Source code for pgmpy.estimators.HillClimbSearch

#!/usr/bin/env python
from itertools import permutations
from collections import deque

import networkx as nx
from import trange

from pgmpy.estimators import (
from pgmpy.base import DAG
from pgmpy.global_vars import SHOW_PROGRESS

[docs]class HillClimbSearch(StructureEstimator): def __init__(self, data, use_cache=True, **kwargs): """ Class for heuristic hill climb searches for DAGs, to learn network structure from data. `estimate` attempts to find a model with optimal score. Parameters ---------- data: pandas DataFrame object datafame object where each column represents one variable. (If some values in the data are missing the data cells should be set to `numpy.NaN`. Note that pandas converts each column containing `numpy.NaN`s to dtype `float`.) state_names: dict (optional) A dict indicating, for each variable, the discrete set of states (or values) that the variable can take. If unspecified, the observed values in the data set are taken to be the only possible states. complete_samples_only: bool (optional, default `True`) Specifies how to deal with missing data, if present. If set to `True` all rows that contain `np.Nan` somewhere are ignored. If `False` then, for each variable, every row where neither the variable nor its parents are `np.NaN` is used. This sets the behavior of the `state_count`-method. use_caching: boolean If True, uses caching of score for faster computation. Note: Caching only works for scoring methods which are decomposible. Can give wrong results in case of custom scoring methods. References ---------- Koller & Friedman, Probabilistic Graphical Models - Principles and Techniques, 2009 Section 18.4.3 (page 811ff) """ self.use_cache = use_cache super(HillClimbSearch, self).__init__(data, **kwargs) def _legal_operations( self, model, score, structure_score, tabu_list, max_indegree, black_list, white_list, fixed_edges, ): """Generates a list of legal (= not in tabu_list) graph modifications for a given model, together with their score changes. Possible graph modifications: (1) add, (2) remove, or (3) flip a single edge. For details on scoring see Koller & Friedman, Probabilistic Graphical Models, Section (page 818). If a number `max_indegree` is provided, only modifications that keep the number of parents for each node below `max_indegree` are considered. A list of edges can optionally be passed as `black_list` or `white_list` to exclude those edges or to limit the search. """ tabu_list = set(tabu_list) # Step 1: Get all legal operations for adding edges. potential_new_edges = ( set(permutations(self.variables, 2)) - set(model.edges()) - set([(Y, X) for (X, Y) in model.edges()]) ) for (X, Y) in potential_new_edges: # Check if adding (X, Y) will create a cycle. if not nx.has_path(model, Y, X): operation = ("+", (X, Y)) if ( (operation not in tabu_list) and ((X, Y) not in black_list) and ((X, Y) in white_list) ): old_parents = model.get_parents(Y) new_parents = old_parents + [X] if len(new_parents) <= max_indegree: score_delta = score(Y, new_parents) - score(Y, old_parents) score_delta += structure_score("+") yield (operation, score_delta) # Step 2: Get all legal operations for removing edges for (X, Y) in model.edges(): operation = ("-", (X, Y)) if (operation not in tabu_list) and ((X, Y) not in fixed_edges): old_parents = model.get_parents(Y) new_parents = old_parents[:] new_parents.remove(X) score_delta = score(Y, new_parents) - score(Y, old_parents) score_delta += structure_score("-") yield (operation, score_delta) # Step 3: Get all legal operations for flipping edges for (X, Y) in model.edges(): # Check if flipping creates any cycles if not any( map(lambda path: len(path) > 2, nx.all_simple_paths(model, X, Y)) ): operation = ("flip", (X, Y)) if ( ((operation not in tabu_list) and ("flip", (Y, X)) not in tabu_list) and ((X, Y) not in fixed_edges) and ((Y, X) not in black_list) and ((Y, X) in white_list) ): old_X_parents = model.get_parents(X) old_Y_parents = model.get_parents(Y) new_X_parents = old_X_parents + [Y] new_Y_parents = old_Y_parents[:] new_Y_parents.remove(X) if len(new_X_parents) <= max_indegree: score_delta = ( score(X, new_X_parents) + score(Y, new_Y_parents) - score(X, old_X_parents) - score(Y, old_Y_parents) ) score_delta += structure_score("flip") yield (operation, score_delta)
[docs] def estimate( self, scoring_method="k2score", start_dag=None, fixed_edges=set(), tabu_length=100, max_indegree=None, black_list=None, white_list=None, epsilon=1e-4, max_iter=1e6, show_progress=True, ): """ Performs local hill climb search to estimates the `DAG` structure that has optimal score, according to the scoring method supplied. Starts at model `start_dag` and proceeds by step-by-step network modifications until a local maximum is reached. Only estimates network structure, no parametrization. Parameters ---------- scoring_method: str or StructureScore instance The score to be optimized during structure estimation. Supported structure scores: k2score, bdeuscore, bdsscore, bicscore. Also accepts a custom score but it should be an instance of `StructureScore`. start_dag: DAG instance The starting point for the local search. By default a completely disconnected network is used. fixed_edges: iterable A list of edges that will always be there in the final learned model. The algorithm will add these edges at the start of the algorithm and will never change it. tabu_length: int If provided, the last `tabu_length` graph modifications cannot be reversed during the search procedure. This serves to enforce a wider exploration of the search space. Default value: 100. max_indegree: int or None If provided and unequal None, the procedure only searches among models where all nodes have at most `max_indegree` parents. Defaults to None. black_list: list or None If a list of edges is provided as `black_list`, they are excluded from the search and the resulting model will not contain any of those edges. Default: None white_list: list or None If a list of edges is provided as `white_list`, the search is limited to those edges. The resulting model will then only contain edges that are in `white_list`. Default: None epsilon: float (default: 1e-4) Defines the exit condition. If the improvement in score is less than `epsilon`, the learned model is returned. max_iter: int (default: 1e6) The maximum number of iterations allowed. Returns the learned model when the number of iterations is greater than `max_iter`. Returns ------- model: `DAG` instance A `DAG` at a (local) score maximum. Examples -------- >>> import pandas as pd >>> import numpy as np >>> from pgmpy.estimators import HillClimbSearch, BicScore >>> # create data sample with 9 random variables: ... data = pd.DataFrame(np.random.randint(0, 5, size=(5000, 9)), columns=list('ABCDEFGHI')) >>> # add 10th dependent variable ... data['J'] = data['A'] * data['B'] >>> est = HillClimbSearch(data) >>> best_model = est.estimate(scoring_method=BicScore(data)) >>> sorted(best_model.nodes()) ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J'] >>> best_model.edges() OutEdgeView([('B', 'J'), ('A', 'J')]) >>> # search a model with restriction on the number of parents: >>> est.estimate(max_indegree=1).edges() OutEdgeView([('J', 'A'), ('B', 'J')]) """ # Step 1: Initial checks and setup for arguments # Step 1.1: Check scoring_method supported_methods = { "k2score": K2Score, "bdeuscore": BDeuScore, "bdsscore": BDsScore, "bicscore": BicScore, } if ( ( isinstance(scoring_method, str) and (scoring_method.lower() not in supported_methods) ) ) and (not isinstance(scoring_method, StructureScore)): raise ValueError( "scoring_method should either be one of k2score, bdeuscore, bicscore, bdsscore, or an instance of StructureScore" ) if isinstance(scoring_method, str): score = supported_methods[scoring_method.lower()]( else: score = scoring_method if self.use_cache: score_fn = ScoreCache.ScoreCache(score, else: score_fn = score.local_score # Step 1.2: Check the start_dag if start_dag is None: start_dag = DAG() start_dag.add_nodes_from(self.variables) elif not isinstance(start_dag, DAG) or not set(start_dag.nodes()) == set( self.variables ): raise ValueError( "'start_dag' should be a DAG with the same variables as the data set, or 'None'." ) # Step 1.3: Check fixed_edges if not hasattr(fixed_edges, "__iter__"): raise ValueError("fixed_edges must be an iterable") else: fixed_edges = set(fixed_edges) start_dag.add_edges_from(fixed_edges) if not nx.is_directed_acyclic_graph(start_dag): raise ValueError( "fixed_edges creates a cycle in start_dag. Please modify either fixed_edges or start_dag." ) # Step 1.4: Check black list and white list black_list = set() if black_list is None else set(black_list) white_list = ( set([(u, v) for u in self.variables for v in self.variables]) if white_list is None else set(white_list) ) # Step 1.5: Initialize max_indegree, tabu_list, and progress bar if max_indegree is None: max_indegree = float("inf") tabu_list = deque(maxlen=tabu_length) current_model = start_dag if show_progress and SHOW_PROGRESS: iteration = trange(int(max_iter)) else: iteration = range(int(max_iter)) # Step 2: For each iteration, find the best scoring operation and # do that to the current model. If no legal operation is # possible, sets best_operation=None. for _ in iteration: best_operation, best_score_delta = max( self._legal_operations( current_model, score_fn, score.structure_prior_ratio, tabu_list, max_indegree, black_list, white_list, fixed_edges, ), key=lambda t: t[1], default=(None, None), ) if best_operation is None or best_score_delta < epsilon: break elif best_operation[0] == "+": current_model.add_edge(*best_operation[1]) tabu_list.append(("-", best_operation[1])) elif best_operation[0] == "-": current_model.remove_edge(*best_operation[1]) tabu_list.append(("+", best_operation[1])) elif best_operation[0] == "flip": X, Y = best_operation[1] current_model.remove_edge(X, Y) current_model.add_edge(Y, X) tabu_list.append(best_operation) # Step 3: Return if no more improvements or maximum iterations reached. return current_model