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Update doc and version 1.30 (#55)
* Add complete classes counts to node and tests * Implement optimized predict and new predict_proba * Add predict_proba test * Add python 3.10 to CI * Update version number and documentation
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Ricardo Montañana Gómez
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@@ -50,7 +50,8 @@ Can be found in [stree.readthedocs.io](https://stree.readthedocs.io/en/stable/)
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| | 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. |
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| | min_samples_split | \<int\> | 0 | The minimum number of samples required to split an internal node. 0 (default) for any |
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| | 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. |
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| | splitter | {"best", "random", "trandom", "mutual", "cfs", "fcbf", "iwss"} | "random" | The strategy used to choose the feature set at each node (only used if max_features < num_features). Supported strategies are: **“best”**: sklearn SelectKBest algorithm is used in every node to choose the max_features best features. **“random”**: The algorithm generates 5 candidates and choose the best (max. info. gain) of them. **“trandom”**: The algorithm generates only one random combination. **"mutual"**: Chooses the best features w.r.t. their mutual info with the label. **"cfs"**: Apply Correlation-based Feature Selection. **"fcbf"**: Apply Fast Correlation-Based Filter. **"iwss"**: IWSS based algorithm |
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| | splitter | {"best", "random", "trandom", "mutual", "cfs", "fcbf", "iwss"} | "random" | The strategy used to choose the feature set at each node (only used if max_features < num_features).
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Supported strategies are: **“best”**: sklearn SelectKBest algorithm is used in every node to choose the max_features best features. **“random”**: The algorithm generates 5 candidates and choose the best (max. info. gain) of them. **“trandom”**: The algorithm generates only one random combination. **"mutual"**: Chooses the best features w.r.t. their mutual info with the label. **"cfs"**: Apply Correlation-based Feature Selection. **"fcbf"**: Apply Fast Correlation-Based Filter. **"iwss"**: IWSS based algorithm |
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| | normalize | \<bool\> | False | If standardization of features should be applied on each node with the samples that reach it |
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| \* | multiclass_strategy | {"ovo", "ovr"} | "ovo" | Strategy to use with multiclass datasets, **"ovo"**: one versus one. **"ovr"**: one versus rest |
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@@ -12,19 +12,18 @@
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#
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import os
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import sys
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import stree
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from stree._version import __version__
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sys.path.insert(0, os.path.abspath("../../stree/"))
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# -- Project information -----------------------------------------------------
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project = "STree"
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copyright = "2020 - 2021, Ricardo Montañana Gómez"
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copyright = "2020 - 2022, Ricardo Montañana Gómez"
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author = "Ricardo Montañana Gómez"
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# The full version, including alpha/beta/rc tags
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version = stree.__version__
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version = __version__
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release = version
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@@ -3,20 +3,20 @@
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| | **Hyperparameter** | **Type/Values** | **Default** | **Meaning** |
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| --- | ------------------- | -------------------------------------------------------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| \* | C | \<float\> | 1.0 | Regularization parameter. The strength of the regularization is inversely proportional to C. Must be strictly positive. |
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| \* | kernel | {"liblinear", "linear", "poly", "rbf", "sigmoid"} | linear | Specifies the kernel type to be used in the algorithm. It must be one of ‘liblinear’, ‘linear’, ‘poly’ or ‘rbf’. liblinear uses [liblinear](https://www.csie.ntu.edu.tw/~cjlin/liblinear/) library and the rest uses [libsvm](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) library through scikit-learn library |
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| \* | kernel | {"liblinear", "linear", "poly", "rbf", "sigmoid"} | linear | Specifies the kernel type to be used in the algorithm. It must be one of ‘liblinear’, ‘linear’, ‘poly’ or ‘rbf’.<br>liblinear uses [liblinear](https://www.csie.ntu.edu.tw/~cjlin/liblinear/) library and the rest uses [libsvm](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) library through scikit-learn library |
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| \* | max_iter | \<int\> | 1e5 | Hard limit on iterations within solver, or -1 for no limit. |
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| \* | 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 |
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| | max_depth | \<int\> | None | Specifies the maximum depth of the tree |
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| \* | tol | \<float\> | 1e-4 | Tolerance for stopping criterion. |
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| \* | degree | \<int\> | 3 | Degree of the polynomial kernel function (‘poly’). Ignored by all other kernels. |
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| \* | gamma | {"scale", "auto"} or \<float\> | scale | Kernel coefficient for ‘rbf’, ‘poly’ and ‘sigmoid’.<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. |
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| | 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\*\*. max_samples is incompatible with 'ovo' multiclass_strategy |
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| | 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. |
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| | 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\*\*.<br>max_samples is incompatible with 'ovo' multiclass_strategy |
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| | 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. |
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| | min_samples_split | \<int\> | 0 | The minimum number of samples required to split an internal node. 0 (default) for any |
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| | 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. |
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| | splitter | {"best", "random", "trandom", "mutual", "cfs", "fcbf", "iwss"} | "random" | The strategy used to choose the feature set at each node (only used if max_features < num_features). Supported strategies are: **“best”**: sklearn SelectKBest algorithm is used in every node to choose the max_features best features. **“random”**: The algorithm generates 5 candidates and choose the best (max. info. gain) of them. **“trandom”**: The algorithm generates only one random combination. **"mutual"**: Chooses the best features w.r.t. their mutual info with the label. **"cfs"**: Apply Correlation-based Feature Selection. **"fcbf"**: Apply Fast Correlation-Based Filter. **"iwss"**: IWSS based algorithm |
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| | splitter | {"best", "random", "trandom", "mutual", "cfs", "fcbf", "iwss"} | "random" | The strategy used to choose the feature set at each node (only used if max_features < num_features).<br>Supported strategies are:<br>**“best”**: sklearn SelectKBest algorithm is used in every node to choose the max_features best features.<br>**“random”**: The algorithm generates 5 candidates and choose the best (max. info. gain) of them.<br>**“trandom”**: The algorithm generates only one random combination.<br>**"mutual"**: Chooses the best features w.r.t. their mutual info with the label.<br>**"cfs"**: Apply Correlation-based Feature Selection.<br>**"fcbf"**: Apply Fast Correlation-Based Filter.<br>**"iwss"**: IWSS based algorithm |
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| | normalize | \<bool\> | False | If standardization of features should be applied on each node with the samples that reach it |
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| \* | multiclass_strategy | {"ovo", "ovr"} | "ovo" | Strategy to use with multiclass datasets, **"ovo"**: one versus one. **"ovr"**: one versus rest |
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| \* | multiclass_strategy | {"ovo", "ovr"} | "ovo" | Strategy to use with multiclass datasets:<br>**"ovo"**: one versus one.<br>**"ovr"**: one versus rest |
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\* Hyperparameter used by the support vector classifier of every node
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12
setup.py
12
setup.py
@@ -7,9 +7,8 @@ def readme():
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return f.read()
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def get_data(field):
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def get_data(field, file_name="__init__.py"):
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item = ""
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file_name = "_version.py" if field == "version" else "__init__.py"
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with open(os.path.join("stree", file_name)) as f:
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for line in f.readlines():
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if line.startswith(f"__{field}__"):
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@@ -21,9 +20,14 @@ def get_data(field):
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return item
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def get_requirements():
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with open("requirements.txt") as f:
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return f.read().splitlines()
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setuptools.setup(
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name="STree",
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version=get_data("version"),
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version=get_data("version", "_version.py"),
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license=get_data("license"),
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description="Oblique decision tree with svm nodes",
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long_description=readme(),
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@@ -46,7 +50,7 @@ setuptools.setup(
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"Topic :: Scientific/Engineering :: Artificial Intelligence",
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"Intended Audience :: Science/Research",
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],
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install_requires=["scikit-learn", "mufs"],
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install_requires=get_requirements(),
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test_suite="stree.tests",
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zip_safe=False,
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)
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@@ -368,6 +368,21 @@ class Stree(BaseEstimator, ClassifierMixin):
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)
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def __predict_class(self, X: np.array) -> np.array:
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"""Compute the predicted class for the samples in X. Returns the number
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of samples of each class in the corresponding leaf node.
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Parameters
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----------
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X : np.array
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Array of samples
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Returns
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-------
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np.array
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Array of shape (n_samples, n_classes) with the number of samples
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of each class in the corresponding leaf node
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"""
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def compute_prediction(xp, indices, node):
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if xp is None:
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return
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@@ -388,6 +403,25 @@ class Stree(BaseEstimator, ClassifierMixin):
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return result
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def check_predict(self, X) -> np.array:
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"""Checks predict and predict_proba preconditions. If input X is not an
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np.array convert it to one.
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Parameters
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----------
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X : np.ndarray
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Array of samples
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Returns
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-------
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np.array
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Array of samples
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Raises
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------
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ValueError
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If number of features of X is different of the number of features
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in training data
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"""
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check_is_fitted(self, ["tree_"])
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# Input validation
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X = check_array(X)
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@@ -1 +1 @@
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__version__ = "1.2.4"
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__version__ = "1.3.0"
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