aisp 0.1.42__tar.gz → 0.2.1__tar.gz

{aisp-0.1.42 → aisp-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.1.42
+Version: 0.2.1
 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>
@@ -26,6 +26,11 @@ Requires-Dist: numpy>=1.22.4
 Requires-Dist: numba>=0.59.0
 Requires-Dist: scipy>=1.8.1
 Requires-Dist: tqdm>=4.64.1
+Provides-Extra: dev
+Requires-Dist: build>=1.2.2.post1; extra == "dev"
+Requires-Dist: ipykernel>=6.29.5; extra == "dev"
+Requires-Dist: twine>=5.1.1; extra == "dev"
+Requires-Dist: pytest>=8.3.5; extra == "dev"
 Dynamic: license-file
 
 <div align = center> 
@@ -79,7 +84,8 @@ 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 +132,14 @@ 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-0.1.42 → aisp-0.2.1}/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-0.1.42 → aisp-0.2.1}/aisp/base/_classifier.py

@@ -16,10 +16,10 @@ class BaseClassifier(ABC):
     ``get_params`` method.
     """
 
-    classes: Optional[Union[npt.NDArray, list]] = None
+    classes: Union[npt.NDArray, list] = []
 
     @abstractmethod
-    def fit(self, X: npt.NDArray, y: npt.NDArray, verbose: bool = True):
+    def fit(self, X: npt.NDArray, y: npt.NDArray, verbose: bool = True) -> "BaseClassifier":
         """
         Train the model using the input data X and corresponding labels y.
 
@@ -83,6 +83,10 @@ class BaseClassifier(ABC):
         if len(y) == 0:
             return 0
         y_pred = self.predict(X)
+
+        if y_pred is None:
+            return 0
+
         return accuracy_score(y, y_pred)
 
     def _slice_index_list_by_class(self, y: npt.NDArray) -> dict:

aisp-0.2.1/aisp/base/mutation.py

@@ -0,0 +1,130 @@
+"""
+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
+
+
+@njit([(types.float64[:], types.int64, types.float64[:, :])], cache=True)
+def clone_and_mutate_ranged(
+    vector: npt.NDArray[np.float64],
+    n: int,
+    bounds: npt.NDArray[np.float64]
+) -> npt.NDArray[np.float64]:
+    """
+    Generate a set of mutated clones from a cell represented by custom ranges per dimension.
+
+    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.bool_]
+        The original immune cell with binary values to be cloned and mutated.
+    n : int
+        The number of mutated clones to be generated.
+    bounds : np.ndarray
+        Array (n_features, 2) with min and max per dimension.
+
+    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]
+            min_limit = bounds[idx, 0]
+            max_limit = bounds[idx, 1]
+            clone[idx] = np.random.uniform(min_limit, max_limit)
+        clone_set[i] = clone
+
+    return clone_set

aisp-0.2.1/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']