Source code for Orange.classification.tree

"""Tree inducers: SKL and Orange's own inducer"""
import numpy as np
import scipy.sparse as sp
import sklearn.tree as skl_tree

from Orange.base import TreeModel as TreeModelInterface
from Orange.classification import SklLearner, SklModel, Learner
from Orange.classification import _tree_scorers
from Orange.statistics import distribution, contingency
from Orange.tree import Node, DiscreteNode, MappedDiscreteNode, \
    NumericNode, TreeModel

__all__ = ["SklTreeLearner", "TreeLearner"]

[docs] class TreeLearner(Learner): """ Tree inducer with proper handling of nominal attributes and binarization. The inducer can handle missing values of attributes and target. For discrete attributes with more than two possible values, each value can get a separate branch (`binarize=False`), or values can be grouped into two groups (`binarize=True`, default). The tree growth can be limited by the required number of instances for internal nodes and for leafs, the sufficient proportion of majority class, and by the maximal depth of the tree. If the tree is not binary, it can contain zero-branches. Args: binarize (bool): if `True` the inducer will find optimal split into two subsets for values of discrete attributes. If `False` (default), each value gets its branch. min_samples_leaf (float): the minimal number of data instances in a leaf min_samples_split (float): the minimal nubmer of data instances that is split into subgroups max_depth (int): the maximal depth of the tree sufficient_majority (float): a majority at which the data is not split further Returns: instance of OrangeTreeModel """ __returns__ = TreeModel # Binarization is exhaustive, so we set a limit on the number of values MAX_BINARIZATION = 16 def __init__( self, *args, binarize=False, max_depth=None, min_samples_leaf=1, min_samples_split=2, sufficient_majority=0.95, preprocessors=None, **kwargs): super().__init__(preprocessors=preprocessors) self.params = {} self.binarize = self.params['binarize'] = binarize self.min_samples_leaf = self.params['min_samples_leaf'] = min_samples_leaf self.min_samples_split = self.params['min_samples_split'] = min_samples_split self.sufficient_majority = self.params['sufficient_majority'] = sufficient_majority self.max_depth = self.params['max_depth'] = max_depth def _select_attr(self, data): """Select the attribute for the next split. Returns: tuple with an instance of Node and a numpy array indicating the branch index for each data instance, or -1 if data instance is dropped """ # Prevent false warnings by pylint attr = attr_no = None col_x = None REJECT_ATTRIBUTE = 0, None, None, 0 def _score_disc(): """Scoring for discrete attributes, no binarization The class computes the entropy itself, not by calling other functions. This is to make sure that it uses the same definition as the below classes that compute entropy themselves for efficiency reasons.""" n_values = len(attr.values) if n_values < 2: return REJECT_ATTRIBUTE cont = _tree_scorers.contingency(col_x, len(data.domain.attributes[attr_no].values), data.Y, len(data.domain.class_var.values)) attr_distr = np.sum(cont, axis=0) null_nodes = attr_distr < self.min_samples_leaf # This is just for speed. If there is only a single non-null-node, # entropy wouldn't decrease anyway. if sum(null_nodes) >= n_values - 1: return REJECT_ATTRIBUTE cont[:, null_nodes] = 0 attr_distr = np.sum(cont, axis=0) cls_distr = np.sum(cont, axis=1) n = np.sum(attr_distr) # Avoid log(0); <= instead of == because we need an array cls_distr[cls_distr <= 0] = 1 attr_distr[attr_distr <= 0] = 1 cont[cont <= 0] = 1 class_entr = n * np.log(n) - np.sum(cls_distr * np.log(cls_distr)) attr_entr = np.sum(attr_distr * np.log(attr_distr)) cont_entr = np.sum(cont * np.log(cont)) score = (class_entr - attr_entr + cont_entr) / n / np.log(2) score *= n / len(data) # punishment for missing values branches = col_x.copy() branches[np.isnan(branches)] = -1 if score == 0: return REJECT_ATTRIBUTE node = DiscreteNode(attr, attr_no, None) return score, node, branches, n_values def _score_disc_bin(): """Scoring for discrete attributes, with binarization""" n_values = len(attr.values) if n_values <= 2: return _score_disc() cont = contingency.Discrete(data, attr) attr_distr = np.sum(cont, axis=0) # Skip instances with missing value of the attribute cls_distr = np.sum(cont, axis=1) if np.sum(attr_distr) == 0: # all values are missing return REJECT_ATTRIBUTE best_score, best_mapping = _tree_scorers.find_binarization_entropy( cont, cls_distr, attr_distr, self.min_samples_leaf) if best_score <= 0: return REJECT_ATTRIBUTE best_score *= 1 - np.sum(cont.unknowns) / len(data) mapping, branches = MappedDiscreteNode.branches_from_mapping( col_x, best_mapping, n_values) node = MappedDiscreteNode(attr, attr_no, mapping, None) return best_score, node, branches, 2 def _score_cont(): """Scoring for numeric attributes""" nans = np.sum(np.isnan(col_x)) non_nans = len(col_x) - nans arginds = np.argsort(col_x)[:non_nans] best_score, best_cut = _tree_scorers.find_threshold_entropy( col_x, data.Y, arginds, len(class_var.values), self.min_samples_leaf) if best_score == 0: return REJECT_ATTRIBUTE best_score *= non_nans / len(col_x) branches = np.full(len(col_x), -1, dtype=int) mask = ~np.isnan(col_x) branches[mask] = (col_x[mask] > best_cut).astype(int) node = NumericNode(attr, attr_no, best_cut, None) return best_score, node, branches, 2 ####################################### # The real _select_attr starts here is_sparse = sp.issparse(data.X) domain = data.domain class_var = domain.class_var best_score, *best_res = REJECT_ATTRIBUTE best_res = [Node(None, None, None)] + best_res[1:] disc_scorer = _score_disc_bin if self.binarize else _score_disc for attr_no, attr in enumerate(domain.attributes): col_x = data.X[:, attr_no] if is_sparse: col_x = col_x.toarray() col_x = col_x.flatten() sc, *res = disc_scorer() if attr.is_discrete else _score_cont() if res[0] is not None and sc > best_score: best_score, best_res = sc, res best_res[0].value = distribution.Discrete(data, class_var) return best_res def _build_tree(self, data, active_inst, level=1): """Induce a tree from the given data Returns: root node (Node)""" node_insts = data[active_inst] distr = distribution.Discrete(node_insts, data.domain.class_var) if len(node_insts) < self.min_samples_leaf: return None if len(node_insts) < self.min_samples_split or \ max(distr) >= sum(distr) * self.sufficient_majority or \ self.max_depth is not None and level > self.max_depth: node, branches, n_children = Node(None, None, distr), None, 0 else: node, branches, n_children = self._select_attr(node_insts) node.subset = active_inst if branches is not None: node.children = [ self._build_tree(data, active_inst[branches == br], level + 1) for br in range(n_children)] return node
[docs] def fit_storage(self, data): if self.binarize and any( attr.is_discrete and len(attr.values) > self.MAX_BINARIZATION for attr in data.domain.attributes): # No fallback in the script; widgets can prevent this error # by providing a fallback and issue a warning about doing so raise ValueError("Exhaustive binarization does not handle " "attributes with more than {} values". format(self.MAX_BINARIZATION)) active_inst = np.nonzero(~np.isnan(data.Y))[0].astype(np.int32) root = self._build_tree(data, active_inst) if root is None: distr = distribution.Discrete(data, data.domain.class_var) if np.sum(distr) == 0: distr[:] = 1 root = Node(None, 0, distr) root.subset = active_inst model = TreeModel(data, root) return model
class SklTreeClassifier(SklModel, TreeModelInterface): """Wrapper for SKL's tree classifier with the interface API for visualizations""" def __init__(self, *args, **kwargs): SklModel.__init__(self, *args, **kwargs) self._cached_sample_assignments = None
[docs] class SklTreeLearner(SklLearner): """Wrapper for SKL's tree inducer""" __wraps__ = skl_tree.DecisionTreeClassifier __returns__ = SklTreeClassifier name = 'tree' supports_weights = True def __init__(self, criterion="gini", splitter="best", max_depth=None, min_samples_split=2, min_samples_leaf=1, max_features=None, random_state=None, max_leaf_nodes=None, preprocessors=None): super().__init__(preprocessors=preprocessors) self.params = vars()