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...

31 Commits

Author SHA1 Message Date
9cb69ebc75 Implement hyperparam. context based normalization 2021-04-15 02:13:30 +02:00
b55f59a3ec Fix compute number of nodes 2021-04-13 22:31:05 +02:00
783d105099 Add another nodes, leaves test 2021-04-09 10:56:54 +02:00
c36f685263 Fix unintended nested if in partition 2021-04-08 08:27:31 +02:00
0f89b044f1 Refactor train method 2021-04-07 01:02:30 +02:00
Ricardo Montañana Gómez
6ba973dfe1 Add a method that return nodes and leaves (#27) (#30)
Add a test
Fix #27
2021-03-23 14:30:32 +01:00
Ricardo Montañana Gómez
460c63a6d0 Fix depth sometimes is wrong (#26) (#29)
Add a test to the tests set
Add depth to node description
Fix iterator and str test due to this addon
2021-03-23 14:08:53 +01:00
Ricardo Montañana Gómez
f438124057 Fix mistakes (#24) (#28)
Put pandas requirements in notebooks
clean requirements.txt
2021-03-23 13:27:32 +01:00
Ricardo Montañana Gómez
147dad684c Weight0samples error (#23)
* Add Hyperparameters description to README
Comment get_subspace method
Add environment info for binder (runtime.txt)

* Complete source comments
Change docstring type to numpy
update hyperameters table and explanation

* Fix problem with zero weighted samples
Solve WARNING: class label x specified in weight is not found
with a different approach

* Allow update of scikitlearn to latest version
2021-01-19 11:40:46 +01:00
Ricardo Montañana Gómez
3bdac9bd60 Complete source comments (#22)
* Add Hyperparameters description to README
Comment get_subspace method
Add environment info for binder (runtime.txt)

* Complete source comments
Change docstring type to numpy
update hyperameters table and explanation

* Update Jupyter notebooks
2021-01-19 10:44:59 +01:00
Ricardo Montañana Gómez
e4ac5075e5 Add main workflow action (#20)
* Add main workflow action

* lock scikit-learn version to 0.23.2

* exchange codeship badge with githubs
2021-01-11 13:46:30 +01:00
Ricardo Montañana Gómez
36816074ff Combinatorial explosion (#19)
* Remove itertools combinations from subspaces

* Generates 5 random subspaces at most
2021-01-10 13:32:22 +01:00
475ad7e752 Fix mistakes in function comments 2020-11-11 19:14:36 +01:00
Ricardo Montañana Gómez
1c869e154e Enhance partition (#16)
#15 Create impurity function in Stree (consistent name, same criteria as other splitter parameter)
Create test for the new function
Update init test
Update test splitter parameters
Rename old impurity function to partition_impurity
close #15
* Complete implementation of splitter_type = impurity with tests
Remove max_distance & min_distance splitter types

* Fix mistake in computing multiclass node belief
Set default criterion for split to entropy instead of gini
Set default max_iter to 1e5 instead of 1e3
change up-down criterion to match SVC multiclass
Fix impurity method of splitting nodes
Update jupyter Notebooks
2020-11-03 11:36:05 +01:00
f5706c3159 Update version and notebooks 2020-06-28 10:44:29 +02:00
be552fdd6c Add test for getting 3 feature_sets in Splitter
Add ensemble notebook
2020-06-28 02:45:08 +02:00
5e3a8e3ec5 Change adaboost notebook 2020-06-27 23:34:15 +02:00
554ec03c32 Get only 3 sets for best split
Fix flaky test in Splitter_test
2020-06-27 18:29:40 +02:00
4b7e4a3fb0 better solution to the sklearn bagging problem
Add better tests
enhance .coveragerc
2020-06-26 11:22:45 +02:00
76723993fd Solve Warning class label not found when bagging 2020-06-25 13:07:50 +02:00
ecd0b86f4d Solve the mistake of min and max distance
The split criteria functions min and max distance return classes while
max_samples return distances positives and negatives to hyperplane of
the class with more samples in node
2020-06-17 00:13:52 +02:00
3e52a4746c Fix entroy and information_gain functions 2020-06-16 13:56:02 +02:00
Ricardo Montañana Gómez
a20e45e8e7 Merge pull request #10 from Doctorado-ML/add_subspaces
#2 Add subspaces
2020-06-15 11:30:53 +02:00
9334951d1b #2 Cosmetic and style updates 2020-06-15 11:09:11 +02:00
736ab7ef20 #2 update benchmark notebook 2020-06-15 10:33:51 +02:00
c94bc068bd #2 Refactor Stree & create Splitter
Add and test splitter parameter
2020-06-15 00:22:57 +02:00
502ee72799 #2 Add predict and score support
Add a test in features notebook
Show max_features in main.py
2020-06-14 14:00:21 +02:00
f1ee4de37b #2 - Add gini and entropy measures
rename get_dataset to load_dataset
add features and impurity to  __str__ of node
2020-06-14 03:08:55 +02:00
ae1c199e21 # 2 - add max_features parameters 2020-06-13 17:58:45 +02:00
1bfe273a70 Fix problem in _min_distance
Remove grapher (moved to another repo)
2020-06-12 00:50:25 +02:00
Ricardo Montañana Gómez
647d21bdb5 Merge pull request #9 from Doctorado-ML/add_multiclass
#6 Add multiclass
2020-06-11 16:30:16 +02:00
23 changed files with 2087 additions and 1840 deletions

View File

@@ -10,5 +10,4 @@ exclude_lines =
if __name__ == .__main__.:
ignore_errors = True
omit =
stree/tests/*
stree/__init__.py

47
.github/workflows/main.yml vendored Normal file
View File

@@ -0,0 +1,47 @@
name: CI
on:
push:
branches: [master]
pull_request:
branches: [master]
workflow_dispatch:
jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [macos-latest, ubuntu-latest]
python: [3.8]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python }}
- name: Install dependencies
run: |
pip install -q --upgrade pip
pip install -q -r requirements.txt
pip install -q --upgrade codecov coverage black flake8 codacy-coverage
- name: Lint
run: |
black --check --diff stree
flake8 --count stree
- name: Tests
run: |
coverage run -m unittest -v stree.tests
coverage xml
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v1
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: ./coverage.xml
- name: Run codacy-coverage-reporter
if: runner.os == 'Linux'
uses: codacy/codacy-coverage-reporter-action@master
with:
project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
coverage-reports: coverage.xml

5
.gitignore vendored
View File

@@ -130,4 +130,7 @@ dmypy.json
.idea
.vscode
.pre-commit-config.yaml
.pre-commit-config.yaml
**.csv
.virtual_documents

View File

@@ -1,6 +1,6 @@
[![Codeship Status for Doctorado-ML/STree](https://app.codeship.com/projects/8b2bd350-8a1b-0138-5f2c-3ad36f3eb318/status?branch=master)](https://app.codeship.com/projects/399170)
![CI](https://github.com/Doctorado-ML/STree/workflows/CI/badge.svg)
[![codecov](https://codecov.io/gh/doctorado-ml/stree/branch/master/graph/badge.svg)](https://codecov.io/gh/doctorado-ml/stree)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/35fa3dfd53a24a339344b33d9f9f2f3d)](https://www.codacy.com/gh/Doctorado-ML/STree?utm_source=github.com&utm_medium=referral&utm_content=Doctorado-ML/STree&utm_campaign=Badge_Grade)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/35fa3dfd53a24a339344b33d9f9f2f3d)](https://www.codacy.com/gh/Doctorado-ML/STree?utm_source=github.com&utm_medium=referral&utm_content=Doctorado-ML/STree&utm_campaign=Badge_Grade)
# Stree
@@ -18,23 +18,43 @@ pip install git+https://github.com/doctorado-ml/stree
### Jupyter notebooks
* [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Doctorado-ML/STree/master?urlpath=lab/tree/notebooks/benchmark.ipynb) Benchmark
- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Doctorado-ML/STree/master?urlpath=lab/tree/notebooks/benchmark.ipynb) Benchmark
* [![Test](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/benchmark.ipynb) Benchmark
- [![benchmark](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/benchmark.ipynb) Benchmark
* [![Test2](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/features.ipynb) Test features
- [![features](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/features.ipynb) Some features
* [![Adaboost](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/adaboost.ipynb) Adaboost
- [![Gridsearch](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/gridsearch.ipynb) Gridsearch
* [![Gridsearch](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/gridsearch.ipynb) Gridsearch
- [![Ensemble](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/ensemble.ipynb) Ensembles
* [![Test Graphics](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/test_graphs.ipynb) Test Graphics
## Hyperparameters
### Command line
| | **Hyperparameter** | **Type/Values** | **Default** | **Meaning** |
| --- | ------------------ | ------------------------------------------------------ | ----------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| \* | C | \<float\> | 1.0 | Regularization parameter. The strength of the regularization is inversely proportional to C. Must be strictly positive. |
| \* | kernel | {"linear", "poly", "rbf"} | linear | Specifies the kernel type to be used in the algorithm. It must be one of linear, poly or rbf. |
| \* | max_iter | \<int\> | 1e5 | Hard limit on iterations within solver, or -1 for no limit. |
| \* | random_state | \<int\> | None | Controls the pseudo random number generation for shuffling the data for probability estimates. Ignored when probability is False.<br>Pass an int for reproducible output across multiple function calls |
| | max_depth | \<int\> | None | Specifies the maximum depth of the tree |
| \* | tol | \<float\> | 1e-4 | Tolerance for stopping criterion. |
| \* | degree | \<int\> | 3 | Degree of the polynomial kernel function (poly). Ignored by all other kernels. |
| \* | gamma | {"scale", "auto"} or \<float\> | scale | Kernel coefficient for rbf and poly.<br>if gamma='scale' (default) is passed then it uses 1 / (n_features \* X.var()) as value of gamma,<br>if auto, uses 1 / n_features. |
| | split_criteria | {"impurity", "max_samples"} | impurity | Decides (just in case of a multi class classification) which column (class) use to split the dataset in a node\*\* |
| | criterion | {“gini”, “entropy”} | entropy | The function to measure the quality of a split (only used if max_features != num_features). <br>Supported criteria are “gini” for the Gini impurity and “entropy” for the information gain. |
| | min_samples_split | \<int\> | 0 | The minimum number of samples required to split an internal node. 0 (default) for any |
| | max_features | \<int\>, \<float\> <br><br>or {“auto”, “sqrt”, “log2”} | None | The number of features to consider when looking for the split:<br>If int, then consider max_features features at each split.<br>If float, then max_features is a fraction and int(max_features \* n_features) features are considered at each split.<br>If “auto”, then max_features=sqrt(n_features).<br>If “sqrt”, then max_features=sqrt(n_features).<br>If “log2”, then max_features=log2(n_features).<br>If None, then max_features=n_features. |
| | splitter | {"best", "random"} | random | The strategy used to choose the feature set at each node (only used if max_features != num_features). <br>Supported strategies are “best” to choose the best feature set and “random” to choose a random combination. <br>The algorithm generates 5 candidates at most to choose from in both strategies. |
```bash
python main.py
```
\* Hyperparameter used by the support vector classifier of every node
\*\* **Splitting in a STree node**
The decision function is applied to the dataset and distances from samples to hyperplanes are computed in a matrix. This matrix has as many columns as classes the samples belongs to (if more than two, i.e. multiclass classification) or 1 column if it's a binary class dataset. In binary classification only one hyperplane is computed and therefore only one column is needed to store the distances of the samples to it. If three or more classes are present in the dataset we need as many hyperplanes as classes are there, and therefore one column per hyperplane is needed.
In case of multiclass classification we have to decide which column take into account to make the split, that depends on hyperparameter _split_criteria_, if "impurity" is chosen then STree computes information gain of every split candidate using each column and chooses the one that maximize the information gain, otherwise STree choses the column with more samples with a predicted class (the column with more positive numbers in it).
Once we have the column to take into account for the split, the algorithm splits samples with positive distances to hyperplane from the rest.
## Tests

76
main.py
View File

@@ -1,74 +1,26 @@
import time
from sklearn.model_selection import train_test_split
from sklearn.datasets import load_iris
from stree import Stree
random_state = 1
X, y = load_iris(return_X_y=True)
def load_creditcard(n_examples=0):
import pandas as pd
import numpy as np
import random
df = pd.read_csv("data/creditcard.csv")
print(
"Fraud: {0:.3f}% {1}".format(
df.Class[df.Class == 1].count() * 100 / df.shape[0],
df.Class[df.Class == 1].count(),
)
)
print(
"Valid: {0:.3f}% {1}".format(
df.Class[df.Class == 0].count() * 100 / df.shape[0],
df.Class[df.Class == 0].count(),
)
)
y = np.expand_dims(df.Class.values, axis=1)
X = df.drop(["Class", "Time", "Amount"], axis=1).values
if n_examples > 0:
# Take first n_examples samples
X = X[:n_examples, :]
y = y[:n_examples, :]
else:
# Take all the positive samples with a number of random negatives
if n_examples < 0:
Xt = X[(y == 1).ravel()]
yt = y[(y == 1).ravel()]
indices = random.sample(range(X.shape[0]), -1 * n_examples)
X = np.append(Xt, X[indices], axis=0)
y = np.append(yt, y[indices], axis=0)
print("X.shape", X.shape, " y.shape", y.shape)
print(
"Fraud: {0:.3f}% {1}".format(
len(y[y == 1]) * 100 / X.shape[0], len(y[y == 1])
)
)
print(
"Valid: {0:.3f}% {1}".format(
len(y[y == 0]) * 100 / X.shape[0], len(y[y == 0])
)
)
Xtrain, Xtest, ytrain, ytest = train_test_split(
X,
y,
train_size=0.7,
shuffle=True,
random_state=random_state,
stratify=y,
)
return Xtrain, Xtest, ytrain, ytest
# data = load_creditcard(-5000) # Take all true samples + 5000 of the others
# data = load_creditcard(5000) # Take the first 5000 samples
data = load_creditcard() # Take all the samples
Xtrain = data[0]
Xtest = data[1]
ytrain = data[2]
ytest = data[3]
Xtrain, Xtest, ytrain, ytest = train_test_split(
X, y, test_size=0.3, random_state=random_state
)
now = time.time()
print("Predicting with max_features=sqrt(n_features)")
clf = Stree(C=0.01, random_state=random_state, max_features="auto")
clf.fit(Xtrain, ytrain)
print(f"Took {time.time() - now:.2f} seconds to train")
print(clf)
print(f"Classifier's accuracy (train): {clf.score(Xtrain, ytrain):.4f}")
print(f"Classifier's accuracy (test) : {clf.score(Xtest, ytest):.4f}")
print("=" * 40)
print("Predicting with max_features=n_features")
clf = Stree(C=0.01, random_state=random_state)
clf.fit(Xtrain, ytrain)
print(f"Took {time.time() - now:.2f} seconds to train")

File diff suppressed because one or more lines are too long

View File

@@ -4,7 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test AdaBoost with different configurations"
"# Test Stree with AdaBoost and Bagging with different configurations"
]
},
{
@@ -17,38 +17,43 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#\n",
"# Google Colab setup\n",
"#\n",
"#!pip install git+https://github.com/doctorado-ml/stree"
"#!pip install git+https://github.com/doctorado-ml/stree\n",
"!pip install pandas"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"from sklearn.ensemble import AdaBoostClassifier\n",
"from sklearn.tree import DecisionTreeClassifier\n",
"from sklearn.svm import LinearSVC, SVC\n",
"from sklearn.model_selection import GridSearchCV, train_test_split\n",
"from sklearn.datasets import load_iris\n",
"from stree import Stree"
"import os\n",
"import random\n",
"import warnings\n",
"import pandas as pd\n",
"import numpy as np\n",
"from sklearn.ensemble import AdaBoostClassifier, BaggingClassifier\n",
"from sklearn.model_selection import train_test_split\n",
"from sklearn.exceptions import ConvergenceWarning\n",
"from stree import Stree\n",
"\n",
"warnings.filterwarnings(\"ignore\", category=ConvergenceWarning)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"if not os.path.isfile('data/creditcard.csv'):\n",
" !wget --no-check-certificate --content-disposition http://nube.jccm.es/index.php/s/Zs7SYtZQJ3RQ2H2/download\n",
" !tar xzf creditcard.tgz"
@@ -56,22 +61,15 @@
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Fraud: 0.173% 492\nValid: 99.827% 284315\nX.shape (100492, 28) y.shape (100492,)\nFraud: 0.659% 662\nValid: 99.341% 99830\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"random_state=1\n",
"\n",
"def load_creditcard(n_examples=0):\n",
" import pandas as pd\n",
" import numpy as np\n",
" import random\n",
" df = pd.read_csv('data/creditcard.csv')\n",
" print(\"Fraud: {0:.3f}% {1}\".format(df.Class[df.Class == 1].count()*100/df.shape[0], df.Class[df.Class == 1].count()))\n",
" print(\"Valid: {0:.3f}% {1}\".format(df.Class[df.Class == 0].count()*100/df.shape[0], df.Class[df.Class == 0].count()))\n",
@@ -117,23 +115,19 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## STree alone on the whole dataset and linear kernel"
"## STree alone with 100.000 samples and linear kernel"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Score Train: 0.9985499829409757\nScore Test: 0.998407854584052\nTook 39.45 seconds\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"now = time.time()\n",
"clf = Stree(max_depth=3, random_state=random_state)\n",
"clf = Stree(max_depth=3, random_state=random_state, max_iter=1e3)\n",
"clf.fit(Xtrain, ytrain)\n",
"print(\"Score Train: \", clf.score(Xtrain, ytrain))\n",
"print(\"Score Test: \", clf.score(Xtest, ytest))\n",
@@ -144,12 +138,12 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Different kernels with different configuations"
"## Adaboost"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -160,19 +154,15 @@
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Kernel: linear\tTime: 87.00 seconds\tScore Train: 0.9982372\tScore Test: 0.9981425\nKernel: rbf\tTime: 60.60 seconds\tScore Train: 0.9934181\tScore Test: 0.9933992\nKernel: poly\tTime: 88.08 seconds\tScore Train: 0.9937450\tScore Test: 0.9938968\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"for kernel in ['linear', 'rbf', 'poly']:\n",
" now = time.time()\n",
" clf = AdaBoostClassifier(Stree(C=7, kernel=kernel, max_depth=max_depth, random_state=random_state), n_estimators=n_estimators, random_state=random_state)\n",
" clf = AdaBoostClassifier(base_estimator=Stree(C=C, kernel=kernel, max_depth=max_depth, random_state=random_state, max_iter=1e3), algorithm=\"SAMME\", n_estimators=n_estimators, random_state=random_state)\n",
" clf.fit(Xtrain, ytrain)\n",
" score_train = clf.score(Xtrain, ytrain)\n",
" score_test = clf.score(Xtest, ytest)\n",
@@ -183,24 +173,31 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test algorithm SAMME in AdaBoost to check speed/accuracy"
"## Bagging"
]
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Kernel: linear\tTime: 58.75 seconds\tScore Train: 0.9980524\tScore Test: 0.9978771\nKernel: rbf\tTime: 12.49 seconds\tScore Train: 0.9934181\tScore Test: 0.9933992\nKernel: poly\tTime: 97.85 seconds\tScore Train: 0.9972137\tScore Test: 0.9971806\n"
}
],
"outputs": [],
"source": [
"n_estimators = 10\n",
"C = 7\n",
"max_depth = 3"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"for kernel in ['linear', 'rbf', 'poly']:\n",
" now = time.time()\n",
" clf = AdaBoostClassifier(Stree(C=7, kernel=kernel, max_depth=max_depth, random_state=random_state), n_estimators=n_estimators, random_state=random_state, algorithm=\"SAMME\")\n",
" clf = BaggingClassifier(base_estimator=Stree(C=C, kernel=kernel, max_depth=max_depth, random_state=random_state, max_iter=1e3), n_estimators=n_estimators, random_state=random_state)\n",
" clf.fit(Xtrain, ytrain)\n",
" score_train = clf.score(Xtrain, ytrain)\n",
" score_test = clf.score(Xtest, ytest)\n",
@@ -209,6 +206,11 @@
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
@@ -219,14 +221,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6-final"
},
"orig_nbformat": 2,
"kernelspec": {
"name": "python37664bitgeneralvenvfbd0a23e74cf4e778460f5ffc6761f39",
"display_name": "Python 3.7.6 64-bit ('general': venv)"
"version": "3.8.2-final"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}

View File

@@ -4,7 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test smple_weight, kernels, C, sklearn estimator"
"# Test sample_weight, kernels, C, sklearn estimator"
]
},
{
@@ -17,22 +17,27 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#\n",
"# Google Colab setup\n",
"#\n",
"#!pip install git+https://github.com/doctorado-ml/stree"
"#!pip install git+https://github.com/doctorado-ml/stree\n",
"!pip install pandas"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"import random\n",
"import warnings\n",
"import os\n",
"import numpy as np\n",
"import pandas as pd\n",
"from sklearn.svm import SVC\n",
@@ -40,17 +45,20 @@
"from sklearn.utils.estimator_checks import check_estimator\n",
"from sklearn.datasets import make_classification, load_iris, load_wine\n",
"from sklearn.model_selection import train_test_split\n",
"from sklearn.utils.class_weight import compute_sample_weight\n",
"from sklearn.exceptions import ConvergenceWarning\n",
"from stree import Stree\n",
"import time"
"warnings.filterwarnings(\"ignore\", category=ConvergenceWarning)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"import os\n",
"if not os.path.isfile('data/creditcard.csv'):\n",
" !wget --no-check-certificate --content-disposition http://nube.jccm.es/index.php/s/Zs7SYtZQJ3RQ2H2/download\n",
" !tar xzf creditcard.tgz"
@@ -58,22 +66,15 @@
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Fraud: 0.173% 492\nValid: 99.827% 284315\nX.shape (1492, 28) y.shape (1492,)\nFraud: 33.110% 494\nValid: 66.890% 998\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"random_state=1\n",
"\n",
"def load_creditcard(n_examples=0):\n",
" import pandas as pd\n",
" import numpy as np\n",
" import random\n",
" df = pd.read_csv('data/creditcard.csv')\n",
" print(\"Fraud: {0:.3f}% {1}\".format(df.Class[df.Class == 1].count()*100/df.shape[0], df.Class[df.Class == 1].count()))\n",
" print(\"Valid: {0:.3f}% {1}\".format(df.Class[df.Class == 0].count()*100/df.shape[0], df.Class[df.Class == 0].count()))\n",
@@ -94,22 +95,20 @@
" print(\"X.shape\", X.shape, \" y.shape\", y.shape)\n",
" print(\"Fraud: {0:.3f}% {1}\".format(len(y[y == 1])*100/X.shape[0], len(y[y == 1])))\n",
" print(\"Valid: {0:.3f}% {1}\".format(len(y[y == 0]) * 100 / X.shape[0], len(y[y == 0])))\n",
" Xtrain, Xtest, ytrain, ytest = train_test_split(X, y, train_size=0.7, shuffle=True, random_state=random_state, stratify=y)\n",
" Xtrain, Xtest, ytrain, ytest = train_test_split(X, y, train_size=0.7, shuffle=True, random_state=random_state)\n",
" return Xtrain, Xtest, ytrain, ytest\n",
"\n",
"# data = load_creditcard(-5000) # Take all true samples + 5000 of the others\n",
"data = load_creditcard(-5000) # Take all true samples with up to 5000 of the others\n",
"# data = load_creditcard(5000) # Take the first 5000 samples\n",
"data = load_creditcard(-1000) # Take all the samples\n",
"# data = load_creditcard(-1000) # Take 1000 samples\n",
"\n",
"Xtrain = data[0]\n",
"Xtest = data[1]\n",
"ytrain = data[2]\n",
"ytest = data[3]\n",
"# Set weights inverse to its count class in dataset\n",
"weights = np.ones(Xtrain.shape[0],) * 1.00244\n",
"weights[ytrain==1] = 1.99755\n",
"weights_test = np.ones(Xtest.shape[0],) * 1.00244\n",
"weights_test[ytest==1] = 1.99755 "
"weights = compute_sample_weight(\"balanced\", ytrain)\n",
"weights_test = compute_sample_weight(\"balanced\", ytest)\n",
"print(weights[:4], weights_test[:4])"
]
},
{
@@ -123,21 +122,17 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test smple_weights\n",
"## Test sample_weights\n",
"Compute accuracy with weights in samples. The weights are set based on the inverse of the number of samples of each class"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Accuracy of Train without weights 0.9789272030651341\nAccuracy of Train with weights 0.9952107279693486\nAccuracy of Tests without weights 0.9598214285714286\nAccuracy of Tests with weights 0.9508928571428571\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"C = 23\n",
"print(\"Accuracy of Train without weights\", Stree(C=C, random_state=1).fit(Xtrain, ytrain).score(Xtrain, ytrain))\n",
@@ -156,15 +151,11 @@
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Time: 0.27s\tKernel: linear\tAccuracy_train: 0.9683908045977011\tAccuracy_test: 0.953125\nTime: 0.09s\tKernel: rbf\tAccuracy_train: 0.9875478927203065\tAccuracy_test: 0.9598214285714286\nTime: 0.06s\tKernel: poly\tAccuracy_train: 0.9885057471264368\tAccuracy_test: 0.9464285714285714\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"random_state=1\n",
"for kernel in ['linear', 'rbf', 'poly']:\n",
@@ -185,19 +176,11 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"metadata": {
"tags": [
"outputPrepend"
]
"tags": []
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "************** C=0.001 ****************************\nClassifier's accuracy (train): 0.9531\nClassifier's accuracy (test) : 0.9621\nroot\nroot - Down, <cgaf> - Leaf class=1 belief= 0.983713 counts=(array([0, 1]), array([ 5, 302]))\nroot - Up, <cgaf> - Leaf class=0 belief= 0.940299 counts=(array([0, 1]), array([693, 44]))\n\n**************************************************\n************** C=0.01 ****************************\nClassifier's accuracy (train): 0.9569\nClassifier's accuracy (test) : 0.9621\nroot\nroot - Down, <cgaf> - Leaf class=1 belief= 0.990228 counts=(array([0, 1]), array([ 3, 304]))\nroot - Up, <cgaf> - Leaf class=0 belief= 0.943012 counts=(array([0, 1]), array([695, 42]))\n\n**************************************************\n************** C=1 ****************************\nClassifier's accuracy (train): 0.9655\nClassifier's accuracy (test) : 0.9643\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([310]))\nroot - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([5]))\nroot - Up, <cgaf> - Leaf class=0 belief= 0.950617 counts=(array([0, 1]), array([693, 36]))\n\n**************************************************\n************** C=5 ****************************\nClassifier's accuracy (train): 0.9684\nClassifier's accuracy (test) : 0.9598\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([311]))\nroot - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([8]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([1]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([2]))\nroot - Up - Up\nroot - Up - Up - Down, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief= 0.954039 counts=(array([0, 1]), array([685, 33]))\n\n**************************************************\n************** C=17 ****************************\nClassifier's accuracy (train): 0.9751\nClassifier's accuracy (test) : 0.9464\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([304]))\nroot - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([8]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([4]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([3]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([4]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([3]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([2]))\nroot - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief= 0.963225 counts=(array([0, 1]), array([681, 26]))\n\n**************************************************\n0.6869 secs\n"
}
],
"outputs": [],
"source": [
"t = time.time()\n",
"for C in (.001, .01, 1, 5, 17):\n",
@@ -216,20 +199,16 @@
"metadata": {},
"source": [
"## Test iterator\n",
"Check different weays of using the iterator"
"Check different ways of using the iterator"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([304]))\nroot - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([8]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([4]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([3]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([4]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([3]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([2]))\nroot - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief= 0.963225 counts=(array([0, 1]), array([681, 26]))\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"#check iterator\n",
"for i in list(clf):\n",
@@ -238,15 +217,11 @@
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([304]))\nroot - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([8]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([4]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([3]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([4]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([3]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down, <pure> - Leaf class=1 belief= 1.000000 counts=(array([1]), array([2]))\nroot - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief= 0.963225 counts=(array([0, 1]), array([681, 26]))\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"#check iterator again\n",
"for i in clf:\n",
@@ -262,15 +237,11 @@
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "1 functools.partial(<function check_no_attributes_set_in_init at 0x1254f13b0>, 'Stree')\n2 functools.partial(<function check_estimators_dtypes at 0x1254e84d0>, 'Stree')\n3 functools.partial(<function check_fit_score_takes_y at 0x1254e83b0>, 'Stree')\n4 functools.partial(<function check_sample_weights_pandas_series at 0x1254e0cb0>, 'Stree')\n5 functools.partial(<function check_sample_weights_not_an_array at 0x1254e0dd0>, 'Stree')\n6 functools.partial(<function check_sample_weights_list at 0x1254e0ef0>, 'Stree')\n7 functools.partial(<function check_sample_weights_shape at 0x1254e2050>, 'Stree')\n8 functools.partial(<function check_sample_weights_invariance at 0x1254e2170>, 'Stree')\n9 functools.partial(<function check_estimators_fit_returns_self at 0x1254eb4d0>, 'Stree')\n10 functools.partial(<function check_estimators_fit_returns_self at 0x1254eb4d0>, 'Stree', readonly_memmap=True)\n11 functools.partial(<function check_complex_data at 0x1254e2320>, 'Stree')\n12 functools.partial(<function check_dtype_object at 0x1254e2290>, 'Stree')\n13 functools.partial(<function check_estimators_empty_data_messages at 0x1254e85f0>, 'Stree')\n14 functools.partial(<function check_pipeline_consistency at 0x1254e8290>, 'Stree')\n15 functools.partial(<function check_estimators_nan_inf at 0x1254e8710>, 'Stree')\n16 functools.partial(<function check_estimators_overwrite_params at 0x1254f1290>, 'Stree')\n17 functools.partial(<function check_estimator_sparse_data at 0x1254e0b90>, 'Stree')\n18 functools.partial(<function check_estimators_pickle at 0x1254e8950>, 'Stree')\n19 functools.partial(<function check_classifier_data_not_an_array at 0x1254f15f0>, 'Stree')\n20 functools.partial(<function check_classifiers_one_label at 0x1254eb050>, 'Stree')\n21 functools.partial(<function check_classifiers_classes at 0x1254eba70>, 'Stree')\n22 functools.partial(<function check_estimators_partial_fit_n_features at 0x1254e8a70>, 'Stree')\n23 functools.partial(<function check_classifiers_train at 0x1254eb170>, 'Stree')\n24 functools.partial(<function check_classifiers_train at 0x1254eb170>, 'Stree', readonly_memmap=True)\n25 functools.partial(<function check_classifiers_train at 0x1254eb170>, 'Stree', readonly_memmap=True, X_dtype='float32')\n26 functools.partial(<function check_classifiers_regression_target at 0x1254f40e0>, 'Stree')\n27 functools.partial(<function check_supervised_y_no_nan at 0x1254da9e0>, 'Stree')\n28 functools.partial(<function check_supervised_y_2d at 0x1254eb710>, 'Stree')\n29 functools.partial(<function check_estimators_unfitted at 0x1254eb5f0>, 'Stree')\n30 functools.partial(<function check_non_transformer_estimators_n_iter at 0x1254f1c20>, 'Stree')\n31 functools.partial(<function check_decision_proba_consistency at 0x1254f4200>, 'Stree')\n32 functools.partial(<function check_fit2d_predict1d at 0x1254e2830>, 'Stree')\n33 functools.partial(<function check_methods_subset_invariance at 0x1254e29e0>, 'Stree')\n34 functools.partial(<function check_fit2d_1sample at 0x1254e2b00>, 'Stree')\n35 functools.partial(<function check_fit2d_1feature at 0x1254e2c20>, 'Stree')\n36 functools.partial(<function check_fit1d at 0x1254e2d40>, 'Stree')\n37 functools.partial(<function check_get_params_invariance at 0x1254f1e60>, 'Stree')\n38 functools.partial(<function check_set_params at 0x1254f1f80>, 'Stree')\n39 functools.partial(<function check_dict_unchanged at 0x1254e2440>, 'Stree')\n40 functools.partial(<function check_dont_overwrite_parameters at 0x1254e2710>, 'Stree')\n41 functools.partial(<function check_fit_idempotent at 0x1254f43b0>, 'Stree')\n42 functools.partial(<function check_n_features_in at 0x1254f4440>, 'Stree')\n43 functools.partial(<function check_requires_y_none at 0x1254f44d0>, 'Stree')\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# Make checks one by one\n",
"c = 0\n",
@@ -283,7 +254,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -300,15 +271,11 @@
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "== Not Weighted ===\nSVC train score ..: 0.9521072796934866\nSTree train score : 0.9578544061302682\nSVC test score ...: 0.9553571428571429\nSTree test score .: 0.9575892857142857\n==== Weighted =====\nSVC train score ..: 0.9616858237547893\nSTree train score : 0.9616858237547893\nSVC test score ...: 0.9642857142857143\nSTree test score .: 0.9598214285714286\n*SVC test score ..: 0.951413553411694\n*STree test score : 0.9480517444389333\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"svc = SVC(C=7, kernel='rbf', gamma=.001, random_state=random_state)\n",
"clf = Stree(C=17, kernel='rbf', gamma=.001, random_state=random_state)\n",
@@ -332,25 +299,47 @@
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "root\nroot - Down\nroot - Down - Down, <cgaf> - Leaf class=1 belief= 0.969325 counts=(array([0, 1]), array([ 10, 316]))\nroot - Down - Up, <pure> - Leaf class=0 belief= 1.000000 counts=(array([0]), array([1]))\nroot - Up, <cgaf> - Leaf class=0 belief= 0.958159 counts=(array([0, 1]), array([687, 30]))\n\n"
}
],
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"print(clf)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test max_features"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"for max_features in [None, \"auto\", \"log2\", 7, .5, .1, .7]:\n",
" now = time.time()\n",
" print(\"*\"*40)\n",
" clf = Stree(random_state=random_state, max_features=max_features)\n",
" clf.fit(Xtrain, ytrain)\n",
" print(f\"max_features {max_features} = {clf.max_features_}\")\n",
" print(\"Train score :\", clf.score(Xtrain, ytrain))\n",
" print(\"Test score .:\", clf.score(Xtest, ytest))\n",
" print(f\"Took {time.time() - now:.2f} seconds\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.7.6 64-bit ('general': venv)",
"display_name": "Python 3",
"language": "python",
"name": "python37664bitgeneralvenvfbd0a23e74cf4e778460f5ffc6761f39"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
@@ -362,9 +351,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6-final"
"version": "3.8.2-final"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}

View File

@@ -1,244 +1,253 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test Gridsearch\n",
"with different kernels and different configurations"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Setup\n",
"Uncomment the next cell if STree is not already installed"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"#\n",
"# Google Colab setup\n",
"#\n",
"#!pip install git+https://github.com/doctorado-ml/stree"
]
},
{
"cell_type": "code",
"metadata": {
"id": "zIHKVxthDZEa",
"colab_type": "code",
"colab": {}
},
"source": [
"from sklearn.ensemble import AdaBoostClassifier\n",
"from sklearn.svm import LinearSVC\n",
"from sklearn.model_selection import GridSearchCV, train_test_split\n",
"from stree import Stree"
],
"execution_count": 2,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "IEmq50QgDZEi",
"colab_type": "code",
"colab": {}
},
"source": [
"import os\n",
"if not os.path.isfile('data/creditcard.csv'):\n",
" !wget --no-check-certificate --content-disposition http://nube.jccm.es/index.php/s/Zs7SYtZQJ3RQ2H2/download\n",
" !tar xzf creditcard.tgz"
],
"execution_count": 3,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "z9Q-YUfBDZEq",
"colab_type": "code",
"colab": {},
"outputId": "afc822fb-f16a-4302-8a67-2b9e2880159b"
},
"source": [
"random_state=1\n",
"\n",
"def load_creditcard(n_examples=0):\n",
" import pandas as pd\n",
" import numpy as np\n",
" import random\n",
" df = pd.read_csv('data/creditcard.csv')\n",
" print(\"Fraud: {0:.3f}% {1}\".format(df.Class[df.Class == 1].count()*100/df.shape[0], df.Class[df.Class == 1].count()))\n",
" print(\"Valid: {0:.3f}% {1}\".format(df.Class[df.Class == 0].count()*100/df.shape[0], df.Class[df.Class == 0].count()))\n",
" y = df.Class\n",
" X = df.drop(['Class', 'Time', 'Amount'], axis=1).values\n",
" if n_examples > 0:\n",
" # Take first n_examples samples\n",
" X = X[:n_examples, :]\n",
" y = y[:n_examples, :]\n",
" else:\n",
" # Take all the positive samples with a number of random negatives\n",
" if n_examples < 0:\n",
" Xt = X[(y == 1).ravel()]\n",
" yt = y[(y == 1).ravel()]\n",
" indices = random.sample(range(X.shape[0]), -1 * n_examples)\n",
" X = np.append(Xt, X[indices], axis=0)\n",
" y = np.append(yt, y[indices], axis=0)\n",
" print(\"X.shape\", X.shape, \" y.shape\", y.shape)\n",
" print(\"Fraud: {0:.3f}% {1}\".format(len(y[y == 1])*100/X.shape[0], len(y[y == 1])))\n",
" print(\"Valid: {0:.3f}% {1}\".format(len(y[y == 0]) * 100 / X.shape[0], len(y[y == 0])))\n",
" Xtrain, Xtest, ytrain, ytest = train_test_split(X, y, train_size=0.7, shuffle=True, random_state=random_state, stratify=y)\n",
" return Xtrain, Xtest, ytrain, ytest\n",
"\n",
"data = load_creditcard(-1000) # Take all true samples + 1000 of the others\n",
"# data = load_creditcard(5000) # Take the first 5000 samples\n",
"# data = load_creditcard(0) # Take all the samples\n",
"\n",
"Xtrain = data[0]\n",
"Xtest = data[1]\n",
"ytrain = data[2]\n",
"ytest = data[3]"
],
"execution_count": 4,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Fraud: 0.173% 492\nValid: 99.827% 284315\nX.shape (1492, 28) y.shape (1492,)\nFraud: 33.244% 496\nValid: 66.756% 996\n"
}
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Tests"
]
},
{
"cell_type": "code",
"metadata": {
"id": "HmX3kR4PDZEw",
"colab_type": "code",
"colab": {}
},
"source": [
"parameters = {\n",
" 'base_estimator': [Stree()],\n",
" 'n_estimators': [10, 25],\n",
" 'learning_rate': [.5, 1],\n",
" 'base_estimator__tol': [.1, 1e-02],\n",
" 'base_estimator__max_depth': [3, 5],\n",
" 'base_estimator__C': [1, 3],\n",
" 'base_estimator__kernel': ['linear', 'poly', 'rbf']\n",
"}"
],
"execution_count": 9,
"outputs": []
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": "{'C': 1.0,\n 'degree': 3,\n 'gamma': 'scale',\n 'kernel': 'linear',\n 'max_depth': None,\n 'max_iter': 1000,\n 'min_samples_split': 0,\n 'random_state': None,\n 'tol': 0.0001}"
},
"metadata": {},
"execution_count": 14
}
],
"source": [
"Stree().get_params()"
]
},
{
"cell_type": "code",
"metadata": {
"id": "CrcB8o6EDZE5",
"colab_type": "code",
"colab": {},
"outputId": "7703413a-d563-4289-a13b-532f38f82762"
},
"source": [
"random_state=2020\n",
"clf = AdaBoostClassifier(random_state=random_state)\n",
"grid = GridSearchCV(clf, parameters, verbose=10, n_jobs=-1, return_train_score=True)\n",
"grid.fit(Xtrain, ytrain)"
],
"execution_count": 11,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Fitting 5 folds for each of 96 candidates, totalling 480 fits\n[Parallel(n_jobs=-1)]: Using backend LokyBackend with 8 concurrent workers.\n[Parallel(n_jobs=-1)]: Done 2 tasks | elapsed: 3.6s\n[Parallel(n_jobs=-1)]: Done 9 tasks | elapsed: 4.2s\n[Parallel(n_jobs=-1)]: Done 16 tasks | elapsed: 4.8s\n[Parallel(n_jobs=-1)]: Done 25 tasks | elapsed: 5.3s\n[Parallel(n_jobs=-1)]: Done 34 tasks | elapsed: 6.2s\n[Parallel(n_jobs=-1)]: Done 45 tasks | elapsed: 7.2s\n[Parallel(n_jobs=-1)]: Done 56 tasks | elapsed: 8.9s\n[Parallel(n_jobs=-1)]: Done 69 tasks | elapsed: 10.7s\n[Parallel(n_jobs=-1)]: Done 82 tasks | elapsed: 12.7s\n[Parallel(n_jobs=-1)]: Done 97 tasks | elapsed: 16.7s\n[Parallel(n_jobs=-1)]: Done 112 tasks | elapsed: 19.4s\n[Parallel(n_jobs=-1)]: Done 129 tasks | elapsed: 24.4s\n[Parallel(n_jobs=-1)]: Done 146 tasks | elapsed: 29.3s\n[Parallel(n_jobs=-1)]: Done 165 tasks | elapsed: 32.7s\n[Parallel(n_jobs=-1)]: Done 184 tasks | elapsed: 36.4s\n[Parallel(n_jobs=-1)]: Done 205 tasks | elapsed: 39.7s\n[Parallel(n_jobs=-1)]: Done 226 tasks | elapsed: 43.7s\n[Parallel(n_jobs=-1)]: Done 249 tasks | elapsed: 46.6s\n[Parallel(n_jobs=-1)]: Done 272 tasks | elapsed: 48.8s\n[Parallel(n_jobs=-1)]: Done 297 tasks | elapsed: 52.0s\n[Parallel(n_jobs=-1)]: Done 322 tasks | elapsed: 55.9s\n[Parallel(n_jobs=-1)]: Done 349 tasks | elapsed: 1.0min\n[Parallel(n_jobs=-1)]: Done 376 tasks | elapsed: 1.2min\n[Parallel(n_jobs=-1)]: Done 405 tasks | elapsed: 1.3min\n[Parallel(n_jobs=-1)]: Done 434 tasks | elapsed: 1.3min\n[Parallel(n_jobs=-1)]: Done 465 tasks | elapsed: 1.4min\n[Parallel(n_jobs=-1)]: Done 480 out of 480 | elapsed: 1.5min finished\n"
},
{
"output_type": "execute_result",
"data": {
"text/plain": "GridSearchCV(estimator=AdaBoostClassifier(random_state=2020), n_jobs=-1,\n param_grid={'base_estimator': [Stree(C=1, max_depth=3, tol=0.1)],\n 'base_estimator__C': [1, 3],\n 'base_estimator__kernel': ['linear', 'poly', 'rbf'],\n 'base_estimator__max_depth': [3, 5],\n 'base_estimator__tol': [0.1, 0.01],\n 'learning_rate': [0.5, 1], 'n_estimators': [10, 25]},\n return_train_score=True, verbose=10)"
},
"metadata": {},
"execution_count": 11
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "ZjX88NoYDZE8",
"colab_type": "code",
"colab": {},
"outputId": "285163c8-fa33-4915-8ae7-61c4f7844344"
},
"source": [
"print(\"Best estimator: \", grid.best_estimator_)\n",
"print(\"Best hyperparameters: \", grid.best_params_)\n",
"print(\"Best accuracy: \", grid.best_score_)"
],
"execution_count": 16,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Best estimator: AdaBoostClassifier(base_estimator=Stree(C=1, max_depth=3, tol=0.1),\n learning_rate=0.5, n_estimators=10, random_state=2020)\nBest hyperparameters: {'base_estimator': Stree(C=1, max_depth=3, tol=0.1), 'base_estimator__C': 1, 'base_estimator__kernel': 'linear', 'base_estimator__max_depth': 3, 'base_estimator__tol': 0.1, 'learning_rate': 0.5, 'n_estimators': 10}\nBest accuracy: 0.9492316893632683\n"
}
]
}
],
"metadata": {
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6-final"
},
"orig_nbformat": 2,
"kernelspec": {
"name": "python37664bitgeneralvenvfbd0a23e74cf4e778460f5ffc6761f39",
"display_name": "Python 3.7.6 64-bit ('general': venv)"
},
"colab": {
"name": "gridsearch.ipynb",
"provenance": []
}
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test Gridsearch\n",
"with different kernels and different configurations"
]
},
"nbformat": 4,
"nbformat_minor": 0
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Setup\n",
"Uncomment the next cell if STree is not already installed"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#\n",
"# Google Colab setup\n",
"#\n",
"#!pip install git+https://github.com/doctorado-ml/stree\n",
"!pip install pandas"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "zIHKVxthDZEa"
},
"outputs": [],
"source": [
"import random\n",
"import os\n",
"import pandas as pd\n",
"import numpy as np\n",
"from sklearn.ensemble import AdaBoostClassifier\n",
"from sklearn.svm import LinearSVC\n",
"from sklearn.model_selection import GridSearchCV, train_test_split\n",
"from stree import Stree"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "IEmq50QgDZEi"
},
"outputs": [],
"source": [
"if not os.path.isfile('data/creditcard.csv'):\n",
" !wget --no-check-certificate --content-disposition http://nube.jccm.es/index.php/s/Zs7SYtZQJ3RQ2H2/download\n",
" !tar xzf creditcard.tgz"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "z9Q-YUfBDZEq",
"outputId": "afc822fb-f16a-4302-8a67-2b9e2880159b",
"tags": []
},
"outputs": [],
"source": [
"random_state=1\n",
"\n",
"def load_creditcard(n_examples=0):\n",
" df = pd.read_csv('data/creditcard.csv')\n",
" print(\"Fraud: {0:.3f}% {1}\".format(df.Class[df.Class == 1].count()*100/df.shape[0], df.Class[df.Class == 1].count()))\n",
" print(\"Valid: {0:.3f}% {1}\".format(df.Class[df.Class == 0].count()*100/df.shape[0], df.Class[df.Class == 0].count()))\n",
" y = df.Class\n",
" X = df.drop(['Class', 'Time', 'Amount'], axis=1).values\n",
" if n_examples > 0:\n",
" # Take first n_examples samples\n",
" X = X[:n_examples, :]\n",
" y = y[:n_examples, :]\n",
" else:\n",
" # Take all the positive samples with a number of random negatives\n",
" if n_examples < 0:\n",
" Xt = X[(y == 1).ravel()]\n",
" yt = y[(y == 1).ravel()]\n",
" indices = random.sample(range(X.shape[0]), -1 * n_examples)\n",
" X = np.append(Xt, X[indices], axis=0)\n",
" y = np.append(yt, y[indices], axis=0)\n",
" print(\"X.shape\", X.shape, \" y.shape\", y.shape)\n",
" print(\"Fraud: {0:.3f}% {1}\".format(len(y[y == 1])*100/X.shape[0], len(y[y == 1])))\n",
" print(\"Valid: {0:.3f}% {1}\".format(len(y[y == 0]) * 100 / X.shape[0], len(y[y == 0])))\n",
" Xtrain, Xtest, ytrain, ytest = train_test_split(X, y, train_size=0.7, shuffle=True, random_state=random_state, stratify=y)\n",
" return Xtrain, Xtest, ytrain, ytest\n",
"\n",
"data = load_creditcard(-1000) # Take all true samples + 1000 of the others\n",
"# data = load_creditcard(5000) # Take the first 5000 samples\n",
"# data = load_creditcard(0) # Take all the samples\n",
"\n",
"Xtrain = data[0]\n",
"Xtest = data[1]\n",
"ytrain = data[2]\n",
"ytest = data[3]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Tests"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "HmX3kR4PDZEw"
},
"outputs": [],
"source": [
"parameters = [{\n",
" 'base_estimator': [Stree(random_state=random_state)],\n",
" 'n_estimators': [10, 25],\n",
" 'learning_rate': [.5, 1],\n",
" 'base_estimator__split_criteria': ['max_samples', 'impurity'],\n",
" 'base_estimator__tol': [.1, 1e-02],\n",
" 'base_estimator__max_depth': [3, 5, 7],\n",
" 'base_estimator__C': [1, 7, 55],\n",
" 'base_estimator__kernel': ['linear']\n",
"},\n",
"{\n",
" 'base_estimator': [Stree(random_state=random_state)],\n",
" 'n_estimators': [10, 25],\n",
" 'learning_rate': [.5, 1],\n",
" 'base_estimator__split_criteria': ['max_samples', 'impurity'],\n",
" 'base_estimator__tol': [.1, 1e-02],\n",
" 'base_estimator__max_depth': [3, 5, 7],\n",
" 'base_estimator__C': [1, 7, 55],\n",
" 'base_estimator__degree': [3, 5, 7],\n",
" 'base_estimator__kernel': ['poly']\n",
"},\n",
"{\n",
" 'base_estimator': [Stree(random_state=random_state)],\n",
" 'n_estimators': [10, 25],\n",
" 'learning_rate': [.5, 1],\n",
" 'base_estimator__split_criteria': ['max_samples', 'impurity'],\n",
" 'base_estimator__tol': [.1, 1e-02],\n",
" 'base_estimator__max_depth': [3, 5, 7],\n",
" 'base_estimator__C': [1, 7, 55],\n",
" 'base_estimator__gamma': [.1, 1, 10],\n",
" 'base_estimator__kernel': ['rbf']\n",
"}]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"Stree().get_params()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "CrcB8o6EDZE5",
"outputId": "7703413a-d563-4289-a13b-532f38f82762",
"tags": []
},
"outputs": [],
"source": [
"clf = AdaBoostClassifier(random_state=random_state, algorithm=\"SAMME\")\n",
"grid = GridSearchCV(clf, parameters, verbose=5, n_jobs=-1, return_train_score=True)\n",
"grid.fit(Xtrain, ytrain)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "ZjX88NoYDZE8",
"outputId": "285163c8-fa33-4915-8ae7-61c4f7844344",
"tags": []
},
"outputs": [],
"source": [
"print(\"Best estimator: \", grid.best_estimator_)\n",
"print(\"Best hyperparameters: \", grid.best_params_)\n",
"print(\"Best accuracy: \", grid.best_score_)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Best estimator: AdaBoostClassifier(algorithm='SAMME',\n",
" base_estimator=Stree(C=55, max_depth=7, random_state=1,\n",
" split_criteria='max_samples', tol=0.1),\n",
" learning_rate=0.5, n_estimators=25, random_state=1)\n",
"Best hyperparameters: {'base_estimator': Stree(C=55, max_depth=7, random_state=1, split_criteria='max_samples', tol=0.1), 'base_estimator__C': 55, 'base_estimator__kernel': 'linear', 'base_estimator__max_depth': 7, 'base_estimator__split_criteria': 'max_samples', 'base_estimator__tol': 0.1, 'learning_rate': 0.5, 'n_estimators': 25}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Best accuracy: 0.9511777695988222"
]
}
],
"metadata": {
"colab": {
"name": "gridsearch.ipynb",
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.2-final"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

File diff suppressed because one or more lines are too long

View File

@@ -1,5 +1 @@
numpy
scikit-learn
pandas
matplotlib
ipympl
scikit-learn>0.24

1
runtime.txt Normal file
View File

@@ -0,0 +1 @@
python-3.8

View File

@@ -1,6 +1,6 @@
import setuptools
__version__ = "0.9rc4"
__version__ = "1.0rc1"
__author__ = "Ricardo Montañana Gómez"
@@ -25,12 +25,12 @@ setuptools.setup(
classifiers=[
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Natural Language :: English",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Intended Audience :: Science/Research",
],
install_requires=["scikit-learn>=0.23.0", "numpy", "matplotlib", "ipympl"],
install_requires=["scikit-learn", "numpy", "ipympl"],
test_suite="stree.tests",
zip_safe=False,
)

View File

@@ -3,16 +3,22 @@ __author__ = "Ricardo Montañana Gómez"
__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
__license__ = "MIT"
__version__ = "0.9"
Build an oblique tree classifier based on SVM Trees
Build an oblique tree classifier based on SVM nodes
"""
import os
import numbers
import random
import warnings
from math import log, factorial
from typing import Optional
import numpy as np
from sklearn.base import BaseEstimator, ClassifierMixin
from sklearn.svm import SVC, LinearSVC
from sklearn.preprocessing import StandardScaler
from sklearn.utils import check_consistent_length
from sklearn.utils.multiclass import check_classification_targets
from sklearn.exceptions import ConvergenceWarning
from sklearn.utils.validation import (
check_X_y,
check_array,
@@ -27,7 +33,17 @@ class Snode:
dataset assigned to it
"""
def __init__(self, clf: SVC, X: np.ndarray, y: np.ndarray, title: str):
def __init__(
self,
clf: SVC,
X: np.ndarray,
y: np.ndarray,
features: np.array,
impurity: float,
title: str,
weight: np.ndarray = None,
scaler: StandardScaler = None,
):
self._clf = clf
self._title = title
self._belief = 0.0
@@ -37,14 +53,61 @@ class Snode:
self._down = None
self._up = None
self._class = None
self._feature = None
self._sample_weight = (
weight if os.environ.get("TESTING", "NS") != "NS" else None
)
self._features = features
self._impurity = impurity
self._partition_column: int = -1
self._scaler = scaler
@classmethod
def copy(cls, node: "Snode") -> "Snode":
return cls(node._clf, node._X, node._y, node._title)
return cls(
node._clf,
node._X,
node._y,
node._features,
node._impurity,
node._title,
node._sample_weight,
node._scaler,
)
def set_partition_column(self, col: int):
self._partition_column = col
def get_partition_column(self) -> int:
return self._partition_column
def set_down(self, son):
self._down = son
def set_title(self, title):
self._title = title
def set_classifier(self, clf):
self._clf = clf
def set_features(self, features):
self._features = features
def set_impurity(self, impurity):
self._impurity = impurity
def get_title(self) -> str:
return self._title
def get_classifier(self) -> SVC:
return self._clf
def get_impurity(self) -> float:
return self._impurity
def get_features(self) -> np.array:
return self._features
def set_up(self, son):
self._up = son
@@ -66,9 +129,8 @@ class Snode:
classes, card = np.unique(self._y, return_counts=True)
if len(classes) > 1:
max_card = max(card)
min_card = min(card)
self._class = classes[card == max_card][0]
self._belief = max_card / (max_card + min_card)
self._belief = max_card / np.sum(card)
else:
self._belief = 1
try:
@@ -77,28 +139,28 @@ class Snode:
self._class = None
def __str__(self) -> str:
count_values = np.unique(self._y, return_counts=True)
if self.is_leaf():
count_values = np.unique(self._y, return_counts=True)
result = (
return (
f"{self._title} - Leaf class={self._class} belief="
f"{self._belief: .6f} counts={count_values}"
f"{self._belief: .6f} impurity={self._impurity:.4f} "
f"counts={count_values}"
)
return result
else:
return f"{self._title}"
return (
f"{self._title} feaures={self._features} impurity="
f"{self._impurity:.4f} "
f"counts={count_values}"
)
class Siterator:
"""Stree preorder iterator
"""
"""Stree preorder iterator"""
def __init__(self, tree: Snode):
self._stack = []
self._push(tree)
def __iter__(self):
return self
def _push(self, node: Snode):
if node is not None:
self._stack.append(node)
@@ -112,6 +174,347 @@ class Siterator:
return node
class Splitter:
def __init__(
self,
clf: SVC = None,
criterion: str = None,
splitter_type: str = None,
criteria: str = None,
min_samples_split: int = None,
random_state=None,
normalize=False,
):
self._clf = clf
self._random_state = random_state
if random_state is not None:
random.seed(random_state)
self._criterion = criterion
self._min_samples_split = min_samples_split
self._criteria = criteria
self._splitter_type = splitter_type
self._normalize = normalize
if clf is None:
raise ValueError(f"clf has to be a sklearn estimator, got({clf})")
if criterion not in ["gini", "entropy"]:
raise ValueError(
f"criterion must be gini or entropy got({criterion})"
)
if criteria not in [
"max_samples",
"impurity",
]:
raise ValueError(
f"criteria has to be max_samples or impurity; got ({criteria})"
)
if splitter_type not in ["random", "best"]:
raise ValueError(
f"splitter must be either random or best, got({splitter_type})"
)
self.criterion_function = getattr(self, f"_{self._criterion}")
self.decision_criteria = getattr(self, f"_{self._criteria}")
def partition_impurity(self, y: np.array) -> np.array:
return self.criterion_function(y)
@staticmethod
def _gini(y: np.array) -> float:
_, count = np.unique(y, return_counts=True)
return 1 - np.sum(np.square(count / np.sum(count)))
@staticmethod
def _entropy(y: np.array) -> float:
"""Compute entropy of a labels set
Parameters
----------
y : np.array
set of labels
Returns
-------
float
entropy
"""
n_labels = len(y)
if n_labels <= 1:
return 0
counts = np.bincount(y)
proportions = counts / n_labels
n_classes = np.count_nonzero(proportions)
if n_classes <= 1:
return 0
entropy = 0.0
# Compute standard entropy.
for prop in proportions:
if prop != 0.0:
entropy -= prop * log(prop, n_classes)
return entropy
def information_gain(
self, labels: np.array, labels_up: np.array, labels_dn: np.array
) -> float:
"""Compute information gain of a split candidate
Parameters
----------
labels : np.array
labels of the dataset
labels_up : np.array
labels of one side
labels_dn : np.array
labels on the other side
Returns
-------
float
information gain
"""
imp_prev = self.criterion_function(labels)
card_up = card_dn = imp_up = imp_dn = 0
if labels_up is not None:
card_up = labels_up.shape[0]
imp_up = self.criterion_function(labels_up)
if labels_dn is not None:
card_dn = labels_dn.shape[0] if labels_dn is not None else 0
imp_dn = self.criterion_function(labels_dn)
samples = card_up + card_dn
if samples == 0:
return 0.0
else:
result = (
imp_prev
- (card_up / samples) * imp_up
- (card_dn / samples) * imp_dn
)
return result
def _select_best_set(
self, dataset: np.array, labels: np.array, features_sets: list
) -> list:
max_gain = 0
selected = None
warnings.filterwarnings("ignore", category=ConvergenceWarning)
for feature_set in features_sets:
self._clf.fit(dataset[:, feature_set], labels)
node = Snode(
self._clf, dataset, labels, feature_set, 0.0, "subset"
)
self.partition(dataset, node, train=True)
y1, y2 = self.part(labels)
gain = self.information_gain(labels, y1, y2)
if gain > max_gain:
max_gain = gain
selected = feature_set
return selected if selected is not None else feature_set
@staticmethod
def _generate_spaces(features: int, max_features: int) -> list:
"""Generate at most 5 feature random combinations
Parameters
----------
features : int
number of features in each combination
max_features : int
number of features in dataset
Returns
-------
list
list with up to 5 combination of features randomly selected
"""
comb = set()
# Generate at most 5 combinations
if max_features == features:
set_length = 1
else:
number = factorial(features) / (
factorial(max_features) * factorial(features - max_features)
)
set_length = min(5, number)
while len(comb) < set_length:
comb.add(
tuple(sorted(random.sample(range(features), max_features)))
)
return list(comb)
def _get_subspaces_set(
self, dataset: np.array, labels: np.array, max_features: int
) -> np.array:
"""Compute the indices of the features selected by splitter depending
on the self._splitter_type hyper parameter
Parameters
----------
dataset : np.array
array of samples
labels : np.array
labels of the dataset
max_features : int
number of features of the subspace
(<= number of features in dataset)
Returns
-------
np.array
indices of the features selected
"""
features_sets = self._generate_spaces(dataset.shape[1], max_features)
if len(features_sets) > 1:
if self._splitter_type == "random":
index = random.randint(0, len(features_sets) - 1)
return features_sets[index]
else:
return self._select_best_set(dataset, labels, features_sets)
else:
return features_sets[0]
def get_subspace(
self, dataset: np.array, labels: np.array, max_features: int
) -> tuple:
"""Return a subspace of the selected dataset of max_features length.
Depending on hyperparmeter
Parameters
----------
dataset : np.array
array of samples (# samples, # features)
labels : np.array
labels of the dataset
max_features : int
number of features to form the subspace
Returns
-------
tuple
tuple with the dataset with only the features selected and the
indices of the features selected
"""
indices = self._get_subspaces_set(dataset, labels, max_features)
return dataset[:, indices], indices
def _impurity(self, data: np.array, y: np.array) -> np.array:
"""return column of dataset to be taken into account to split dataset
Parameters
----------
data : np.array
distances to hyper plane of every class
y : np.array
vector of labels (classes)
Returns
-------
np.array
column of dataset to be taken into account to split dataset
"""
max_gain = 0
selected = -1
for col in range(data.shape[1]):
tup = y[data[:, col] > 0]
tdn = y[data[:, col] <= 0]
info_gain = self.information_gain(y, tup, tdn)
if info_gain > max_gain:
selected = col
max_gain = info_gain
return selected
@staticmethod
def _max_samples(data: np.array, y: np.array) -> np.array:
"""return column of dataset to be taken into account to split dataset
Parameters
----------
data : np.array
distances to hyper plane of every class
y : np.array
column of dataset to be taken into account to split dataset
Returns
-------
np.array
column of dataset to be taken into account to split dataset
"""
# select the class with max number of samples
_, samples = np.unique(y, return_counts=True)
return np.argmax(samples)
def partition(self, samples: np.array, node: Snode, train: bool):
"""Set the criteria to split arrays. Compute the indices of the samples
that should go to one side of the tree (up)
"""
# data contains the distances of every sample to every class hyperplane
# array of (m, nc) nc = # classes
data = self._distances(node, samples)
if data.shape[0] < self._min_samples_split:
# there aren't enough samples to split
self._up = np.ones((data.shape[0]), dtype=bool)
return
if data.ndim > 1:
# split criteria for multiclass
# Convert data to a (m, 1) array selecting values for samples
if train:
# in train time we have to compute the column to take into
# account to split the dataset
col = self.decision_criteria(data, node._y)
node.set_partition_column(col)
else:
# in predcit time just use the column computed in train time
# is taking the classifier of class <col>
col = node.get_partition_column()
if col == -1:
# No partition is producing information gain
data = np.ones(data.shape)
data = data[:, col]
self._up = data > 0
def part(self, origin: np.array) -> list:
"""Split an array in two based on indices (self._up) and its complement
partition has to be called first to establish up indices
Parameters
----------
origin : np.array
dataset to split
Returns
-------
list
list with two splits of the array
"""
down = ~self._up
return [
origin[self._up] if any(self._up) else None,
origin[down] if any(down) else None,
]
def _distances(self, node: Snode, data: np.ndarray) -> np.array:
"""Compute distances of the samples to the hyperplane of the node
Parameters
----------
node : Snode
node containing the svm classifier
data : np.ndarray
samples to compute distance to hyperplane
Returns
-------
np.array
array of shape (m, nc) with the distances of every sample to
the hyperplane of every class. nc = # of classes
"""
X_transformed = data[:, node._features]
if self._normalize:
X_transformed = node._scaler.transform(X_transformed)
return node._clf.decision_function(X_transformed)
class Stree(BaseEstimator, ClassifierMixin):
"""Estimator that is based on binary trees of svm nodes
can deal with sample_weights in predict, used in boosting sklearn methods
@@ -124,14 +527,18 @@ class Stree(BaseEstimator, ClassifierMixin):
self,
C: float = 1.0,
kernel: str = "linear",
max_iter: int = 1000,
max_iter: int = 1e5,
random_state: int = None,
max_depth: int = None,
tol: float = 1e-4,
degree: int = 3,
gamma="scale",
split_criteria="max_samples",
split_criteria: str = "impurity",
criterion: str = "entropy",
min_samples_split: int = 0,
max_features=None,
splitter: str = "random",
normalize: bool = False,
):
self.max_iter = max_iter
self.C = C
@@ -143,90 +550,38 @@ class Stree(BaseEstimator, ClassifierMixin):
self.degree = degree
self.min_samples_split = min_samples_split
self.split_criteria = split_criteria
self.max_features = max_features
self.criterion = criterion
self.splitter = splitter
self.normalize = normalize
def _more_tags(self) -> dict:
"""Required by sklearn to supply features of the classifier
make mandatory the labels array
:return: the tag required
:rtype: dict
"""
return {"requires_y": True}
def _split_array(self, origin: np.array, down: np.array) -> list:
"""Split an array in two based on indices (down) and its complement
:param origin: dataset to split
:type origin: np.array
:param down: indices to use to split array
:type down: np.array
:return: list with two splits of the array
:rtype: list
"""
up = ~down
return (
origin[up] if any(up) else None,
origin[down] if any(down) else None,
)
def _distances(self, node: Snode, data: np.ndarray) -> np.array:
"""Compute distances of the samples to the hyperplane of the node
:param node: node containing the svm classifier
:type node: Snode
:param data: samples to find out distance to hyperplane
:type data: np.ndarray
:return: array of shape (m, 1) with the distances of every sample to
the hyperplane of the node
:rtype: np.array
"""
return node._clf.decision_function(data)
def _min_distance(self, data: np.array, _) -> np.array:
# chooses the lowest distance of every sample
indices = np.argmin(np.abs(data), axis=1)
return np.take(data, indices)
def _max_samples(self, data: np.array, y: np.array) -> np.array:
# select the class with max number of samples
_, samples = np.unique(y, return_counts=True)
selected = np.argmax(samples)
return data[:, selected]
def _split_criteria(self, data: np.array, node: Snode) -> np.array:
"""Set the criteria to split arrays
:param data: distances of samples to hyperplanes shape (m, nclasses)
if nclasses > 2 else (m,)
:type data: np.array
:param node: node containing the svm classifier
:type node: Snode
:return: array of booleans of samples under or above zero
:rtype: np.array
"""
if data.shape[0] < self.min_samples_split:
return np.ones((data.shape[0]), dtype=bool)
if data.ndim > 1:
# split criteria for multiclass
data = getattr(self, f"_{self.split_criteria}")(data, node._y)
res = data > 0
return res
def fit(
self, X: np.ndarray, y: np.ndarray, sample_weight: np.array = None
) -> "Stree":
"""Build the tree based on the dataset of samples and its labels
:param X: dataset of samples to make predictions
:type X: np.array
:param y: samples labels
:type y: np.array
:param sample_weight: weights of the samples. Rescale C per sample.
Hi' weights force the classifier to put more emphasis on these points
:type sample_weight: np.array optional
:raises ValueError: if parameters C or max_depth are out of bounds
:return: itself to be able to chain actions: fit().predict() ...
:rtype: Stree
Returns
-------
Stree
itself to be able to chain actions: fit().predict() ...
Raises
------
ValueError
if C < 0
ValueError
if max_depth < 1
ValueError
if all samples have 0 or negative weights
"""
# Check parameters are Ok.
if self.C < 0:
@@ -243,24 +598,40 @@ class Stree(BaseEstimator, ClassifierMixin):
f"Maximum depth has to be greater than 1... got (max_depth=\
{self.max_depth})"
)
if self.split_criteria not in ["min_distance", "max_samples"]:
raise ValueError(
f"split_criteria has to be min_distance or \
max_samples got ({self.split_criteria})"
)
check_classification_targets(y)
X, y = check_X_y(X, y)
sample_weight = _check_sample_weight(sample_weight, X)
sample_weight = _check_sample_weight(
sample_weight, X, dtype=np.float64
)
if not any(sample_weight):
raise ValueError(
"Invalid input - all samples have zero or negative weights."
)
check_classification_targets(y)
# Initialize computed parameters
self.splitter_ = Splitter(
clf=self._build_clf(),
criterion=self.criterion,
splitter_type=self.splitter,
criteria=self.split_criteria,
random_state=self.random_state,
min_samples_split=self.min_samples_split,
normalize=self.normalize,
)
if self.random_state is not None:
random.seed(self.random_state)
self.classes_, y = np.unique(y, return_inverse=True)
self.n_classes_ = self.classes_.shape[0]
self.n_iter_ = self.max_iter
self.depth_ = 0
self.n_features_ = X.shape[1]
self.n_features_in_ = X.shape[1]
self.max_features_ = self._initialize_max_features()
self.tree_ = self.train(X, y, sample_weight, 1, "root")
self._build_predictor()
self.X_ = X
self.y_ = y
return self
def train(
@@ -270,48 +641,73 @@ class Stree(BaseEstimator, ClassifierMixin):
sample_weight: np.ndarray,
depth: int,
title: str,
) -> Snode:
) -> Optional[Snode]:
"""Recursive function to split the original dataset into predictor
nodes (leaves)
:param X: samples dataset
:type X: np.ndarray
:param y: samples labels
:type y: np.ndarray
:param sample_weight: weight of samples. Rescale C per sample.
Hi weights force the classifier to put more emphasis on these points.
:type sample_weight: np.ndarray
:param depth: actual depth in the tree
:type depth: int
:param title: description of the node
:type title: str
:return: binary tree
:rtype: Snode
Parameters
----------
X : np.ndarray
samples dataset
y : np.ndarray
samples labels
sample_weight : np.ndarray
weight of samples. Rescale C per sample.
depth : int
actual depth in the tree
title : str
description of the node
Returns
-------
Optional[Snode]
binary tree
"""
if depth > self.__max_depth:
return None
# Mask samples with 0 weight
if any(sample_weight == 0):
indices_zero = sample_weight == 0
X = X[~indices_zero, :]
y = y[~indices_zero]
sample_weight = sample_weight[~indices_zero]
self.depth_ = max(depth, self.depth_)
scaler = StandardScaler()
node = Snode(None, X, y, X.shape[1], 0.0, title, sample_weight, scaler)
if np.unique(y).shape[0] == 1:
# only 1 class => pure dataset
return Snode(None, X, y, title + ", <pure>")
node.set_title(title + ", <pure>")
return node
# Train the model
clf = self._build_clf()
clf.fit(X, y, sample_weight=sample_weight)
node = Snode(clf, X, y, title)
self.depth_ = max(depth, self.depth_)
down = self._split_criteria(self._distances(node, X), node)
X_U, X_D = self._split_array(X, down)
y_u, y_d = self._split_array(y, down)
sw_u, sw_d = self._split_array(sample_weight, down)
Xs, features = self.splitter_.get_subspace(X, y, self.max_features_)
if self.normalize:
scaler.fit(Xs)
Xs = scaler.transform(Xs)
clf.fit(Xs, y, sample_weight=sample_weight)
node.set_impurity(self.splitter_.partition_impurity(y))
node.set_classifier(clf)
node.set_features(features)
self.splitter_.partition(X, node, True)
X_U, X_D = self.splitter_.part(X)
y_u, y_d = self.splitter_.part(y)
sw_u, sw_d = self.splitter_.part(sample_weight)
if X_U is None or X_D is None:
# didn't part anything
return Snode(clf, X, y, title + ", <cgaf>")
node.set_up(self.train(X_U, y_u, sw_u, depth + 1, title + " - Up"))
node.set_down(self.train(X_D, y_d, sw_d, depth + 1, title + " - Down"))
node.set_title(title + ", <cgaf>")
return node
node.set_up(
self.train(X_U, y_u, sw_u, depth + 1, title + f" - Up({depth+1})")
)
node.set_down(
self.train(
X_D, y_d, sw_d, depth + 1, title + f" - Down({depth+1})"
)
)
return node
def _build_predictor(self):
"""Process the leaves to make them predictors
"""
"""Process the leaves to make them predictors"""
def run_tree(node: Snode):
if node.is_leaf():
@@ -323,8 +719,7 @@ class Stree(BaseEstimator, ClassifierMixin):
run_tree(self.tree_)
def _build_clf(self):
""" Build the correct classifier for the node
"""
"""Build the correct classifier for the node"""
return (
LinearSVC(
max_iter=self.max_iter,
@@ -343,15 +738,21 @@ class Stree(BaseEstimator, ClassifierMixin):
)
)
def _reorder_results(self, y: np.array, indices: np.array) -> np.array:
@staticmethod
def _reorder_results(y: np.array, indices: np.array) -> np.array:
"""Reorder an array based on the array of indices passed
:param y: data untidy
:type y: np.array
:param indices: indices used to set order
:type indices: np.array
:return: array y ordered
:rtype: np.array
Parameters
----------
y : np.array
data untidy
indices : np.array
indices used to set order
Returns
-------
np.array
array y ordered
"""
# return array of same type given in y
y_ordered = y.copy()
@@ -363,10 +764,22 @@ class Stree(BaseEstimator, ClassifierMixin):
def predict(self, X: np.array) -> np.array:
"""Predict labels for each sample in dataset passed
:param X: dataset of samples
:type X: np.array
:return: array of labels
:rtype: np.array
Parameters
----------
X : np.array
dataset of samples
Returns
-------
np.array
array of labels
Raises
------
ValueError
if dataset with inconsistent number of features
NotFittedError
if model is not fitted
"""
def predict_class(
@@ -378,9 +791,9 @@ class Stree(BaseEstimator, ClassifierMixin):
# set a class for every sample in dataset
prediction = np.full((xp.shape[0], 1), node._class)
return prediction, indices
down = self._split_criteria(self._distances(node, xp), node)
x_u, x_d = self._split_array(xp, down)
i_u, i_d = self._split_array(indices, down)
self.splitter_.partition(xp, node, train=False)
x_u, x_d = self.splitter_.part(xp)
i_u, i_d = self.splitter_.part(indices)
prx_u, prin_u = predict_class(x_u, i_u, node.get_up())
prx_d, prin_d = predict_class(x_d, i_d, node.get_down())
return np.append(prx_u, prx_d), np.append(prin_u, prin_d)
@@ -389,6 +802,11 @@ class Stree(BaseEstimator, ClassifierMixin):
check_is_fitted(self, ["tree_"])
# Input validation
X = check_array(X)
if X.shape[1] != self.n_features_:
raise ValueError(
f"Expected {self.n_features_} features but got "
f"({X.shape[1]})"
)
# setup prediction & make it happen
indices = np.arange(X.shape[0])
result = (
@@ -403,15 +821,19 @@ class Stree(BaseEstimator, ClassifierMixin):
) -> float:
"""Compute accuracy of the prediction
:param X: dataset of samples to make predictions
:type X: np.array
:param y_true: samples labels
:type y_true: np.array
:param sample_weight: weights of the samples. Rescale C per sample.
Hi' weights force the classifier to put more emphasis on these points
:type sample_weight: np.array optional
:return: accuracy of the prediction
:rtype: float
Parameters
----------
X : np.array
dataset of samples to make predictions
y : np.array
samples labels
sample_weight : np.array, optional
weights of the samples. Rescale C per sample, by default None
Returns
-------
float
accuracy of the prediction
"""
# sklearn check
check_is_fitted(self)
@@ -419,17 +841,35 @@ class Stree(BaseEstimator, ClassifierMixin):
X, y = check_X_y(X, y)
y_pred = self.predict(X).reshape(y.shape)
# Compute accuracy for each possible representation
y_type, y_true, y_pred = _check_targets(y, y_pred)
_, y_true, y_pred = _check_targets(y, y_pred)
check_consistent_length(y_true, y_pred, sample_weight)
score = y_true == y_pred
return _weighted_sum(score, sample_weight, normalize=True)
def nodes_leaves(self) -> tuple:
"""Compute the number of nodes and leaves in the built tree
Returns
-------
[tuple]
tuple with the number of nodes and the number of leaves
"""
nodes = 0
leaves = 0
for node in self:
nodes += 1
if node.is_leaf():
leaves += 1
return nodes, leaves
def __iter__(self) -> Siterator:
"""Create an iterator to be able to visit the nodes of the tree in
preorder, can make a list with all the nodes in preorder
:return: an iterator, can for i in... and list(...)
:rtype: Siterator
Returns
-------
Siterator
an iterator, can for i in... and list(...)
"""
try:
tree = self.tree_
@@ -440,10 +880,43 @@ class Stree(BaseEstimator, ClassifierMixin):
def __str__(self) -> str:
"""String representation of the tree
:return: description of nodes in the tree in preorder
:rtype: str
Returns
-------
str
description of nodes in the tree in preorder
"""
output = ""
for i in self:
output += str(i) + "\n"
return output
def _initialize_max_features(self) -> int:
if isinstance(self.max_features, str):
if self.max_features == "auto":
max_features = max(1, int(np.sqrt(self.n_features_)))
elif self.max_features == "sqrt":
max_features = max(1, int(np.sqrt(self.n_features_)))
elif self.max_features == "log2":
max_features = max(1, int(np.log2(self.n_features_)))
else:
raise ValueError(
"Invalid value for max_features. "
"Allowed string values are 'auto', "
"'sqrt' or 'log2'."
)
elif self.max_features is None:
max_features = self.n_features_
elif isinstance(self.max_features, numbers.Integral):
max_features = self.max_features
else: # float
if self.max_features > 0.0:
max_features = max(
1, int(self.max_features * self.n_features_)
)
else:
raise ValueError(
"Invalid value for max_features."
"Allowed float must be in range (0, 1] "
f"got ({self.max_features})"
)
return max_features

View File

@@ -1,205 +0,0 @@
"""
__author__ = "Ricardo Montañana Gómez"
__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
__license__ = "MIT"
__version__ = "0.9"
Plot 3D views of nodes in Stree
"""
import os
import matplotlib.pyplot as plt
import numpy as np
from sklearn.decomposition import PCA
from mpl_toolkits.mplot3d import Axes3D
from .Strees import Stree, Snode, Siterator
class Snode_graph(Snode):
def __init__(self, node: Stree):
self._plot_size = (8, 8)
self._xlimits = (None, None)
self._ylimits = (None, None)
self._zlimits = (None, None)
n = Snode.copy(node)
super().__init__(n._clf, n._X, n._y, n._title)
def set_plot_size(self, size: tuple):
self._plot_size = size
def get_plot_size(self) -> tuple:
return self._plot_size
def _is_pure(self) -> bool:
"""is considered pure a leaf node with one label
"""
if self.is_leaf():
return self._belief == 1.0
return False
def set_axis_limits(self, limits: tuple):
self._xlimits, self._ylimits, self._zlimits = limits
def get_axis_limits(self) -> tuple:
return self._xlimits, self._ylimits, self._zlimits
def _set_graphics_axis(self, ax: Axes3D):
ax.set_xlim(self._xlimits)
ax.set_ylim(self._ylimits)
ax.set_zlim(self._zlimits)
def save_hyperplane(
self, save_folder: str = "./", save_prefix: str = "", save_seq: int = 1
):
_, fig = self.plot_hyperplane()
name = os.path.join(save_folder, f"{save_prefix}STnode{save_seq}.png")
fig.savefig(name, bbox_inches="tight")
plt.close(fig)
def _get_cmap(self):
cmap = "jet"
if self._is_pure() and self._class == 1:
cmap = "jet_r"
return cmap
def _graph_title(self):
n_class, card = np.unique(self._y, return_counts=True)
return f"{self._title} {n_class} {card}"
def plot_hyperplane(self, plot_distribution: bool = True):
fig = plt.figure(figsize=self._plot_size)
ax = fig.add_subplot(1, 1, 1, projection="3d")
if not self._is_pure():
# Can't plot hyperplane of leaves with one label because it hasn't
# classiffier
# get the splitting hyperplane
def hyperplane(x, y):
return (
-self._clf.intercept_
- self._clf.coef_[0][0] * x
- self._clf.coef_[0][1] * y
) / self._clf.coef_[0][2]
tmpx = np.linspace(self._X[:, 0].min(), self._X[:, 0].max())
tmpy = np.linspace(self._X[:, 1].min(), self._X[:, 1].max())
xx, yy = np.meshgrid(tmpx, tmpy)
ax.plot_surface(
xx,
yy,
hyperplane(xx, yy),
alpha=0.5,
antialiased=True,
rstride=1,
cstride=1,
cmap="seismic",
)
self._set_graphics_axis(ax)
if plot_distribution:
self.plot_distribution(ax)
else:
plt.title(self._graph_title())
plt.show()
return ax, fig
def plot_distribution(self, ax: Axes3D = None):
if ax is None:
fig = plt.figure(figsize=self._plot_size)
ax = fig.add_subplot(1, 1, 1, projection="3d")
plt.title(self._graph_title())
cmap = self._get_cmap()
ax.scatter(
self._X[:, 0], self._X[:, 1], self._X[:, 2], c=self._y, cmap=cmap
)
ax.set_xlabel("X0")
ax.set_ylabel("X1")
ax.set_zlabel("X2")
plt.show()
class Stree_grapher(Stree):
"""Build 3d graphs of any dataset, if it's more than 3 features PCA shall
make its magic
"""
def __init__(self, params: dict):
self._plot_size = (8, 8)
self._tree_gr = None
# make Snode store X's
os.environ["TESTING"] = "1"
self._fitted = False
self._pca = None
super().__init__(**params)
def __del__(self):
try:
os.environ.pop("TESTING")
except KeyError:
pass
def _copy_tree(self, node: Snode) -> Snode_graph:
mirror = Snode_graph(node)
# clone node
mirror._class = node._class
mirror._belief = node._belief
if node.get_down() is not None:
mirror.set_down(self._copy_tree(node.get_down()))
if node.get_up() is not None:
mirror.set_up(self._copy_tree(node.get_up()))
return mirror
def fit(
self, X: np.array, y: np.array, sample_weight: np.array = None
) -> "Stree_grapher":
"""Fit the Stree and copy the tree in a Snode_graph tree
:param X: Dataset
:type X: np.array
:param y: Labels
:type y: np.array
:return: Stree model
:rtype: Stree
"""
if X.shape[1] != 3:
self._pca = PCA(n_components=3)
X = self._pca.fit_transform(X)
super().fit(X, y, sample_weight=sample_weight)
self._tree_gr = self._copy_tree(self.tree_)
self._fitted = True
return self
def score(self, X: np.array, y: np.array) -> float:
self._check_fitted()
if X.shape[1] != 3:
X = self._pca.transform(X)
return super().score(X, y)
def _check_fitted(self):
if not self._fitted:
raise Exception("Have to fit the grapher first!")
def save_all(self, save_folder: str = "./", save_prefix: str = ""):
"""Save all the node plots in png format, each with a sequence number
:param save_folder: folder where the plots are saved, defaults to './'
:type save_folder: str, optional
"""
self._check_fitted()
if not os.path.isdir(save_folder):
os.mkdir(save_folder)
seq = 1
for node in self:
node.save_hyperplane(
save_folder=save_folder, save_prefix=save_prefix, save_seq=seq
)
seq += 1
def plot_all(self):
"""Plots all the nodes
"""
self._check_fitted()
for node in self:
node.plot_hyperplane()
def __iter__(self):
return Siterator(self._tree_gr)

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@@ -1,4 +1,3 @@
from .Strees import Stree, Snode, Siterator
from .Strees_grapher import Stree_grapher, Snode_graph
from .Strees import Stree, Snode, Siterator, Splitter
__all__ = ["Stree", "Snode", "Siterator", "Stree_grapher", "Snode_graph"]
__all__ = ["Stree", "Snode", "Siterator", "Splitter"]

121
stree/tests/Snode_test.py Normal file
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import os
import unittest
import numpy as np
from stree import Stree, Snode
from .utils import load_dataset
class Snode_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
self._clf = Stree(random_state=self._random_state)
self._clf.fit(*load_dataset(self._random_state))
super().__init__(*args, **kwargs)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def test_attributes_in_leaves(self):
"""Check if the attributes in leaves have correct values so they form a
predictor
"""
def check_leave(node: Snode):
if not node.is_leaf():
check_leave(node.get_down())
check_leave(node.get_up())
return
# Check Belief in leave
classes, card = np.unique(node._y, return_counts=True)
max_card = max(card)
min_card = min(card)
if len(classes) > 1:
belief = max_card / (max_card + min_card)
else:
belief = 1
self.assertEqual(belief, node._belief)
# Check Class
class_computed = classes[card == max_card]
self.assertEqual(class_computed, node._class)
# Check Partition column
self.assertEqual(node._partition_column, -1)
check_leave(self._clf.tree_)
def test_nodes_coefs(self):
"""Check if the nodes of the tree have the right attributes filled"""
def run_tree(node: Snode):
if node._belief < 1:
# only exclude pure leaves
self.assertIsNotNone(node._clf)
self.assertIsNotNone(node._clf.coef_)
if node.is_leaf():
return
run_tree(node.get_up())
run_tree(node.get_down())
model = Stree(self._random_state)
model.fit(*load_dataset(self._random_state, 3, 4))
run_tree(model.tree_)
def test_make_predictor_on_leaf(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test")
test.make_predictor()
self.assertEqual(1, test._class)
self.assertEqual(0.75, test._belief)
self.assertEqual(-1, test._partition_column)
def test_set_title(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test")
self.assertEqual("test", test.get_title())
test.set_title("another")
self.assertEqual("another", test.get_title())
def test_set_classifier(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test")
clf = Stree()
self.assertIsNone(test.get_classifier())
test.set_classifier(clf)
self.assertEqual(clf, test.get_classifier())
def test_set_impurity(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test")
self.assertEqual(0.0, test.get_impurity())
test.set_impurity(54.7)
self.assertEqual(54.7, test.get_impurity())
def test_set_features(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [0, 1], 0.0, "test")
self.assertListEqual([0, 1], test.get_features())
test.set_features([1, 2])
self.assertListEqual([1, 2], test.get_features())
def test_make_predictor_on_not_leaf(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test")
test.set_up(Snode(None, [1], [1], [], 0.0, "another_test"))
test.make_predictor()
self.assertIsNone(test._class)
self.assertEqual(0, test._belief)
self.assertEqual(-1, test._partition_column)
self.assertEqual(-1, test.get_up()._partition_column)
def test_make_predictor_on_leaf_bogus_data(self):
test = Snode(None, [1, 2, 3, 4], [], [], 0.0, "test")
test.make_predictor()
self.assertIsNone(test._class)
self.assertEqual(-1, test._partition_column)
def test_copy_node(self):
px = [1, 2, 3, 4]
py = [1]
test = Snode(Stree(), px, py, [], 0.0, "test")
computed = Snode.copy(test)
self.assertListEqual(computed._X, px)
self.assertListEqual(computed._y, py)
self.assertEqual("test", computed._title)
self.assertIsInstance(computed._clf, Stree)
self.assertEqual(test._partition_column, computed._partition_column)
self.assertEqual(test._sample_weight, computed._sample_weight)
self.assertEqual(test._scaler, computed._scaler)

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import os
import unittest
import random
import numpy as np
from sklearn.svm import SVC
from sklearn.datasets import load_wine, load_iris
from stree import Splitter
class Splitter_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
super().__init__(*args, **kwargs)
@staticmethod
def build(
clf=SVC,
min_samples_split=0,
splitter_type="random",
criterion="gini",
criteria="max_samples",
random_state=None,
):
return Splitter(
clf=clf(random_state=random_state, kernel="rbf"),
min_samples_split=min_samples_split,
splitter_type=splitter_type,
criterion=criterion,
criteria=criteria,
random_state=random_state,
)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def test_init(self):
with self.assertRaises(ValueError):
self.build(criterion="duck")
with self.assertRaises(ValueError):
self.build(splitter_type="duck")
with self.assertRaises(ValueError):
self.build(criteria="duck")
with self.assertRaises(ValueError):
_ = Splitter(clf=None)
for splitter_type in ["best", "random"]:
for criterion in ["gini", "entropy"]:
for criteria in ["max_samples", "impurity"]:
tcl = self.build(
splitter_type=splitter_type,
criterion=criterion,
criteria=criteria,
)
self.assertEqual(splitter_type, tcl._splitter_type)
self.assertEqual(criterion, tcl._criterion)
self.assertEqual(criteria, tcl._criteria)
def test_gini(self):
expected_values = [
([0, 1, 1, 1, 1, 1, 0, 0, 0, 1], 0.48),
([0, 1, 1, 2, 2, 3, 4, 5, 3, 2, 1, 1], 0.7777777777777778),
([0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 2, 2, 2], 0.520408163265306),
([0, 0, 1, 1, 1, 1, 0, 0], 0.5),
([0, 0, 1, 1, 2, 2, 3, 3], 0.75),
([0, 0, 1, 1, 1, 1, 1, 1], 0.375),
([0], 0),
([1, 1, 1, 1], 0),
]
for labels, expected in expected_values:
self.assertAlmostEqual(expected, Splitter._gini(labels))
tcl = self.build(criterion="gini")
self.assertAlmostEqual(expected, tcl.criterion_function(labels))
def test_entropy(self):
expected_values = [
([0, 1, 1, 1, 1, 1, 0, 0, 0, 1], 0.9709505944546686),
([0, 1, 1, 2, 2, 3, 4, 5, 3, 2, 1, 1], 0.9111886696810589),
([0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 2, 2, 2], 0.8120406807940999),
([0, 0, 1, 1, 1, 1, 0, 0], 1),
([0, 0, 1, 1, 2, 2, 3, 3], 1),
([0, 0, 1, 1, 1, 1, 1, 1], 0.8112781244591328),
([1], 0),
([0, 0, 0, 0], 0),
]
for labels, expected in expected_values:
self.assertAlmostEqual(expected, Splitter._entropy(labels))
tcl = self.build(criterion="entropy")
self.assertAlmostEqual(expected, tcl.criterion_function(labels))
def test_information_gain(self):
expected_values = [
(
[0, 1, 1, 1, 1, 1],
[0, 0, 0, 1],
0.16333333333333333,
0.25642589168200297,
),
(
[0, 1, 1, 2, 2, 3, 4, 5, 3, 2, 1, 1],
[5, 3, 2, 1, 1],
0.007381776239907684,
-0.03328610916207225,
),
([], [], 0.0, 0.0),
([1], [], 0.0, 0.0),
([], [1], 0.0, 0.0),
([0, 0, 0, 0], [0, 0], 0.0, 0.0),
([], [1, 1, 1, 2], 0.0, 0.0),
(None, [1, 2, 3], 0.0, 0.0),
([1, 2, 3], None, 0.0, 0.0),
]
for yu, yd, expected_gini, expected_entropy in expected_values:
yu = np.array(yu, dtype=np.int32) if yu is not None else None
yd = np.array(yd, dtype=np.int32) if yd is not None else None
if yu is not None and yd is not None:
complete = np.append(yu, yd)
elif yd is not None:
complete = yd
else:
complete = yu
tcl = self.build(criterion="gini")
computed = tcl.information_gain(complete, yu, yd)
self.assertAlmostEqual(expected_gini, computed)
tcl = self.build(criterion="entropy")
computed = tcl.information_gain(complete, yu, yd)
self.assertAlmostEqual(expected_entropy, computed)
def test_max_samples(self):
tcl = self.build(criteria="max_samples")
data = np.array(
[
[-0.1, 0.2, -0.3],
[0.7, 0.01, -0.1],
[0.7, -0.9, 0.5],
[0.1, 0.2, 0.3],
[-0.1, 0.2, 0.3],
[-0.1, 0.2, 0.3],
]
)
expected = data[:, 0]
y = [1, 2, 1, 0, 0, 0]
computed = tcl._max_samples(data, y)
self.assertEqual(0, computed)
computed_data = data[:, computed]
self.assertEqual((6,), computed_data.shape)
self.assertListEqual(expected.tolist(), computed_data.tolist())
def test_impurity(self):
tcl = self.build(criteria="impurity")
data = np.array(
[
[-0.1, 0.2, -0.3],
[0.7, 0.01, -0.1],
[0.7, -0.9, 0.5],
[0.1, 0.2, 0.3],
[-0.1, 0.2, 0.3],
[-0.1, 0.2, 0.3],
]
)
expected = data[:, 2]
y = np.array([1, 2, 1, 0, 0, 0])
computed = tcl._impurity(data, y)
self.assertEqual(2, computed)
computed_data = data[:, computed]
self.assertEqual((6,), computed_data.shape)
self.assertListEqual(expected.tolist(), computed_data.tolist())
def test_generate_subspaces(self):
features = 250
for max_features in range(2, features):
num = len(Splitter._generate_spaces(features, max_features))
self.assertEqual(5, num)
self.assertEqual(3, len(Splitter._generate_spaces(3, 2)))
self.assertEqual(4, len(Splitter._generate_spaces(4, 3)))
def test_best_splitter_few_sets(self):
X, y = load_iris(return_X_y=True)
X = np.delete(X, 3, 1)
tcl = self.build(splitter_type="best", random_state=self._random_state)
dataset, computed = tcl.get_subspace(X, y, max_features=2)
self.assertListEqual([0, 2], list(computed))
self.assertListEqual(X[:, computed].tolist(), dataset.tolist())
def test_splitter_parameter(self):
expected_values = [
[1, 4, 9, 12], # best entropy max_samples
[1, 3, 6, 10], # best entropy impurity
[6, 8, 10, 12], # best gini max_samples
[7, 8, 10, 11], # best gini impurity
[0, 3, 8, 12], # random entropy max_samples
[0, 3, 9, 11], # random entropy impurity
[0, 4, 7, 12], # random gini max_samples
[0, 2, 5, 6], # random gini impurity
]
X, y = load_wine(return_X_y=True)
rn = 0
for splitter_type in ["best", "random"]:
for criterion in ["entropy", "gini"]:
for criteria in [
"max_samples",
"impurity",
]:
tcl = self.build(
splitter_type=splitter_type,
criterion=criterion,
criteria=criteria,
)
expected = expected_values.pop(0)
random.seed(rn)
rn += 1
dataset, computed = tcl.get_subspace(X, y, max_features=4)
# print(
# "{}, # {:7s}{:8s}{:15s}".format(
# list(computed),
# splitter_type,
# criterion,
# criteria,
# )
# )
self.assertListEqual(expected, list(computed))
self.assertListEqual(
X[:, computed].tolist(), dataset.tolist()
)

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import os
import unittest
import warnings
import numpy as np
from sklearn.datasets import load_iris, load_wine
from sklearn.exceptions import ConvergenceWarning
from sklearn.svm import LinearSVC
from stree import Stree, Snode
from .utils import load_dataset
class Stree_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
self._kernels = ["linear", "rbf", "poly"]
super().__init__(*args, **kwargs)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def _check_tree(self, node: Snode):
"""Check recursively that the nodes that are not leaves have the
correct number of labels and its sons have the right number of elements
in their dataset
Parameters
----------
node : Snode
node to check
"""
if node.is_leaf():
return
y_prediction = node._clf.predict(node._X)
y_down = node.get_down()._y
y_up = node.get_up()._y
# Is a correct partition in terms of cadinality?
# i.e. The partition algorithm didn't forget any sample
self.assertEqual(node._y.shape[0], y_down.shape[0] + y_up.shape[0])
unique_y, count_y = np.unique(node._y, return_counts=True)
_, count_d = np.unique(y_down, return_counts=True)
_, count_u = np.unique(y_up, return_counts=True)
#
for i in unique_y:
number_up = count_u[i]
try:
number_down = count_d[i]
except IndexError:
number_down = 0
self.assertEqual(count_y[i], number_down + number_up)
# Is the partition made the same as the prediction?
# as the node is not a leaf...
_, count_yp = np.unique(y_prediction, return_counts=True)
self.assertEqual(count_yp[1], y_up.shape[0])
self.assertEqual(count_yp[0], y_down.shape[0])
self._check_tree(node.get_down())
self._check_tree(node.get_up())
def test_build_tree(self):
"""Check if the tree is built the same way as predictions of models"""
warnings.filterwarnings("ignore")
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
clf.fit(*load_dataset(self._random_state))
self._check_tree(clf.tree_)
def test_single_prediction(self):
X, y = load_dataset(self._random_state)
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
yp = clf.fit(X, y).predict((X[0, :].reshape(-1, X.shape[1])))
self.assertEqual(yp[0], y[0])
def test_multiple_prediction(self):
# First 27 elements the predictions are the same as the truth
num = 27
X, y = load_dataset(self._random_state)
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
yp = clf.fit(X, y).predict(X[:num, :])
self.assertListEqual(y[:num].tolist(), yp.tolist())
def test_single_vs_multiple_prediction(self):
"""Check if predicting sample by sample gives the same result as
predicting all samples at once
"""
X, y = load_dataset(self._random_state)
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
clf.fit(X, y)
# Compute prediction line by line
yp_line = np.array([], dtype=int)
for xp in X:
yp_line = np.append(
yp_line, clf.predict(xp.reshape(-1, X.shape[1]))
)
# Compute prediction at once
yp_once = clf.predict(X)
self.assertListEqual(yp_line.tolist(), yp_once.tolist())
def test_iterator_and_str(self):
"""Check preorder iterator"""
expected = [
"root feaures=(0, 1, 2) impurity=1.0000 counts=(array([0, 1]), "
"array([750, 750]))",
"root - Down(2), <cgaf> - Leaf class=0 belief= 0.928297 impurity="
"0.3722 counts=(array([0, 1]), array([725, 56]))",
"root - Up(2) feaures=(0, 1, 2) impurity=0.2178 counts=(array([0, "
"1]), array([ 25, 694]))",
"root - Up(2) - Down(3) feaures=(0, 1, 2) impurity=0.8454 counts="
"(array([0, 1]), array([8, 3]))",
"root - Up(2) - Down(3) - Down(4), <pure> - Leaf class=0 belief= "
"1.000000 impurity=0.0000 counts=(array([0]), array([7]))",
"root - Up(2) - Down(3) - Up(4), <cgaf> - Leaf class=1 belief= "
"0.750000 impurity=0.8113 counts=(array([0, 1]), array([1, 3]))",
"root - Up(2) - Up(3), <cgaf> - Leaf class=1 belief= 0.975989 "
"impurity=0.1634 counts=(array([0, 1]), array([ 17, 691]))",
]
computed = []
expected_string = ""
clf = Stree(kernel="linear", random_state=self._random_state)
clf.fit(*load_dataset(self._random_state))
for node in clf:
computed.append(str(node))
expected_string += str(node) + "\n"
self.assertListEqual(expected, computed)
self.assertEqual(expected_string, str(clf))
@staticmethod
def test_is_a_sklearn_classifier():
warnings.filterwarnings("ignore", category=ConvergenceWarning)
warnings.filterwarnings("ignore", category=RuntimeWarning)
from sklearn.utils.estimator_checks import check_estimator
check_estimator(Stree())
def test_exception_if_C_is_negative(self):
tclf = Stree(C=-1)
with self.assertRaises(ValueError):
tclf.fit(*load_dataset(self._random_state))
def test_exception_if_bogus_split_criteria(self):
tclf = Stree(split_criteria="duck")
with self.assertRaises(ValueError):
tclf.fit(*load_dataset(self._random_state))
def test_check_max_depth_is_positive_or_None(self):
tcl = Stree()
self.assertIsNone(tcl.max_depth)
tcl = Stree(max_depth=1)
self.assertGreaterEqual(1, tcl.max_depth)
with self.assertRaises(ValueError):
tcl = Stree(max_depth=-1)
tcl.fit(*load_dataset(self._random_state))
def test_check_max_depth(self):
depths = (3, 4)
for depth in depths:
tcl = Stree(random_state=self._random_state, max_depth=depth)
tcl.fit(*load_dataset(self._random_state))
self.assertEqual(depth, tcl.depth_)
def test_unfitted_tree_is_iterable(self):
tcl = Stree()
self.assertEqual(0, len(list(tcl)))
def test_min_samples_split(self):
dataset = [[1], [2], [3]], [1, 1, 0]
tcl_split = Stree(min_samples_split=3).fit(*dataset)
self.assertIsNotNone(tcl_split.tree_.get_down())
self.assertIsNotNone(tcl_split.tree_.get_up())
tcl_nosplit = Stree(min_samples_split=4).fit(*dataset)
self.assertIsNone(tcl_nosplit.tree_.get_down())
self.assertIsNone(tcl_nosplit.tree_.get_up())
def test_simple_muticlass_dataset(self):
for kernel in self._kernels:
clf = Stree(
kernel=kernel,
split_criteria="max_samples",
random_state=self._random_state,
)
px = [[1, 2], [5, 6], [9, 10]]
py = [0, 1, 2]
clf.fit(px, py)
self.assertEqual(1.0, clf.score(px, py))
self.assertListEqual(py, clf.predict(px).tolist())
self.assertListEqual(py, clf.classes_.tolist())
def test_muticlass_dataset(self):
datasets = {
"Synt": load_dataset(random_state=self._random_state, n_classes=3),
"Iris": load_wine(return_X_y=True),
}
outcomes = {
"Synt": {
"max_samples linear": 0.9606666666666667,
"max_samples rbf": 0.7133333333333334,
"max_samples poly": 0.618,
"impurity linear": 0.9606666666666667,
"impurity rbf": 0.7133333333333334,
"impurity poly": 0.618,
},
"Iris": {
"max_samples linear": 1.0,
"max_samples rbf": 0.6910112359550562,
"max_samples poly": 0.6966292134831461,
"impurity linear": 1,
"impurity rbf": 0.6910112359550562,
"impurity poly": 0.6966292134831461,
},
}
for name, dataset in datasets.items():
px, py = dataset
for criteria in ["max_samples", "impurity"]:
for kernel in self._kernels:
clf = Stree(
C=55,
max_iter=1e5,
kernel=kernel,
random_state=self._random_state,
)
clf.fit(px, py)
outcome = outcomes[name][f"{criteria} {kernel}"]
# print(
# f"{name} {criteria} {kernel} {outcome} {clf.score(px"
# ", py)}"
# )
self.assertAlmostEqual(outcome, clf.score(px, py))
def test_max_features(self):
n_features = 16
expected_values = [
("auto", 4),
("log2", 4),
("sqrt", 4),
(0.5, 8),
(3, 3),
(None, 16),
]
clf = Stree()
clf.n_features_ = n_features
for max_features, expected in expected_values:
clf.set_params(**dict(max_features=max_features))
computed = clf._initialize_max_features()
self.assertEqual(expected, computed)
# Check bogus max_features
values = ["duck", -0.1, 0.0]
for max_features in values:
clf.set_params(**dict(max_features=max_features))
with self.assertRaises(ValueError):
_ = clf._initialize_max_features()
def test_get_subspaces(self):
dataset = np.random.random((10, 16))
y = np.random.randint(0, 2, 10)
expected_values = [
("auto", 4),
("log2", 4),
("sqrt", 4),
(0.5, 8),
(3, 3),
(None, 16),
]
clf = Stree()
for max_features, expected in expected_values:
clf.set_params(**dict(max_features=max_features))
clf.fit(dataset, y)
computed, indices = clf.splitter_.get_subspace(
dataset, y, clf.max_features_
)
self.assertListEqual(
dataset[:, indices].tolist(), computed.tolist()
)
self.assertEqual(expected, len(indices))
def test_bogus_criterion(self):
clf = Stree(criterion="duck")
with self.assertRaises(ValueError):
clf.fit(*load_dataset())
def test_predict_feature_dimensions(self):
X = np.random.rand(10, 5)
y = np.random.randint(0, 2, 10)
clf = Stree()
clf.fit(X, y)
with self.assertRaises(ValueError):
clf.predict(X[:, :3])
# Tests of score
def test_score_binary(self):
X, y = load_dataset(self._random_state)
accuracies = [
0.9506666666666667,
0.9606666666666667,
0.9433333333333334,
]
for kernel, accuracy_expected in zip(self._kernels, accuracies):
clf = Stree(
random_state=self._random_state,
kernel=kernel,
)
clf.fit(X, y)
accuracy_score = clf.score(X, y)
yp = clf.predict(X)
accuracy_computed = np.mean(yp == y)
self.assertEqual(accuracy_score, accuracy_computed)
self.assertAlmostEqual(accuracy_expected, accuracy_score)
def test_score_max_features(self):
X, y = load_dataset(self._random_state)
clf = Stree(random_state=self._random_state, max_features=2)
clf.fit(X, y)
self.assertAlmostEqual(0.9246666666666666, clf.score(X, y))
def test_bogus_splitter_parameter(self):
clf = Stree(splitter="duck")
with self.assertRaises(ValueError):
clf.fit(*load_dataset())
def test_multiclass_classifier_integrity(self):
"""Checks if the multiclass operation is done right"""
X, y = load_iris(return_X_y=True)
clf = Stree(random_state=0)
clf.fit(X, y)
score = clf.score(X, y)
# Check accuracy of the whole model
self.assertAlmostEquals(0.98, score, 5)
svm = LinearSVC(random_state=0)
svm.fit(X, y)
self.assertAlmostEquals(0.9666666666666667, svm.score(X, y), 5)
data = svm.decision_function(X)
expected = [
0.4444444444444444,
0.35777777777777775,
0.4569777777777778,
]
ty = data.copy()
ty[data <= 0] = 0
ty[data > 0] = 1
ty = ty.astype(int)
for i in range(3):
self.assertAlmostEquals(
expected[i],
clf.splitter_._gini(ty[:, i]),
)
# 1st Branch
# up has to have 50 samples of class 0
# down should have 100 [50, 50]
up = data[:, 2] > 0
resup = np.unique(y[up], return_counts=True)
resdn = np.unique(y[~up], return_counts=True)
self.assertListEqual([1, 2], resup[0].tolist())
self.assertListEqual([3, 50], resup[1].tolist())
self.assertListEqual([0, 1], resdn[0].tolist())
self.assertListEqual([50, 47], resdn[1].tolist())
# 2nd Branch
# up should have 53 samples of classes [1, 2] [3, 50]
# down shoud have 47 samples of class 1
node_up = clf.tree_.get_down().get_up()
node_dn = clf.tree_.get_down().get_down()
resup = np.unique(node_up._y, return_counts=True)
resdn = np.unique(node_dn._y, return_counts=True)
self.assertListEqual([1, 2], resup[0].tolist())
self.assertListEqual([3, 50], resup[1].tolist())
self.assertListEqual([1], resdn[0].tolist())
self.assertListEqual([47], resdn[1].tolist())
def test_score_multiclass_rbf(self):
X, y = load_dataset(
random_state=self._random_state,
n_classes=3,
n_features=5,
n_samples=500,
)
clf = Stree(kernel="rbf", random_state=self._random_state)
clf2 = Stree(
kernel="rbf", random_state=self._random_state, normalize=True
)
self.assertEqual(0.768, clf.fit(X, y).score(X, y))
self.assertEqual(0.814, clf2.fit(X, y).score(X, y))
X, y = load_wine(return_X_y=True)
self.assertEqual(0.6741573033707865, clf.fit(X, y).score(X, y))
self.assertEqual(1.0, clf2.fit(X, y).score(X, y))
def test_score_multiclass_poly(self):
X, y = load_dataset(
random_state=self._random_state,
n_classes=3,
n_features=5,
n_samples=500,
)
clf = Stree(
kernel="poly", random_state=self._random_state, C=10, degree=5
)
clf2 = Stree(
kernel="poly",
random_state=self._random_state,
normalize=True,
)
self.assertEqual(0.786, clf.fit(X, y).score(X, y))
self.assertEqual(0.818, clf2.fit(X, y).score(X, y))
X, y = load_wine(return_X_y=True)
self.assertEqual(0.702247191011236, clf.fit(X, y).score(X, y))
self.assertEqual(0.6067415730337079, clf2.fit(X, y).score(X, y))
def test_score_multiclass_linear(self):
X, y = load_dataset(
random_state=self._random_state,
n_classes=3,
n_features=5,
n_samples=1500,
)
clf = Stree(kernel="linear", random_state=self._random_state)
self.assertEqual(0.9533333333333334, clf.fit(X, y).score(X, y))
# Check with context based standardization
clf2 = Stree(
kernel="linear", random_state=self._random_state, normalize=True
)
self.assertEqual(0.9526666666666667, clf2.fit(X, y).score(X, y))
X, y = load_wine(return_X_y=True)
self.assertEqual(0.9831460674157303, clf.fit(X, y).score(X, y))
self.assertEqual(1.0, clf2.fit(X, y).score(X, y))
def test_zero_all_sample_weights(self):
X, y = load_dataset(self._random_state)
with self.assertRaises(ValueError):
Stree().fit(X, y, np.zeros(len(y)))
def test_mask_samples_weighted_zero(self):
X = np.array(
[
[1, 1],
[1, 1],
[1, 1],
[2, 2],
[2, 2],
[2, 2],
[3, 3],
[3, 3],
[3, 3],
]
)
y = np.array([1, 1, 1, 2, 2, 2, 5, 5, 5])
yw = np.array([1, 1, 1, 5, 5, 5, 5, 5, 5])
w = [1, 1, 1, 0, 0, 0, 1, 1, 1]
model1 = Stree().fit(X, y)
model2 = Stree().fit(X, y, w)
predict1 = model1.predict(X)
predict2 = model2.predict(X)
self.assertListEqual(y.tolist(), predict1.tolist())
self.assertListEqual(yw.tolist(), predict2.tolist())
self.assertEqual(model1.score(X, y), 1)
self.assertAlmostEqual(model2.score(X, y), 0.66666667)
self.assertEqual(model2.score(X, y, w), 1)
def test_depth(self):
X, y = load_dataset(
random_state=self._random_state,
n_classes=3,
n_features=5,
n_samples=1500,
)
clf = Stree(random_state=self._random_state)
clf.fit(X, y)
self.assertEqual(6, clf.depth_)
X, y = load_wine(return_X_y=True)
clf = Stree(random_state=self._random_state)
clf.fit(X, y)
self.assertEqual(4, clf.depth_)
def test_nodes_leaves(self):
X, y = load_dataset(
random_state=self._random_state,
n_classes=3,
n_features=5,
n_samples=1500,
)
clf = Stree(random_state=self._random_state)
clf.fit(X, y)
nodes, leaves = clf.nodes_leaves()
self.assertEqual(25, nodes)
self.assertEquals(13, leaves)
X, y = load_wine(return_X_y=True)
clf = Stree(random_state=self._random_state)
clf.fit(X, y)
nodes, leaves = clf.nodes_leaves()
self.assertEqual(9, nodes)
self.assertEquals(5, leaves)
def test_nodes_leaves_artificial(self):
n1 = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test1")
n2 = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test2")
n3 = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test3")
n4 = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test4")
n5 = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test5")
n6 = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], [], 0.0, "test6")
n1.set_up(n2)
n2.set_up(n3)
n2.set_down(n4)
n3.set_up(n5)
n4.set_down(n6)
clf = Stree(random_state=self._random_state)
clf.tree_ = n1
nodes, leaves = clf.nodes_leaves()
self.assertEqual(6, nodes)
self.assertEqual(2, leaves)

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@@ -1,226 +0,0 @@
import os
import imghdr
import unittest
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import warnings
from sklearn.datasets import make_classification
from stree import Stree_grapher, Snode_graph, Snode
def get_dataset(random_state=0, n_features=3):
X, y = make_classification(
n_samples=1500,
n_features=n_features,
n_informative=3,
n_redundant=0,
n_repeated=0,
n_classes=2,
n_clusters_per_class=2,
class_sep=1.5,
flip_y=0,
weights=[0.5, 0.5],
random_state=random_state,
)
return X, y
class Stree_grapher_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
self._clf = Stree_grapher(dict(random_state=self._random_state))
self._clf.fit(*get_dataset(self._random_state, n_features=4))
super().__init__(*args, **kwargs)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def test_iterator(self):
"""Check preorder iterator
"""
expected = [
"root",
"root - Down",
"root - Down - Down, <cgaf> - Leaf class=1 belief= 0.976023 counts"
"=(array([0, 1]), array([ 17, 692]))",
"root - Down - Up",
"root - Down - Up - Down, <cgaf> - Leaf class=0 belief= 0.500000 "
"counts=(array([0, 1]), array([1, 1]))",
"root - Down - Up - Up, <cgaf> - Leaf class=0 belief= 0.888889 "
"counts=(array([0, 1]), array([8, 1]))",
"root - Up, <cgaf> - Leaf class=0 belief= 0.928205 counts=(array("
"[0, 1]), array([724, 56]))",
]
computed = []
for node in self._clf:
computed.append(str(node))
self.assertListEqual(expected, computed)
def test_score(self):
X, y = get_dataset(self._random_state)
accuracy_score = self._clf.score(X, y)
yp = self._clf.predict(X)
accuracy_computed = np.mean(yp == y)
self.assertEqual(accuracy_score, accuracy_computed)
self.assertGreater(accuracy_score, 0.86)
def test_score_4dims(self):
X, y = get_dataset(self._random_state, n_features=4)
accuracy_score = self._clf.score(X, y)
self.assertEqual(accuracy_score, 0.95)
def test_save_all(self):
folder_name = os.path.join(os.sep, "tmp", "stree")
if os.path.isdir(folder_name):
os.rmdir(folder_name)
file_names = [
os.path.join(folder_name, f"STnode{i}.png") for i in range(1, 8)
]
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
self._clf.save_all(save_folder=folder_name)
for file_name in file_names:
self.assertTrue(os.path.exists(file_name))
self.assertEqual("png", imghdr.what(file_name))
os.remove(file_name)
os.rmdir(folder_name)
def test_plot_all(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf.plot_all()
num_figures_after = plt.gcf().number
self.assertEqual(7, num_figures_after - num_figures_before)
class Snode_graph_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
self._clf = Stree_grapher(dict(random_state=self._random_state))
self._clf.fit(*get_dataset(self._random_state))
super().__init__(*args, **kwargs)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def test_plot_size(self):
default = self._clf._tree_gr.get_plot_size()
expected = (17, 3)
self._clf._tree_gr.set_plot_size(expected)
self.assertEqual(expected, self._clf._tree_gr.get_plot_size())
self._clf._tree_gr.set_plot_size(default)
self.assertEqual(default, self._clf._tree_gr.get_plot_size())
def test_attributes_in_leaves_graph(self):
"""Check if the attributes in leaves have correct values so they form a
predictor
"""
def check_leave(node: Snode_graph):
if not node.is_leaf():
check_leave(node.get_down())
check_leave(node.get_up())
return
# Check Belief in leave
classes, card = np.unique(node._y, return_counts=True)
max_card = max(card)
min_card = min(card)
if len(classes) > 1:
try:
belief = max_card / (max_card + min_card)
except ZeroDivisionError:
belief = 0.0
else:
belief = 1
self.assertEqual(belief, node._belief)
# Check Class
class_computed = classes[card == max_card]
self.assertEqual(class_computed, node._class)
check_leave(self._clf._tree_gr)
def test_nodes_graph_coefs(self):
"""Check if the nodes of the tree have the right attributes filled
"""
def run_tree(node: Snode_graph):
if node._belief < 1:
# only exclude pure leaves
self.assertIsNotNone(node._clf)
self.assertIsNotNone(node._clf.coef_)
if node.is_leaf():
return
run_tree(node.get_down())
run_tree(node.get_up())
run_tree(self._clf._tree_gr)
def test_save_hyperplane(self):
folder_name = "/tmp/"
file_name = os.path.join(folder_name, "STnode1.png")
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
self._clf._tree_gr.save_hyperplane(folder_name)
self.assertTrue(os.path.exists(file_name))
self.assertEqual("png", imghdr.what(file_name))
os.remove(file_name)
def test_plot_hyperplane_with_distribution(self):
plt.close()
# select a pure node
node = self._clf._tree_gr.get_down().get_up().get_up()
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
node.plot_hyperplane(plot_distribution=True)
num_figures_after = plt.gcf().number
self.assertEqual(1, num_figures_after - num_figures_before)
def test_plot_hyperplane_without_distribution(self):
plt.close()
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf._tree_gr.plot_hyperplane(plot_distribution=False)
num_figures_after = plt.gcf().number
self.assertEqual(1, num_figures_after - num_figures_before)
def test_plot_distribution(self):
plt.close()
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf._tree_gr.plot_distribution()
num_figures_after = plt.gcf().number
self.assertEqual(1, num_figures_after - num_figures_before)
def test_set_axis_limits(self):
node = Snode_graph(Snode(None, None, None, "test"))
limits = (-2, 2), (-3, 3), (-4, 4)
node.set_axis_limits(limits)
computed = node.get_axis_limits()
x, y, z = limits
xx, yy, zz = computed
self.assertEqual(x, xx)
self.assertEqual(y, yy)
self.assertEqual(z, zz)
def test_cmap_change(self):
node = Snode_graph(Snode(None, None, None, "test"))
self.assertEqual("jet", node._get_cmap())
# make node pure
node._belief = 1.0
node._class = 1
self.assertEqual("jet_r", node._get_cmap())

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@@ -1,355 +0,0 @@
import os
import unittest
import numpy as np
from sklearn.datasets import make_classification, load_iris
from stree import Stree, Snode
def get_dataset(random_state=0, n_classes=2):
X, y = make_classification(
n_samples=1500,
n_features=3,
n_informative=3,
n_redundant=0,
n_repeated=0,
n_classes=n_classes,
n_clusters_per_class=2,
class_sep=1.5,
flip_y=0,
random_state=random_state,
)
return X, y
class Stree_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
self._kernels = ["linear", "rbf", "poly"]
super().__init__(*args, **kwargs)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def _check_tree(self, node: Snode):
"""Check recursively that the nodes that are not leaves have the
correct number of labels and its sons have the right number of elements
in their dataset
Arguments:
node {Snode} -- node to check
"""
if node.is_leaf():
return
y_prediction = node._clf.predict(node._X)
y_down = node.get_down()._y
y_up = node.get_up()._y
# Is a correct partition in terms of cadinality?
# i.e. The partition algorithm didn't forget any sample
self.assertEqual(node._y.shape[0], y_down.shape[0] + y_up.shape[0])
unique_y, count_y = np.unique(node._y, return_counts=True)
_, count_d = np.unique(y_down, return_counts=True)
_, count_u = np.unique(y_up, return_counts=True)
#
for i in unique_y:
try:
number_down = count_d[i]
except IndexError:
number_down = 0
try:
number_up = count_u[i]
except IndexError:
number_up = 0
self.assertEqual(count_y[i], number_down + number_up)
# Is the partition made the same as the prediction?
# as the node is not a leaf...
_, count_yp = np.unique(y_prediction, return_counts=True)
self.assertEqual(count_yp[0], y_up.shape[0])
self.assertEqual(count_yp[1], y_down.shape[0])
self._check_tree(node.get_down())
self._check_tree(node.get_up())
def test_build_tree(self):
"""Check if the tree is built the same way as predictions of models
"""
import warnings
warnings.filterwarnings("ignore")
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
clf.fit(*get_dataset(self._random_state))
self._check_tree(clf.tree_)
def _find_out(
self, px: np.array, x_original: np.array, y_original
) -> list:
"""Find the original values of y for a given array of samples
Arguments:
px {np.array} -- array of samples to search for
x_original {np.array} -- original dataset
y_original {[type]} -- original classes
Returns:
np.array -- classes of the given samples
"""
res = []
for needle in px:
for row in range(x_original.shape[0]):
if all(x_original[row, :] == needle):
res.append(y_original[row])
return res
def test_single_prediction(self):
X, y = get_dataset(self._random_state)
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
yp = clf.fit(X, y).predict((X[0, :].reshape(-1, X.shape[1])))
self.assertEqual(yp[0], y[0])
def test_multiple_prediction(self):
# First 27 elements the predictions are the same as the truth
num = 27
X, y = get_dataset(self._random_state)
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
yp = clf.fit(X, y).predict(X[:num, :])
self.assertListEqual(y[:num].tolist(), yp.tolist())
def test_score(self):
X, y = get_dataset(self._random_state)
accuracies = [
0.9506666666666667,
0.9606666666666667,
0.9433333333333334,
]
for kernel, accuracy_expected in zip(self._kernels, accuracies):
clf = Stree(random_state=self._random_state, kernel=kernel,)
clf.fit(X, y)
accuracy_score = clf.score(X, y)
yp = clf.predict(X)
accuracy_computed = np.mean(yp == y)
self.assertEqual(accuracy_score, accuracy_computed)
self.assertAlmostEqual(accuracy_expected, accuracy_score)
def test_single_vs_multiple_prediction(self):
"""Check if predicting sample by sample gives the same result as
predicting all samples at once
"""
X, y = get_dataset(self._random_state)
for kernel in self._kernels:
clf = Stree(kernel=kernel, random_state=self._random_state)
clf.fit(X, y)
# Compute prediction line by line
yp_line = np.array([], dtype=int)
for xp in X:
yp_line = np.append(
yp_line, clf.predict(xp.reshape(-1, X.shape[1]))
)
# Compute prediction at once
yp_once = clf.predict(X)
self.assertListEqual(yp_line.tolist(), yp_once.tolist())
def test_iterator_and_str(self):
"""Check preorder iterator
"""
expected = [
"root",
"root - Down",
"root - Down - Down, <cgaf> - Leaf class=1 belief= 0.975989 counts"
"=(array([0, 1]), array([ 17, 691]))",
"root - Down - Up",
"root - Down - Up - Down, <cgaf> - Leaf class=1 belief= 0.750000 "
"counts=(array([0, 1]), array([1, 3]))",
"root - Down - Up - Up, <pure> - Leaf class=0 belief= 1.000000 "
"counts=(array([0]), array([7]))",
"root - Up, <cgaf> - Leaf class=0 belief= 0.928297 counts=(array("
"[0, 1]), array([725, 56]))",
]
computed = []
expected_string = ""
clf = Stree(kernel="linear", random_state=self._random_state)
clf.fit(*get_dataset(self._random_state))
for node in clf:
computed.append(str(node))
expected_string += str(node) + "\n"
self.assertListEqual(expected, computed)
self.assertEqual(expected_string, str(clf))
def test_is_a_sklearn_classifier(self):
import warnings
from sklearn.exceptions import ConvergenceWarning
warnings.filterwarnings("ignore", category=ConvergenceWarning)
warnings.filterwarnings("ignore", category=RuntimeWarning)
from sklearn.utils.estimator_checks import check_estimator
check_estimator(Stree())
def test_exception_if_C_is_negative(self):
tclf = Stree(C=-1)
with self.assertRaises(ValueError):
tclf.fit(*get_dataset(self._random_state))
def test_exception_if_bogus_split_criteria(self):
tclf = Stree(split_criteria="duck")
with self.assertRaises(ValueError):
tclf.fit(*get_dataset(self._random_state))
def test_check_max_depth_is_positive_or_None(self):
tcl = Stree()
self.assertIsNone(tcl.max_depth)
tcl = Stree(max_depth=1)
self.assertGreaterEqual(1, tcl.max_depth)
with self.assertRaises(ValueError):
tcl = Stree(max_depth=-1)
tcl.fit(*get_dataset(self._random_state))
def test_check_max_depth(self):
depths = (3, 4)
for depth in depths:
tcl = Stree(random_state=self._random_state, max_depth=depth)
tcl.fit(*get_dataset(self._random_state))
self.assertEqual(depth, tcl.depth_)
def test_unfitted_tree_is_iterable(self):
tcl = Stree()
self.assertEqual(0, len(list(tcl)))
def test_min_samples_split(self):
tcl_split = Stree(min_samples_split=3)
tcl_nosplit = Stree(min_samples_split=4)
dataset = [[1], [2], [3]], [1, 1, 0]
tcl_split.fit(*dataset)
self.assertIsNotNone(tcl_split.tree_.get_down())
self.assertIsNotNone(tcl_split.tree_.get_up())
tcl_nosplit.fit(*dataset)
self.assertIsNone(tcl_nosplit.tree_.get_down())
self.assertIsNone(tcl_nosplit.tree_.get_up())
def test_simple_muticlass_dataset(self):
for kernel in self._kernels:
clf = Stree(
kernel=kernel,
split_criteria="max_samples",
random_state=self._random_state,
)
px = [[1, 2], [5, 6], [9, 10]]
py = [0, 1, 2]
clf.fit(px, py)
self.assertEqual(1.0, clf.score(px, py))
self.assertListEqual(py, clf.predict(px).tolist())
self.assertListEqual(py, clf.classes_.tolist())
def test_muticlass_dataset(self):
datasets = {
"Synt": get_dataset(random_state=self._random_state, n_classes=3),
"Iris": load_iris(return_X_y=True),
}
outcomes = {
"Synt": {
"max_samples linear": 0.9533333333333334,
"max_samples rbf": 0.836,
"max_samples poly": 0.9473333333333334,
"min_distance linear": 0.9533333333333334,
"min_distance rbf": 0.836,
"min_distance poly": 0.9473333333333334,
},
"Iris": {
"max_samples linear": 0.98,
"max_samples rbf": 1.0,
"max_samples poly": 1.0,
"min_distance linear": 0.98,
"min_distance rbf": 1.0,
"min_distance poly": 1.0,
},
}
for name, dataset in datasets.items():
px, py = dataset
for criteria in ["max_samples", "min_distance"]:
for kernel in self._kernels:
clf = Stree(
C=1e4,
max_iter=1e4,
kernel=kernel,
random_state=self._random_state,
)
clf.fit(px, py)
outcome = outcomes[name][f"{criteria} {kernel}"]
self.assertAlmostEqual(outcome, clf.score(px, py))
class Snode_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
self._random_state = 1
self._clf = Stree(random_state=self._random_state)
self._clf.fit(*get_dataset(self._random_state))
super().__init__(*args, **kwargs)
@classmethod
def setUp(cls):
os.environ["TESTING"] = "1"
def test_attributes_in_leaves(self):
"""Check if the attributes in leaves have correct values so they form a
predictor
"""
def check_leave(node: Snode):
if not node.is_leaf():
check_leave(node.get_down())
check_leave(node.get_up())
return
# Check Belief in leave
classes, card = np.unique(node._y, return_counts=True)
max_card = max(card)
min_card = min(card)
if len(classes) > 1:
try:
belief = max_card / (max_card + min_card)
except ZeroDivisionError:
belief = 0.0
else:
belief = 1
self.assertEqual(belief, node._belief)
# Check Class
class_computed = classes[card == max_card]
self.assertEqual(class_computed, node._class)
check_leave(self._clf.tree_)
def test_nodes_coefs(self):
"""Check if the nodes of the tree have the right attributes filled
"""
def run_tree(node: Snode):
if node._belief < 1:
# only exclude pure leaves
self.assertIsNotNone(node._clf)
self.assertIsNotNone(node._clf.coef_)
if node.is_leaf():
return
run_tree(node.get_down())
run_tree(node.get_up())
run_tree(self._clf.tree_)
def test_make_predictor_on_leaf(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], "test")
test.make_predictor()
self.assertEqual(1, test._class)
self.assertEqual(0.75, test._belief)
def test_make_predictor_on_not_leaf(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], "test")
test.set_up(Snode(None, [1], [1], "another_test"))
test.make_predictor()
self.assertIsNone(test._class)
self.assertEqual(0, test._belief)
def test_make_predictor_on_leaf_bogus_data(self):
test = Snode(None, [1, 2, 3, 4], [], "test")
test.make_predictor()
self.assertIsNone(test._class)

View File

@@ -1,9 +1,5 @@
from .Strees_test import Stree_test, Snode_test
from .Strees_grapher_test import Stree_grapher_test, Snode_graph_test
from .Stree_test import Stree_test
from .Snode_test import Snode_test
from .Splitter_test import Splitter_test
__all__ = [
"Stree_test",
"Snode_test",
"Stree_grapher_test",
"Snode_graph_test",
]
__all__ = ["Stree_test", "Snode_test", "Splitter_test"]

17
stree/tests/utils.py Normal file
View File

@@ -0,0 +1,17 @@
from sklearn.datasets import make_classification
def load_dataset(random_state=0, n_classes=2, n_features=3, n_samples=1500):
X, y = make_classification(
n_samples=n_samples,
n_features=n_features,
n_informative=3,
n_redundant=0,
n_repeated=0,
n_classes=n_classes,
n_clusters_per_class=2,
class_sep=1.5,
flip_y=0,
random_state=random_state,
)
return X, y