mlquantify 0.1.3__tar.gz → 0.1.4__tar.gz

{mlquantify-0.1.3/mlquantify.egg-info → mlquantify-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlquantify
-Version: 0.1.3
+Version: 0.1.4
 Summary: Quantification Library
 Home-page: https://github.com/luizfernandolj/QuantifyML/tree/master
 Maintainer: Luiz Fernando Luth Junior
@@ -40,9 +40,9 @@ ___
 
 ## Latest Release
 
-- **Version 0.0.11.6**: Inicial beta version. For a detailed list of changes, check the [changelog](#).
-- In case you need any help, refer to the [wiki](https://github.com/luizfernandolj/mlquantify/wiki).
-- Explore the [API documentation](#) for detailed developer information.
+- **Version 0.1.3**: Inicial beta version. For a detailed list of changes, check the [changelog](#).
+- In case you need any help, refer to the [User Guide](https://luizfernandolj.github.io/mlquantify/user_guide.html).
+- Explore the [API documentation](https://luizfernandolj.github.io/mlquantify/api/index.html) for detailed developer information.
 - See also the library in the pypi site in [pypi mlquantify](https://pypi.org/project/mlquantify/)
 
 ___
@@ -70,7 +70,7 @@ ___
 | **21 Quantification Methods** | Methods for quantification, such as classify & Count Correct methods, Threshold Optimization, Mixture Models and more.|
 | **Dynamic class management** | All methods are dynamic, and handles multiclass and binary problems, in case of binary it makes One-Vs-All (OVA) automatically. |
 | **Model Selection** | Criteria and processes used to select the best model, such as grid-search for the case of quantification|
-| **Evaluation Metrics** | Specific metrics used to evaluate quantification performance, (e.g., AE, BIAS, NAE, SE, KLD, etc.). |
+| **Evaluation Metrics** | Specific metrics used to evaluate quantification performance, (e.g., AE, MAE, NAE, SE, KLD, etc.). |
 | **Evaluation Protocols** | Evaluation protocols used, based on sampling generation (e.g., APP, NPP, etc.).. |
 | **Plotting Results** | Tools and techniques used to visualize results, such as the protocol results.|
 | **Comprehensive Documentation** | Complete documentation of the project, including code, data, and results. |
@@ -82,7 +82,10 @@ ___
 This code first loads the breast cancer dataset from _sklearn_, which is then split into training and testing sets. It uses the _Expectation Maximisation Quantifier (EMQ)_ with a RandomForest classifier to predict class prevalence. After training the model, it evaluates performance by calculating and printing the absolute error and bias between the real and predicted prevalences.
 
 ```python
-import mlquantify as mq
+from mlquantify.methods import EMQ
+from mlquantify.evaluation.measures import absolute_error, mean_absolute_error
+from mlquantify.utils import get_real_prev
+
 from sklearn.ensemble import RandomForestClassifier
 from sklearn.datasets import load_breast_cancer
 from sklearn.model_selection import train_test_split
@@ -94,19 +97,19 @@ features, target = load_breast_cancer(return_X_y=True)
 X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.3)
 
 #Create the model, here it is the Expectation Maximisation Quantifier (EMQ) with a classifier
-model = mq.methods.EMQ(RandomForestClassifier())
+model = EMQ(RandomForestClassifier())
 model.fit(X_train, y_train)
 
 #Predict the class prevalence for X_test
 pred_prevalence = model.predict(X_test)
-real_prevalence = mq.utils.get_real_prev(y_test)
+real_prevalence = get_real_prev(y_test)
 
 #Get the error for the prediction
-ae = mq.evaluation.absolute_error(real_prevalence, pred_prevalence)
-bias = mq.evaluation.bias(real_prevalence, pred_prevalence)
+ae = absolute_error(real_prevalence, pred_prevalence)
+mae = mean_absolute_error(real_prevalence, pred_prevalence)
 
-print(f"Mean Squared Error (MSE) -> {ae:.4f}")
-print(f"Bias -> {bias}")
+print(f"Absolute Error -> {ae}")
+print(f"Mean Absolute Error -> {mae}")
 ```
 
 ___
@@ -125,7 +128,7 @@ ___
 
 ## Documentation
 
-##### API is avaliable [here](#)
+##### API is avaliable [here](https://luizfernandolj.github.io/mlquantify/api/index.html)
 
 - [Methods](https://github.com/luizfernandolj/mlquantify/wiki/Methods)
 - [Model Selection](https://github.com/luizfernandolj/mlquantify/wiki/Model-Selection)

{mlquantify-0.1.3 → mlquantify-0.1.4}/README.md

@@ -9,9 +9,9 @@ ___
 
 ## Latest Release
 
-- **Version 0.0.11.6**: Inicial beta version. For a detailed list of changes, check the [changelog](#).
-- In case you need any help, refer to the [wiki](https://github.com/luizfernandolj/mlquantify/wiki).
-- Explore the [API documentation](#) for detailed developer information.
+- **Version 0.1.3**: Inicial beta version. For a detailed list of changes, check the [changelog](#).
+- In case you need any help, refer to the [User Guide](https://luizfernandolj.github.io/mlquantify/user_guide.html).
+- Explore the [API documentation](https://luizfernandolj.github.io/mlquantify/api/index.html) for detailed developer information.
 - See also the library in the pypi site in [pypi mlquantify](https://pypi.org/project/mlquantify/)
 
 ___
@@ -39,7 +39,7 @@ ___
 | **21 Quantification Methods** | Methods for quantification, such as classify & Count Correct methods, Threshold Optimization, Mixture Models and more.|
 | **Dynamic class management** | All methods are dynamic, and handles multiclass and binary problems, in case of binary it makes One-Vs-All (OVA) automatically. |
 | **Model Selection** | Criteria and processes used to select the best model, such as grid-search for the case of quantification|
-| **Evaluation Metrics** | Specific metrics used to evaluate quantification performance, (e.g., AE, BIAS, NAE, SE, KLD, etc.). |
+| **Evaluation Metrics** | Specific metrics used to evaluate quantification performance, (e.g., AE, MAE, NAE, SE, KLD, etc.). |
 | **Evaluation Protocols** | Evaluation protocols used, based on sampling generation (e.g., APP, NPP, etc.).. |
 | **Plotting Results** | Tools and techniques used to visualize results, such as the protocol results.|
 | **Comprehensive Documentation** | Complete documentation of the project, including code, data, and results. |
@@ -51,7 +51,10 @@ ___
 This code first loads the breast cancer dataset from _sklearn_, which is then split into training and testing sets. It uses the _Expectation Maximisation Quantifier (EMQ)_ with a RandomForest classifier to predict class prevalence. After training the model, it evaluates performance by calculating and printing the absolute error and bias between the real and predicted prevalences.
 
 ```python
-import mlquantify as mq
+from mlquantify.methods import EMQ
+from mlquantify.evaluation.measures import absolute_error, mean_absolute_error
+from mlquantify.utils import get_real_prev
+
 from sklearn.ensemble import RandomForestClassifier
 from sklearn.datasets import load_breast_cancer
 from sklearn.model_selection import train_test_split
@@ -63,19 +66,19 @@ features, target = load_breast_cancer(return_X_y=True)
 X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.3)
 
 #Create the model, here it is the Expectation Maximisation Quantifier (EMQ) with a classifier
-model = mq.methods.EMQ(RandomForestClassifier())
+model = EMQ(RandomForestClassifier())
 model.fit(X_train, y_train)
 
 #Predict the class prevalence for X_test
 pred_prevalence = model.predict(X_test)
-real_prevalence = mq.utils.get_real_prev(y_test)
+real_prevalence = get_real_prev(y_test)
 
 #Get the error for the prediction
-ae = mq.evaluation.absolute_error(real_prevalence, pred_prevalence)
-bias = mq.evaluation.bias(real_prevalence, pred_prevalence)
+ae = absolute_error(real_prevalence, pred_prevalence)
+mae = mean_absolute_error(real_prevalence, pred_prevalence)
 
-print(f"Mean Squared Error (MSE) -> {ae:.4f}")
-print(f"Bias -> {bias}")
+print(f"Absolute Error -> {ae}")
+print(f"Mean Absolute Error -> {mae}")
 ```
 
 ___
@@ -94,7 +97,7 @@ ___
 
 ## Documentation
 
-##### API is avaliable [here](#)
+##### API is avaliable [here](https://luizfernandolj.github.io/mlquantify/api/index.html)
 
 - [Methods](https://github.com/luizfernandolj/mlquantify/wiki/Methods)
 - [Model Selection](https://github.com/luizfernandolj/mlquantify/wiki/Model-Selection)

mlquantify-0.1.4/VERSION.txt

@@ -0,0 +1 @@
+0.1.4

mlquantify-0.1.4/mlquantify/evaluation/protocol.py

@@ -0,0 +1,297 @@
+from abc import ABC, abstractmethod
+import numpy as np
+from typing import Generator, Tuple
+from tqdm import tqdm
+
+from ..utils.general import *
+
+class Protocol(ABC):
+    """Base class for evaluation protocols.
+    
+    Parameters
+    ----------
+    batch_size : int or list of int
+        The size of the batches to be used in the evaluation.
+    random_state : int, optional
+        The random seed for reproducibility.
+
+    Attributes
+    ----------
+    n_combinations : int
+
+    Raises
+    ------
+    ValueError
+        If the batch size is not a positive integer or list of positive integers.
+
+    Notes
+    -----
+    This class serves as a base class for different evaluation protocols, each with its own strategy for splitting the data into batches.
+    
+    Examples
+    --------
+    >>> class MyCustomProtocol(Protocol):
+    ...     def _iter_indices(self, X: np.ndarray, y: np.ndarray) -> Generator[np.ndarray]:
+    ...         for batch_size in self.batch_size:
+    ...             yield np.random.choice(X.shape[0], batch_size, replace=True)
+    ...
+    >>> protocol = MyCustomProtocol(batch_size=100, random_state=42)
+    >>> for train_idx, test_idx in protocol.split(X, y):
+    ...     # Train and evaluate model
+    ...     pass
+
+    """
+
+    def __init__(self, batch_size, random_state=None, **kwargs):
+        if isinstance(batch_size, int):
+            self.n_combinations = 1
+        else:
+            self.n_combinations = len(batch_size)
+
+        self.batch_size = [batch_size] if isinstance(batch_size, int) else batch_size
+        self.random_state = random_state
+
+        for name, value in kwargs.items():
+            setattr(self, name, value)
+            if isinstance(value, list):
+                self.n_combinations *= len(value)
+            elif isinstance(value, (int, float)):
+                self.n_combinations *= value
+            else:
+                raise ValueError(f"Invalid argument {name}={value}: must be int/float or list of int/float.")
+                 
+
+    def split(self, X: np.ndarray, y: np.ndarray) -> Generator[np.ndarray, np.ndarray]:
+        """
+        Split the data into samples for evaluation.
+
+        Parameters
+        ----------
+        X : np.ndarray
+            The input features.
+        y : np.ndarray
+            The target labels.
+
+        Yields
+        ------
+        Generator[np.ndarray, np.ndarray]
+            A generator that yields the indices for each split.
+        """
+        indices = np.arange(X.shape[0])
+        for idx in self._split_indices_masks(X, y):
+            indexes = indices[idx]
+            yield indexes
+
+    def _split_indices_masks(self, X: np.ndarray, y: np.ndarray) -> Generator[Tuple[np.ndarray, np.ndarray]]:
+        for idx in self._iter_indices(X, y):
+
+            mask = np.zeros(X.shape[0], dtype=bool)
+            mask[idx] = True 
+
+            yield mask
+
+    @abstractmethod
+    def _iter_indices(self, X, y):
+        """Abstract method to be implemented by subclasses to yield indices for each batch."""
+        pass
+    
+    def get_n_combinations(self) -> int:
+        """
+        Get the number of combinations for the current protocol.
+        """
+        return self.n_combinations
+
+
+class APP(Protocol):
+    """Artificial Prevalence Protocol (APP) for evaluation.
+    This protocol generates artificial prevalence distributions for the evaluation in an exhaustive manner, testing all possible combinations of prevalences.
+    
+    Parameters
+    ----------
+    batch_size : int or list of int
+        The size of the batches to be used in the evaluation.
+    n_prevalences : int
+        The number of artificial prevalences to generate.
+    repeats : int, optional
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int, optional
+        The random seed for reproducibility.
+        
+    Attributes
+    ----------
+    n_prevalences : int
+        The number of artificial prevalences to generate.
+    repeats : int
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int
+        The random seed for reproducibility.
+        
+    Notes
+    -----
+    It is important to note that in case of multiclass problems, the time complexity of this protocol can be significantly higher due to the increased number of combinations to evaluate.
+
+    Examples
+    --------
+    >>> protocol = APP(batch_size=[100, 200], n_prevalences=5, repeats=3, random_state=42)
+    >>> for train_idx, test_idx in protocol.split(X, y):
+    ...     # Train and evaluate model
+    ...     pass
+
+    """
+
+    def __init__(self, batch_size, n_prevalences, repeats=1, random_state=None):
+        super().__init__(batch_size=batch_size, 
+                            random_state=random_state,
+                            n_prevalences=n_prevalences, 
+                            repeats=repeats)
+
+    def _iter_indices(self, X: np.ndarray, y: np.ndarray) -> Generator[np.ndarray]:
+        
+        n_dim = len(np.unique(y))
+        
+        for batch_size in self.batch_size:
+            prevalences = generate_artificial_prevalences(n_dim=n_dim,
+                                                           n_prev=self.n_prevalences,
+                                                           n_iter=self.repeats)
+            for prev in prevalences:
+                indexes = get_indexes_with_prevalence(y, prev, batch_size)
+                yield indexes
+                
+
+            
+
+class NPP(Protocol):
+    """No Prevalence Protocol (NPP) for evaluation.
+    This protocol just samples the data without any consideration for prevalence, with all instances having equal probability of being selected.
+
+    Parameters
+    ----------
+    batch_size : int or list of int
+        The size of the batches to be used in the evaluation.
+    random_state : int, optional
+        The random seed for reproducibility.
+
+    Attributes
+    ----------
+    n_prevalences : int
+        The number of artificial prevalences to generate.
+    repeats : int
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int
+        The random seed for reproducibility.
+
+    Examples
+    --------
+    >>> protocol = NPP(batch_size=100, random_state=42)
+    >>> for train_idx, test_idx in protocol.split(X, y):
+    ...     # Train and evaluate model
+    ...     pass
+    """
+
+    def _iter_indices(self, X: np.ndarray, y: np.ndarray) -> Generator[np.ndarray]:
+        
+        for batch_size in self.batch_size:
+            yield np.random.choice(X.shape[0], batch_size, replace=True)
+            
+
+class UPP(Protocol):
+    """Uniform Prevalence Protocol (UPP) for evaluation.
+    An extension of the APP that generates artificial prevalence distributions uniformly across all classes utilizing the kraemer sampling method.
+
+    Parameters
+    ----------
+    batch_size : int or list of int
+        The size of the batches to be used in the evaluation.
+    n_prevalences : int
+        The number of artificial prevalences to generate.
+    repeats : int
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int, optional
+        The random seed for reproducibility.
+
+    Attributes
+    ----------
+    n_prevalences : int
+        The number of artificial prevalences to generate.
+    repeats : int
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int
+        The random seed for reproducibility.
+
+    Examples
+    --------
+    >>> protocol = UPP(batch_size=100, n_prevalences=5, repeats=3, random_state=42)
+    >>> for train_idx, test_idx in protocol.split(X, y):
+    ...     # Train and evaluate model
+    ...     pass
+    """
+
+    def __init__(self, batch_size, n_prevalences, repeats=1, random_state=None):
+        super().__init__(batch_size=batch_size, 
+                            random_state=random_state,
+                            n_prevalences=n_prevalences, 
+                            repeats=repeats)
+
+    def _iter_indices(self, X: np.ndarray, y: np.ndarray) -> Generator[np.ndarray]:
+        
+        n_dim = len(np.unique(y))
+        
+        for batch_size in self.batch_size:
+            
+            prevalences = kraemer_sampling(n_dim=n_dim,
+                                           n_prev=self.n_prevalences,
+                                           n_iter=self.repeats)
+            
+            for prev in prevalences:
+                indexes = get_indexes_with_prevalence(y, prev, batch_size)
+                yield indexes
+
+
+class PPP(Protocol):
+    """ Personalized Prevalence Protocol (PPP) for evaluation.
+    This protocol generates artificial prevalence distributions personalized for each class.
+
+    Parameters
+    ----------
+    batch_size : int or list of int
+        The size of the batches to be used in the evaluation.
+    prevalences : list of float
+        The list of artificial prevalences to generate for each class.
+    repeats : int
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int, optional
+        The random seed for reproducibility.
+
+    Attributes
+    ----------
+    prevalences : list of float
+        The list of artificial prevalences to generate for each class.
+    repeats : int
+        The number of times to repeat the evaluation with different random seeds.
+    random_state : int
+        The random seed for reproducibility.
+
+    Examples
+    --------
+    >>> protocol = PPP(batch_size=100, prevalences=[0.1, 0.9], repeats=3, random_state=42)
+    >>> for train_idx, test_idx in protocol.split(X, y):
+    ...     # Train and evaluate model
+    ...     pass
+    """
+    
+    def __init__(self, batch_size, prevalences, repeats=1, random_state=None):
+        super().__init__(batch_size=batch_size, 
+                        random_state=random_state,
+                        prevalences=prevalences, 
+                        repeats=repeats)
+    
+    def _iter_indices(self, X: np.ndarray, y: np.ndarray) -> Generator[np.ndarray]:
+        
+        for batch_size in self.batch_size:    
+            for prev in self.prevalences:
+                if isinstance(prev, float):
+                    prev = [1-prev, prev]
+                
+                indexes = get_indexes_with_prevalence(y, prev, batch_size)
+                yield indexes
+        

{mlquantify-0.1.3 → mlquantify-0.1.4}/mlquantify/utils/general.py

@@ -26,12 +26,9 @@ def convert_columns_to_arrays(df, columns:list = ['PRED_PREVS', 'REAL_PREVS']):
     return df
 
 
-
-
-
-def generate_artificial_indexes(y, prevalence: list, sample_size:int, classes:list):
+def get_indexes_with_prevalence(y, prevalence: list, sample_size:int):
     """
-    Generate indexes for a stratified sample based on the prevalence of each class.
+    Get indexes for a stratified sample based on the prevalence of each class.
     
     Parameters
     ----------
@@ -48,10 +45,13 @@ def generate_artificial_indexes(y, prevalence: list, sample_size:int, classes:li
     -------
     list
         List of indexes for the stratified sample.
-    """        
+    """      
+    classes = np.unique(y)
+        
     # Ensure the sum of prevalences is 1
     assert np.isclose(sum(prevalence), 1), "The sum of prevalences must be 1"
     # Ensure the number of prevalences matches the number of classes
+    assert len(prevalence) == len(classes), "The number of prevalences must match the number of classes"
 
     sampled_indexes = []
     total_sampled = 0
@@ -78,6 +78,43 @@ def generate_artificial_indexes(y, prevalence: list, sample_size:int, classes:li
 
 
 
+def kraemer_sampling(n_dim: int, n_prev: int, n_iter: int = 1) -> np.ndarray:
+    """
+    Uniform sampling from the unit simplex using Kraemer's algorithm.
+
+    Parameters
+    ----------
+    n_dim : int
+        Number of dimensions.
+    n_prev : int
+        Size of the sample.
+    n_iter : int
+        Number of iterations.
+
+    Returns
+    -------
+    np.ndarray
+        Array of sampled prevalences.
+    """
+
+    def _sampling(n_dim: int, n_prev: int) -> np.ndarray:
+        if n_dim == 2:
+            u = np.random.rand(n_prev)
+            return np.vstack([1 - u, u]).T
+        else:
+            u = np.random.rand(n_prev, n_dim - 1)
+            u.sort(axis=-1)   # sort each row
+            _0s = np.zeros((n_prev, 1))
+            _1s = np.ones((n_prev, 1))
+            a = np.hstack([_0s, u])
+            b = np.hstack([u, _1s])
+            return b - a
+
+    # repeat n_iter times
+    prevs = _sampling(n_dim, n_prev)
+
+    return np.repeat(prevs, n_iter, axis=0) if n_iter > 1 else prevs
+ 
 
 def generate_artificial_prevalences(n_dim: int, n_prev: int, n_iter: int) -> np.ndarray:
     """Generates n artificial prevalences with n dimensions.

{mlquantify-0.1.3 → mlquantify-0.1.4/mlquantify.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlquantify
-Version: 0.1.3
+Version: 0.1.4
 Summary: Quantification Library
 Home-page: https://github.com/luizfernandolj/QuantifyML/tree/master
 Maintainer: Luiz Fernando Luth Junior
@@ -40,9 +40,9 @@ ___
 
 ## Latest Release
 
-- **Version 0.0.11.6**: Inicial beta version. For a detailed list of changes, check the [changelog](#).
-- In case you need any help, refer to the [wiki](https://github.com/luizfernandolj/mlquantify/wiki).
-- Explore the [API documentation](#) for detailed developer information.
+- **Version 0.1.3**: Inicial beta version. For a detailed list of changes, check the [changelog](#).
+- In case you need any help, refer to the [User Guide](https://luizfernandolj.github.io/mlquantify/user_guide.html).
+- Explore the [API documentation](https://luizfernandolj.github.io/mlquantify/api/index.html) for detailed developer information.
 - See also the library in the pypi site in [pypi mlquantify](https://pypi.org/project/mlquantify/)
 
 ___
@@ -70,7 +70,7 @@ ___
 | **21 Quantification Methods** | Methods for quantification, such as classify & Count Correct methods, Threshold Optimization, Mixture Models and more.|
 | **Dynamic class management** | All methods are dynamic, and handles multiclass and binary problems, in case of binary it makes One-Vs-All (OVA) automatically. |
 | **Model Selection** | Criteria and processes used to select the best model, such as grid-search for the case of quantification|
-| **Evaluation Metrics** | Specific metrics used to evaluate quantification performance, (e.g., AE, BIAS, NAE, SE, KLD, etc.). |
+| **Evaluation Metrics** | Specific metrics used to evaluate quantification performance, (e.g., AE, MAE, NAE, SE, KLD, etc.). |
 | **Evaluation Protocols** | Evaluation protocols used, based on sampling generation (e.g., APP, NPP, etc.).. |
 | **Plotting Results** | Tools and techniques used to visualize results, such as the protocol results.|
 | **Comprehensive Documentation** | Complete documentation of the project, including code, data, and results. |
@@ -82,7 +82,10 @@ ___
 This code first loads the breast cancer dataset from _sklearn_, which is then split into training and testing sets. It uses the _Expectation Maximisation Quantifier (EMQ)_ with a RandomForest classifier to predict class prevalence. After training the model, it evaluates performance by calculating and printing the absolute error and bias between the real and predicted prevalences.
 
 ```python
-import mlquantify as mq
+from mlquantify.methods import EMQ
+from mlquantify.evaluation.measures import absolute_error, mean_absolute_error
+from mlquantify.utils import get_real_prev
+
 from sklearn.ensemble import RandomForestClassifier
 from sklearn.datasets import load_breast_cancer
 from sklearn.model_selection import train_test_split
@@ -94,19 +97,19 @@ features, target = load_breast_cancer(return_X_y=True)
 X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.3)
 
 #Create the model, here it is the Expectation Maximisation Quantifier (EMQ) with a classifier
-model = mq.methods.EMQ(RandomForestClassifier())
+model = EMQ(RandomForestClassifier())
 model.fit(X_train, y_train)
 
 #Predict the class prevalence for X_test
 pred_prevalence = model.predict(X_test)
-real_prevalence = mq.utils.get_real_prev(y_test)
+real_prevalence = get_real_prev(y_test)
 
 #Get the error for the prediction
-ae = mq.evaluation.absolute_error(real_prevalence, pred_prevalence)
-bias = mq.evaluation.bias(real_prevalence, pred_prevalence)
+ae = absolute_error(real_prevalence, pred_prevalence)
+mae = mean_absolute_error(real_prevalence, pred_prevalence)
 
-print(f"Mean Squared Error (MSE) -> {ae:.4f}")
-print(f"Bias -> {bias}")
+print(f"Absolute Error -> {ae}")
+print(f"Mean Absolute Error -> {mae}")
 ```
 
 ___
@@ -125,7 +128,7 @@ ___
 
 ## Documentation
 
-##### API is avaliable [here](#)
+##### API is avaliable [here](https://luizfernandolj.github.io/mlquantify/api/index.html)
 
 - [Methods](https://github.com/luizfernandolj/mlquantify/wiki/Methods)
 - [Model Selection](https://github.com/luizfernandolj/mlquantify/wiki/Model-Selection)

mlquantify-0.1.3/VERSION.txt

@@ -1 +0,0 @@
-0.1.3

mlquantify-0.1.3/mlquantify/evaluation/protocol.py

@@ -1,647 +0,0 @@
-from abc import ABC, abstractmethod
-import numpy as np
-import pandas as pd
-from typing import Union, List, Tuple, Any
-from sklearn.base import BaseEstimator
-from time import time
-from tqdm import tqdm
-
-from ..methods import METHODS, AGGREGATIVE, NON_AGGREGATIVE
-from ..utils.general import *
-from ..utils.method import *
-from . import MEASURES
-from ..base import Quantifier
-
-import mlquantify as mq
-
-class Protocol(ABC):
-    """Base class for evaluation protocols.
-    
-    Parameters
-    ----------
-    models : Union[List[Union[str, Quantifier]], str, Quantifier]
-        List of quantification models, a single model name, or 'all' for all models.
-    learner : BaseEstimator, optional
-        Machine learning model to be used with the quantifiers. Required for model methods.
-    n_jobs : int, optional
-        Number of jobs to run in parallel. Default is 1.
-    random_state : int, optional
-        Seed for random number generation. Default is 32.
-    verbose : bool, optional
-        Whether to print progress messages. Default is False.
-    return_type : str, optional
-        Type of return value ('predictions' or 'table'). Default is 'predictions'.
-    measures : List[str], optional
-        List of error measures to calculate. Must be in MEASURES or None. Default is None.
-    columns : List[str], optional
-        Columns to be included in the table. Default is ['ITERATION', 'QUANTIFIER', 'REAL_PREVS', 'PRED_PREVS', 'BATCH_SIZE'].
-    
-    Attributes
-    ----------
-    models : List[Quantifier]
-        List of quantification models.
-    learner : BaseEstimator
-        Machine learning model to be used with the quantifiers.
-    n_jobs : int
-        Number of jobs to run in parallel.
-    random_state : int
-        Seed for random number generation.
-    verbose : bool
-        Whether to print progress messages.
-    return_type : str
-        Type of return value ('predictions' or 'table').
-    measures : List[str]
-        List of error measures to calculate.
-    columns : List[str]
-        Columns to be included in the table.
-    
-    Raises
-    ------
-    AssertionError
-        If measures contain invalid error measures.
-        If return_type is invalid.
-        If columns does not contain ['QUANTIFIER', 'REAL_PREVS', 'PRED_PREVS'].
-    
-    Notes
-    -----
-    - The 'models' parameter can be a list of Quantifiers, a single Quantifier, a list of model names, a single model name, or 'all'.
-    - If 'models' is a list of model names or 'all', 'learner' must be provided.
-    - The 'all' option for 'models' will use all quantification models available in the library.
-    - If 'models' is a Quantifier or list of Quantifier, 'learner' is not required. But the models must be initializated
-    - You can pass your own model by passing a Quantifier object.
-    - Columns must contain ['QUANTIFIER', 'REAL_PREVS', 'PRED_PREVS'].
-    - If 'return_type' is 'table', the table will contain the columns specified in 'columns' and the error measures in 'measures'.
-    - For creating your own protocol, you must have the attributes 'models', 'learner', 'n_jobs', 'random_state', 'verbose', 'return_type', 'measures', and 'columns'., but columns can be changed, as long as it contains ['QUANTIFIER', 'REAL_PREVS', 'PRED_PREVS'].
-    
-    See Also
-    --------
-    APP : Artificial Prevalence Protocol.
-    NPP : Natural Prevalence Protocol.
-    Quantifier : Base class for quantification methods.
-    
-    Examples
-    --------
-    import numpy as np
-    >>> from mlquantify.evaluation.protocol import Protocol
-    >>> from mlquantify.utils import get_real_prev
-    >>> from sklearn.ensemble import RandomForestClassifier
-    >>> from sklearn.datasets import load_breast_cancer
-    >>> from sklearn.model_selection import train_test_split
-    >>> import time as t
-    >>> 
-    >>> class MyProtocol(Protocol):
-    ...    def __init__(self, 
-    ...                models, 
-    ...                learner, 
-    ...                n_jobs, 
-    ...                random_state, 
-    ...                verbose, 
-    ...                return_type, 
-    ...                measures,
-    ...                sample_size,
-    ...                iterations=10):
-    ...        super().__init__(models, 
-    ...                         learner, 
-    ...                         n_jobs, 
-    ...                         random_state, 
-    ...                         verbose, 
-    ...                         return_type, 
-    ...                         measures, 
-    ...                         columns=['QUANTIFIER', 'REAL_PREVS', 'PRED_PREVS', 'TIME'])
-    ...        self.sample_size = sample_size
-    ...        self.iterations = iterations
-    ...        
-    ...    def predict_protocol(self, X_test, y_test):
-    ...        predictions = []
-    ...        
-    ...        X_sample, y_sample = self._new_sample(X_test, y_test)
-    ...        
-    ...        for _ in range(self.iterations):
-    ...            for model in self.models:
-    ...                quantifier = model.__class__.__name__
-    ...
-    ...                real_prev = get_real_prev(y_sample)
-    ...
-    ...                start_time = t.time()
-    ...                pred_prev = model.predict(X_sample)
-    ...                end_time = t.time()
-    ...                time = end_time - start_time
-    ...                
-    ...                predictions.append([quantifier, real_prev, pred_prev, time])
-    ...        
-    ...        return predictions
-    ...    
-    ...    def _new_sample(self, X_test, y_test):
-    ...        indexes = np.random.choice(len(X_test), size=self.sample_size, replace=False)
-    ...        return X_test[indexes], y_test[indexes]
-    >>>     
-    >>> 
-    >>> features, target = load_breast_cancer(return_X_y=True)
-    >>> 
-    >>> X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.5, random_state=42)
-    >>> 
-    >>> protocol = MyProtocol(models=["CC", "EMQ", "DyS"], # or [CC(learner), EMQ(learner), DyS(learner)]
-    ...                    learner=RandomForestClassifier(),
-    ...                    n_jobs=1,
-    ...                    random_state=42,
-    ...                    verbose=True,
-    ...                    return_type="table",
-    ...                    measures=None,
-    ...                    sample_size=100)
-    >>>
-    >>> protocol.fit(X_train, y_train)
-    >>> table = protocol.predict(X_test, y_test)
-    >>> print(table)
-    
-    """
-    
-    def __init__(self,
-                 models: Union[List[Union[str, Quantifier]], str, Quantifier],
-                 learner: BaseEstimator = None,
-                 n_jobs: int = 1,
-                 random_state: int = 32,
-                 verbose: bool = False,
-                 return_type: str = "predictions",
-                 measures: List[str] = None,
-                 columns: List[str] = ["ITERATION", "QUANTIFIER", "REAL_PREVS", "PRED_PREVS", "BATCH_SIZE"]):
-        
-        assert not measures or all(m in MEASURES for m in measures), \
-            f"Invalid measure(s) provided. Valid options: {list(MEASURES.keys())} or None"
-        assert return_type in ["predictions", "table"], \
-            "Invalid return_type. Valid options: ['predictions', 'table']"
-        assert all(col in columns for col in ["QUANTIFIER", "REAL_PREVS", "PRED_PREVS"]), \
-            "Columns must contain ['QUANTIFIER', 'REAL_PREVS', 'PRED_PREVS']"
-
-        # Fixed parameters
-        self.models = self._initialize_models(models, learner)
-        self.learner = learner
-        self.n_jobs = n_jobs
-        self.random_state = random_state
-        self.verbose = verbose
-        self.return_type = return_type
-        self.measures = measures
-        self.columns = columns
-        
-    def _initialize_models(self, models, learner):
-        """Initializes the quantification models.
-        
-        Parameters
-        ----------
-        models : Union[List[Union[str, Quantifier]], str, Quantifier]
-            List of quantification models, a single model name, or 'all' for all models.
-        learner : BaseEstimator
-            Machine learning model to be used with the quantifiers.
-        
-        Returns
-        -------
-        List[Quantifier]
-            List of quantification models.
-        """
-        if isinstance(models, list):
-            if all(isinstance(model, Quantifier) for model in models):
-                return models
-            return [get_method(model)(learner) for model in models]
-        
-        if isinstance(models, Quantifier):
-            return [models]
-
-        assert learner is not None, "Learner is required for model methods."
-
-        model_dict = {
-            "all": METHODS.values,
-            "aggregative": AGGREGATIVE.values,
-            "non_aggregative": NON_AGGREGATIVE.values
-        }
-
-        if models in model_dict:
-            return [model(learner) if hasattr(model, "learner") else model() for model in model_dict[models]()]
-        return [get_method(models)(learner)]
-    
-    def sout(self, msg):
-        """Prints a message if verbose is True."""
-        if self.verbose:
-            print('[APP]' + msg)
-    
-    def fit(self, X_train, y_train):
-        """Fits the models with the training data.
-        
-        Parameters
-        ----------
-        X_train : np.ndarray
-            Features of the training set.
-        y_train : np.ndarray
-            Labels of the training set.
-        
-        Returns
-        -------
-        Protocol
-            Fitted protocol.
-        """
-        self.sout("Fitting models")
-
-        args = ((model, X_train, y_train) for model in self.models)
-        
-        wrapper = tqdm if self.verbose else lambda x, **kwargs: x
-    
-        self.models = Parallel(n_jobs=self.n_jobs)(  # Parallel processing of models
-            delayed(self._delayed_fit)(*arg) for arg in wrapper(args, desc="Fitting models", total=len(self.models))
-        )
-        self.sout("Fit [Done]")
-        return self
-    
-    
-    def predict(self, X_test: np.ndarray, y_test: np.ndarray) -> Any:
-        """Predicts the prevalence for the test set.
-        
-        Parameters
-        ----------
-        X_test : np.ndarray
-            Features of the test set.
-        y_test : np.ndarray
-            Labels of the test set.
-        
-        Returns
-        -------
-        Any
-            Predictions for the test set. Can be a table or a tuple with the quantifier names, real prevalence, and predicted prevalence.
-        """
-        predictions = self.predict_protocol(X_test, y_test)
-        predictions_df = pd.DataFrame(predictions, columns=self.columns)
-
-        if self.return_type == "table":
-            if self.measures:
-                smoothed_factor = 1 / (2 * len(X_test))
-
-                def smooth(values: np.ndarray) -> np.ndarray:
-                    return (values + smoothed_factor) / (smoothed_factor * len(values) + 1)
-
-                for metric in self.measures:
-                    predictions_df[metric] = predictions_df.apply(
-                        lambda row: get_measure(metric)( 
-                            smooth(np.array(row["REAL_PREVS"])),
-                            smooth(np.array(row["PRED_PREVS"]))
-                        ),
-                        axis=1
-                    )
-            return predictions_df
-
-        return (
-            predictions_df["QUANTIFIER"].to_numpy(),  # Quantifier names
-            np.stack(predictions_df["REAL_PREVS"].to_numpy()),  # REAL_PREVS
-            np.stack(predictions_df["PRED_PREVS"].to_numpy())   # PRED_PREVS
-        )
-
-    @abstractmethod
-    def predict_protocol(self, X_test: np.ndarray, y_test: np.ndarray) -> np.ndarray:
-        """Abstract method that every protocol must implement
-        
-        Parameters
-        ----------
-        X_test : np.ndarray
-            Features of the test set.
-        y_test : np.ndarray
-            Labels of the test set.
-        
-        Returns
-        -------
-        np.ndarray
-            Predictions for the test set. With the same format as the column names attribute.
-        """
-        ...
-
-    @abstractmethod
-    def _new_sample(self) -> Tuple[np.ndarray, np.ndarray]:
-        """Abstract method of sample extraction for each protocol.
-
-        Returns:
-            Tuple[np.ndarray, np.ndarray]: Tuple containing X_sample and y_sample.
-        """
-        ...
-
-    @staticmethod
-    def _delayed_fit(model, X_train, y_train):
-        """Method to fit the model in parallel.
-        
-        Parameters
-        ----------
-        model : Quantifier
-            Quantification model.
-        X_train : np.ndarray
-            Features of the training set.
-        y_train : np.ndarray
-            Labels of the training set.
-        
-        Returns
-        -------
-        Quantifier
-            Fitted quantification model
-        """
-        model_name = model.__class__.__name__
-        if model_name == "Ensemble" and isinstance(model.base_quantifier, Quantifier):
-            model_name = f"{model.__class__.__name__}_{model.base_quantifier.__class__.__name__}_{model.size}"
-        
-        start = time()
-        model = model.fit(X=X_train, y=y_train)
-        duration = time() - start
-        print(f"\tFitted {model_name} in {duration:.3f} seconds")
-        return model
-
-
-    
-    
-    
-
-
-class APP(Protocol):
-    """Artificial Prevalence Protocol. 
-    
-    This approach splits a test into several samples varying prevalence and sample size, 
-    with n iterations. For a list of Quantifiers, it computes training and testing for 
-    each one and returns either a table of results with error measures or just the predictions.
-    
-    Parameters
-    ----------
-    models : Union[List[Union[str, Quantifier]], str, Quantifier]
-        List of quantification models, a single model name, or 'all' for all models.
-    batch_size : Union[List[int], int]
-        Size of the batches to be processed, or a list of sizes.
-    learner : BaseEstimator, optional
-        Machine learning model to be used with the quantifiers. Required for model methods.
-    n_prevs : int, optional
-        Number of prevalence points to generate. Default is 100.
-    n_iterations : int, optional
-        Number of iterations for the protocol. Default is 1.
-    n_jobs : int, optional
-        Number of jobs to run in parallel. Default is 1.
-    random_state : int, optional
-        Seed for random number generation. Default is 32.
-    verbose : bool, optional
-        Whether to print progress messages. Default is False.
-    return_type : str, optional
-        Type of return value ('predictions' or 'table'). Default is 'predictions'.
-    measures : List[str], optional
-        List of error measures to calculate. Must be in MEASURES or None. Default is None.
-    
-    Attributes
-    ----------
-    models : List[Quantifier]
-        List of quantification models.
-    batch_size : Union[List[int], int]
-        Size of the batches to be processed.
-    learner : BaseEstimator
-        Machine learning model to be used with the quantifiers.
-    n_prevs : int
-        Number of prevalence points to generate.
-    n_iterations : int
-        Number of iterations for the protocol.
-    n_jobs : int
-        Number of jobs to run in parallel.
-    random_state : int
-        Seed for random number generation.
-    verbose : bool
-        Whether to print progress messages.
-    return_type : str
-        Type of return value ('predictions' or 'table').
-    measures : List[str]
-        List of error measures to calculate.
-        
-    Raises
-    ------
-    AssertionError
-        If return_type is invalid.
-    
-    See Also
-    --------
-    Protocol : Base class for evaluation protocols.
-    NPP : Natural Prevalence Protocol.
-    Quantifier : Base class for quantification methods.
-    
-    Examples
-    --------
-    >>> from mlquantify.evaluation.protocol import APP
-    >>> from sklearn.ensemble import RandomForestClassifier
-    >>> from sklearn.datasets import load_breast_cancer
-    >>> from sklearn.model_selection import train_test_split
-    >>>
-    >>> # Loading dataset from sklearn
-    >>> features, target = load_breast_cancer(return_X_y=True)
-    >>> 
-    >>> #Splitting into train and test
-    >>> X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.3)
-    >>>
-    >>> app = APP(models=["CC", "EMQ", "DyS"],
-    ...           batch_size=[10, 50, 100],
-    ...           learner=RandomForestClassifier(),
-    ...           n_prevs=100, # Default
-    ...           n_jobs=-1,
-    ...           return_type="table",
-    ...           measures=["ae", "se"],
-    ...           verbose=True)
-    >>>
-    >>> app.fit(X_train, y_train)
-    >>>
-    >>> table = app.predict(X_test, y_test)
-    >>>
-    >>> print(table)
-    """
-    
-    def __init__(self,     
-                 models: Union[List[Union[str, Quantifier]], str, Quantifier], 
-                 batch_size: Union[List[int], int],
-                 learner: BaseEstimator = None, 
-                 n_prevs: int = 100,
-                 n_iterations: int = 1,
-                 n_jobs: int = 1,
-                 random_state: int = 32,
-                 verbose: bool = False,
-                 return_type: str = "predictions",
-                 measures: List[str] = None):
-        
-        super().__init__(models, learner, n_jobs, random_state, verbose, return_type, measures)
-        self.n_prevs = n_prevs
-        self.batch_size = batch_size if isinstance(batch_size, list) else [batch_size]
-        self.n_prevs = n_prevs
-        self.n_iterations = n_iterations
-
-
-    def predict_protocol(self, X_test: np.ndarray, y_test: np.ndarray) -> Tuple:
-        """Generates several samples with artificial prevalences and sizes.
-        For each model, predicts with this sample, aggregating all together
-        with a pandas dataframe if requested, or else just the predictions.
-
-        Parameters
-        ----------
-        X_test : np.ndarray
-            Features of the test set.
-        y_test : np.ndarray
-            Labels of the test set.
-        
-        Returns
-        -------
-        Tuple
-            Tuple containing the (iteration, model name, prev, prev_pred, and batch size).
-        """
-        
-        n_dim = len(np.unique(y_test))
-        prevs = generate_artificial_prevalences(n_dim, self.n_prevs, self.n_iterations)
-
-        args = [
-            (iteration, X_test, y_test, model, prev, bs, self.verbose)
-            for prev in prevs for bs in self.batch_size for model in self.models for iteration in range(self.n_iterations)
-        ]
-        
-        size = len(prevs) * len(self.models) * len(self.batch_size) * self.n_iterations
-
-        predictions = []
-        for arg in tqdm(args, desc="Running APP", total=size):
-            predictions.append(self._predict(*arg))
-        
-        return predictions
-
-    def _predict(self, iteration:int, X: np.ndarray, y: np.ndarray, model: Any, prev: List[float], batch_size: int, verbose: bool) -> Tuple:
-        """Method predicts into the new sample for each model and prevalence.
-
-        Parameters
-        ----------
-        iteration : int
-            Current iteration.
-        X : np.ndarray
-            Features of the test set.
-        y : np.ndarray
-            Labels of the test set.
-        model : Any
-            Quantification model.
-        prev : List[float]
-            Prevalence values for the sample.
-        batch_size : int
-            Batch size for the sample.
-        verbose : bool
-            Whether to print progress messages.
-        
-        Returns
-        -------
-        Tuple
-            Tuple containing the iteration, model name, prev, prev_pred, and batch size.
-        """
-        model_name = model.__class__.__name__
-        if model_name == "Ensemble" and isinstance(model.base_quantifier, Quantifier):
-            model_name = f"{model.__class__.__name__}_{model.base_quantifier.__class__.__name__}_{model.size}"
-        
-        if verbose:
-            print(f'\t {model_name} with {batch_size} instances and prev {prev}')
-        
-        X_sample, _ = self._new_sample(X, y, prev, batch_size)
-        prev_pred = np.asarray(list(model.predict(X_sample).values()))
-        
-        if verbose:
-            print(f'\t \\--Ending {model_name} with {batch_size} instances and prev {prev}\n')
-        
-        return (iteration+1, model_name, prev, prev_pred, batch_size)
-
-
-    def _new_sample(self, X: np.ndarray, y: np.ndarray, prev: List[float], batch_size: int) -> Tuple[np.ndarray, np.ndarray]:
-        """Generates a new sample with a specified prevalence and size.
-
-        Parameters
-        ----------
-        X : np.ndarray
-            Features of the test set.
-        y : np.ndarray
-            Labels of the test set.
-        prev : List[float]
-            Prevalence values for the sample.
-        batch_size : int
-            Batch size for the sample.
-        
-        Returns
-        -------
-        Tuple[np.ndarray, np.ndarray]
-            Tuple containing the new sample features and labels.
-        """
-        sample_index = generate_artificial_indexes(y, prev, batch_size, np.unique(y))
-        return (np.take(X, sample_index, axis=0), np.take(y, sample_index, axis=0))
- 
-
-
-
-
-
-
-
-
-
-
-
-class NPP(Protocol):
-    """Natural Prevalence Protocol.
-    
-    This approach splits a test into several samples varying sample size,
-    with n iterations. For a list of Quantifiers, it computes training and testing for
-    each one and returns either a table of results with error measures or just the predictions.
-    
-    Parameters
-    ----------
-    models : Union[List[Union[str, Quantifier]], str, Quantifier]
-        List of quantification models, a single model name, or 'all' for all models.
-    batch_size : Union[List[int], int]
-        Size of the batches to be processed, or a list of sizes.
-    learner : BaseEstimator, optional
-        Machine learning model to be used with the quantifiers. Required for model methods.
-    n_iterations : int, optional
-        Number of iterations for the protocol. Default is 1.
-    n_jobs : int, optional
-        Number of jobs to run in parallel. Default is 1.
-    random_state : int, optional
-        Seed for random number generation. Default is 32.
-    verbose : bool, optional
-        Whether to print progress messages. Default is False.
-    return_type : str, optional
-        Type of return value ('predictions' or 'table'). Default is 'predictions'.
-    measures : List[str], optional
-        List of error measures to calculate. Must be in MEASURES or None. Default is None.
-    
-    Attributes
-    ----------
-    models : List[Quantifier]
-        List of quantification models.
-    batch_size : Union[List[int], int]
-        Size of the batches to be processed.
-    learner : BaseEstimator
-        Machine learning model to be used with the quantifiers.
-    n_iterations : int
-        Number of iterations for the protocol.
-    n_jobs : int
-        Number of jobs to run in parallel.
-    random_state : int
-        Seed for random number generation.
-    verbose : bool
-        Whether to print progress messages.
-    return_type : str
-        Type of return value ('predictions' or 'table').
-    measures : List[str]
-        List of error measures to calculate.    
-    """
-    
-    
-    def __init__(self,     
-                 models: Union[List[Union[str, Quantifier]], str, Quantifier], 
-                 learner: BaseEstimator = None, 
-                 n_jobs: int = 1,
-                 random_state: int = 32,
-                 verbose: bool = False,
-                 return_type: str = "predictions",
-                 measures: List[str] = None):
-        
-        super().__init__(models, learner, n_jobs, random_state, verbose, return_type, measures)
-        
-    
-    def predict_protocol(self, X_test, y_test) -> tuple:
-        raise NotImplementedError
-        
-    
-    def _new_sample(self, X, y, prev: List[float], batch_size: int) -> tuple:
-        raise NotImplementedError
-        
-    
-    def _delayed_predict(self, args) -> tuple:
-        raise NotImplementedError