Merge pull request #19 from arminwitte/algorithm_kwargs

entropy tolerance

binarybeech/attributehandler.py

@@ -12,10 +12,11 @@
 
 
 class AttributeHandlerBase(ABC):
-    def __init__(self, y_name, attribute, metrics):
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
         self.y_name = y_name
         self.attribute = attribute
         self.metrics = metrics
+        self.algorithm_kwargs = algorithm_kwargs
 
         self.loss = None
         self.split_df = []
@@ -44,8 +45,8 @@ def check(x):
 
 
 class NominalAttributeHandler(AttributeHandlerBase):
-    def __init__(self, y_name, attribute, metrics):
-        super().__init__(y_name, attribute, metrics)
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
+        super().__init__(y_name, attribute, metrics, algorithm_kwargs)
 
     def split(self, df):
         self.loss = np.Inf
@@ -105,8 +106,8 @@ def check(x):
 
 
 class DichotomousAttributeHandler(AttributeHandlerBase):
-    def __init__(self, y_name, attribute, metrics):
-        super().__init__(y_name, attribute, metrics)
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
+        super().__init__(y_name, attribute, metrics, algorithm_kwargs)
 
     def split(self, df):
         self.loss = np.Inf
@@ -155,8 +156,8 @@ def check(x):
 
 
 class IntervalAttributeHandler(AttributeHandlerBase):
-    def __init__(self, y_name, attribute, metrics):
-        super().__init__(y_name, attribute, metrics)
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
+        super().__init__(y_name, attribute, metrics, algorithm_kwargs)
 
     def split(self, df):
         self.loss = np.Inf
@@ -212,8 +213,8 @@ def check(x):
 
 
 class NullAttributeHandler(AttributeHandlerBase):
-    def __init__(self, y_name, attribute, metrics):
-        super().__init__(y_name, attribute, metrics)
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
+        super().__init__(y_name, attribute, metrics, algorithm_kwargs)
 
     def split(self, df):
         self.loss = np.Inf
@@ -240,8 +241,8 @@ def check(x):
 
 
 class UnsupervisedIntervalAttributeHandler(AttributeHandlerBase):
-    def __init__(self, y_name, attribute, metrics):
-        super().__init__(y_name, attribute, metrics)
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
+        super().__init__(y_name, attribute, metrics, algorithm_kwargs)
 
     def split(self, df):
         self.loss = np.Inf
@@ -258,15 +259,41 @@ def split(self, df):
         valleys = math.valley(df[name])
         if not valleys:
             return success
-        else:
-            success = True
 
-        self.threshold = valleys[0]
-        self.split_df = [
-            df[df[self.attribute] < self.threshold],
-            df[df[self.attribute] >= self.threshold],
-        ]
-        self.loss = math.shannon_entropy_histogram(df[name])
+        loss = np.Inf
+        for v in valleys:
+            threshold_candidate = v
+            split_df_candidate = [
+                df[df[self.attribute] < threshold_candidate],
+                df[df[self.attribute] >= threshold_candidate],
+            ]
+            H = math.shannon_entropy_histogram(df[name], normalized=False)
+            H_ = [
+                math.shannon_entropy_histogram(df_[name], normalized=False)
+                for df_ in split_df_candidate
+            ]
+            loss_candidate = (-np.sum(H_) + H) / np.abs(H)
+            if loss_candidate < loss:
+                loss = loss_candidate
+                split_df = split_df_candidate
+                threshold = threshold_candidate
+
+        # loss = math.shannon_entropy_histogram(df[name], normalized=True)
+
+        print(f"{self.attribute} loss: {loss}")
+
+        tol = self.algorithm_kwargs.get(
+            "unsupervised_minimum_relative_entropy_improvement"
+        )
+
+        if tol is not None and loss > tol:
+            return success
+
+        success = True
+
+        self.threshold = threshold
+        self.split_df = split_df
+        self.loss = loss
         return success
 
     def handle_missings(self, df):
@@ -284,8 +311,8 @@ def check(x):
 
 
 class UnsupervisedNominalAttributeHandler(AttributeHandlerBase):
-    def __init__(self, y_name, attribute, metrics):
-        super().__init__(y_name, attribute, metrics)
+    def __init__(self, y_name, attribute, metrics, algorithm_kwargs):
+        super().__init__(y_name, attribute, metrics, algorithm_kwargs)
 
     def split(self, df):
         self.loss = np.Inf
@@ -362,21 +389,21 @@ def get_attribute_handler_class(self, arr, group_name="default"):
 
         raise ValueError("no data handler class for this type of data")
 
-    def create_attribute_handlers(self, training_data, metrics):
+    def create_attribute_handlers(self, training_data, metrics, algorithm_kwargs):
         df = training_data.df
         y_name = training_data.y_name
         X_names = training_data.X_names
-        dhc = self.get_attribute_handler_class(
+        ahc = self.get_attribute_handler_class(
             df[y_name], group_name=metrics.attribute_handler_group()
         )
 
-        d = {y_name: dhc(y_name, y_name, metrics)}
+        d = {y_name: ahc(y_name, y_name, metrics, algorithm_kwargs)}
 
         for name in X_names:
-            dhc = self.get_attribute_handler_class(
+            ahc = self.get_attribute_handler_class(
                 df[name], group_name=metrics.attribute_handler_group()
             )
-            d[name] = dhc(y_name, name, metrics)
+            d[name] = ahc(y_name, name, metrics, algorithm_kwargs)
 
         return d
 

binarybeech/datamanager.py

@@ -12,17 +12,17 @@ def __init__(self, training_data, method, attribute_handlers, algorithm_kwargs):
 
         if method is None:
             metrics_type, metrics = metrics_factory.from_data(
-                training_data.df[training_data.y_name]
+                training_data.df[training_data.y_name], self.algorithm_kwargs
             )
         else:
-            metrics = metrics_factory.create_metrics(method)
+            metrics = metrics_factory.create_metrics(method, self.algorithm_kwargs)
             metrics_type = method
         self.metrics = metrics
         self.metrics_type = metrics_type
 
         if attribute_handlers is None:
             attribute_handlers = attribute_handler_factory.create_attribute_handlers(
-                training_data, self.metrics
+                training_data, self.metrics, self.algorithm_kwargs
             )
         self.attribute_handlers = attribute_handlers
         self.items = self.attribute_handlers.items

binarybeech/math.py

@@ -122,16 +122,28 @@ def ambiguity(X):
 
 
 def valley(x):
-    hist, bin_edges = np.histogram(x, bins="auto")
+    hist, bin_edges = np.histogram(x, bins="sturges", density=False)
     valley_ind, _ = scipy.signal.find_peaks(-hist)
+    # if len(valley_ind) < 1:
+    #    return []
+    # prom = scipy.signal.peak_prominences(-hist,valley_ind)[0]
+    # ind_max = np.argmax(prom)
     v = [(bin_edges[i] + bin_edges[i + 1]) * 0.5 for i in valley_ind]
-    return v
+    return v  # [ind_max]
 
 
-def shannon_entropy_histogram(x):
-    hist, bin_edges = np.histogram(x, bins="auto")
+def shannon_entropy_histogram(x: np.ndarray, normalized=False):
+    hist, bin_edges = np.histogram(x, bins="sturges", density=False)
     hist = np.maximum(hist, 1e-12)
-    return -np.sum(hist * np.log2(hist))
+    s = -np.sum(hist * np.log2(hist))
+
+    if normalized:
+        n_bins = bin_edges.size - 1
+        n_samples = x.size
+        s_ref = n_samples * np.log2(n_samples / n_bins)
+        s /= s_ref
+
+    return s
 
 
 # =====================================

binarybeech/metrics.py

@@ -287,13 +287,13 @@ def __init__(self):
     def register(self, metrics_type, metrics_class):
         self.metrics[metrics_type] = metrics_class
 
-    def create_metrics(self, metrics_type):
+    def create_metrics(self, metrics_type, algorithm_kwargs):
         if metrics_type in self.metrics:
             return self.metrics[metrics_type]()
         else:
             raise ValueError("Invalid metrics type")
 
-    def from_data(self, y):
+    def from_data(self, y, algorithm_kwargs):
         for name, cls in self.metrics.items():
             if cls.check_data_type(y):
                 return cls(), name

binarybeech/utils.py

@@ -82,3 +82,17 @@ def model_missings(df, y_name, X_names=None, cart_settings={}):
         df_.loc[df[x_name].isnull(), x_name] = mod.predict(df[df[x_name].isnull()])
 
     return df_
+
+
+# def plot_areas(df):
+#     x, y = np.meshgrid(np.linspace(1,7,101),np.linspace(0,2.5,101))
+#     col = []
+#     for i in range(len(x.ravel())):
+#         d = df_iris.iloc[120].copy()
+#         d["petal_length"] = x.ravel()[i]
+#         d["petal_width"] = y.ravel()[i]
+#         col.append(c_iris.tree.traverse(d).value)
+#     unique = [u for u in np.unique(col)]
+#     for i, c in enumerate(col):
+#         col[i] = unique.index(c)
+#     z = np.array(col).reshape(x.shape)