mlquantify 0.1.7__py3-none-any.whl → 0.1.9__py3-none-any.whl

mlquantify/mixture/_classes.py

@@ -0,0 +1,400 @@
+import numpy as np
+from abc import abstractmethod
+
+from mlquantify.base import BaseQuantifier
+from mlquantify.base_aggregative import AggregationMixin, SoftLearnerQMixin, _get_learner_function
+from mlquantify.mixture._base import BaseMixture
+from mlquantify.multiclass import define_binary
+from mlquantify.utils._constraints import Interval, Options
+from mlquantify.utils._decorators import _fit_context
+from mlquantify.utils._get_scores import apply_cross_validation
+from mlquantify.utils._validation import check_classes_attribute, validate_predictions, validate_prevalences, validate_y
+from mlquantify.mixture._utils import (
+    getHist,
+    ternary_search,
+)
+
+
+
+# =====================================================
+# Base class
+# =====================================================
+@define_binary
+class AggregativeMixture(SoftLearnerQMixin, AggregationMixin, BaseMixture):
+    """
+    Base class for Mixture-based Quantification Methods.
+
+    These methods assume that the test score distribution is a mixture
+    of the positive and negative score distributions from the training data.
+    """
+    
+    _parameter_constraints = {
+        "strategy": [Options(["ovr", "ovo"])]
+    }
+
+    def __init__(self, learner = None, strategy="ovr"):
+        super().__init__()
+        self.learner = learner
+        self.pos_scores = None
+        self.neg_scores = None
+        self.distances = None
+        self.strategy = strategy
+    
+    def _fit(self, X, y, learner_fitted=False, *args, **kwargs):
+        learner_function = _get_learner_function(self)
+        
+        if learner_fitted:
+            train_predictions = getattr(self.learner, learner_function)(X)
+            train_y_values = y
+        else:
+            train_predictions, train_y_values = apply_cross_validation(
+                self.learner,
+                X,
+                y,
+                function= learner_function,
+                cv= 5,
+                stratified= True,
+                random_state= None,
+                shuffle= True
+            )
+            
+        self.train_predictions = train_predictions
+        self.train_y_values = train_y_values
+
+        self._precompute_training(train_predictions, train_y_values)
+        return self
+
+    def _precompute_training(self, train_predictions, train_y_values):
+        """
+        Fit learner and store score distributions for positive and negative classes.
+        """ 
+        # Store scores for positive and negative classes
+        self.pos_scores = train_predictions[train_y_values == self.classes_[1], 1]
+        self.neg_scores = train_predictions[train_y_values == self.classes_[0], 1]
+        self._precomputed = True
+        return self
+    
+    def _predict(self, X):
+        """Predict class prevalences for the given data."""
+        predictions = getattr(self.learner, _get_learner_function(self))(X)
+        prevalences = self.aggregate(predictions, self.train_predictions, self.train_y_values)
+
+        return prevalences
+    
+    def aggregate(self, predictions, train_predictions, train_y_values):
+        predictions = validate_predictions(self, predictions)
+        self.classes_ = check_classes_attribute(self, np.unique(train_y_values))
+
+        if not self._precomputed:
+            self._precompute_training(train_predictions, train_y_values)
+            self._precomputed = True
+        
+        pos_test_scores = predictions[:, 1]
+        
+        best_alpha, _ = self.best_mixture(pos_test_scores, self.pos_scores, self.neg_scores)
+        prevalence = np.array([1 - best_alpha, best_alpha])
+        prevalence = validate_prevalences(self, prevalence, self.classes_)
+        return prevalence
+    
+    @abstractmethod
+    def best_mixture(self, predictions, pos_scores, neg_scores):
+        ...
+
+# =====================================================
+# DyS
+# =====================================================
+
+class DyS(AggregativeMixture):
+    """Distribution y-Similarity (DyS) quantification method.
+
+    Uses mixture modeling with a dissimilarity measure between distributions
+    computed on histograms of classifier scores. This method optimizes mixture 
+    weights by minimizing a chosen distance measure: Hellinger, Topsoe, or ProbSymm.
+
+    Parameters
+    ----------
+    learner : estimator, optional
+        Base probabilistic classifier.
+    measure : {'hellinger', 'topsoe', 'probsymm'}, default='topsoe'
+        Distance function to minimize.
+    bins_size : array-like or None
+        Histogram bin sizes to try for score representation. Defaults to a set of 
+        bin sizes between 2 and 30.
+
+    References
+    ----------
+    [1] Maletzke et al. (2019). DyS: A Framework for Mixture Models in Quantification. AAAI 2019.
+    [2] Esuli et al. (2023). Learning to Quantify. Springer.
+
+    Examples
+    --------
+    >>> q = DyS(learner=my_learner, measure="hellinger")
+    >>> q.fit(X_train, y_train)
+    >>> prevalences = q.predict(X_test)
+    """
+    
+    _parameter_constraints = {
+        "measure": [Options(["hellinger", "topsoe", "probsymm"])],
+        "bins_size": ["array-like", None]
+    }
+
+    def __init__(self, learner=None, measure="topsoe", bins_size=None):
+        super().__init__(learner)
+        if bins_size is None:
+            bins_size = np.append(np.linspace(2, 20, 10), 30)
+            
+        self.measure = measure
+        self.bins_size = np.asarray(bins_size, dtype=int)
+
+    def best_mixture(self, predictions, pos_scores, neg_scores):
+        
+        prevs = []
+        self.distances = []
+        for bins in self.bins_size:
+            pos = getHist(pos_scores, bins)
+            neg = getHist(neg_scores, bins)
+            test = getHist(predictions, bins)
+
+            def f(alpha):
+                mix = self._mix(pos, neg, alpha)
+                return BaseMixture.get_distance(mix, test, measure=self.measure)
+
+            alpha = ternary_search(0, 1, f)
+            prevs.append(alpha)
+            self.distances.append(f(alpha))
+        alpha = np.median(prevs)
+        best_distance = np.median(self.distances)
+        return alpha, best_distance
+        
+    def _mix(self, pos_hist, neg_hist, alpha):
+        return alpha * pos_hist + (1 - alpha) * neg_hist
+
+
+# =====================================================
+# HDy
+# =====================================================
+
+class HDy(AggregativeMixture):
+    """Hellinger Distance Minimization (HDy) quantification method.
+
+    Estimates class prevalences by finding mixture weights that minimize
+    the Hellinger distance between the histogram of test scores and the mixture
+    of positive and negative class score histograms, evaluated over multiple bin sizes.
+
+    Parameters
+    ----------
+    learner : estimator, optional
+        Base probabilistic classifier.
+
+    References
+    ----------
+    [2] Esuli et al. (2023). Learning to Quantify. Springer.
+
+    """
+    
+    def best_mixture(self, predictions, pos_scores, neg_scores):
+        bins_size = np.arange(10, 110, 11)
+        alpha_values = np.round(np.linspace(0, 1, 101), 2)
+        
+        alphas, self.distances = [], []
+        for bins in bins_size:
+            pos = getHist(pos_scores, bins)
+            neg = getHist(neg_scores, bins)
+            test = getHist(predictions, bins)
+            dists = []
+            for a in alpha_values:
+                mix = self._mix(pos, neg, a)
+                dists.append(BaseMixture.get_distance(mix, test, measure="hellinger"))
+            a = alpha_values[np.argmin(dists)]
+            alphas.append(a)
+            self.distances.append(np.min(dists))
+        
+        best_alpha = np.median(alphas)
+        best_distance = np.median(self.distances)    
+        
+        return best_alpha, best_distance
+    
+    def _mix(self, pos_hist, neg_hist, alpha):
+        return alpha * pos_hist + (1 - alpha) * neg_hist
+
+
+
+# =====================================================
+# SMM
+# =====================================================
+
+class SMM(AggregativeMixture):
+    r"""Sample Mean Matching (SMM) quantification method.
+
+    Estimates class prevalence by matching the mean score of the test samples 
+    to a convex combination of positive and negative training scores. The mixture 
+    weight \( \alpha \) is computed as:
+
+    \[
+    \alpha = \frac{\bar{s}_{test} - \bar{s}_{neg}}{\bar{s}_{pos} - \bar{s}_{neg}}
+    \]
+
+    where \( \bar{s} \) denotes the sample mean.
+
+    Parameters
+    ----------
+    learner : estimator, optional
+        Base probabilistic classifier.
+
+    References
+    ----------
+    [2] Esuli et al. (2023). Learning to Quantify. Springer.
+    """
+    
+    def best_mixture(self, predictions, pos_scores, neg_scores):
+        mean_pos = np.mean(pos_scores)
+        mean_neg = np.mean(neg_scores)
+        mean_test = np.mean(predictions)
+        
+        alpha = (mean_test - mean_neg) / (mean_pos - mean_neg)
+        return alpha, None
+
+
+# =====================================================
+# SORD
+# =====================================================
+
+class SORD(AggregativeMixture):
+    """Sample Ordinal Distance (SORD) quantification method.
+
+    Estimates prevalence by minimizing the weighted sum of absolute score differences
+    between test data and training classes. The method creates weighted score 
+    vectors for positive, negative, and test samples, sorts them, and computes
+    a cumulative absolute difference as the distance measure.
+
+    Parameters
+    ----------
+    learner : estimator, optional
+        Base probabilistic classifier.
+
+    References
+    ----------
+    [2] Esuli et al. (2023). Learning to Quantify. Springer.
+    """
+
+    def best_mixture(self, predictions, pos_scores, neg_scores):
+        alphas = np.linspace(0, 1, 101)
+        self.distances = []
+        
+        pos, neg, test = pos_scores, neg_scores, predictions
+        n_pos, n_neg, n_test = len(pos), len(neg), len(test)
+        for a in alphas:
+            pos_w = np.full(n_pos, a / n_pos)
+            neg_w = np.full(n_neg, (1 - a) / n_neg)
+            test_w = np.full(n_test, -1 / n_test)
+            scores = np.concatenate([pos, neg, test])
+            weights = np.concatenate([pos_w, neg_w, test_w])
+            idx = np.argsort(scores)
+            sorted_scores = scores[idx]
+            sorted_weights = weights[idx]
+            cum_w = sorted_weights[0]
+            total = 0
+            for i in range(1, len(sorted_scores)):
+                seg = sorted_scores[i] - sorted_scores[i - 1]
+                total += abs(seg * cum_w)
+                cum_w += sorted_weights[i]
+            self.distances.append(total)
+            
+        best_distance_index = np.argmin(self.distances)
+        best_alpha = alphas[best_distance_index]
+        best_distance = self.distances[best_distance_index]
+        return best_alpha, best_distance
+
+
+
+
+
+# =====================================================
+# Non aggregative Mixture-based Quantifiers
+# =====================================================
+
+class HDx(BaseMixture):
+    """
+    Hellinger Distance-based Quantifier (HDx).
+
+    A non-aggregative mixture quantifier that estimates class prevalences by 
+    minimizing the average Hellinger distance between class-wise feature histograms 
+    of training data and test data. It iterates over mixture weights and histogram bin sizes,
+    evaluating distance per feature and aggregates the results.
+
+    Parameters
+    ----------
+    bins_size : array-like, optional
+        Histogram bin sizes to consider for discretizing features.
+    strategy : {'ovr', 'ovo'}, default='ovr'
+        Multiclass quantification strategy.
+
+    Attributes
+    ----------
+    pos_features : ndarray
+        Training samples of the positive class.
+    neg_features : ndarray
+        Training samples of the negative class.
+
+    References
+    ----------
+    [2] Esuli et al. (2023). Learning to Quantify. Springer.
+    """
+    
+    _parameter_constraints = {
+        "bins_size": ["array-like", None],
+        "strategy": [Options(["ovr", "ovo"])]
+    }
+
+    def __init__(self, bins_size=None, strategy="ovr"):
+        super().__init__()
+        if bins_size is None:
+            bins_size = np.append(np.linspace(2, 20, 10), 30)
+
+        self.bins_size = bins_size
+        self.neg_features = None
+        self.pos_features = None
+        self.strategy = strategy
+        
+    
+    def _fit(self, X, y, *args, **kwargs):
+        self.pos_features = X[y == self.classes_[1]]
+        self.neg_features = X[y == self.classes_[0]]
+        return self
+    
+    def _predict(self, X) -> np.ndarray:
+        alpha, _ = self.best_mixture(X, self.pos_features, self.neg_features)
+        prevalence = np.array([1 - alpha, alpha])
+        prevalence = validate_prevalences(self, prevalence, self.classes_)
+        return prevalence
+    
+    def best_mixture(self, X, pos, neg):
+        alpha_values = np.round(np.linspace(0, 1, 101), 2)
+        self.distances = []
+
+        # Iterate over alpha values to compute the prevalence
+        for alpha in alpha_values:
+            distances = []
+
+            # For each feature, compute the Hellinger distance
+            for feature_idx in range(X.shape[1]):
+                
+                for bins in self.bins_size:
+                
+                    pos_feature = pos[:, feature_idx]
+                    neg_feature = neg[:, feature_idx]
+                    test_feature = X[:, feature_idx]
+
+                    pos_hist = getHist(pos_feature, bins)
+                    neg_hist = getHist(neg_feature, bins)
+                    test_hist = getHist(test_feature, bins)
+
+                    mix_hist = alpha * pos_hist + (1 - alpha) * neg_hist
+                    distance = BaseMixture.get_distance(mix_hist, test_hist, measure="hellinger")
+                    distances.append(distance)
+
+            avg_distance = np.mean(distances)
+            self.distances.append(avg_distance)
+        best_alpha = alpha_values[np.argmin(self.distances)]
+        best_distance = np.min(self.distances)
+        return best_alpha, best_distance

mlquantify/mixture/_utils.py

@@ -0,0 +1,112 @@
+import numpy as np
+
+
+# =====================================================
+# Utility functions
+# =====================================================
+
+def getHist(scores, nbins):
+    """
+    Calculate histogram-like bin probabilities for a given set of scores.
+
+    This function divides the score range into equal bins and computes the proportion 
+    of scores in each bin, normalized by the total count.
+
+    Parameters
+    ----------
+    scores : np.ndarray
+        A 1-dimensional array of scores.
+    nbins : int
+        Number of bins for dividing the score range.
+
+    Returns
+    -------
+    np.ndarray
+        An array containing the normalized bin probabilities.
+
+    Notes
+    -----
+    - The bins are equally spaced between 0 and 1, with an additional upper boundary 
+      to include the maximum score.
+    - The returned probabilities are normalized to account for the total number of scores.
+    """
+    breaks = np.linspace(0, 1, int(nbins) + 1)
+    breaks = np.delete(breaks, -1)
+    breaks = np.append(breaks, 1.1)
+
+    re = np.repeat(1 / (len(breaks) - 1), (len(breaks) - 1))
+    for i in range(1, len(breaks)):
+        re[i - 1] = (re[i - 1] + len(np.where((scores >= breaks[i - 1]) & (scores < breaks[i]))[0])) / (len(scores) + 1)
+
+    return re
+
+
+def ternary_search(left: float, right: float, func, tol: float = 1e-4) -> float:
+    """
+    Ternary search to find the minimum of a unimodal function in [left, right].
+
+    Parameters
+    ----------
+    left : float
+        Left bound.
+    right : float
+        Right bound.
+    func : callable
+        Function to minimize.
+    tol : float
+        Tolerance for termination.
+
+    Returns
+    -------
+    float
+        Approximate position of the minimum.
+    """
+    while right - left > tol:
+        m1 = left + (right - left) / 3
+        m2 = right - (right - left) / 3
+        f1, f2 = func(m1), func(m2)
+        if f1 < f2:
+            right = m2
+        else:
+            left = m1
+    return (left + right) / 2
+
+
+def topsoe(p: np.ndarray, q: np.ndarray) -> float:
+    """
+    Topsoe distance between two probability distributions.
+
+    D_T(p, q) = sum( p*log(2p/(p+q)) + q*log(2q/(p+q)) )
+    """
+    p = np.maximum(p, 1e-20)
+    q = np.maximum(q, 1e-20)
+    return np.sum(p * np.log(2 * p / (p + q)) + q * np.log(2 * q / (p + q)))
+
+
+def probsymm(p: np.ndarray, q: np.ndarray) -> float:
+    """
+    Probabilistic Symmetric distance.
+
+    D_PS(p, q) = sum( (p - q) * log(p / q) )
+    """
+    p = np.maximum(p, 1e-20)
+    q = np.maximum(q, 1e-20)
+    return np.sum((p - q) * np.log(p / q))
+
+
+def hellinger(p: np.ndarray, q: np.ndarray) -> float:
+    """
+    Hellinger distance between two probability distributions.
+
+    H(p, q) = (1/sqrt(2)) * sqrt( sum( (sqrt(p) - sqrt(q))^2 ) )
+    """
+    p = np.maximum(p, 1e-20)
+    q = np.maximum(q, 1e-20)
+    return np.sqrt(0.5 * np.sum((np.sqrt(p) - np.sqrt(q)) ** 2))
+
+
+def sqEuclidean(p: np.ndarray, q: np.ndarray) -> float:
+    """
+    Squared Euclidean distance between two vectors.
+    """
+    return np.sum((p - q) ** 2)

mlquantify/model_selection/__init__.py

@@ -0,0 +1,9 @@
+from ._protocol import (
+    BaseProtocol,
+    APP,
+    NPP,
+    UPP,
+    PPP
+)
+
+from ._search import GridSearchQ