aisp 0.1.35__tar.gz → 0.1.41__tar.gz

{aisp-0.1.35 → aisp-0.1.41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.1.35
+Version: 0.1.41
 Summary: Package with techniques of artificial immune systems.
 Author-email: João Paulo da Silva Barros <jpsilvabarr@gmail.com>
 Maintainer-email: Alison Zille Lopes <alisonzille@gmail.com>
@@ -9,18 +9,21 @@ Project-URL: Homepage, https://ais-package.github.io/
 Project-URL: Documentation, https://ais-package.github.io/docs/intro
 Project-URL: Source Code, https://github.com/AIS-Package/aisp
 Project-URL: Tracker, https://github.com/AIS-Package/aisp/issues
-Keywords: Artificial Immune Systems,classification,Natural computing,machine learning,artificial intelligence
+Keywords: Artificial Immune Systems,classification,Natural computing,machine learning,artificial intelligence,AIS
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8.10
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.22.4
+Requires-Dist: numba>=0.59.0
 Requires-Dist: scipy>=1.8.1
 Requires-Dist: tqdm>=4.64.1
 Dynamic: license-file
@@ -86,7 +89,7 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 
 #### **Installation**
 
-The module requires installation of [python 3.8.10](https://www.python.org/downloads/) or higher.
+The module requires installation of [python 3.10](https://www.python.org/downloads/) or higher.
 
 <section id='dependencies'>
 
@@ -99,6 +102,7 @@ The module requires installation of [python 3.8.10](https://www.python.org/downl
 |    numpy      |    ≥ 1.22.4   |
 |    scipy      |    ≥ 1.8.1    |
 |    tqdm       |    ≥ 4.64.1   |
+|    numba      |    ≥ 0.59.0   |
 
 </div>
 

{aisp-0.1.35 → aisp-0.1.41}/README.md

@@ -59,7 +59,7 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 
 #### **Installation**
 
-The module requires installation of [python 3.8.10](https://www.python.org/downloads/) or higher.
+The module requires installation of [python 3.10](https://www.python.org/downloads/) or higher.
 
 <section id='dependencies'>
 
@@ -72,6 +72,7 @@ The module requires installation of [python 3.8.10](https://www.python.org/downl
 |    numpy      |    ≥ 1.22.4   |
 |    scipy      |    ≥ 1.8.1    |
 |    tqdm       |    ≥ 4.64.1   |
+|    numba      |    ≥ 0.59.0   |
 
 </div>
 

{aisp-0.1.35 → aisp-0.1.41}/aisp/__init__.py

@@ -1,4 +1,4 @@
 """Artificial Immune Systems Package"""
 
 __author__ = "João Paulo da Silva Barros"
-__version__ = "0.1.35"
+__version__ = "0.1.40"

aisp-0.1.41/aisp/base/__init__.py

@@ -0,0 +1,4 @@
+"""Base class modules."""
+from ._classifier import BaseClassifier
+
+__all__ = ['BaseClassifier']

aisp-0.1.41/aisp/base/_classifier.py

@@ -0,0 +1,110 @@
+"""Base class for classification algorithm."""
+
+from abc import ABC, abstractmethod
+from typing import Optional, Union
+
+import numpy.typing as npt
+
+from ..utils import slice_index_list_by_class
+from ..utils.metrics import accuracy_score
+
+
+class BaseClassifier(ABC):
+    """
+    Base class for classification algorithms, defining the abstract methods ``fit`` and ``predict``,
+    and implementing the ``get_params`` method.
+    """
+
+    classes: Optional[Union[npt.NDArray, list]] = None
+
+    @abstractmethod
+    def fit(self, X: npt.NDArray, y: npt.NDArray, verbose: bool = True):
+        """
+        Function to train the model using the input data ``X`` and corresponding labels ``y``.
+
+        This abstract method is implemented by the class that inherits it.
+
+        Parameters
+        ----------
+        * X (``npt.NDArray``): Input data used for training the model, previously normalized to the
+            range [0, 1].
+        * y (``npt.NDArray``): Corresponding labels or target values for the input data.
+        * verbose (``bool``, optional): Flag to enable or disable detailed output during training.
+            Default is ``True``.
+
+        Returns
+        ----------
+        * self: Returns the instance of the class that implements this method.
+        """
+
+    @abstractmethod
+    def predict(self, X) -> Optional[npt.NDArray]:
+        """
+        Function to generate predictions based on the input data ``X``.
+
+        This abstract method is implemented by the class that inherits it.
+
+        Parameters
+        ----------
+        * X (``npt.NDArray``): Input data for which predictions will be generated.
+
+        Returns
+        ----------
+        * Predictions (``Optional[npt.NDArray]``): Predicted values for each input sample, or
+            ``None`` if the prediction fails.
+        """
+
+    def score(self, X: npt.NDArray, y: list) -> float:
+        """
+        Score function calculates forecast accuracy.
+
+        Details
+        ----------
+        This function performs the prediction of X and checks how many elements are equal
+        between vector y and y_predicted. This function was added for compatibility with some
+        scikit-learn functions.
+
+        Parameters
+        ----------
+        * X (``np.ndarray``):
+            Feature set with shape (n_samples, n_features).
+        * y (``np.ndarray``):
+            True values with shape (n_samples,).
+
+        Returns
+        ----------
+        * accuracy (``float``): The accuracy of the model.
+        """
+        if len(y) == 0:
+            return 0
+        y_pred = self.predict(X)
+        return accuracy_score(y, y_pred)
+
+    def _slice_index_list_by_class(self, y: npt.NDArray) -> dict:
+        """
+        The function ``_slice_index_list_by_class(...)``, separates the indices of the lines \
+        according to the output class, to loop through the sample array, only in positions where \
+        the output is the class being trained.
+
+        Parameters
+        ----------
+        * y (npt.NDArray): Receives a ``y``[``N sample``] array with the output classes of the \
+            ``X`` sample array.
+
+        returns
+        ----------
+        * dict: A dictionary with the list of array positions(``y``), with the classes as key.
+        """
+        return slice_index_list_by_class(self.classes, y)
+
+    def get_params(self, deep: bool = True) -> dict:  # pylint: disable=W0613
+        """
+        The get_params function Returns a dictionary with the object's main parameters.
+
+        This function is required to ensure compatibility with scikit-learn functions.
+        """
+        return {
+            key: value
+            for key, value in self.__dict__.items()
+            if not key.startswith("_")
+        }

{aisp-0.1.35 → aisp-0.1.41}/aisp/nsa/__init__.py

@@ -8,4 +8,4 @@ from ._negative_selection import BNSA, RNSA
 
 __author__ = "João Paulo da Silva Barros"
 __all__ = ["RNSA", "BNSA"]
-__version__ = "0.1.35"
+__version__ = "0.1.40"

aisp-0.1.41/aisp/nsa/_base.py

@@ -0,0 +1,118 @@
+"""Base Class for Negative Selection Algorithm."""
+
+from abc import ABC
+from dataclasses import dataclass
+from typing import Literal, Optional
+
+import numpy as np
+import numpy.typing as npt
+
+from ..base import BaseClassifier
+from ..exceptions import FeatureDimensionMismatch
+
+
+class BaseNSA(BaseClassifier, ABC):
+    """
+    The base class contains functions that are used by more than one class in the package, and
+    therefore are considered essential for the overall functioning of the system.
+    """
+
+    @staticmethod
+    def _check_and_raise_exceptions_fit(
+        X: npt.NDArray = None,
+        y: npt.NDArray = None,
+        _class_: Literal["RNSA", "BNSA"] = "RNSA",
+    ) -> None:
+        """
+        Function responsible for verifying fit function parameters and throwing exceptions if the
+        verification is not successful.
+
+        Parameters
+        ----------
+        * X (``npt.NDArray``) Training array, containing the samples and their
+            characteristics, [``N samples`` (rows)][``N features`` (columns)].
+        * y (``npt.NDArray``) Array of target classes of ``X`` with [``N samples`` (lines)].
+        * _class_ (``Literal[RNSA, BNSA], optional``) Current class. Defaults to 'RNSA'.
+
+        Raises
+        ----------
+        * TypeError: If X or y are not ndarrays or have incompatible shapes.
+        * ValueError: If _class_ is BNSA and X contains values that are not composed only of
+            0 and 1.
+        """
+        if isinstance(X, list):
+            X = np.array(X)
+        if isinstance(y, list):
+            y = np.array(y)
+
+        if not isinstance(X, np.ndarray):
+            raise TypeError("X is not an ndarray or list.")
+        if not isinstance(y, np.ndarray):
+            raise TypeError("y is not an ndarray or list.")
+
+        if X.shape[0] != y.shape[0]:
+            raise TypeError(
+                "X does not have the same amount of sample for the output classes in y."
+            )
+
+        if _class_ == "BNSA" and not np.isin(X, [0, 1]).all():
+            raise ValueError(
+                "The array X contains values that are not composed only of 0 and 1."
+            )
+
+    @staticmethod
+    def _check_and_raise_exceptions_predict(
+        X: npt.NDArray = None,
+        expected: int = 0,
+        _class_: Literal["RNSA", "BNSA"] = "RNSA",
+    ) -> None:
+        """
+        Function responsible for verifying predict function parameters and throwing exceptions if
+        the verification is not successful.
+
+        Parameters
+        ----------
+        * X (``npt.NDArray``)
+            Input array for prediction, containing the samples and their characteristics,
+            [``N samples`` (rows)][``N features`` (columns)].
+        * expected (``int``)
+            Expected number of features per sample (columns in X).
+        * _class_ (``Literal[RNSA, BNSA], optional``)
+            Current class. Defaults to 'RNSA'.
+
+        Raises
+        ----------
+        * TypeError: If X is not an ndarray or list.
+        * FeatureDimensionMismatch: If the number of features in X does not match the expected
+            number.
+        * ValueError: If _class_ is BNSA and X contains values that are not composed only of 0
+        and 1.
+        """
+        if not isinstance(X, (np.ndarray, list)):
+            raise TypeError("X is not an ndarray or list")
+        if expected != len(X[0]):
+            raise FeatureDimensionMismatch(expected, len(X[0]), "X")
+
+        if _class_ != "BNSA":
+            return
+
+        # Checks if matrix X contains only binary samples. Otherwise, raises an exception.
+        if not np.isin(X, [0, 1]).all():
+            raise ValueError(
+                "The array X contains values that are not composed only of 0 and 1."
+            )
+
+
+@dataclass(slots=True)
+class Detector:
+    """
+    Represents a non-self detector of the RNSA class.
+
+    Attributes
+    ----------
+    * position (``npt.NDArray[np.float64]``): Detector feature vector.
+    * radius (``float, optional``): Detector radius, used in the V-detector algorithm.
+    """
+
+    position: npt.NDArray[np.float64]
+    radius: Optional[float] = None