aisp 0.2.1__tar.gz → 0.3.0__tar.gz

{aisp-0.2.1 → aisp-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.2.1
+Version: 0.3.0
 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>
@@ -84,10 +84,11 @@ 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/)
-> - [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.*
+> - [x] [**Clonal Selection Algorithms.**](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
+>     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/airs/)
+> - [ ] *Danger Theory.*
+> - [x] [*Immune Network Theory.*](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory)
+>   - [AiNet - Artificial Immune Network para Clustering and Compression](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory/ainet)
 
 </section>
 

{aisp-0.2.1 → aisp-0.3.0}/README.md

@@ -49,10 +49,11 @@ 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/)
-> - [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.*
+> - [x] [**Clonal Selection Algorithms.**](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
+>     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/airs/)
+> - [ ] *Danger Theory.*
+> - [x] [*Immune Network Theory.*](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory)
+>   - [AiNet - Artificial Immune Network para Clustering and Compression](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory/ainet)
 
 </section>
 

{aisp-0.2.1 → aisp-0.3.0}/aisp/__init__.py

@@ -1,4 +1,4 @@
 """Artificial Immune Systems Package."""
 
 __author__ = "João Paulo da Silva Barros"
-__version__ = "0.1.42"
+__version__ = "0.3.0"

aisp-0.3.0/aisp/base/__init__.py

@@ -0,0 +1,7 @@
+"""Base class modules."""
+
+from ._classifier import BaseClassifier
+from ._clusterer import BaseClusterer
+from ._base import set_seed_numba
+
+__all__ = ['BaseClassifier', 'BaseClusterer', 'set_seed_numba']

aisp-0.3.0/aisp/base/_base.py

@@ -0,0 +1,65 @@
+"""Base class for parameter introspection compatible with the scikit-learn API."""
+import random
+
+import numpy as np
+from numba import njit
+
+
+class Base:
+    """
+    Generic base class for models with a common interface.
+
+    Provides the ``get_params`` and ``set_params`` method for compatibility with
+    the scikit-learn API, allowing access to the model's public parameters.
+    """
+
+    def set_params(self, **params):
+        """
+        Set the parameters of the instance.
+
+        This method is required to ensure compatibility with scikit-learn functions
+
+        Parameters
+        ----------
+        **params
+            set as attributes on the instance.
+
+        Returns
+        -------
+        self
+        """
+        for key, value in params.items():
+            if not key.startswith("_") and hasattr(self, key):
+                setattr(self, key, value)
+        return self
+
+    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.
+
+        Returns
+        -------
+        dict
+            Dictionary containing the object's attributes that do not start with "_".
+        """
+        return {
+            key: value
+            for key, value in self.__dict__.items()
+            if not key.startswith("_")
+        }
+
+
+@njit(cache=True)
+def set_seed_numba(seed: int):
+    """
+    Set the seed for random numbers used by functions compiled with Numba.
+
+    Parameters
+    ----------
+    seed : int
+        Integer value used to initialize Numba's random number generator.
+    """
+    np.random.seed(seed)
+    random.seed(seed)

{aisp-0.2.1 → aisp-0.3.0}/aisp/base/_classifier.py

@@ -5,15 +5,15 @@ from typing import Optional, Union
 
 import numpy.typing as npt
 
+from ._base import Base
 from ..utils import slice_index_list_by_class
 from ..utils.metrics import accuracy_score
 
 
-class BaseClassifier(ABC):
+class BaseClassifier(ABC, Base):
     """Base class for classification algorithms.
 
-    Defines the abstract methods ``fit`` and ``predict``, and implements the ``score``,
-    ``get_params`` method.
+    Defines the abstract methods ``fit`` and ``predict``, and implements the ``score`` method.
     """
 
     classes: Union[npt.NDArray, list] = []
@@ -106,15 +106,3 @@ class BaseClassifier(ABC):
             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-0.3.0/aisp/base/_clusterer.py

@@ -0,0 +1,76 @@
+"""Base class for clustering algorithms."""
+
+from abc import ABC, abstractmethod
+from typing import Optional
+
+import numpy.typing as npt
+
+from ._base import Base
+
+
+class BaseClusterer(ABC, Base):
+    """Abstract base class for clustering algorithms.
+
+    This class defines the core interface for clustering models. It enforces
+    the implementation of the `fit` and `predict` methods in all derived classes,
+    and provides a default implementation for `fit_predict` and `get_params`.
+    """
+
+    @abstractmethod
+    def fit(self, X: npt.NDArray, verbose: bool = True) -> "BaseClusterer":
+        """
+        Train the model using the input data X.
+
+        This abstract method is implemented by the class that inherits it.
+
+        Parameters
+        ----------
+        X : npt.NDArray
+            Input data used for training the model.
+        verbose : bool, default=True
+            Flag to enable or disable detailed output during training.
+
+        Returns
+        -------
+        self : BaseClusterer
+            Returns the instance of the class that implements this method.
+        """
+
+    @abstractmethod
+    def predict(self, X: npt.NDArray) -> 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 cluster labels for each input sample, or None if prediction is not possible.
+        """
+
+    def fit_predict(self, X, verbose: bool = True):
+        """Fit the clustering model to the data and return cluster labels.
+
+        This is a convenience method that combines `fit` and `predict`
+        into a single call.
+
+        Parameters
+        ----------
+        X : npt.NDArray
+            Input data for which predictions will be generated.
+        verbose : bool, default=True
+            Flag to enable or disable detailed output during training.
+
+        Returns
+        -------
+        predictions : Optional[npt.NDArray]
+            Predicted cluster labels for each input sample, or None if prediction is not possible.
+        """
+        self.fit(X, verbose)
+        return self.predict(X)

{aisp-0.2.1 → aisp-0.3.0}/aisp/csa/__init__.py

@@ -3,7 +3,7 @@
 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
+from ._ai_recognition_sys import AIRS
 
 __author__ = 'João Paulo da Silva Barros'
 __all__ = ['AIRS']

aisp-0.2.1/aisp/csa/_ai_immune_recognition_sys.py → aisp-0.3.0/aisp/csa/_ai_recognition_sys.py

@@ -11,7 +11,7 @@ import numpy.typing as npt
 from scipy.spatial.distance import pdist
 from tqdm import tqdm
 
-
+from ..base import set_seed_numba
 from ._cell import Cell
 from ..utils.sanitizers import sanitize_param, sanitize_seed, sanitize_choice
 from ..utils.distance import hamming, compute_metric_distance, get_metric_code
@@ -178,6 +178,7 @@ class AIRS(BaseAIRS):
         self.seed: Optional[int] = sanitize_seed(seed)
         if self.seed is not None:
             np.random.seed(self.seed)
+            set_seed_numba(self.seed)
 
         self._feature_type: FeatureType = "continuous-features"
 
@@ -219,8 +220,6 @@ class AIRS(BaseAIRS):
         AIRS
             Returns the instance itself.
         """
-        progress = None
-
         self._feature_type = detect_vector_data_type(X)
 
         super()._check_and_raise_exceptions_fit(X, y)
@@ -234,18 +233,17 @@ class AIRS(BaseAIRS):
 
         self.classes = np.unique(y)
         sample_index = self._slice_index_list_by_class(y)
-        if verbose:
-            progress = tqdm(
-                total=len(y),
-                postfix="\n",
-                bar_format="{desc} ┇{bar}┇ {n}/{total} memory cells for each aᵢ",
-            )
+        progress = tqdm(
+            total=len(y),
+            postfix="\n",
+            disable=not verbose,
+            bar_format="{desc} ┇{bar}┇ {n}/{total} memory cells for each aᵢ",
+        )
         pool_cells_classes = {}
         for _class_ in self.classes:
-            if verbose and progress is not None:
-                progress.set_description_str(
-                    f"Generating the memory cells for the {_class_} class:"
-                )
+            progress.set_description_str(
+                f"Generating the memory cells for the {_class_} class:"
+            )
 
             x_class = X[sample_index[_class_]]
             # Calculating the similarity threshold between antigens
@@ -294,15 +292,14 @@ class AIRS(BaseAIRS):
                     if self._affinity(c_candidate.vector, c_match.vector) < sufficiently_similar:
                         pool_c.remove(c_match)
 
-                if verbose and progress is not None:
-                    progress.update(1)
+                progress.update(1)
             pool_cells_classes[_class_] = pool_c
 
-        if verbose and progress is not None:
-            progress.set_description(
-                f"\033[92m✔ Set of memory cells for classes ({', '.join(map(str, self.classes))}) "
-                f"successfully generated\033[0m"
-            )
+        progress.set_description(
+            f"\033[92m✔ Set of memory cells for classes ({', '.join(map(str, self.classes))}) "
+            f"successfully generated\033[0m"
+        )
+        progress.close()
         self._cells_memory = pool_cells_classes
         return self
 

aisp-0.3.0/aisp/ina/__init__.py

@@ -0,0 +1,14 @@
+"""Module (ina) Immune Network Algorithm.
+
+This module implements algorithms based on Network Theory Algorithms proposed by Jerne.
+
+Classes
+-------
+AiNet
+    Artificial Immune Network implementation for clustering.
+"""
+
+from ._ai_network import AiNet
+
+__author__ = 'João Paulo da Silva Barros'
+__all__ = ['AiNet']