentsInitializer):
|
||||||
@ -62,58 +83,95 @@ class MeanInitializer(PositionAwareInitializer):
|
|||||||
|
|
||||||
|
|
||||||
class ClassAwareInitializer(ComponentsInitializer):
|
class ClassAwareInitializer(ComponentsInitializer):
|
||||||
def __init__(self, positions, classes):
|
def __init__(self, arg):
|
||||||
super().__init__()
|
super().__init__()
|
||||||
self.data = positions
|
data, labels = parse_init_arg(arg)
|
||||||
self.classes = classes
|
self.data = data
|
||||||
|
self.labels = labels
|
||||||
|
|
||||||
self.names = torch.unique(self.classes)
|
self.clabels = torch.unique(self.labels)
|
||||||
self.num_classes = len(self.names)
|
self.num_classes = len(self.clabels)
|
||||||
|
|
||||||
|
def _get_samples_from_initializer(self, length, dist):
|
||||||
|
if not dist:
|
||||||
|
per_class = length // self.num_classes
|
||||||
|
dist = self.num_classes * [per_class]
|
||||||
|
samples_list = [
|
||||||
|
init.generate(n) for init, n in zip(self.initializers, dist)
|
||||||
|
]
|
||||||
|
return torch.vstack(samples_list)
|
||||||
|
|
||||||
|
|
||||||
class StratifiedMeanInitializer(ClassAwareInitializer):
|
class StratifiedMeanInitializer(ClassAwareInitializer):
|
||||||
def __init__(self, positions, classes):
|
def __init__(self, arg):
|
||||||
super().__init__(positions, classes)
|
super().__init__(arg)
|
||||||
|
|
||||||
self.initializers = []
|
self.initializers = []
|
||||||
for name in self.names:
|
for clabel in self.clabels:
|
||||||
class_data = self.data[self.classes == name]
|
class_data = self.data[self.labels == clabel]
|
||||||
class_initializer = MeanInitializer(class_data)
|
class_initializer = MeanInitializer(class_data)
|
||||||
self.initializers.append(class_initializer)
|
self.initializers.append(class_initializer)
|
||||||
|
|
||||||
def generate(self, length):
|
def generate(self, length, dist=[]):
|
||||||
per_class = length // self.num_classes
|
samples = self._get_samples_from_initializer(length, dist)
|
||||||
return torch.vstack(
|
return samples
|
||||||
[init.generate(per_class) for init in self.initializers])
|
|
||||||
|
|
||||||
|
|
||||||
class StratifiedSelectionInitializer(ClassAwareInitializer):
|
class StratifiedSelectionInitializer(ClassAwareInitializer):
|
||||||
def __init__(self, positions, classes):
|
def __init__(self, arg, *, noise=None):
|
||||||
super().__init__(positions, classes)
|
super().__init__(arg)
|
||||||
|
self.noise = noise
|
||||||
|
|
||||||
self.initializers = []
|
self.initializers = []
|
||||||
for name in self.names:
|
for clabel in self.clabels:
|
||||||
class_data = self.data[self.classes == name]
|
class_data = self.data[self.labels == clabel]
|
||||||
class_initializer = SelectionInitializer(class_data)
|
class_initializer = SelectionInitializer(class_data)
|
||||||
self.initializers.append(class_initializer)
|
self.initializers.append(class_initializer)
|
||||||
|
|
||||||
def generate(self, length):
|
def add_noise(self, x):
|
||||||
per_class = length // self.num_classes
|
"""Shifts some dimensions of the data randomly."""
|
||||||
return torch.vstack(
|
n1 = torch.rand_like(x)
|
||||||
[init.generate(per_class) for init in self.initializers])
|
n2 = torch.rand_like(x)
|
||||||
|
mask = torch.bernoulli(n1) - torch.bernoulli(n2)
|
||||||
|
return x + (self.noise * mask)
|
||||||
|
|
||||||
|
def generate(self, length, dist=[]):
|
||||||
|
samples = self._get_samples_from_initializer(length, dist)
|
||||||
|
if self.noise is not None:
|
||||||
|
# samples = self.add_noise(samples)
|
||||||
|
samples = samples + self.noise
|
||||||
|
return samples
|
||||||
|
|
||||||
|
|
||||||
# Labels
|
# Labels
|
||||||
class LabelsInitializer:
|
class LabelsInitializer:
|
||||||
def generate(self):
|
def generate(self):
|
||||||
pass
|
raise NotImplementedError("Subclasses should implement this!")
|
||||||
|
|
||||||
|
|
||||||
class EqualLabelInitializer(LabelsInitializer):
|
class UnequalLabelsInitializer(LabelsInitializer):
|
||||||
|
def __init__(self, dist):
|
||||||
|
self.dist = dist
|
||||||
|
|
||||||
|
@property
|
||||||
|
def distribution(self):
|
||||||
|
return self.dist
|
||||||
|
|
||||||
|
def generate(self):
|
||||||
|
clabels = range(len(self.dist))
|
||||||
|
labels = list(chain(*[[i] * n for i, n in zip(clabels, self.dist)]))
|
||||||
|
return torch.tensor(labels)
|
||||||
|
|
||||||
|
|
||||||
|
class EqualLabelsInitializer(LabelsInitializer):
|
||||||
def __init__(self, classes, per_class):
|
def __init__(self, classes, per_class):
|
||||||
self.classes = classes
|
self.classes = classes
|
||||||
self.per_class = per_class
|
self.per_class = per_class
|
||||||
|
|
||||||
|
@property
|
||||||
|
def distribution(self):
|
||||||
|
return self.classes * [self.per_class]
|
||||||
|
|
||||||
def generate(self):
|
def generate(self):
|
||||||
return torch.arange(self.classes).repeat(self.per_class, 1).T.flatten()
|
return torch.arange(self.classes).repeat(self.per_class, 1).T.flatten()
|
||||||
|
|
||||||
@ -121,7 +179,7 @@ class EqualLabelInitializer(LabelsInitializer):
|
|||||||
# Reasonings
|
# Reasonings
|
||||||
class ReasoningsInitializer:
|
class ReasoningsInitializer:
|
||||||
def generate(self, length):
|
def generate(self, length):
|
||||||
pass
|
raise NotImplementedError("Subclasses should implement this!")
|
||||||
|
|
||||||
|
|
||||||
class ZeroReasoningsInitializer(ReasoningsInitializer):
|
class ZeroReasoningsInitializer(ReasoningsInitializer):
|
||||||
@ -131,3 +189,9 @@ class ZeroReasoningsInitializer(ReasoningsInitializer):
|
|||||||
|
|
||||||
def generate(self):
|
def generate(self):
|
||||||
return torch.zeros((self.length, self.classes, 2))
|
return torch.zeros((self.length, self.classes, 2))
|
||||||
|
|
||||||
|
|
||||||
|
# Aliases
|
||||||
|
SSI = StratifiedSampleInitializer = StratifiedSelectionInitializer
|
||||||
|
SMI = StratifiedMeanInitializer
|
||||||
|
Random = RandomInitializer = UniformInitializer
|
||||||
|
@ -1,7 +1,11 @@
|
|||||||
"""ProtoTorch datasets."""
|
"""ProtoTorch datasets."""
|
||||||
|
|
||||||
|
from .abstract import NumpyDataset
|
||||||
|
from .spiral import Spiral
|
||||||
from .tecator import Tecator
|
from .tecator import Tecator
|
||||||
|
|
||||||
__all__ = [
|
__all__ = [
|
||||||
|
"NumpyDataset",
|
||||||
|
"Spiral",
|
||||||
"Tecator",
|
"Tecator",
|
||||||
]
|
]
|
||||||
|
@ -13,6 +13,7 @@ import torch
|
|||||||
|
|
||||||
|
|
||||||
class NumpyDataset(torch.utils.data.TensorDataset):
|
class NumpyDataset(torch.utils.data.TensorDataset):
|
||||||
|
"""Create a PyTorch TensorDataset from NumPy arrays."""
|
||||||
def __init__(self, *arrays):
|
def __init__(self, *arrays):
|
||||||
tensors = [torch.Tensor(arr) for arr in arrays]
|
tensors = [torch.Tensor(arr) for arr in arrays]
|
||||||
super().__init__(*tensors)
|
super().__init__(*tensors)
|
||||||
|
33
prototorch/datasets/spiral.py
Normal file
33
prototorch/datasets/spiral.py
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
"""Spiral dataset for binary classification."""
|
||||||
|
|
||||||
|
import numpy as np
|
||||||
|
import torch
|
||||||
|
|
||||||
|
|
||||||
|
def make_spiral(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
|
||||||
|
|
||||||
|
|
||||||
|
class Spiral(torch.utils.data.TensorDataset):
|
||||||
|
"""Spiral dataset for binary classification."""
|
||||||
|
def __init__(self, n_samples=500, noise=0.3):
|
||||||
|
x, y = make_spiral(n_samples, noise)
|
||||||
|
super().__init__(torch.Tensor(x), torch.LongTensor(y))
|
@ -52,7 +52,7 @@ class Tecator(ProtoDataset):
|
|||||||
"""
|
"""
|
||||||
|
|
||||||
_resources = [
|
_resources = [
|
||||||
("1MMuUK8V41IgNpnPDbg3E-QAL6wlErTk0",
|
("1P9WIYnyxFPh6f1vqAbnKfK8oYmUgyV83",
|
||||||
"ba5607c580d0f91bb27dc29d13c2f8df"),
|
"ba5607c580d0f91bb27dc29d13c2f8df"),
|
||||||
] # (google_storage_id, md5hash)
|
] # (google_storage_id, md5hash)
|
||||||
classes = ["0 - low_fat", "1 - high_fat"]
|
classes = ["0 - low_fat", "1 - high_fat"]
|
||||||
|
@ -16,40 +16,43 @@ def register_activation(function):
|
|||||||
|
|
||||||
@register_activation
|
@register_activation
|
||||||
# @torch.jit.script
|
# @torch.jit.script
|
||||||
def identity(x, beta=torch.tensor(0)):
|
def identity(x, beta=0.0):
|
||||||
"""Identity activation function.
|
"""Identity activation function.
|
||||||
|
|
||||||
Definition:
|
Definition:
|
||||||
:math:`f(x) = x`
|
:math:`f(x) = x`
|
||||||
|
|
||||||
|
Keyword Arguments:
|
||||||
|
beta (`float`): Ignored.
|
||||||
"""
|
"""
|
||||||
return x
|
return x
|
||||||
|
|
||||||
|
|
||||||
@register_activation
|
@register_activation
|
||||||
# @torch.jit.script
|
# @torch.jit.script
|
||||||
def sigmoid_beta(x, beta=torch.tensor(10)):
|
def sigmoid_beta(x, beta=10.0):
|
||||||
r"""Sigmoid activation function with scaling.
|
r"""Sigmoid activation function with scaling.
|
||||||
|
|
||||||
Definition:
|
Definition:
|
||||||
:math:`f(x) = \frac{1}{1 + e^{-\beta x}}`
|
:math:`f(x) = \frac{1}{1 + e^{-\beta x}}`
|
||||||
|
|
||||||
Keyword Arguments:
|
Keyword Arguments:
|
||||||
beta (`torch.tensor`): Scaling parameter :math:`\beta`
|
beta (`float`): Scaling parameter :math:`\beta`
|
||||||
"""
|
"""
|
||||||
out = torch.reciprocal(1.0 + torch.exp(-int(beta.item()) * x))
|
out = 1.0 / (1.0 + torch.exp(-1.0 * beta * x))
|
||||||
return out
|
return out
|
||||||
|
|
||||||
|
|
||||||
@register_activation
|
@register_activation
|
||||||
# @torch.jit.script
|
# @torch.jit.script
|
||||||
def swish_beta(x, beta=torch.tensor(10)):
|
def swish_beta(x, beta=10.0):
|
||||||
r"""Swish activation function with scaling.
|
r"""Swish activation function with scaling.
|
||||||
|
|
||||||
Definition:
|
Definition:
|
||||||
:math:`f(x) = \frac{x}{1 + e^{-\beta x}}`
|
:math:`f(x) = \frac{x}{1 + e^{-\beta x}}`
|
||||||
|
|
||||||
Keyword Arguments:
|
Keyword Arguments:
|
||||||
beta (`torch.tensor`): Scaling parameter :math:`\beta`
|
beta (`float`): Scaling parameter :math:`\beta`
|
||||||
"""
|
"""
|
||||||
out = x * sigmoid_beta(x, beta=beta)
|
out = x * sigmoid_beta(x, beta=beta)
|
||||||
return out
|
return out
|
||||||
|
@ -3,12 +3,19 @@
|
|||||||
import torch
|
import torch
|
||||||
|
|
||||||
|
|
||||||
def _get_dp_dm(distances, targets, plabels):
|
def _get_matcher(targets, labels):
|
||||||
matcher = torch.eq(targets.unsqueeze(dim=1), plabels)
|
"""Returns a boolean tensor."""
|
||||||
if plabels.ndim == 2:
|
matcher = torch.eq(targets.unsqueeze(dim=1), labels)
|
||||||
|
if labels.ndim == 2:
|
||||||
# if the labels are one-hot vectors
|
# if the labels are one-hot vectors
|
||||||
nclasses = targets.size()[1]
|
nclasses = targets.size()[1]
|
||||||
matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
|
matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
|
||||||
|
return matcher
|
||||||
|
|
||||||
|
|
||||||
|
def _get_dp_dm(distances, targets, plabels):
|
||||||
|
"""Returns the d+ and d- values for a batch of distances."""
|
||||||
|
matcher = _get_matcher(targets, plabels)
|
||||||
not_matcher = torch.bitwise_not(matcher)
|
not_matcher = torch.bitwise_not(matcher)
|
||||||
|
|
||||||
inf = torch.full_like(distances, fill_value=float("inf"))
|
inf = torch.full_like(distances, fill_value=float("inf"))
|
||||||
@ -24,3 +31,26 @@ def glvq_loss(distances, target_labels, prototype_labels):
|
|||||||
dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
|
dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
|
||||||
mu = (dp - dm) / (dp + dm)
|
mu = (dp - dm) / (dp + dm)
|
||||||
return mu
|
return mu
|
||||||
|
|
||||||
|
|
||||||
|
def lvq1_loss(distances, target_labels, prototype_labels):
|
||||||
|
"""LVQ1 loss function with support for one-hot labels.
|
||||||
|
|
||||||
|
See Section 4 [Sado&Yamada]
|
||||||
|
https://papers.nips.cc/paper/1995/file/9c3b1830513cc3b8fc4b76635d32e692-Paper.pdf
|
||||||
|
"""
|
||||||
|
dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
|
||||||
|
mu = dp
|
||||||
|
mu[dp > dm] = -dm[dp > dm]
|
||||||
|
return mu
|
||||||
|
|
||||||
|
|
||||||
|
def lvq21_loss(distances, target_labels, prototype_labels):
|
||||||
|
"""LVQ2.1 loss function with support for one-hot labels.
|
||||||
|
|
||||||
|
See Section 4 [Sado&Yamada]
|
||||||
|
https://papers.nips.cc/paper/1995/file/9c3b1830513cc3b8fc4b76635d32e692-Paper.pdf
|
||||||
|
"""
|
||||||
|
dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
|
||||||
|
mu = dp - dm
|
||||||
|
return mu
|
@ -1,5 +0,0 @@
|
|||||||
matplotlib==3.1.2
|
|
||||||
pytest==5.3.4
|
|
||||||
requests==2.22.0
|
|
||||||
codecov==2.0.22
|
|
||||||
tqdm==4.44.1
|
|
22
setup.py
22
setup.py
@ -1,8 +1,8 @@
|
|||||||
"""
|
"""
|
||||||
_____ _ _______ _
|
_____ _ _______ _
|
||||||
| __ \ | | |__ __| | |
|
| __ \ | | |__ __| | |
|
||||||
| |__) | __ ___ | |_ ___ | | ___ _ __ ___| |__
|
| |__) | __ ___ | |_ ___ | | ___ _ __ ___| |__
|
||||||
| ___/ '__/ _ \| __/ _ \| |/ _ \| '__/ __| '_ \
|
| ___/ '__/ _ \| __/ _ \| |/ _ \| '__/ __| '_ \
|
||||||
| | | | | (_) | || (_) | | (_) | | | (__| | | |
|
| | | | | (_) | || (_) | | (_) | | | (__| | | |
|
||||||
|_| |_| \___/ \__\___/|_|\___/|_| \___|_| |_|
|
|_| |_| \___/ \__\___/|_|\___/|_| \___|_| |_|
|
||||||
|
|
||||||
@ -21,27 +21,28 @@ INSTALL_REQUIRES = [
|
|||||||
"torchvision>=0.5.0",
|
"torchvision>=0.5.0",
|
||||||
"numpy>=1.9.1",
|
"numpy>=1.9.1",
|
||||||
]
|
]
|
||||||
|
DATASETS = [
|
||||||
|
"requests",
|
||||||
|
"tqdm",
|
||||||
|
]
|
||||||
|
DEV = ["bumpversion"]
|
||||||
DOCS = [
|
DOCS = [
|
||||||
"recommonmark",
|
"recommonmark",
|
||||||
"sphinx",
|
"sphinx",
|
||||||
"sphinx_rtd_theme",
|
"sphinx_rtd_theme",
|
||||||
"sphinxcontrib-katex",
|
"sphinxcontrib-katex",
|
||||||
]
|
]
|
||||||
DATASETS = [
|
|
||||||
"requests",
|
|
||||||
"tqdm",
|
|
||||||
]
|
|
||||||
EXAMPLES = [
|
EXAMPLES = [
|
||||||
"sklearn",
|
"sklearn",
|
||||||
"matplotlib",
|
"matplotlib",
|
||||||
"torchinfo",
|
"torchinfo",
|
||||||
]
|
]
|
||||||
TESTS = ["pytest"]
|
TESTS = ["codecov", "pytest"]
|
||||||
ALL = DOCS + DATASETS + EXAMPLES + TESTS
|
ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
|
||||||
|
|
||||||
setup(
|
setup(
|
||||||
name="prototorch",
|
name="prototorch",
|
||||||
version="0.3.0-dev0",
|
version="0.4.2",
|
||||||
description="Highly extensible, GPU-supported "
|
description="Highly extensible, GPU-supported "
|
||||||
"Learning Vector Quantization (LVQ) toolbox "
|
"Learning Vector Quantization (LVQ) toolbox "
|
||||||
"built using PyTorch and its nn API.",
|
"built using PyTorch and its nn API.",
|
||||||
@ -71,6 +72,7 @@ setup(
|
|||||||
"Programming Language :: Python :: 3.6",
|
"Programming Language :: Python :: 3.6",
|
||||||
"Programming Language :: Python :: 3.7",
|
"Programming Language :: Python :: 3.7",
|
||||||
"Programming Language :: Python :: 3.8",
|
"Programming Language :: Python :: 3.8",
|
||||||
|
"Programming Language :: Python :: 3.9",
|
||||||
"Operating System :: OS Independent",
|
"Operating System :: OS Independent",
|
||||||
"Topic :: Scientific/Engineering :: Artificial Intelligence",
|
"Topic :: Scientific/Engineering :: Artificial Intelligence",
|
||||||
"Topic :: Software Development :: Libraries",
|
"Topic :: Software Development :: Libraries",
|
||||||
|
@ -57,7 +57,7 @@ class TestActivations(unittest.TestCase):
|
|||||||
self.assertIsNone(mismatch)
|
self.assertIsNone(mismatch)
|
||||||
|
|
||||||
def test_sigmoid_beta1(self):
|
def test_sigmoid_beta1(self):
|
||||||
actual = activations.sigmoid_beta(self.x, beta=torch.tensor(1))
|
actual = activations.sigmoid_beta(self.x, beta=1.0)
|
||||||
desired = torch.sigmoid(self.x)
|
desired = torch.sigmoid(self.x)
|
||||||
mismatch = np.testing.assert_array_almost_equal(actual,
|
mismatch = np.testing.assert_array_almost_equal(actual,
|
||||||
desired,
|
desired,
|
||||||
@ -65,7 +65,7 @@ class TestActivations(unittest.TestCase):
|
|||||||
self.assertIsNone(mismatch)
|
self.assertIsNone(mismatch)
|
||||||
|
|
||||||
def test_swish_beta1(self):
|
def test_swish_beta1(self):
|
||||||
actual = activations.swish_beta(self.x, beta=torch.tensor(1))
|
actual = activations.swish_beta(self.x, beta=1.0)
|
||||||
desired = self.x * torch.sigmoid(self.x)
|
desired = self.x * torch.sigmoid(self.x)
|
||||||
mismatch = np.testing.assert_array_almost_equal(actual,
|
mismatch = np.testing.assert_array_almost_equal(actual,
|
||||||
desired,
|
desired,
|
||||||
|
15
tox.ini
15
tox.ini
@ -1,15 +0,0 @@
|
|||||||
# tox (https://tox.readthedocs.io/) is a tool for running tests
|
|
||||||
# in multiple virtualenvs. This configuration file will run the
|
|
||||||
# test suite on all supported python versions. To use it, "pip install tox"
|
|
||||||
# and then run "tox" from this directory.
|
|
||||||
|
|
||||||
[tox]
|
|
||||||
envlist = py36,py37,py38
|
|
||||||
|
|
||||||
[testenv]
|
|
||||||
deps =
|
|
||||||
pytest
|
|
||||||
coverage
|
|
||||||
commands =
|
|
||||||
pip install -e .
|
|
||||||
coverage run -m pytest
|
|
Loading…
Reference in New Issue
Block a user