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40 Commits

Author SHA1 Message Date
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
1d392d534f #6 - Update tests and codecov conf 2020-06-11 13:45:24 +02:00
f360a2640c #6 - Add multiclass support
Removed (by now) predict_proba. Created a notebook in jupyter
Added split_criteria parameter with min_distance and max_samples values
Refactor _distances
Refactor _split_criteria
Refactor _reorder_results
2020-06-11 13:10:52 +02:00
Ricardo Montañana Gómez
45510b43bc Merge pull request #5 from Doctorado-ML/add_kernels
#3 Add kernels to STree
2020-06-09 13:43:31 +02:00
286a91a3d7 #3 refactor unneeded code and new test 2020-06-09 13:01:01 +02:00
5c31c2b2a5 #3 update features notebook 2020-06-09 02:12:56 +02:00
7e932de072 #3 Add sample_weights to score, update notebooks
Update readme to use new names of notebooks
2020-06-09 01:46:38 +02:00
26273e936a #3 Add degree hyperparam and update notebooks
Update readme to add new  notebooks
2020-06-08 20:16:42 +02:00
d7c0bc3bc5 #3 Complete multiclass in Stree
Add multiclass dimensions management in distances method
Add gamma hyperparameter for non linear kernels
2020-06-08 13:54:24 +02:00
3a48d8b405 #3 Rewrite some tests & remove use_predictions
Remove use_predictions parameter as of now, the model always use it
2020-06-08 01:51:21 +02:00
05b462716e #3 First try, change LinearSVC to SVC
make a builder
start changing tests
2020-06-07 20:26:59 +02:00
b824229121 #1 Add min_samples_split
Fix #1
2020-06-07 16:12:25 +02:00
8ba9b1b6a1 Remove travis ci and set codecov percentage 2020-06-06 19:47:00 +02:00
37577849db Fix parameter missing in method overload 2020-06-06 18:18:03 +02:00
cb10aea36e remove unneed test and cosmetic 2020-06-06 14:20:07 +02:00
b9f14aec05 #4 Add code coverage & codacy badge
Add code coverage configuration in codecov
Add some tests
2020-06-06 03:04:18 +02:00
b4816b2995 Show sample_weight use in test2 notebook
Update revision to RC4
Lint Stree grapher
2020-05-30 23:59:40 +02:00
5e5fea9c6a Document & lint code 2020-05-30 23:10:10 +02:00
29 changed files with 3347 additions and 2048 deletions

13
.coveragerc Normal file
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@@ -0,0 +1,13 @@
[run]
branch = True
source = stree
[report]
exclude_lines =
if self.debug:
pragma: no cover
raise NotImplementedError
if __name__ == .__main__.:
ignore_errors = True
omit =
stree/__init__.py

47
.github/workflows/main.yml vendored Normal file
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@@ -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

6
.gitignore vendored
View File

@@ -129,4 +129,8 @@ dmypy.json
.pyre/
.idea
.vscode
.vscode
.pre-commit-config.yaml
**.csv
.virtual_documents

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@@ -1,13 +0,0 @@
language: python
os: linux
dist: xenial
install:
- pip install -r requirements.txt
notifications:
email:
recipients:
- ricardo.montanana@alu.uclm.es
on_success: never # default: change
on_failure: always # default: always
# command to run tests
script: python -m unittest stree.tests

View File

@@ -1,8 +1,10 @@
[![Build Status](https://travis-ci.com/Doctorado-ML/STree.svg?branch=master)](https://travis-ci.com/Doctorado-ML/STree)
![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)
# Stree
Oblique Tree classifier based on SVM nodes. The nodes are built and splitted with sklearn LinearSVC models.Stree is a sklearn estimator and can be integrated in pipelines, grid searches, etc.
Oblique Tree classifier based on SVM nodes. The nodes are built and splitted with sklearn SVC models. Stree is a sklearn estimator and can be integrated in pipelines, grid searches, etc.
![Stree](https://raw.github.com/doctorado-ml/stree/master/example.png)
@@ -16,23 +18,45 @@ pip install git+https://github.com/doctorado-ml/stree
### Jupyter notebooks
##### Slow launch but better integration
- [![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/test.ipynb) Test notebook
- [![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
##### Fast launch but have to run first commented out cell for setup
- [![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
* [![Test](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/test.ipynb) Test notebook
- [![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
* [![Test2](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/STree/blob/master/notebooks/test2.ipynb) Another Test notebook
- [![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
* [![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 notebook
- [![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
### Command line
## Hyperparameters
```bash
python main.py
```
| | **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. |
\* 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

12
codecov.yml Normal file
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@@ -0,0 +1,12 @@
overage:
status:
project:
default:
target: 90%
comment:
layout: "reach, diff, flags, files"
behavior: default
require_changes: false
require_base: yes
require_head: yes
branches: null

60
main.py
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@@ -1,57 +1,29 @@
import time
from sklearn.model_selection import train_test_split
from sklearn.datasets import load_iris
from stree import Stree
random_state=1
random_state = 1
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
X, y = load_iris(return_X_y=True)
# 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()
clf = Stree(C=.01, random_state=random_state)
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")
print(clf)
print(f"Classifier's accuracy (train): {clf.score(Xtrain, ytrain):.4f}")
print(f"Classifier's accuracy (test) : {clf.score(Xtest, ytest):.4f}")
proba = clf.predict_proba(Xtest)
print("Checking that we have correct probabilities, these are probabilities of sample belonging to class 1")
res0 = proba[proba[:, 0] == 0]
res1 = proba[proba[:, 0] == 1]
print("++++++++++res0 > .8++++++++++++")
print(res0[res0[:, 1] > .8])
print("**********res1 < .4************")
print(res1[res1[:, 1] < .4])

View File

@@ -1,190 +0,0 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"from sklearn.ensemble import AdaBoostClassifier\n",
"from sklearn.tree import DecisionTreeClassifier\n",
"from sklearn.svm import LinearSVC\n",
"from sklearn.model_selection import GridSearchCV, train_test_split\n",
"from sklearn.datasets import load_iris\n",
"from stree import Stree"
]
},
{
"cell_type": "code",
"execution_count": 2,
"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"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Fraud: 0.244% 196\nValid: 99.755% 80234\nX.shape (1196, 28) y.shape (1196,)\nFraud: 16.722% 200\nValid: 83.278% 996\n"
}
],
"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]"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Score Train: 0.986857825567503\nScore Test: 0.9805013927576601\nTook 0.12 seconds\n"
}
],
"source": [
"now = time.time()\n",
"clf = Stree(max_depth=3, random_state=random_state)\n",
"clf.fit(Xtrain, ytrain)\n",
"print(\"Score Train: \", clf.score(Xtrain, ytrain))\n",
"print(\"Score Test: \", clf.score(Xtest, ytest))\n",
"print(f\"Took {time.time() - now:.2f} seconds\")"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Score Train: 0.997610513739546\nScore Test: 0.9721448467966574\nTook 7.80 seconds\n"
}
],
"source": [
"now = time.time()\n",
"clf2 = AdaBoostClassifier(Stree(max_depth=3, random_state=random_state), n_estimators=100, random_state=random_state)\n",
"clf2.fit(Xtrain, ytrain)\n",
"print(\"Score Train: \", clf2.score(Xtrain, ytrain))\n",
"print(\"Score Test: \", clf2.score(Xtest, ytest))\n",
"print(f\"Took {time.time() - now:.2f} seconds\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Score Train: 0.9796893667861409\nScore Test: 0.9554317548746518\nTook 0.48 seconds\n"
}
],
"source": [
"now = time.time()\n",
"clf3 = AdaBoostClassifier(LinearSVC(random_state=random_state), n_estimators=100, random_state=random_state, algorithm='SAMME')\n",
"clf3.fit(Xtrain, ytrain)\n",
"print(\"Score Train: \", clf3.score(Xtrain, ytrain))\n",
"print(\"Score Test: \", clf3.score(Xtest, ytest))\n",
"print(f\"Took {time.time() - now:.2f} seconds\")"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Score Train: 1.0\nScore Test: 0.9721448467966574\nTook 0.86 seconds\n"
}
],
"source": [
"now = time.time()\n",
"clf4 = AdaBoostClassifier(DecisionTreeClassifier(max_depth=1, random_state=random_state), n_estimators=100, random_state=random_state)\n",
"clf4.fit(Xtrain, ytrain)\n",
"print(\"Score Train: \", clf4.score(Xtrain, ytrain))\n",
"print(\"Score Test: \", clf4.score(Xtest, ytest))\n",
"print(f\"Took {time.time() - now:.2f} seconds\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"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)"
}
},
"nbformat": 4,
"nbformat_minor": 2
}

613
notebooks/benchmark.ipynb Normal file
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Compare STree with different estimators"
]
},
{
"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",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import datetime, time\n",
"import numpy as np\n",
"import pandas as pd\n",
"from sklearn.model_selection import train_test_split\n",
"from sklearn.metrics import classification_report, confusion_matrix, f1_score\n",
"from sklearn.tree import DecisionTreeClassifier\n",
"from sklearn.naive_bayes import GaussianNB\n",
"from sklearn.neural_network import MLPClassifier\n",
"from sklearn.svm import LinearSVC\n",
"from stree import Stree"
]
},
{
"cell_type": "code",
"execution_count": 3,
"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"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Tests"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2021-01-14 11:30:51\n"
]
}
],
"source": [
"print(datetime.date.today(), time.strftime(\"%H:%M:%S\"))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Load dataset and normalize values"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"# Load Dataset\n",
"df = pd.read_csv('data/creditcard.csv')\n",
"df.shape\n",
"random_state = 2020"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Fraud: 0.173% 492\n",
"Valid: 99.827% 284,315\n"
]
}
],
"source": [
"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()))"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"# Normalize Amount\n",
"from sklearn.preprocessing import RobustScaler\n",
"values = RobustScaler().fit_transform(df.Amount.values.reshape(-1, 1))\n",
"df['Amount_Scaled'] = values"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"X shape: (284807, 29)\n",
"y shape: (284807,)\n"
]
}
],
"source": [
"# Remove unneeded features\n",
"y = df.Class.values\n",
"X = df.drop(['Class', 'Time', 'Amount'], axis=1).values\n",
"print(f\"X shape: {X.shape}\\ny shape: {y.shape}\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Build the models"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# Divide dataset\n",
"train_size = .7\n",
"Xtrain, Xtest, ytrain, ytest = train_test_split(X, y, train_size=train_size, shuffle=True, random_state=random_state, stratify=y)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"# Linear Tree\n",
"linear_tree = DecisionTreeClassifier(random_state=random_state)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"# Naive Bayes\n",
"naive_bayes = GaussianNB()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"# Stree\n",
"stree = Stree(random_state=random_state, C=.01, max_iter=1e3)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"# Neural Network\n",
"mlp = MLPClassifier(random_state=random_state, alpha=1)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"# SVC (linear)\n",
"svc = LinearSVC(random_state=random_state, C=.01, max_iter=1e3)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Do the test"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"def try_model(name, model):\n",
" print(f\"************************** {name} **********************\")\n",
" now = time.time()\n",
" model.fit(Xtrain, ytrain)\n",
" spent = time.time() - now\n",
" print(f\"Train Model {name} took: {spent:.4} seconds\")\n",
" predict = model.predict(Xtrain)\n",
" predictt = model.predict(Xtest)\n",
" print(f\"=========== {name} - Train {Xtrain.shape[0]:,} samples =============\",)\n",
" print(classification_report(ytrain, predict, digits=6))\n",
" print(f\"=========== {name} - Test {Xtest.shape[0]:,} samples =============\")\n",
" print(classification_report(ytest, predictt, digits=6))\n",
" print(\"Confusion Matrix in Train\")\n",
" print(confusion_matrix(ytrain, predict))\n",
" print(\"Confusion Matrix in Test\")\n",
" print(confusion_matrix(ytest, predictt))\n",
" return f1_score(ytest, predictt), spent"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"************************** Linear Tree **********************\n",
"Train Model Linear Tree took: 10.25 seconds\n",
"=========== Linear Tree - Train 199,364 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 1.000000 1.000000 1.000000 199020\n",
" 1 1.000000 1.000000 1.000000 344\n",
"\n",
" accuracy 1.000000 199364\n",
" macro avg 1.000000 1.000000 1.000000 199364\n",
"weighted avg 1.000000 1.000000 1.000000 199364\n",
"\n",
"=========== Linear Tree - Test 85,443 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999578 0.999613 0.999596 85295\n",
" 1 0.772414 0.756757 0.764505 148\n",
"\n",
" accuracy 0.999192 85443\n",
" macro avg 0.885996 0.878185 0.882050 85443\n",
"weighted avg 0.999184 0.999192 0.999188 85443\n",
"\n",
"Confusion Matrix in Train\n",
"[[199020 0]\n",
" [ 0 344]]\n",
"Confusion Matrix in Test\n",
"[[85262 33]\n",
" [ 36 112]]\n",
"************************** Naive Bayes **********************\n",
"Train Model Naive Bayes took: 0.09943 seconds\n",
"=========== Naive Bayes - Train 199,364 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999692 0.978238 0.988849 199020\n",
" 1 0.061538 0.825581 0.114539 344\n",
"\n",
" accuracy 0.977975 199364\n",
" macro avg 0.530615 0.901910 0.551694 199364\n",
"weighted avg 0.998073 0.977975 0.987340 199364\n",
"\n",
"=========== Naive Bayes - Test 85,443 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999712 0.977994 0.988734 85295\n",
" 1 0.061969 0.837838 0.115403 148\n",
"\n",
" accuracy 0.977751 85443\n",
" macro avg 0.530841 0.907916 0.552068 85443\n",
"weighted avg 0.998088 0.977751 0.987221 85443\n",
"\n",
"Confusion Matrix in Train\n",
"[[194689 4331]\n",
" [ 60 284]]\n",
"Confusion Matrix in Test\n",
"[[83418 1877]\n",
" [ 24 124]]\n",
"************************** Stree (SVM Tree) **********************\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/rmontanana/.virtualenvs/general/lib/python3.8/site-packages/sklearn/svm/_base.py:976: ConvergenceWarning: Liblinear failed to converge, increase the number of iterations.\n",
" warnings.warn(\"Liblinear failed to converge, increase \"\n",
"/Users/rmontanana/.virtualenvs/general/lib/python3.8/site-packages/sklearn/svm/_base.py:976: ConvergenceWarning: Liblinear failed to converge, increase the number of iterations.\n",
" warnings.warn(\"Liblinear failed to converge, increase \"\n",
"/Users/rmontanana/.virtualenvs/general/lib/python3.8/site-packages/sklearn/svm/_base.py:976: ConvergenceWarning: Liblinear failed to converge, increase the number of iterations.\n",
" warnings.warn(\"Liblinear failed to converge, increase \"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Train Model Stree (SVM Tree) took: 28.47 seconds\n",
"=========== Stree (SVM Tree) - Train 199,364 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999623 0.999864 0.999744 199020\n",
" 1 0.908784 0.781977 0.840625 344\n",
"\n",
" accuracy 0.999488 199364\n",
" macro avg 0.954204 0.890921 0.920184 199364\n",
"weighted avg 0.999467 0.999488 0.999469 199364\n",
"\n",
"=========== Stree (SVM Tree) - Test 85,443 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999637 0.999918 0.999777 85295\n",
" 1 0.943548 0.790541 0.860294 148\n",
"\n",
" accuracy 0.999555 85443\n",
" macro avg 0.971593 0.895229 0.930036 85443\n",
"weighted avg 0.999540 0.999555 0.999536 85443\n",
"\n",
"Confusion Matrix in Train\n",
"[[198993 27]\n",
" [ 75 269]]\n",
"Confusion Matrix in Test\n",
"[[85288 7]\n",
" [ 31 117]]\n",
"************************** Neural Network **********************\n",
"Train Model Neural Network took: 9.76 seconds\n",
"=========== Neural Network - Train 199,364 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999247 0.999844 0.999545 199020\n",
" 1 0.862222 0.563953 0.681898 344\n",
"\n",
" accuracy 0.999092 199364\n",
" macro avg 0.930734 0.781899 0.840722 199364\n",
"weighted avg 0.999010 0.999092 0.998997 199364\n",
"\n",
"=========== Neural Network - Test 85,443 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999356 0.999871 0.999613 85295\n",
" 1 0.894231 0.628378 0.738095 148\n",
"\n",
" accuracy 0.999228 85443\n",
" macro avg 0.946793 0.814125 0.868854 85443\n",
"weighted avg 0.999173 0.999228 0.999160 85443\n",
"\n",
"Confusion Matrix in Train\n",
"[[198989 31]\n",
" [ 150 194]]\n",
"Confusion Matrix in Test\n",
"[[85284 11]\n",
" [ 55 93]]\n",
"************************** SVC (linear) **********************\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/rmontanana/.virtualenvs/general/lib/python3.8/site-packages/sklearn/svm/_base.py:976: ConvergenceWarning: Liblinear failed to converge, increase the number of iterations.\n",
" warnings.warn(\"Liblinear failed to converge, increase \"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Train Model SVC (linear) took: 8.207 seconds\n",
"=========== SVC (linear) - Train 199,364 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999237 0.999859 0.999548 199020\n",
" 1 0.872727 0.558140 0.680851 344\n",
"\n",
" accuracy 0.999097 199364\n",
" macro avg 0.935982 0.778999 0.840199 199364\n",
"weighted avg 0.999018 0.999097 0.998998 199364\n",
"\n",
"=========== SVC (linear) - Test 85,443 samples =============\n",
" precision recall f1-score support\n",
"\n",
" 0 0.999344 0.999894 0.999619 85295\n",
" 1 0.910891 0.621622 0.738956 148\n",
"\n",
" accuracy 0.999239 85443\n",
" macro avg 0.955117 0.810758 0.869287 85443\n",
"weighted avg 0.999191 0.999239 0.999168 85443\n",
"\n",
"Confusion Matrix in Train\n",
"[[198992 28]\n",
" [ 152 192]]\n",
"Confusion Matrix in Test\n",
"[[85286 9]\n",
" [ 56 92]]\n"
]
}
],
"source": [
"# Train & Test models\n",
"models = {\n",
" 'Linear Tree':linear_tree, 'Naive Bayes': naive_bayes, 'Stree (SVM Tree)': stree, \n",
" 'Neural Network': mlp, 'SVC (linear)': svc\n",
"}\n",
"\n",
"best_f1 = 0\n",
"outcomes = []\n",
"for name, model in models.items():\n",
" f1, time_spent = try_model(name, model)\n",
" outcomes.append((name, f1, time_spent))\n",
" if f1 > best_f1:\n",
" best_model = name\n",
" best_time = time_spent\n",
" best_f1 = f1"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"**************************************************************************************************************\n",
"*The best f1 model is Stree (SVM Tree), with a f1 score: 0.8603 in 28.4743 seconds with 0.7 samples in train dataset\n",
"**************************************************************************************************************\n",
"Model: Linear Tree\t Time: 10.25 seconds\t f1: 0.7645\n",
"Model: Naive Bayes\t Time: 0.10 seconds\t f1: 0.1154\n",
"Model: Stree (SVM Tree)\t Time: 28.47 seconds\t f1: 0.8603\n",
"Model: Neural Network\t Time: 9.76 seconds\t f1: 0.7381\n",
"Model: SVC (linear)\t Time: 8.21 seconds\t f1: 0.739\n"
]
}
],
"source": [
"print(\"*\"*110)\n",
"print(f\"*The best f1 model is {best_model}, with a f1 score: {best_f1:.4} in {best_time:.6} seconds with {train_size:,} samples in train dataset\")\n",
"print(\"*\"*110)\n",
"for name, f1, time_spent in outcomes:\n",
" print(f\"Model: {name}\\t Time: {time_spent:6.2f} seconds\\t f1: {f1:.4}\")"
]
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"**************************************************************************************************************\n",
"*The best f1 model is Stree (SVM Tree), with a f1 score: 0.8603 in 28.4743 seconds with 0.7 samples in train dataset\n",
"**************************************************************************************************************\n",
"Model: Linear Tree\t Time: 10.25 seconds\t f1: 0.7645\n",
"Model: Naive Bayes\t Time: 0.10 seconds\t f1: 0.1154\n",
"Model: Stree (SVM Tree)\t Time: 28.47 seconds\t f1: 0.8603\n",
"Model: Neural Network\t Time: 9.76 seconds\t f1: 0.7381\n",
"Model: SVC (linear)\t Time: 8.21 seconds\t f1: 0.739"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'C': 0.01,\n",
" 'criterion': 'entropy',\n",
" 'degree': 3,\n",
" 'gamma': 'scale',\n",
" 'kernel': 'linear',\n",
" 'max_depth': None,\n",
" 'max_features': None,\n",
" 'max_iter': 1000.0,\n",
" 'min_samples_split': 0,\n",
" 'random_state': 2020,\n",
" 'split_criteria': 'impurity',\n",
" 'splitter': 'random',\n",
" 'tol': 0.0001}"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"stree.get_params()"
]
}
],
"metadata": {
"hide_input": false,
"kernelspec": {
"display_name": "Python 3",
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"nav_menu": {},
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"title_cell": "Table of Contents",
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test Stree with AdaBoost and Bagging with 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",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"import warnings\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",
"warnings.filterwarnings(\"ignore\", category=ConvergenceWarning)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"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"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Fraud: 0.173% 492\n",
"Valid: 99.827% 284315\n",
"X.shape (100492, 28) y.shape (100492,)\n",
"Fraud: 0.651% 654\n",
"Valid: 99.349% 99838\n"
]
}
],
"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",
"data = load_creditcard(-100000)\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": "markdown",
"metadata": {},
"source": [
"## STree alone with 100.000 samples and linear kernel"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Score Train: 0.9984504719663368\n",
"Score Test: 0.9983415151917209\n",
"Took 26.09 seconds\n"
]
}
],
"source": [
"now = time.time()\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",
"print(f\"Took {time.time() - now:.2f} seconds\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Adaboost"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"n_estimators = 10\n",
"C = 7\n",
"max_depth = 3"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Kernel: linear\tTime: 43.49 seconds\tScore Train: 0.9980098\tScore Test: 0.9980762\n",
"Kernel: rbf\tTime: 8.86 seconds\tScore Train: 0.9934891\tScore Test: 0.9934987\n",
"Kernel: poly\tTime: 41.14 seconds\tScore Train: 0.9972279\tScore Test: 0.9973133\n"
]
}
],
"source": [
"for kernel in ['linear', 'rbf', 'poly']:\n",
" now = time.time()\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",
" print(f\"Kernel: {kernel}\\tTime: {time.time() - now:.2f} seconds\\tScore Train: {score_train:.7f}\\tScore Test: {score_test:.7f}\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Bagging"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"n_estimators = 10\n",
"C = 7\n",
"max_depth = 3"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Kernel: linear\tTime: 187.51 seconds\tScore Train: 0.9984505\tScore Test: 0.9983083\n",
"Kernel: rbf\tTime: 73.65 seconds\tScore Train: 0.9993461\tScore Test: 0.9985074\n",
"Kernel: poly\tTime: 52.19 seconds\tScore Train: 0.9993461\tScore Test: 0.9987727\n"
]
}
],
"source": [
"for kernel in ['linear', 'rbf', 'poly']:\n",
" now = time.time()\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",
" print(f\"Kernel: {kernel}\\tTime: {time.time() - now:.2f} seconds\\tScore Train: {score_train:.7f}\\tScore Test: {score_test:.7f}\")"
]
}
],
"metadata": {
"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"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test sample_weight, kernels, C, sklearn estimator"
]
},
{
"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",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"import warnings\n",
"import numpy as np\n",
"import pandas as pd\n",
"from sklearn.svm import SVC\n",
"from sklearn.tree import DecisionTreeClassifier\n",
"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.exceptions import ConvergenceWarning\n",
"from stree import Stree\n",
"warnings.filterwarnings(\"ignore\", category=ConvergenceWarning)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"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"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Fraud: 0.173% 492\n",
"Valid: 99.827% 284315\n",
"X.shape (5492, 28) y.shape (5492,)\n",
"Fraud: 9.086% 499\n",
"Valid: 90.914% 4993\n",
"[0.09079084 0.09079084 0.09079084 0.09079084] [0.09101942 0.09101942 0.09101942 0.09101942]\n"
]
}
],
"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)\n",
" return Xtrain, Xtest, ytrain, ytest\n",
"\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 1000 samples\n",
"\n",
"Xtrain = data[0]\n",
"Xtest = data[1]\n",
"ytrain = data[2]\n",
"ytest = data[3]\n",
"_, data = np.unique(ytrain, return_counts=True)\n",
"wtrain = (data[1] / np.sum(data), data[0] / np.sum(data))\n",
"_, data = np.unique(ytest, return_counts=True)\n",
"wtest = (data[1] / np.sum(data), data[0] / np.sum(data))\n",
"# Set weights inverse to its count class in dataset\n",
"weights = np.ones(Xtrain.shape[0],)\n",
"weights[ytrain==0] = wtrain[0]\n",
"weights[ytrain==1] = wtrain[1]\n",
"weights_test = np.ones(Xtest.shape[0],)\n",
"weights_test[ytest==0] = wtest[0]\n",
"weights_test[ytest==1] = wtest[1]\n",
"print(weights[:4], weights_test[:4])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Tests"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 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": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Accuracy of Train without weights 0.9849115504682622\n",
"Accuracy of Train with weights 0.9849115504682622\n",
"Accuracy of Tests without weights 0.9848300970873787\n",
"Accuracy of Tests with weights 0.9805825242718447\n"
]
}
],
"source": [
"C = 23\n",
"print(\"Accuracy of Train without weights\", Stree(C=C, random_state=1).fit(Xtrain, ytrain).score(Xtrain, ytrain))\n",
"print(\"Accuracy of Train with weights\", Stree(C=C, random_state=1).fit(Xtrain, ytrain, sample_weight=weights).score(Xtrain, ytrain))\n",
"print(\"Accuracy of Tests without weights\", Stree(C=C, random_state=1).fit(Xtrain, ytrain).score(Xtest, ytest))\n",
"print(\"Accuracy of Tests with weights\", Stree(C=C, random_state=1).fit(Xtrain, ytrain, sample_weight=weights).score(Xtest, ytest))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test accuracy with different kernels\n",
"Compute accuracy on train and test set with default hyperparmeters of every kernel"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Time: 26.59s\tKernel: linear\tAccuracy_train: 0.9846514047866806\tAccuracy_test: 0.9848300970873787\n",
"Time: 0.56s\tKernel: rbf\tAccuracy_train: 0.9947970863683663\tAccuracy_test: 0.9866504854368932\n",
"Time: 0.23s\tKernel: poly\tAccuracy_train: 0.9955775234131113\tAccuracy_test: 0.9824029126213593\n"
]
}
],
"source": [
"random_state=1\n",
"for kernel in ['linear', 'rbf', 'poly']:\n",
" now = time.time()\n",
" clf = Stree(C=7, kernel=kernel, random_state=random_state).fit(Xtrain, ytrain)\n",
" accuracy_train = clf.score(Xtrain, ytrain)\n",
" accuracy_test = clf.score(Xtest, ytest)\n",
" time_spent = time.time() - now\n",
" print(f\"Time: {time_spent:.2f}s\\tKernel: {kernel}\\tAccuracy_train: {accuracy_train}\\tAccuracy_test: {accuracy_test}\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test diferent values of C"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"************** C=0.001 ****************************\n",
"Classifier's accuracy (train): 0.9823\n",
"Classifier's accuracy (test) : 0.9836\n",
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down, <cgaf> - Leaf class=0 belief= 0.981455 impurity=0.1332 counts=(array([0, 1]), array([3493, 66]))\n",
"root - Up, <cgaf> - Leaf class=1 belief= 0.992982 impurity=0.0603 counts=(array([0, 1]), array([ 2, 283]))\n",
"\n",
"**************************************************\n",
"************** C=0.01 ****************************\n",
"Classifier's accuracy (train): 0.9834\n",
"Classifier's accuracy (test) : 0.9842\n",
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down, <cgaf> - Leaf class=0 belief= 0.982288 impurity=0.1284 counts=(array([0, 1]), array([3494, 63]))\n",
"root - Up, <cgaf> - Leaf class=1 belief= 0.996516 impurity=0.0335 counts=(array([0, 1]), array([ 1, 286]))\n",
"\n",
"**************************************************\n",
"************** C=1 ****************************\n",
"Classifier's accuracy (train): 0.9844\n",
"Classifier's accuracy (test) : 0.9848\n",
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1236 counts=(array([0, 1]), array([3493, 60]))\n",
"root - Down - Down, <cgaf> - Leaf class=0 belief= 0.983108 impurity=0.1236 counts=(array([0, 1]), array([3492, 60]))\n",
"root - Down - Up, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.0593 counts=(array([0, 1]), array([ 2, 289]))\n",
"root - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([2]))\n",
"root - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([289]))\n",
"\n",
"**************************************************\n",
"************** C=5 ****************************\n",
"Classifier's accuracy (train): 0.9847\n",
"Classifier's accuracy (test) : 0.9848\n",
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1236 counts=(array([0, 1]), array([3493, 60]))\n",
"root - Down - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1236 counts=(array([0, 1]), array([3492, 60]))\n",
"root - Down - Down - Down, <cgaf> - Leaf class=0 belief= 0.983385 impurity=0.1220 counts=(array([0, 1]), array([3492, 59]))\n",
"root - Down - Down - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([1]))\n",
"root - Down - Up, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.0593 counts=(array([0, 1]), array([ 2, 289]))\n",
"root - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([2]))\n",
"root - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([289]))\n",
"\n",
"**************************************************\n",
"************** C=17 ****************************\n",
"Classifier's accuracy (train): 0.9847\n",
"Classifier's accuracy (test) : 0.9848\n",
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1236 counts=(array([0, 1]), array([3493, 60]))\n",
"root - Down - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1220 counts=(array([0, 1]), array([3492, 59]))\n",
"root - Down - Down - Down, <cgaf> - Leaf class=0 belief= 0.983380 impurity=0.1220 counts=(array([0, 1]), array([3491, 59]))\n",
"root - Down - Down - Up, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Down - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=1.0000 counts=(array([0, 1]), array([1, 1]))\n",
"root - Down - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Down - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([1]))\n",
"root - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.0593 counts=(array([0, 1]), array([ 2, 289]))\n",
"root - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([2]))\n",
"root - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([289]))\n",
"\n",
"**************************************************\n",
"59.0161 secs\n"
]
}
],
"source": [
"t = time.time()\n",
"for C in (.001, .01, 1, 5, 17):\n",
" clf = Stree(C=C, kernel=\"linear\", random_state=random_state)\n",
" clf.fit(Xtrain, ytrain)\n",
" print(f\"************** C={C} ****************************\")\n",
" print(f\"Classifier's accuracy (train): {clf.score(Xtrain, ytrain):.4f}\")\n",
" print(f\"Classifier's accuracy (test) : {clf.score(Xtest, ytest):.4f}\")\n",
" print(clf)\n",
" print(f\"**************************************************\")\n",
"print(f\"{time.time() - t:.4f} secs\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test iterator\n",
"Check different ways of using the iterator"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1236 counts=(array([0, 1]), array([3493, 60]))\n",
"root - Down - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1220 counts=(array([0, 1]), array([3492, 59]))\n",
"root - Down - Down - Down, <cgaf> - Leaf class=0 belief= 0.983380 impurity=0.1220 counts=(array([0, 1]), array([3491, 59]))\n",
"root - Down - Down - Up, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Down - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=1.0000 counts=(array([0, 1]), array([1, 1]))\n",
"root - Down - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Down - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([1]))\n",
"root - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.0593 counts=(array([0, 1]), array([ 2, 289]))\n",
"root - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([2]))\n",
"root - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([289]))\n"
]
}
],
"source": [
"#check iterator\n",
"for i in list(clf):\n",
" print(i)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"root feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.4391 counts=(array([0, 1]), array([3495, 349]))\n",
"root - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1236 counts=(array([0, 1]), array([3493, 60]))\n",
"root - Down - Down feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.1220 counts=(array([0, 1]), array([3492, 59]))\n",
"root - Down - Down - Down, <cgaf> - Leaf class=0 belief= 0.983380 impurity=0.1220 counts=(array([0, 1]), array([3491, 59]))\n",
"root - Down - Down - Up, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Down - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=1.0000 counts=(array([0, 1]), array([1, 1]))\n",
"root - Down - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([1]))\n",
"root - Down - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([1]))\n",
"root - Up feaures=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) impurity=0.0593 counts=(array([0, 1]), array([ 2, 289]))\n",
"root - Up - Down, <pure> - Leaf class=0 belief= 1.000000 impurity=0.0000 counts=(array([0]), array([2]))\n",
"root - Up - Up, <pure> - Leaf class=1 belief= 1.000000 impurity=0.0000 counts=(array([1]), array([289]))\n"
]
}
],
"source": [
"#check iterator again\n",
"for i in clf:\n",
" print(i)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Test STree is a sklearn estimator"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1 functools.partial(<function check_no_attributes_set_in_init at 0x16817f670>, 'Stree')\n",
"2 functools.partial(<function check_estimators_dtypes at 0x168179820>, 'Stree')\n",
"3 functools.partial(<function check_fit_score_takes_y at 0x168179700>, 'Stree')\n",
"4 functools.partial(<function check_sample_weights_pandas_series at 0x168174040>, 'Stree')\n",
"5 functools.partial(<function check_sample_weights_not_an_array at 0x168174160>, 'Stree')\n",
"6 functools.partial(<function check_sample_weights_list at 0x168174280>, 'Stree')\n",
"7 functools.partial(<function check_sample_weights_shape at 0x1681743a0>, 'Stree')\n",
"8 functools.partial(<function check_sample_weights_invariance at 0x1681744c0>, 'Stree', kind='ones')\n",
"10 functools.partial(<function check_estimators_fit_returns_self at 0x16817b8b0>, 'Stree')\n",
"11 functools.partial(<function check_estimators_fit_returns_self at 0x16817b8b0>, 'Stree', readonly_memmap=True)\n",
"12 functools.partial(<function check_complex_data at 0x168174670>, 'Stree')\n",
"13 functools.partial(<function check_dtype_object at 0x1681745e0>, 'Stree')\n",
"14 functools.partial(<function check_estimators_empty_data_messages at 0x1681799d0>, 'Stree')\n",
"15 functools.partial(<function check_pipeline_consistency at 0x1681795e0>, 'Stree')\n",
"16 functools.partial(<function check_estimators_nan_inf at 0x168179af0>, 'Stree')\n",
"17 functools.partial(<function check_estimators_overwrite_params at 0x16817f550>, 'Stree')\n",
"18 functools.partial(<function check_estimator_sparse_data at 0x168172ee0>, 'Stree')\n",
"19 functools.partial(<function check_estimators_pickle at 0x168179d30>, 'Stree')\n",
"20 functools.partial(<function check_estimator_get_tags_default_keys at 0x168181790>, 'Stree')\n",
"21 functools.partial(<function check_classifier_data_not_an_array at 0x16817f8b0>, 'Stree')\n",
"22 functools.partial(<function check_classifiers_one_label at 0x16817b430>, 'Stree')\n",
"23 functools.partial(<function check_classifiers_classes at 0x16817bd30>, 'Stree')\n",
"24 functools.partial(<function check_estimators_partial_fit_n_features at 0x168179e50>, 'Stree')\n",
"25 functools.partial(<function check_classifiers_train at 0x16817b550>, 'Stree')\n",
"26 functools.partial(<function check_classifiers_train at 0x16817b550>, 'Stree', readonly_memmap=True)\n",
"27 functools.partial(<function check_classifiers_train at 0x16817b550>, 'Stree', readonly_memmap=True, X_dtype='float32')\n",
"28 functools.partial(<function check_classifiers_regression_target at 0x168181280>, 'Stree')\n",
"29 functools.partial(<function check_supervised_y_no_nan at 0x1681720d0>, 'Stree')\n",
"30 functools.partial(<function check_supervised_y_2d at 0x16817baf0>, 'Stree')\n",
"31 functools.partial(<function check_estimators_unfitted at 0x16817b9d0>, 'Stree')\n",
"32 functools.partial(<function check_non_transformer_estimators_n_iter at 0x16817fdc0>, 'Stree')\n",
"33 functools.partial(<function check_decision_proba_consistency at 0x1681813a0>, 'Stree')\n",
"34 functools.partial(<function check_parameters_default_constructible at 0x16817fb80>, 'Stree')\n",
"35 functools.partial(<function check_methods_sample_order_invariance at 0x168174d30>, 'Stree')\n",
"36 functools.partial(<function check_methods_subset_invariance at 0x168174c10>, 'Stree')\n",
"37 functools.partial(<function check_fit2d_1sample at 0x168174e50>, 'Stree')\n",
"38 functools.partial(<function check_fit2d_1feature at 0x168174f70>, 'Stree')\n",
"39 functools.partial(<function check_get_params_invariance at 0x168181040>, 'Stree')\n",
"40 functools.partial(<function check_set_params at 0x168181160>, 'Stree')\n",
"41 functools.partial(<function check_dict_unchanged at 0x168174790>, 'Stree')\n",
"42 functools.partial(<function check_dont_overwrite_parameters at 0x168174940>, 'Stree')\n",
"43 functools.partial(<function check_fit_idempotent at 0x168181550>, 'Stree')\n",
"44 functools.partial(<function check_n_features_in at 0x1681815e0>, 'Stree')\n",
"45 functools.partial(<function check_fit1d at 0x1681790d0>, 'Stree')\n",
"46 functools.partial(<function check_fit2d_predict1d at 0x168174a60>, 'Stree')\n",
"47 functools.partial(<function check_requires_y_none at 0x168181670>, 'Stree')\n"
]
}
],
"source": [
"# Make checks one by one\n",
"c = 0\n",
"checks = check_estimator(Stree(), generate_only=True)\n",
"for check in checks:\n",
" c += 1\n",
" if c == 9:\n",
" pass\n",
" else:\n",
" print(c, check[1])\n",
" check[1](check[0])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Check if the classifier is a sklearn estimator\n",
"check_estimator(Stree())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Compare to SVM"
]
},
{
"cell_type": "code",
"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",
"svc.fit(Xtrain, ytrain)\n",
"clf.fit(Xtrain, ytrain)\n",
"print(\"== Not Weighted ===\")\n",
"print(\"SVC train score ..:\", svc.score(Xtrain, ytrain))\n",
"print(\"STree train score :\", clf.score(Xtrain, ytrain))\n",
"print(\"SVC test score ...:\", svc.score(Xtest, ytest))\n",
"print(\"STree test score .:\", clf.score(Xtest, ytest))\n",
"svc.fit(Xtrain, ytrain, weights)\n",
"clf.fit(Xtrain, ytrain, weights)\n",
"print(\"==== Weighted =====\")\n",
"print(\"SVC train score ..:\", svc.score(Xtrain, ytrain))\n",
"print(\"STree train score :\", clf.score(Xtrain, ytrain))\n",
"print(\"SVC test score ...:\", svc.score(Xtest, ytest))\n",
"print(\"STree test score .:\", clf.score(Xtest, ytest))\n",
"print(\"*SVC test score ..:\", svc.score(Xtest, ytest, weights_test))\n",
"print(\"*STree test score :\", clf.score(Xtest, ytest, weights_test))"
]
},
{
"cell_type": "code",
"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",
"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": "3.9.1"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

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{
"cells": [
{
"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",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"from sklearn.svm import LinearSVC\n",
"from sklearn.tree import DecisionTreeClassifier\n",
"from sklearn.datasets import make_classification, load_iris, load_wine\n",
"from sklearn.model_selection import train_test_split\n",
"from stree import Stree\n",
"import time"
]
},
{
"cell_type": "code",
"execution_count": 3,
"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"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "Fraud: 0.244% 196\nValid: 99.755% 80234\nX.shape (1196, 28) y.shape (1196,)\nFraud: 16.722% 200\nValid: 83.278% 996\n"
}
],
"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(-5000) # Take all true samples + 5000 of the others\n",
"# data = load_creditcard(5000) # Take the first 5000 samples\n",
"data = load_creditcard(-1000) # Take all the samples\n",
"\n",
"Xtrain = data[0]\n",
"Xtest = data[1]\n",
"ytrain = data[2]\n",
"ytest = data[3]"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"tags": [
"outputPrepend"
]
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "************** C=0.001 ****************************\nClassifier's accuracy (train): 0.9797\nClassifier's accuracy (test) : 0.9749\nroot\nroot - Down\nroot - Down - Down, <cgaf> - Leaf class=1.0 belief=0.984127 counts=(array([0., 1.]), array([ 2, 124]))\nroot - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([5]))\nroot - Up\nroot - Up - Down, <cgaf> - Leaf class=0.0 belief=0.750000 counts=(array([0., 1.]), array([3, 1]))\nroot - Up - Up\nroot - Up - Up - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Up, <cgaf> - Leaf class=0.0 belief=0.980029 counts=(array([0., 1.]), array([687, 14]))\n\n**************************************************\n************** C=0.01 ****************************\nClassifier's accuracy (train): 0.9809\nClassifier's accuracy (test) : 0.9749\nroot\nroot - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([124]))\nroot - Up, <cgaf> - Leaf class=0.0 belief=0.977560 counts=(array([0., 1.]), array([697, 16]))\n\n**************************************************\n************** C=1 ****************************\nClassifier's accuracy (train): 0.9869\nClassifier's accuracy (test) : 0.9749\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([129]))\nroot - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([2]))\nroot - Up, <cgaf> - Leaf class=0.0 belief=0.984419 counts=(array([0., 1.]), array([695, 11]))\n\n**************************************************\n************** C=5 ****************************\nClassifier's accuracy (train): 0.9869\nClassifier's accuracy (test) : 0.9777\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([129]))\nroot - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([2]))\nroot - Up, <cgaf> - Leaf class=0.0 belief=0.984419 counts=(array([0., 1.]), array([695, 11]))\n\n**************************************************\n************** C=17 ****************************\nClassifier's accuracy (train): 0.9916\nClassifier's accuracy (test) : 0.9833\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([131]))\nroot - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([8]))\nroot - Up\nroot - Up - Down, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([1]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([5]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Up - Up, <cgaf> - Leaf class=0.0 belief=0.989855 counts=(array([0., 1.]), array([683, 7]))\n\n**************************************************\n0.2235 secs\n"
}
],
"source": [
"t = time.time()\n",
"for C in (.001, .01, 1, 5, 17):\n",
" clf = Stree(C=C, random_state=random_state)\n",
" clf.fit(Xtrain, ytrain)\n",
" print(f\"************** C={C} ****************************\")\n",
" print(f\"Classifier's accuracy (train): {clf.score(Xtrain, ytrain):.4f}\")\n",
" print(f\"Classifier's accuracy (test) : {clf.score(Xtest, ytest):.4f}\")\n",
" print(clf)\n",
" print(f\"**************************************************\")\n",
"print(f\"{time.time() - t:.4f} secs\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from sklearn.preprocessing import StandardScaler\n",
"from sklearn.svm import LinearSVC\n",
"from sklearn.calibration import CalibratedClassifierCV\n",
"scaler = StandardScaler()\n",
"cclf = CalibratedClassifierCV(base_estimator=LinearSVC(), cv=5)\n",
"cclf.fit(Xtrain, ytrain)\n",
"res = cclf.predict_proba(Xtest)\n",
"#an array containing probabilities of belonging to the 1st class"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([131]))\nroot - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([8]))\nroot - Up\nroot - Up - Down, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([1]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([5]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Up - Up, <cgaf> - Leaf class=0.0 belief=0.989855 counts=(array([0., 1.]), array([683, 7]))\n"
}
],
"source": [
"#check iterator\n",
"for i in list(clf):\n",
" print(i)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([131]))\nroot - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([8]))\nroot - Up\nroot - Up - Down, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([1]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0.0 belief=1.000000 counts=(array([0.]), array([5]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1.0 belief=1.000000 counts=(array([1.]), array([1]))\nroot - Up - Up - Up - Up, <cgaf> - Leaf class=0.0 belief=0.989855 counts=(array([0., 1.]), array([683, 7]))\n"
}
],
"source": [
"#check iterator again\n",
"for i in clf:\n",
" print(i)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# Check if the classifier is a sklearn estimator\n",
"from sklearn.utils.estimator_checks import check_estimator\n",
"check_estimator(Stree())"
]
},
{
"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 0x12aabb320>, 'Stree')\n2 functools.partial(<function check_estimators_dtypes at 0x12aab0440>, 'Stree')\n3 functools.partial(<function check_fit_score_takes_y at 0x12aab0320>, 'Stree')\n4 functools.partial(<function check_sample_weights_pandas_series at 0x12aaaac20>, 'Stree')\n5 functools.partial(<function check_sample_weights_not_an_array at 0x12aaaad40>, 'Stree')\n6 functools.partial(<function check_sample_weights_list at 0x12aaaae60>, 'Stree')\n7 functools.partial(<function check_sample_weights_shape at 0x12aaaaf80>, 'Stree')\n8 functools.partial(<function check_sample_weights_invariance at 0x12aaac0e0>, 'Stree')\n9 functools.partial(<function check_estimators_fit_returns_self at 0x12aab6440>, 'Stree')\n10 functools.partial(<function check_estimators_fit_returns_self at 0x12aab6440>, 'Stree', readonly_memmap=True)\n11 functools.partial(<function check_complex_data at 0x12aaac290>, 'Stree')\n12 functools.partial(<function check_dtype_object at 0x12aaac200>, 'Stree')\n13 functools.partial(<function check_estimators_empty_data_messages at 0x12aab0560>, 'Stree')\n14 functools.partial(<function check_pipeline_consistency at 0x12aab0200>, 'Stree')\n15 functools.partial(<function check_estimators_nan_inf at 0x12aab0680>, 'Stree')\n16 functools.partial(<function check_estimators_overwrite_params at 0x12aabb200>, 'Stree')\n17 functools.partial(<function check_estimator_sparse_data at 0x12aaaab00>, 'Stree')\n18 functools.partial(<function check_estimators_pickle at 0x12aab08c0>, 'Stree')\n19 functools.partial(<function check_classifier_data_not_an_array at 0x12aabb560>, 'Stree')\n20 functools.partial(<function check_classifiers_one_label at 0x12aab0f80>, 'Stree')\n21 functools.partial(<function check_classifiers_classes at 0x12aab69e0>, 'Stree')\n22 functools.partial(<function check_estimators_partial_fit_n_features at 0x12aab09e0>, 'Stree')\n23 functools.partial(<function check_classifiers_train at 0x12aab60e0>, 'Stree')\n24 functools.partial(<function check_classifiers_train at 0x12aab60e0>, 'Stree', readonly_memmap=True)\n25 functools.partial(<function check_classifiers_train at 0x12aab60e0>, 'Stree', readonly_memmap=True, X_dtype='float32')\n26 functools.partial(<function check_classifiers_regression_target at 0x12aabf050>, 'Stree')\n27 functools.partial(<function check_supervised_y_no_nan at 0x12aaa0c20>, 'Stree')\n28 functools.partial(<function check_supervised_y_2d at 0x12aab6680>, 'Stree')\n29 functools.partial(<function check_estimators_unfitted at 0x12aab6560>, 'Stree')\n30 functools.partial(<function check_non_transformer_estimators_n_iter at 0x12aabbb90>, 'Stree')\n31 functools.partial(<function check_decision_proba_consistency at 0x12aabf170>, 'Stree')\n32 functools.partial(<function check_fit2d_predict1d at 0x12aaac7a0>, 'Stree')\n33 functools.partial(<function check_methods_subset_invariance at 0x12aaac950>, 'Stree')\n34 functools.partial(<function check_fit2d_1sample at 0x12aaaca70>, 'Stree')\n35 functools.partial(<function check_fit2d_1feature at 0x12aaacb90>, 'Stree')\n36 functools.partial(<function check_fit1d at 0x12aaaccb0>, 'Stree')\n37 functools.partial(<function check_get_params_invariance at 0x12aabbdd0>, 'Stree')\n38 functools.partial(<function check_set_params at 0x12aabbef0>, 'Stree')\n39 functools.partial(<function check_dict_unchanged at 0x12aaac3b0>, 'Stree')\n40 functools.partial(<function check_dont_overwrite_parameters at 0x12aaac680>, 'Stree')\n41 functools.partial(<function check_fit_idempotent at 0x12aabf320>, 'Stree')\n42 functools.partial(<function check_n_features_in at 0x12aabf3b0>, 'Stree')\n"
}
],
"source": [
"# Make checks one by one\n",
"c = 0\n",
"checks = check_estimator(Stree(), generate_only=True)\n",
"for check in checks:\n",
" c += 1\n",
" print(c, check[1])\n",
" check[1](check[0])"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.7.6 64-bit ('general': venv)",
"language": "python",
"name": "python37664bitgeneralvenvfbd0a23e74cf4e778460f5ffc6761f39"
},
"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"
}
},
"nbformat": 4,
"nbformat_minor": 2
}

View File

@@ -1,197 +0,0 @@
{
"cells": [
{
"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",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"output_type": "error",
"ename": "ModuleNotFoundError",
"evalue": "No module named 'stree'",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-12-36af63297651>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0msklearn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdatasets\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmake_blobs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0msklearn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msvm\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLinearSVC\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mstree\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mStree\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mStree_grapher\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'stree'"
]
}
],
"source": [
"import time\n",
"import random\n",
"import numpy as np\n",
"from sklearn.datasets import make_blobs\n",
"from sklearn.svm import LinearSVC\n",
"from stree import Stree, Stree_grapher"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"def build_data(random_state):\n",
" random.seed(random_state)\n",
" X, y = make_blobs(centers=10, n_features=3, n_samples=500, random_state=random_state)\n",
" def make_binary(y):\n",
" for i in range(2, 10):\n",
" y[y==i] = random.randint(0, 1)\n",
" return y\n",
" y = make_binary(y)\n",
" #print(X.shape, np.unique(y), y[y==0].shape, y[y==1].shape)\n",
" return X, y"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"output_type": "error",
"ename": "NameError",
"evalue": "name 'Stree_grapher' is not defined",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-4-b909470cb406>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mX\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0my\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbuild_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mgr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mStree_grapher\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mC\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m.01\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmax_iter\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m200\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3\u001b[0m \u001b[0mgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mX\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0my\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;31m#gr.save_all(save_folder='data/', save_prefix='7')\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'Stree_grapher' is not defined"
]
}
],
"source": [
"X, y = build_data(10)\n",
"gr = Stree_grapher(dict(C=.01, max_iter=200))\n",
"gr.fit(X, y)\n",
"#gr.save_all(save_folder='data/', save_prefix='7')"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"output_type": "error",
"ename": "NameError",
"evalue": "name 'gr' is not defined",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-5-efa3db892bfd>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'gr' is not defined"
]
}
],
"source": [
"print(gr)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"output_type": "error",
"ename": "NameError",
"evalue": "name 'gr' is not defined",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-6-0e62f081c9aa>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0muse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Agg'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave_all\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msave_folder\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'data/'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'gr' is not defined"
]
}
],
"source": [
"import matplotlib\n",
"matplotlib.use('Agg')\n",
"gr.save_all(save_folder='data/')"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"output_type": "error",
"ename": "NameError",
"evalue": "name 'gr' is not defined",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-7-b0484cfe9d26>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;31m#%matplotlib inline\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'matplotlib'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'widget'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_tree_gr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot_hyperplane\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'gr' is not defined"
]
}
],
"source": [
"#Uncomment one of the following lines to display graphics: static(inline), dynamic(widget)\n",
"#%matplotlib inline\n",
"%matplotlib widget\n",
"gr._tree_gr.plot_hyperplane()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"output_type": "error",
"ename": "NameError",
"evalue": "name 'gr' is not defined",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-8-4277c1aacbe2>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'matplotlib'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'inline'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;31m#%matplotlib widget\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot_all\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'gr' is not defined"
]
}
],
"source": [
"#Uncomment one of the following lines to display graphics: static(inline), dynamic(widget)\n",
"%matplotlib inline\n",
"#%matplotlib widget\n",
"gr.plot_all()"
]
}
],
"metadata": {
"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": "3.7.6-final"
}
},
"nbformat": 4,
"nbformat_minor": 2
}

16
pyproject.toml Normal file
View File

@@ -0,0 +1,16 @@
[tool.black]
line-length = 79
include = '\.pyi?$'
exclude = '''
/(
\.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
'''

View File

@@ -1,5 +1,4 @@
numpy
scikit-learn
pandas
matplotlib
ipympl

1
runtime.txt Normal file
View File

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

View File

@@ -1,39 +1,36 @@
import setuptools
__version__ = "0.9rc3"
__version__ = "1.0rc1"
__author__ = "Ricardo Montañana Gómez"
def readme():
with open('README.md') as f:
with open("README.md") as f:
return f.read()
setuptools.setup(
name='STree',
name="STree",
version=__version__,
license='MIT License',
description='Oblique decision tree with svm nodes',
license="MIT License",
description="Oblique decision tree with svm nodes",
long_description=readme(),
long_description_content_type='text/markdown',
long_description_content_type="text/markdown",
packages=setuptools.find_packages(),
url='https://github.com/doctorado-ml/stree',
url="https://github.com/doctorado-ml/stree",
author=__author__,
author_email='ricardo.montanana@alu.uclm.es',
keywords='scikit-learn oblique-classifier oblique-decision-tree decision-tree svm svc',
author_email="ricardo.montanana@alu.uclm.es",
keywords="scikit-learn oblique-classifier oblique-decision-tree decision-\
tree svm svc",
classifiers=[
'Development Status :: 4 - Beta',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 3.7',
'Natural Language :: English',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
'Intended Audience :: Science/Research'
],
install_requires=[
'scikit-learn>=0.23.0',
'numpy',
'matplotlib',
'ipympl'
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3.8",
"Natural Language :: English",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Intended Audience :: Science/Research",
],
install_requires=["scikit-learn", "numpy", "ipympl"],
test_suite="stree.tests",
zip_safe=False
zip_safe=False,
)

File diff suppressed because it is too large Load Diff

View File

@@ -1,184 +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 _is_pure(self) -> bool:
"""is considered pure a leaf node with one label
"""
if self.is_leaf():
return self._belief == 1.
return False
def set_axis_limits(self, limits: tuple):
self._xlimits = limits[0]
self._ylimits = limits[1]
self._zlimits = limits[2]
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 = f"{save_folder}{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():
if 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._interceptor - self._vector[0][0] * x
- self._vector[0][1] * y) / self._vector[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=.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:
pass
plt.close('all')
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) -> Stree:
"""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)
res = super().fit(X, y)
self._tree_gr = self._copy_tree(self.tree_)
self._fitted = True
return res
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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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", "Splitter"]

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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_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)

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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]), arr"
"ay([750, 750]))",
"root - Down, <cgaf> - Leaf class=0 belief= 0.928297 impurity=0.37"
"22 counts=(array([0, 1]), array([725, 56]))",
"root - Up feaures=(0, 1, 2) impurity=0.2178 counts=(array([0, 1])"
", array([ 25, 694]))",
"root - Up - Down feaures=(0, 1, 2) impurity=0.8454 counts=(array("
"[0, 1]), array([8, 3]))",
"root - Up - Down - Down, <pure> - Leaf class=0 belief= 1.000000 i"
"mpurity=0.0000 counts=(array([0]), array([7]))",
"root - Up - Down - Up, <cgaf> - Leaf class=1 belief= 0.750000 imp"
"urity=0.8113 counts=(array([0, 1]), array([1, 3]))",
"root - Up - Up, <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": 0.49066666666666664,
"impurity linear": 0.9606666666666667,
"impurity rbf": 0.7133333333333334,
"impurity poly": 0.49066666666666664,
},
"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)
self.assertEqual(0.824, clf.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))
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
)
self.assertEqual(0.786, clf.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))
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))
X, y = load_wine(return_X_y=True)
self.assertEqual(0.9550561797752809, clf.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)

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@@ -1,333 +0,0 @@
import csv
import os
import unittest
import numpy as np
from sklearn.datasets import make_classification
from stree import Stree, Snode
class Stree_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
os.environ['TESTING'] = '1'
self._random_state = 1
self._clf = Stree(random_state=self._random_state,
use_predictions=False)
self._clf.fit(*self._get_Xy())
super().__init__(*args, **kwargs)
@classmethod
def tearDownClass(cls):
try:
os.environ.pop('TESTING')
except:
pass
def _get_Xy(self):
X, y = make_classification(n_samples=1500, n_features=3, 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=self._random_state)
return X, y
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:
number_down = 0
try:
number_up = count_u[i]
except:
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
"""
self._check_tree(self._clf.tree_)
def _get_file_data(self, file_name: str) -> tuple:
"""Return X, y from data, y is the last column in array
Arguments:
file_name {str} -- the file name
Returns:
tuple -- tuple with samples, categories
"""
data = np.genfromtxt(file_name, delimiter=',')
data = np.array(data)
column_y = data.shape[1] - 1
fy = data[:, column_y]
fx = np.delete(data, column_y, axis=1)
return fx, fy
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 = self._get_Xy()
yp = self._clf.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 = self._get_Xy()
yp = self._clf.predict(X[:num, :])
self.assertListEqual(y[:num].tolist(), yp.tolist())
def test_score(self):
X, y = self._get_Xy()
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, 0.9)
def test_single_predict_proba(self):
"""Check that element 28 has a prediction different that the current label
"""
# Element 28 has a different prediction than the truth
decimals = 5
prob = 0.29026400766
X, y = self._get_Xy()
yp = self._clf.predict_proba(X[28, :].reshape(-1, X.shape[1]))
self.assertEqual(np.round(1 - prob, decimals), np.round(yp[0:, 0], decimals))
self.assertEqual(1, y[28])
self.assertAlmostEqual(
round(prob, decimals),
round(yp[0, 1], decimals),
decimals
)
def test_multiple_predict_proba(self):
# First 27 elements the predictions are the same as the truth
num = 27
decimals = 5
X, y = self._get_Xy()
yp = self._clf.predict_proba(X[:num, :])
self.assertListEqual(y[:num].tolist(), np.argmax(yp[:num], axis=1).tolist())
expected_proba = [0.88395641, 0.36746962, 0.84158767, 0.34106833, 0.14269291, 0.85193236,
0.29876058, 0.7282164, 0.85958616, 0.89517877, 0.99745224, 0.18860349,
0.30756427, 0.8318412, 0.18981198, 0.15564624, 0.25740655, 0.22923355,
0.87365959, 0.49928689, 0.95574351, 0.28761257, 0.28906333, 0.32643692,
0.29788483, 0.01657364, 0.81149083]
expected = np.round(expected_proba, decimals=decimals).tolist()
computed = np.round(yp[:, 1], decimals=decimals).tolist()
for i in range(len(expected)):
self.assertAlmostEqual(expected[i], computed[i], decimals)
def build_models(self):
"""Build and train two models, model_clf will use the sklearn classifier to
compute predictions and split data. model_computed will use vector of
coefficients to compute both predictions and splitted data
"""
model_clf = Stree(random_state=self._random_state,
use_predictions=True)
model_computed = Stree(random_state=self._random_state,
use_predictions=False)
X, y = self._get_Xy()
model_clf.fit(X, y)
model_computed.fit(X, y)
return model_clf, model_computed, X, y
def test_use_model_predict(self):
"""Check that we get the same results wether we use the estimator in nodes
to compute labels or we use the hyperplane and the position of samples wrt to it
"""
use_clf, use_math, X, _ = self.build_models()
self.assertListEqual(
use_clf.predict(X).tolist(),
use_math.predict(X).tolist()
)
def test_use_model_score(self):
use_clf, use_math, X, y = self.build_models()
b = use_math.score(X, y)
self.assertEqual(
use_clf.score(X, y),
b
)
self.assertGreater(b, .95)
def test_use_model_predict_proba(self):
use_clf, use_math, X, _ = self.build_models()
self.assertListEqual(
use_clf.predict_proba(X).tolist(),
use_math.predict_proba(X).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, _ = self._get_Xy()
# Compute prediction line by line
yp_line = np.array([], dtype=int)
for xp in X:
yp_line = np.append(yp_line, self._clf.predict(xp.reshape(-1, X.shape[1])))
# Compute prediction at once
yp_once = self._clf.predict(X)
#
self.assertListEqual(yp_line.tolist(), yp_once.tolist())
def test_iterator(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 = []
for node in self._clf:
computed.append(str(node))
self.assertListEqual(expected, computed)
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(*self._get_Xy())
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(*self._get_Xy())
def test_check_max_depth(self):
depth = 3
tcl = Stree(random_state=self._random_state, max_depth=depth)
tcl.fit(*self._get_Xy())
self.assertEqual(depth, tcl.depth_)
def test_unfitted_tree_is_iterable(self):
tcl = Stree()
self.assertEqual(0, len(list(tcl)))
class Snode_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
os.environ['TESTING'] = '1'
self._random_state = 1
self._clf = Stree(random_state=self._random_state,
use_predictions=True)
self._clf.fit(*self._get_Xy())
super().__init__(*args, **kwargs)
@classmethod
def tearDownClass(cls):
try:
os.environ.pop('TESTING')
except:
pass
def _get_Xy(self):
X, y = make_classification(n_samples=1500, n_features=3, 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=self._random_state)
return X, y
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:
belief = 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_)
self.assertIsNotNone(node._vector)
self.assertIsNotNone(node._interceptor)
if node.is_leaf():
return
run_tree(node.get_down())
run_tree(node.get_up())
run_tree(self._clf.tree_)

View File

@@ -1 +1,5 @@
from .Strees_test import Stree_test, Snode_test
from .Stree_test import Stree_test
from .Snode_test import Snode_test
from .Splitter_test import Splitter_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