[ENH v2] Add partial fit to the correct branch for decisiontreeclassifier (#54)

Supersedes: #50 

Implements partial_fit API for all classification decision trees.

---------

Signed-off-by: Adam Li <adam2392@gmail.com>
Co-authored-by: Haoyin Xu <haoyinxu@gmail.com>

Author: adam2392

sklearn/tree/_classes.py

@@ -11,12 +11,12 @@
 #          Joly Arnaud <arnaud.v.joly@gmail.com>
 #          Fares Hedayati <fares.hedayati@gmail.com>
 #          Nelson Liu <nelson@nelsonliu.me>
+#          Haoyin Xu <haoyinxu@gmail.com>
 #
 # License: BSD 3 clause
 
 import copy
 import numbers
-import warnings
 from abc import ABCMeta, abstractmethod
 from math import ceil
 from numbers import Integral, Real
@@ -35,7 +35,10 @@
 )
 from sklearn.utils import Bunch, check_random_state, compute_sample_weight
 from sklearn.utils._param_validation import Hidden, Interval, RealNotInt, StrOptions
-from sklearn.utils.multiclass import check_classification_targets
+from sklearn.utils.multiclass import (
+    _check_partial_fit_first_call,
+    check_classification_targets,
+)
 from sklearn.utils.validation import (
     _assert_all_finite_element_wise,
     _check_sample_weight,
@@ -237,6 +240,7 @@ def _fit(
         self,
         X,
         y,
+        classes=None,
         sample_weight=None,
         check_input=True,
         missing_values_in_feature_mask=None,
@@ -291,7 +295,6 @@ def _fit(
         is_classification = False
         if y is not None:
             is_classification = is_classifier(self)
-
             y = np.atleast_1d(y)
             expanded_class_weight = None
 
@@ -313,10 +316,28 @@ def _fit(
                     y_original = np.copy(y)
 
                 y_encoded = np.zeros(y.shape, dtype=int)
-                for k in range(self.n_outputs_):
-                    classes_k, y_encoded[:, k] = np.unique(y[:, k], return_inverse=True)
-                    self.classes_.append(classes_k)
-                    self.n_classes_.append(classes_k.shape[0])
+                if classes is not None:
+                    classes = np.atleast_1d(classes)
+                    if classes.ndim == 1:
+                        classes = np.array([classes])
+
+                    for k in classes:
+                        self.classes_.append(np.array(k))
+                        self.n_classes_.append(np.array(k).shape[0])
+
+                    for i in range(n_samples):
+                        for j in range(self.n_outputs_):
+                            y_encoded[i, j] = np.where(self.classes_[j] == y[i, j])[0][
+                                0
+                            ]
+                else:
+                    for k in range(self.n_outputs_):
+                        classes_k, y_encoded[:, k] = np.unique(
+                            y[:, k], return_inverse=True
+                        )
+                        self.classes_.append(classes_k)
+                        self.n_classes_.append(classes_k.shape[0])
+
                 y = y_encoded
 
                 if self.class_weight is not None:
@@ -355,24 +376,8 @@ def _fit(
             if self.max_features == "auto":
                 if is_classification:
                     max_features = max(1, int(np.sqrt(self.n_features_in_)))
-                    warnings.warn(
-                        (
-                            "`max_features='auto'` has been deprecated in 1.1 "
-                            "and will be removed in 1.3. To keep the past behaviour, "
-                            "explicitly set `max_features='sqrt'`."
-                        ),
-                        FutureWarning,
-                    )
                 else:
                     max_features = self.n_features_in_
-                    warnings.warn(
-                        (
-                            "`max_features='auto'` has been deprecated in 1.1 "
-                            "and will be removed in 1.3. To keep the past behaviour, "
-                            "explicitly set `max_features=1.0'`."
-                        ),
-                        FutureWarning,
-                    )
             elif self.max_features == "sqrt":
                 max_features = max(1, int(np.sqrt(self.n_features_in_)))
             elif self.max_features == "log2":
@@ -538,7 +543,7 @@ def _build_tree(
 
         # Use BestFirst if max_leaf_nodes given; use DepthFirst otherwise
         if max_leaf_nodes < 0:
-            builder = DepthFirstTreeBuilder(
+            self.builder_ = DepthFirstTreeBuilder(
                 splitter,
                 min_samples_split,
                 min_samples_leaf,
@@ -548,7 +553,7 @@ def _build_tree(
                 self.store_leaf_values,
             )
         else:
-            builder = BestFirstTreeBuilder(
+            self.builder_ = BestFirstTreeBuilder(
                 splitter,
                 min_samples_split,
                 min_samples_leaf,
@@ -558,7 +563,9 @@ def _build_tree(
                 self.min_impurity_decrease,
                 self.store_leaf_values,
             )
-        builder.build(self.tree_, X, y, sample_weight, missing_values_in_feature_mask)
+        self.builder_.build(
+            self.tree_, X, y, sample_weight, missing_values_in_feature_mask
+        )
 
         if self.n_outputs_ == 1 and is_classifier(self):
             self.n_classes_ = self.n_classes_[0]
@@ -1119,6 +1126,9 @@ class DecisionTreeClassifier(ClassifierMixin, BaseDecisionTree):
         :ref:`sphx_glr_auto_examples_tree_plot_unveil_tree_structure.py`
         for basic usage of these attributes.
 
+    builder_ : TreeBuilder instance
+        The underlying TreeBuilder object.
+
     See Also
     --------
     DecisionTreeRegressor : A decision tree regressor.
@@ -1209,7 +1219,14 @@ def __init__(
         )
 
     @_fit_context(prefer_skip_nested_validation=True)
-    def fit(self, X, y, sample_weight=None, check_input=True):
+    def fit(
+        self,
+        X,
+        y,
+        sample_weight=None,
+        check_input=True,
+        classes=None,
+    ):
         """Build a decision tree classifier from the training set (X, y).
 
         Parameters
@@ -1233,6 +1250,11 @@ def fit(self, X, y, sample_weight=None, check_input=True):
             Allow to bypass several input checking.
             Don't use this parameter unless you know what you're doing.
 
+        classes : array-like of shape (n_classes,), default=None
+            List of all the classes that can possibly appear in the y vector.
+            Must be provided at the first call to partial_fit, can be omitted
+            in subsequent calls.
+
         Returns
         -------
         self : DecisionTreeClassifier
@@ -1243,9 +1265,112 @@ def fit(self, X, y, sample_weight=None, check_input=True):
             y,
             sample_weight=sample_weight,
             check_input=check_input,
+            classes=classes,
         )
         return self
 
+    def partial_fit(self, X, y, classes=None, sample_weight=None, check_input=True):
+        """Update a decision tree classifier from the training set (X, y).
+
+        Parameters
+        ----------
+        X : {array-like, sparse matrix} of shape (n_samples, n_features)
+            The training input samples. Internally, it will be converted to
+            ``dtype=np.float32`` and if a sparse matrix is provided
+            to a sparse ``csc_matrix``.
+
+        y : array-like of shape (n_samples,) or (n_samples, n_outputs)
+            The target values (class labels) as integers or strings.
+
+        classes : array-like of shape (n_classes,), default=None
+            List of all the classes that can possibly appear in the y vector.
+            Must be provided at the first call to partial_fit, can be omitted
+            in subsequent calls.
+
+        sample_weight : array-like of shape (n_samples,), default=None
+            Sample weights. If None, then samples are equally weighted. Splits
+            that would create child nodes with net zero or negative weight are
+            ignored while searching for a split in each node. Splits are also
+            ignored if they would result in any single class carrying a
+            negative weight in either child node.
+
+        check_input : bool, default=True
+            Allow to bypass several input checking.
+            Don't use this parameter unless you know what you do.
+
+        Returns
+        -------
+        self : DecisionTreeClassifier
+            Fitted estimator.
+        """
+        self._validate_params()
+
+        # validate input parameters
+        first_call = _check_partial_fit_first_call(self, classes=classes)
+
+        # Fit if no tree exists yet
+        if first_call:
+            self.fit(
+                X,
+                y,
+                sample_weight=sample_weight,
+                check_input=check_input,
+                classes=classes,
+            )
+            return self
+
+        if check_input:
+            # Need to validate separately here.
+            # We can't pass multi_ouput=True because that would allow y to be
+            # csr.
+            check_X_params = dict(dtype=DTYPE, accept_sparse="csc")
+            check_y_params = dict(ensure_2d=False, dtype=None)
+            X, y = self._validate_data(
+                X, y, reset=False, validate_separately=(check_X_params, check_y_params)
+            )
+            if issparse(X):
+                X.sort_indices()
+
+                if X.indices.dtype != np.intc or X.indptr.dtype != np.intc:
+                    raise ValueError(
+                        "No support for np.int64 index based sparse matrices"
+                    )
+
+        if X.shape[1] != self.n_features_in_:
+            msg = "Number of features %d does not match previous data %d."
+            raise ValueError(msg % (X.shape[1], self.n_features_in_))
+
+        y = np.atleast_1d(y)
+
+        if y.ndim == 1:
+            # reshape is necessary to preserve the data contiguity against vs
+            # [:, np.newaxis] that does not.
+            y = np.reshape(y, (-1, 1))
+
+        check_classification_targets(y)
+        y = np.copy(y)
+
+        classes = self.classes_
+        if self.n_outputs_ == 1:
+            classes = [classes]
+
+        y_encoded = np.zeros(y.shape, dtype=int)
+        for i in range(X.shape[0]):
+            for j in range(self.n_outputs_):
+                y_encoded[i, j] = np.where(classes[j] == y[i, j])[0][0]
+        y = y_encoded
+
+        if getattr(y, "dtype", None) != DOUBLE or not y.flags.contiguous:
+            y = np.ascontiguousarray(y, dtype=DOUBLE)
+
+        # Update tree
+        self.builder_.initialize_node_queue(self.tree_, X, y, sample_weight)
+        self.builder_.build(self.tree_, X, y, sample_weight)
+
+        self._prune_tree()
+
+        return self
+
     def predict_proba(self, X, check_input=True):
         """Predict class probabilities of the input samples X.
 
@@ -1518,6 +1643,9 @@ class DecisionTreeRegressor(RegressorMixin, BaseDecisionTree):
         :ref:`sphx_glr_auto_examples_tree_plot_unveil_tree_structure.py`
         for basic usage of these attributes.
 
+    builder_ : TreeBuilder instance
+        The underlying TreeBuilder object.
+
     See Also
     --------
     DecisionTreeClassifier : A decision tree classifier.
@@ -1600,7 +1728,14 @@ def __init__(
         )
 
     @_fit_context(prefer_skip_nested_validation=True)
-    def fit(self, X, y, sample_weight=None, check_input=True):
+    def fit(
+        self,
+        X,
+        y,
+        sample_weight=None,
+        check_input=True,
+        classes=None,
+    ):
         """Build a decision tree regressor from the training set (X, y).
 
         Parameters
@@ -1623,6 +1758,9 @@ def fit(self, X, y, sample_weight=None, check_input=True):
             Allow to bypass several input checking.
             Don't use this parameter unless you know what you're doing.
 
+        classes : array-like of shape (n_classes,), default=None
+            List of all the classes that can possibly appear in the y vector.
+
         Returns
         -------
         self : DecisionTreeRegressor
@@ -1634,6 +1772,7 @@ def fit(self, X, y, sample_weight=None, check_input=True):
             y,
             sample_weight=sample_weight,
             check_input=check_input,
+            classes=classes,
         )
         return self
 
@@ -1885,6 +2024,9 @@ class ExtraTreeClassifier(DecisionTreeClassifier):
         :ref:`sphx_glr_auto_examples_tree_plot_unveil_tree_structure.py`
         for basic usage of these attributes.
 
+    builder_ : TreeBuilder instance
+        The underlying TreeBuilder object.
+
     See Also
     --------
     ExtraTreeRegressor : An extremely randomized tree regressor.
@@ -2147,6 +2289,9 @@ class ExtraTreeRegressor(DecisionTreeRegressor):
         :ref:`sphx_glr_auto_examples_tree_plot_unveil_tree_structure.py`
         for basic usage of these attributes.
 
+    builder_ : TreeBuilder instance
+        The underlying TreeBuilder object.
+
     See Also
     --------
     ExtraTreeClassifier : An extremely randomized tree classifier.