bayesian plot

BayesianKDEy/bayesian_kdey.py

@@ -7,9 +7,10 @@ from quapy.protocol import UPP
 import quapy.functional as F
 import numpy as np
 from tqdm import tqdm
+from scipy.stats import dirichlet
 
 
-def bayesian(kdes, data, prob_classifier, init=None, MAX_ITER=100_000, warmup=3_000):
+def bayesian(kdes, data, probabilistic_classifier, init=None, MAX_ITER=100_000, warmup=3_000):
     """
     Bayes:
         P(prev|data) = P(data|prev) P(prev) / P(data)
@@ -23,26 +24,32 @@ def bayesian(kdes, data, prob_classifier, init=None, MAX_ITER=100_000, warmup=3_
         # todo: remove exp, since we are then doing the log every time? (not sure)
         return np.exp(kde.score_samples(X))
 
-    X = prob_classifier.predict_proba(data)
+    X = probabilistic_classifier.predict_proba(data)
-    test_densities = [pdf(kde_i, X) for kde_i in kdes]
+    test_densities = np.asarray([pdf(kde_i, X) for kde_i in kdes])
 
-    def log_likelihood(prev, epsilon=1e-8):
+    def log_likelihood(prev, epsilon=1e-10):
-        # test_likelihoods = sum(prev_i*dens_i for prev_i, dens_i in zip (prev, test_densities))
         test_likelihoods = prev @ test_densities
         test_loglikelihood = np.log(test_likelihoods + epsilon)
         return np.sum(test_loglikelihood)
 
-    def log_prior(prev):
+    # def log_prior(prev):
         # todo: adapt to arbitrary prior knowledge (e.g., something around training prevalence)
-        return 1 # it is not 1 but we assume uniform, son anyway is an useless constant
+        # return 1/np.sum((prev-init)**2) # it is not 1 but we assume uniform, son anyway is an useless constant
+
+    # def log_prior(prev, alpha_scale=1000):
+    #     alpha = np.array(init) * alpha_scale
+    #     return dirichlet.logpdf(prev, alpha)
+
+    def log_prior(prev):
+        return 0
 
     def sample_neighbour(prev):
-        rand_prev = F.uniform_prevalence_sampling(n_classes=len(prev), size=1)
+        dir_noise = np.random.normal(scale=0.05, size=len(prev))
-        rand_direction = rand_prev - prev
+        # neighbour = F.normalize_prevalence(prev + dir_noise, method='clip')
-        neighbour = F.normalize_prevalence(prev + rand_direction*0.05)
+        neighbour = F.normalize_prevalence(prev + dir_noise, method='mapsimplex')
         return neighbour
 
-    n_classes = len(prob_classifier.classes_)
+    n_classes = len(probabilistic_classifier.classes_)
     current_prev = F.uniform_prevalence(n_classes) if init is None else init
     current_likelihood = log_likelihood(current_prev) + log_prior(current_prev)
 
@@ -74,23 +81,25 @@ if __name__ == '__main__':
     kdey = KDEyML(cls)
 
     train, test = qp.datasets.fetch_UCIMulticlassDataset('waveform-v1', standardize=True).train_test
+    # train, test = qp.datasets.fetch_UCIMulticlassDataset('phishing', standardize=True).train_test
 
-    with qp.util.temp_seed(0):
+    with qp.util.temp_seed(2):
         print('fitting KDEy')
         kdey.fit(*train.Xy)
 
-        shifted = test.sampling(500, *[0.1, 0.1, 0.8])
+        shifted = test.sampling(500, *[0.7, 0.1, 0.2])
         prev_hat = kdey.predict(shifted.X)
         mae = qp.error.mae(shifted.prevalence(), prev_hat)
         print(f'true_prev={strprev(shifted.prevalence())}, prev_hat={strprev(prev_hat)}, {mae=:.4f}')
 
         kdes = kdey.mix_densities
         h = kdey.classifier
-        samples = bayesian(kdes, shifted.X, h, init=prev_hat, MAX_ITER=100_000, warmup=0)
+        samples = bayesian(kdes, shifted.X, h, init=None, MAX_ITER=5_000, warmup=1_000)
 
         print(f'mean posterior {strprev(samples.mean(axis=0))}')
 
-        plot_prev_points(samples, true_prev=shifted.prevalence())
+        plot_prev_points(samples, true_prev=shifted.prevalence(), point_estim=prev_hat, train_prev=train.prevalence())
+        # plot_prev_points_matplot(samples)
 
 
         # report = qp.evaluation.evaluation_report(kdey, protocol=UPP(test), verbose=True)

BayesianKDEy/plot_simplex.py

@@ -3,7 +3,15 @@ import matplotlib.pyplot as plt
 from scipy.stats import gaussian_kde
 
 
-def plot_prev_points(prevs, true_prev):
+def plot_prev_points(prevs, true_prev, point_estim, train_prev):
+    plt.rcParams.update({
+        'font.size': 10,  # tamaño base de todo el texto
+        'axes.titlesize': 12,  # título del eje
+        'axes.labelsize': 10,  # etiquetas de ejes
+        'xtick.labelsize': 8,  # etiquetas de ticks
+        'ytick.labelsize': 8,
+        'legend.fontsize': 9,  # leyenda
+    })
 
     def cartesian(p):
         dim = p.shape[-1]
@@ -17,13 +25,13 @@ def plot_prev_points(prevs, true_prev):
     v2 = np.array([1, 0])
     v3 = np.array([0.5, np.sqrt(3)/2])
 
-    # transform (a,b,c) -> Cartesian coordinates
-    x, y = cartesian(prevs)
-
     # Plot
     fig, ax = plt.subplots(figsize=(6, 6))
-    ax.scatter(x, y, s=50, alpha=0.05, edgecolors='none')
+    ax.scatter(*cartesian(prevs), s=50, alpha=0.05, edgecolors='none', label='samples')
-    ax.scatter(*cartesian(true_prev), s=5, alpha=1)
+    ax.scatter(*cartesian(prevs.mean(axis=0)), s=10, alpha=1, label='sample-mean', edgecolors='black')
+    ax.scatter(*cartesian(true_prev), s=10, alpha=1, label='true-prev', edgecolors='black')
+    ax.scatter(*cartesian(point_estim), s=10, alpha=1, label='KDEy-estim', edgecolors='black')
+    ax.scatter(*cartesian(train_prev), s=10, alpha=1, label='train-prev', edgecolors='black')
 
     # edges
     triangle = np.array([v1, v2, v3, v1])
@@ -36,6 +44,13 @@ def plot_prev_points(prevs, true_prev):
 
     ax.set_aspect('equal')
     ax.axis('off')
+    plt.legend(
+        loc='center left',
+        bbox_to_anchor=(1.05, 0.5),
+        # ncol=3,
+        # frameon=False
+    )
+    plt.tight_layout()
     plt.show()
 
 
@@ -50,7 +65,7 @@ def plot_prev_points_matplot(points):
 
     # kde
     xy = np.vstack([x, y])
-    kde = gaussian_kde(xy)
+    kde = gaussian_kde(xy, bw_method=0.25)
     xmin, xmax = 0, 1
     ymin, ymax = 0, np.sqrt(3) / 2
 
@@ -91,4 +106,7 @@ def plot_prev_points_matplot(points):
     ax.axis('off')
     plt.show()
 
-
+if __name__ == '__main__':
+    n = 1000
+    points = np.random.dirichlet([2, 3, 4], size=n)
+    plot_prev_points_matplot(points)

quapy/method/_kdey.py

@@ -190,7 +190,8 @@ class KDEyML(AggregativeSoftQuantifier, KDEBase):
             test_densities = [self.pdf(kde_i, posteriors, self.kernel) for kde_i in self.mix_densities]
 
             def neg_loglikelihood(prev):
-                test_mixture_likelihood = sum(prev_i * dens_i for prev_i, dens_i in zip (prev, test_densities))
+                # test_mixture_likelihood = sum(prev_i * dens_i for prev_i, dens_i in zip (prev, test_densities))
+                test_mixture_likelihood = prev @ test_densities
                 test_loglikelihood = np.log(test_mixture_likelihood + epsilon)
                 return  -np.sum(test_loglikelihood)