aisp 0.1.41__tar.gz → 0.2.0__tar.gz

{aisp-0.1.41 → aisp-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.1.41
+Version: 0.2.0
 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>
@@ -79,7 +79,8 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 ##### Algorithms implemented:
 
 > - [x] [**Negative Selection.**](https://ais-package.github.io/docs/aisp-techniques/Negative%20Selection/)
-> - [ ] *Clonal Selection Algorithms.*
+> - [x] **Clonal Selection Algorithms.**
+>     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
 > - [ ] *Dendritic Cells.*
 > - [ ] *Immune Network Theory.*
 
@@ -126,22 +127,14 @@ pip install aisp
 
 ---
 
-##### Example using the negative selection technique (**nsa**):
+Explore the example notebooks available in the [AIS-Package/aisp repository](https://github.com/AIS-Package/aisp/tree/main/examples).
+These notebooks demonstrate how to utilize the package's functionalities in various scenarios, including applications of the RNSA,
+BNSA and AIRS algorithms on datasets such as Iris, Geyser, and Mushrooms.
 
-In the example present in this [notebook](https://github.com/AIS-Package/aisp/blob/main/examples/RNSA/example_with_randomly_generated_dataset-en.ipynb), **500** random samples were generated, arranged in two groups, one for each class.
+You can run the notebooks directly in your browser without any local installation using Binder:
 
-Below are some examples that use a database for classification with the [Jupyter notebook](https://jupyter.org/) tool.
-
-
-##### **Negative Selection:**
-
-+ **RNSA** Application of negative selection techniques for classification using the Iris family flower database and Old Faithful Geyser:
-    + [iris_dataBase_example](https://github.com/AIS-Package/aisp/blob/main/examples/RNSA/iris_dataBase_example_en.ipynb)
-    + [geyser_dataBase_example](https://github.com/AIS-Package/aisp/blob/main/examples/RNSA/geyser_dataBase_example_en.ipynb)
-+ **BNSA** 
-    + [mushrooms_dataBase_example](https://github.com/AIS-Package/aisp/blob/main/examples/BNSA/mushrooms_dataBase_example_en.ipynb)
-
----
+[![Launch on Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AIS-Package/aisp/HEAD?labpath=%2Fexamples)
 
+> 💡 **Tip**: Binder may take a few minutes to load the environment, especially on the first launch.
 </section>
 </section>

{aisp-0.1.41 → aisp-0.2.0}/README.md

@@ -49,7 +49,8 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 ##### Algorithms implemented:
 
 > - [x] [**Negative Selection.**](https://ais-package.github.io/docs/aisp-techniques/Negative%20Selection/)
-> - [ ] *Clonal Selection Algorithms.*
+> - [x] **Clonal Selection Algorithms.**
+>     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
 > - [ ] *Dendritic Cells.*
 > - [ ] *Immune Network Theory.*
 
@@ -96,22 +97,14 @@ pip install aisp
 
 ---
 
-##### Example using the negative selection technique (**nsa**):
+Explore the example notebooks available in the [AIS-Package/aisp repository](https://github.com/AIS-Package/aisp/tree/main/examples).
+These notebooks demonstrate how to utilize the package's functionalities in various scenarios, including applications of the RNSA,
+BNSA and AIRS algorithms on datasets such as Iris, Geyser, and Mushrooms.
 
-In the example present in this [notebook](https://github.com/AIS-Package/aisp/blob/main/examples/RNSA/example_with_randomly_generated_dataset-en.ipynb), **500** random samples were generated, arranged in two groups, one for each class.
+You can run the notebooks directly in your browser without any local installation using Binder:
 
-Below are some examples that use a database for classification with the [Jupyter notebook](https://jupyter.org/) tool.
-
-
-##### **Negative Selection:**
-
-+ **RNSA** Application of negative selection techniques for classification using the Iris family flower database and Old Faithful Geyser:
-    + [iris_dataBase_example](https://github.com/AIS-Package/aisp/blob/main/examples/RNSA/iris_dataBase_example_en.ipynb)
-    + [geyser_dataBase_example](https://github.com/AIS-Package/aisp/blob/main/examples/RNSA/geyser_dataBase_example_en.ipynb)
-+ **BNSA** 
-    + [mushrooms_dataBase_example](https://github.com/AIS-Package/aisp/blob/main/examples/BNSA/mushrooms_dataBase_example_en.ipynb)
-
----
+[![Launch on Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AIS-Package/aisp/HEAD?labpath=%2Fexamples)
 
+> 💡 **Tip**: Binder may take a few minutes to load the environment, especially on the first launch.
 </section>
 </section>

aisp-0.2.0/aisp/__init__.py

@@ -0,0 +1,4 @@
+"""Artificial Immune Systems Package."""
+
+__author__ = "João Paulo da Silva Barros"
+__version__ = "0.1.42"

{aisp-0.1.41 → aisp-0.2.0}/aisp/base/__init__.py

@@ -1,4 +1,5 @@
 """Base class modules."""
+
 from ._classifier import BaseClassifier
 
 __all__ = ['BaseClassifier']

aisp-0.2.0/aisp/base/_classifier.py

@@ -0,0 +1,116 @@
+"""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.
+
+    Defines the abstract methods ``fit`` and ``predict``, and implements the ``score``,
+    ``get_params`` method.
+    """
+
+    classes: Optional[Union[npt.NDArray, list]] = None
+
+    @abstractmethod
+    def fit(self, X: npt.NDArray, y: npt.NDArray, verbose: bool = True):
+        """
+        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.
+        y : npt.NDArray
+            Corresponding labels or target values for the input data.
+        verbose : bool, default=True
+            Flag to enable or disable detailed output during training.
+
+        Returns
+        -------
+        self : BaseClassifier
+            Returns the instance of the class that implements this method.
+        """
+
+    @abstractmethod
+    def predict(self, X) -> Optional[npt.NDArray]:
+        """
+        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:
+        """Separate the indices of the lines according to the output class.
+
+        Loop through the sample array only in positions where the output matches 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: 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
+        """
+        Return a dictionary with the object's main parameters.
+
+        This method is required to ensure compatibility with scikit-learn functions.
+        """
+        return {
+            key: value
+            for key, value in self.__dict__.items()
+            if not key.startswith("_")
+        }

aisp-0.2.0/aisp/base/mutation.py

@@ -0,0 +1,86 @@
+"""
+The functions perform utilize Numba decorators for Just-In-Time compilation.
+
+Contains functions that generate sets of mutated clones from continuous or binary vectors,
+simulating the clonal expansion process in artificial immune systems.
+"""
+
+import numpy as np
+import numpy.typing as npt
+from numba import njit, types
+
+
+@njit([(types.float64[:], types.int64)], cache=True)
+def clone_and_mutate_continuous(
+    vector: npt.NDArray[np.float64],
+    n: int
+) -> npt.NDArray[np.float64]:
+    """
+    Generate a set of mutated clones from a cell represented by a continuous vector.
+
+    This function creates `n` clones of the input vector and applies random mutations to each of
+    them, simulating the process of clonal expansion in artificial immune systems. Each clone
+    will have a random number of mutations applied in distinct positions of the original vector.
+
+    Parameters
+    ----------
+    vector : npt.NDArray[np.float64]
+        The original immune cell with continuous values to be cloned and mutated.
+    n : int
+        The number of mutated clones to be generated.
+
+    Returns
+    -------
+    clone_set : npt.NDArray
+        An Array(n, len(vector)) containing the `n` mutated clones of the original vector.
+    """
+    n_features = vector.shape[0]
+    clone_set = np.empty((n, n_features), dtype=np.float64)
+    for i in range(n):
+        n_mutations = np.random.randint(1, n_features)
+        clone = vector.copy()
+        position_mutations = np.random.permutation(n_features)[:n_mutations]
+        for j in range(n_mutations):
+            idx = position_mutations[j]
+            clone[idx] = np.float64(np.random.random())
+        clone_set[i] = clone
+
+    return clone_set
+
+
+@njit([(types.boolean[:], types.int64)], cache=True)
+def clone_and_mutate_binary(
+    vector: npt.NDArray[np.bool_],
+    n: int
+) -> npt.NDArray[np.bool_]:
+    """
+    Generate a set of mutated clones from a cell represented by a binary vector.
+
+    This function creates `n` clones of the input vector and applies random mutations to each of
+    them, changing some bits randomly. The process simulates clonal expansion in artificial
+    immune systems with discrete representations.
+
+    Parameters
+    ----------
+    vector : npt.NDArray[np.bool_]
+        The original immune cell with binary values to be cloned and mutated.
+    n : int
+        The number of mutated clones to be generated.
+
+    Returns
+    -------
+    clone_set : npt.NDArray[np.bool_]
+        An Array(n, len(vector)) containing the `n` mutated clones of the original vector.
+    """
+    n_features = vector.shape[0]
+    clone_set = np.empty((n, n_features), dtype=np.bool_)
+    for i in range(n):
+        n_mutations = np.random.randint(1, n_features)
+        clone = vector.copy()
+        position_mutations = np.random.permutation(n_features)[:n_mutations]
+        for j in range(n_mutations):
+            idx = position_mutations[j]
+            clone[idx] = np.bool_(np.random.randint(0, 2))
+        clone_set[i] = clone
+
+    return clone_set

aisp-0.2.0/aisp/csa/__init__.py

@@ -0,0 +1,9 @@
+"""Module (CSA) Clonal Selection Algorithm.
+
+CSAs are inspired by the process of antibody proliferation upon detecting an antigen, during which
+the generated antibodies undergo mutations in an attempt to enhance pathogen recognition.
+"""
+from ._ai_immune_recognition_sys import AIRS
+
+__author__ = 'João Paulo da Silva Barros'
+__all__ = ['AIRS']