Source code for ontolearn.search

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# Copyright (c) 2024 Ontolearn Team
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"""Node representation."""
import weakref
from _weakref import ReferenceType
from abc import abstractmethod, ABCMeta
from functools import total_ordering
from queue import PriorityQueue
from typing import List, Optional, ClassVar, Final, Iterable, TypeVar, Generic, Set, Tuple, Dict
from owlapy.owl_object import OWLObjectRenderer
from owlapy.class_expression import OWLClassExpression
from owlapy.render import DLSyntaxObjectRenderer
from owlapy.utils import as_index, OrderedOWLObject
from .abstracts import AbstractNode, AbstractHeuristic, AbstractScorer, AbstractOEHeuristicNode, LBLSearchTree, \
    AbstractConceptNode, EncodedLearningProblem, DRILLAbstractTree

_N = TypeVar('_N')  #:

from owlapy import owl_expression_to_dl


# Due to a bug in Python, we cannot use the slots like we should be able to. Hence, the attribute access is also
# invalid but there is nothing we can do. See https://mail.python.org/pipermail/python-list/2002-December/126637.html

# noinspection PyUnresolvedReferences
# noinspection PyDunderSlots
class _NodeConcept(metaclass=ABCMeta):
    __slots__ = ()

    renderer: ClassVar[OWLObjectRenderer] = DLSyntaxObjectRenderer()

    _concept: OWLClassExpression

    @abstractmethod
    def __init__(self, concept: OWLClassExpression):
        self._concept = concept

    @property
    def concept(self) -> OWLClassExpression:
        return self._concept

    @abstractmethod
    def __str__(self):
        return _NodeConcept.renderer.render(self.concept)

    @property
    def str(self):
        return _NodeConcept.__str__(self)


# noinspection PyUnresolvedReferences
# noinspection PyDunderSlots
class _NodeLen(metaclass=ABCMeta):  # pragma: no cover
    __slots__ = ()

    _len: int

    @abstractmethod
    def __init__(self, length: int):
        self._len = length

    @property
    def len(self) -> int:
        return self._len


# noinspection PyUnresolvedReferences
# noinspection PyDunderSlots
class _NodeIndividualsCount(metaclass=ABCMeta):  # pragma: no cover
    __slots__ = ()

    _individuals_count: Optional[int]

    @abstractmethod
    def __init__(self, individuals_count: Optional[int] = None):
        self._individuals_count = individuals_count

    @property
    def individuals_count(self) -> Optional[int]:
        return self._individuals_count

    @individuals_count.setter
    def individuals_count(self, v: int):
        if self._individuals_count is not None:
            raise ValueError("Individuals already counted", self)
        self._individuals_count = v

    @abstractmethod
    def __str__(self):
        return f'|Indv.|:{self.individuals_count}'


# noinspection PyUnresolvedReferences
# noinspection PyDunderSlots
class _NodeHeuristic(metaclass=ABCMeta):
    __slots__ = ()

    _heuristic: Optional[float]

    @abstractmethod
    def __init__(self, heuristic: Optional[float] = None):
        self._heuristic = heuristic

    @property
    def heuristic(self) -> float:
        return self._heuristic

    @heuristic.setter
    def heuristic(self, v: float):
        if v is not None and self._heuristic is not None:
            raise ValueError("Node heuristic already calculated", self)
        self._heuristic = v

    @abstractmethod
    def __str__(self):
        return f'Heuristic:{self.heuristic}'


class _NodeParentRef(Generic[_N], metaclass=ABCMeta):
    __slots__ = ()

    _parent_ref: Optional[ReferenceType]  # Optional[ReferenceType[OENode]]

    @abstractmethod
    def __init__(self, parent_node: Optional[_N] = None, is_root: bool = False):
        if is_root:
            self._parent_ref = None
        else:
            self._parent_ref = weakref.ref(parent_node)

    @property
    def is_root(self) -> bool:
        return self._parent_ref is None

    @property
    def parent_node(self) -> Optional[_N]:
        if self._parent_ref is None:
            return None
        return self._parent_ref()

    def depth(self) -> int:
        d = 0
        n = self
        while True:
            n = n.parent_node
            if not n:
                break
            d += 1
        return d

    @abstractmethod
    def __str__(self):
        return f'Depth:{self.depth()}'


# noinspection PyUnresolvedReferences
# noinspection PyDunderSlots
class _NodeQuality(metaclass=ABCMeta):
    __slots__ = ()

    _quality: Optional[float]

    @abstractmethod
    def __init__(self, quality: Optional[float] = None):
        self._quality = quality

    @property
    def quality(self) -> float:
        return self._quality

    @quality.setter
    def quality(self, v: float):
        if self._quality is not None:
            raise ValueError("Node already evaluated", self)
        self._quality = v

    @abstractmethod
    def __str__(self):
        return f'Quality:{self.quality}'


[docs] class Node(_NodeConcept, _NodeLen, _NodeIndividualsCount, AbstractNode): """ Simple node. """ __slots__ = '_concept', '_len', '_individuals_count' def __init__(self, concept: OWLClassExpression, length: int): # pragma: no cover _NodeConcept.__init__(self, concept) _NodeLen.__init__(self, length) _NodeIndividualsCount.__init__(self) AbstractNode.__init__(self)
[docs] def __str__(self): return "\t".join(( AbstractNode.__str__(self), _NodeConcept.__str__(self), _NodeIndividualsCount.__str__(self), ))
[docs] class OENode(_NodeConcept, _NodeLen, _NodeIndividualsCount, _NodeQuality, _NodeHeuristic, _NodeParentRef['OENode'], AbstractNode, AbstractConceptNode, AbstractOEHeuristicNode): """OENode search tree node.""" __slots__ = '_concept', '_len', '_individuals_count', '_quality', '_heuristic', \ '_parent_ref', '_horizontal_expansion', \ '_refinement_count', '__weakref__' renderer: ClassVar[OWLObjectRenderer] = DLSyntaxObjectRenderer() _horizontal_expansion: int _refinement_count: int def __init__(self, concept: OWLClassExpression, length: int, parent_node: Optional['OENode'] = None, is_root: bool = False): _NodeConcept.__init__(self, concept) _NodeLen.__init__(self, length) _NodeIndividualsCount.__init__(self) _NodeQuality.__init__(self) _NodeHeuristic.__init__(self) _NodeParentRef.__init__(self, parent_node, is_root) self._horizontal_expansion = length self._refinement_count = 0 AbstractNode.__init__(self) @property def h_exp(self) -> int: return self._horizontal_expansion
[docs] def increment_h_exp(self): self._heuristic = None self._horizontal_expansion += 1
@property def refinement_count(self) -> int: return self._refinement_count @refinement_count.setter def refinement_count(self, v: int): self._heuristic = None self._refinement_count = v
[docs] def __str__(self): return "\t".join(( AbstractNode.__str__(self), _NodeConcept.__str__(self), _NodeQuality.__str__(self), _NodeHeuristic.__str__(self), _NodeParentRef.__str__(self), f'H_exp:{self.h_exp}', f'|RC|:{self.refinement_count}', _NodeIndividualsCount.__str__(self), ))
[docs] class EvoLearnerNode(_NodeConcept, _NodeLen, _NodeIndividualsCount, _NodeQuality, AbstractNode, AbstractConceptNode): """ EvoLearner search tree node. """ __slots__ = '_concept', '_len', '_individuals_count', '_quality', '_tree_length', '_tree_depth' _tree_length: int _tree_depth: int def __init__(self, concept: OWLClassExpression, length: int, individuals_count: int, quality: float, tree_length: int, tree_depth: int): _NodeConcept.__init__(self, concept) _NodeLen.__init__(self, length) _NodeIndividualsCount.__init__(self, individuals_count) _NodeQuality.__init__(self, quality) AbstractNode.__init__(self) self._tree_length = tree_length self._tree_depth = tree_depth @property def tree_length(self): return self._tree_length @property def tree_depth(self): return self._tree_depth
[docs] def __str__(self): return "\t".join(( AbstractNode.__str__(self), _NodeConcept.__str__(self), _NodeQuality.__str__(self), f'Length:{self._len}', f'Tree Length:{self._tree_length}', f'Tree Depth:{self._tree_depth}', _NodeIndividualsCount.__str__(self), ))
[docs] class NCESNode(_NodeConcept, _NodeLen, _NodeIndividualsCount, _NodeQuality, AbstractNode, AbstractConceptNode): """ EvoLearner search tree node. """ __slots__ = '_concept', '_len', '_individuals_count', '_quality' def __init__(self, concept: OWLClassExpression, length: int, individuals_count: int, quality: float): _NodeConcept.__init__(self, concept) _NodeLen.__init__(self, length) _NodeIndividualsCount.__init__(self, individuals_count) _NodeQuality.__init__(self, quality) AbstractNode.__init__(self)
[docs] def __str__(self): return "\t".join(( AbstractNode.__str__(self), _NodeConcept.__str__(self), _NodeQuality.__str__(self), f'Length:{self._len}', _NodeIndividualsCount.__str__(self), ))
[docs] class RL_State(_NodeConcept, _NodeQuality, _NodeHeuristic, AbstractNode, _NodeParentRef['RL_State']): renderer: ClassVar[OWLObjectRenderer] = DLSyntaxObjectRenderer() """RL_State node.""" __slots__ = '_concept', 'embeddings', '_quality', '_heuristic', 'length', 'parent_node', 'is_root', '_parent_ref', '__weakref__' def __init__(self, concept: OWLClassExpression, parent_node: Optional['RL_State'] = None, embeddings=None, is_root: bool = False, length=None): _NodeConcept.__init__(self, concept) _NodeQuality.__init__(self) _NodeHeuristic.__init__(self) _NodeParentRef.__init__(self, parent_node=parent_node, is_root=is_root) AbstractNode.__init__(self) self.parent_node = parent_node self.is_root = is_root self.length = length self.embeddings = embeddings self.__sanity_checking() def __sanity_checking(self): assert self.concept if self.is_root is False: assert self.parent_node
[docs] def __str__(self): # pragma: no cover if self.embeddings is None: return "\t".join(( AbstractNode.__str__(self), _NodeConcept.__str__(self), _NodeQuality.__str__(self), _NodeHeuristic.__str__(self), f'Length:{self.length}')) else: return "\t".join(( AbstractNode.__str__(self), _NodeConcept.__str__(self), _NodeQuality.__str__(self), _NodeHeuristic.__str__(self), f'Length:{self.length}', f'Embeddings:{self.embeddings.shape}',))
[docs] def __lt__(self, other): return self.heuristic <= other.heuristic
[docs] def __gt__(self, other): return self.heuristic > other.heuristic
# noinspection PyUnresolvedReferences # noinspection PyDunderSlots class _NodeIndividuals(metaclass=ABCMeta): __slots__ = () _individuals: Optional[set] @abstractmethod def __init__(self, individuals: Optional[set] = None): self._individuals = individuals @property def individuals(self): return self._individuals @property def individuals_count(self) -> Optional[int]: return len(self._individuals)
[docs] class LBLNode(_NodeIndividuals, OENode): """ LBL search tree node.""" __slots__ = '_children', '_individuals' def __init__(self, concept: OWLClassExpression, length: int, individuals, parent_node: Optional['LBLNode'] = None, is_root: bool = False): OENode.__init__(self, concept=concept, length=length, parent_node=parent_node, is_root=is_root) _NodeIndividuals.__init__(self, individuals) self._children = set()
[docs] def add_child(self, n): self._children.add(n)
[docs] def remove_child(self, n): self._children.remove(n)
@property def children(self): return self._children @property def parent_node(self) -> Optional['LBLNode']: return SuperProp(super()).parent_node @parent_node.setter def parent_node(self, parent_node: Optional['LBLNode']): self._parent_ref = weakref.ref(parent_node)
[docs] @total_ordering class LengthOrderedNode(Generic[_N]): __slots__ = 'node', 'len' node: Final[_N] len: Final[int] def __init__(self, node: _N, length: int): self.node = node self.len = length
[docs] def __lt__(self, other): if type(other) is not type(self): return NotImplemented if self.len < other.len: return True elif other.len < self.len: return False else: return OrderedOWLObject(as_index(self.node.concept)) < OrderedOWLObject(as_index(other.node.concept))
[docs] def __eq__(self, other): return self.len == other.len and self.node == other.node
[docs] @total_ordering class HeuristicOrderedNode(Generic[_N]): """A comparator that orders the Nodes based on Heuristic, then OrderedOWLObject of the concept""" __slots__ = 'node' node: Final[_N] def __init__(self, node: _N): self.node = node
[docs] def __lt__(self: _N, other: _N): if self.node.heuristic is None: raise ValueError("node heuristic not calculated", self.node) if other.node.heuristic is None: raise ValueError("other node heuristic not calculcated", other.node) if self.node.heuristic < other.node.heuristic: return True elif self.node.heuristic > other.node.heuristic: return False else: return OrderedOWLObject(as_index(self.node.concept)) < OrderedOWLObject(as_index(other.node.concept))
[docs] def __eq__(self: _N, other: _N): return self.node == other.node
[docs] @total_ordering class QualityOrderedNode: """QualityOrderedNode search tree node.""" __slots__ = 'node' node: Final[OENode] def __init__(self, node: OENode): self.node = node
[docs] def __lt__(self, other): if self.node.quality is None: raise ValueError("node not evaluated", self.node) if other.node.quality is None: raise ValueError("other node not evaluated", other.node) if self.node.quality < other.node.quality: return True elif self.node.quality > other.node.quality: return False else: if self.node.len > other.node.len: # shorter is better, ie. greater return True elif self.node.len < other.node.len: return False else: return OrderedOWLObject(as_index(self.node.concept)) < OrderedOWLObject(as_index(other.node.concept))
[docs] def __eq__(self, other): return self.node == other.node
def _node_and_all_children(n: _N) -> Iterable[_N]: # pragma: no cover """Get a node and all of its children (recursively) in an iterable""" yield n for c in n.children: yield from _node_and_all_children(c)
[docs] class SearchTreePriorityQueue(LBLSearchTree[LBLNode]): """ Search tree based on priority queue. Args: quality_func: An instance of a subclass of AbstractScorer that measures the quality of a node. heuristic_func: An instance of a subclass of AbstractScorer that measures the promise of a node. Attributes: quality_func: An instance of a subclass of AbstractScorer that measures the quality of a node. heuristic_func: An instance of a subclass of AbstractScorer that measures the promise of a node. items_in_queue: An instance of PriorityQueue Class. .nodes: A dictionary where keys are string representation of nodes and values are corresponding node objects. nodes: A property method for ._nodes. expressionTests: not being used . str_to_obj_instance_mapping: not being used. """ quality_func: AbstractScorer heuristic_func: AbstractHeuristic nodes: Dict[OWLClassExpression, LBLNode] items_in_queue: 'PriorityQueue[Tuple[float, HeuristicOrderedNode[LBLNode]]]' def __init__(self, quality_func, heuristic_func): # pragma: no cover self.quality_func = quality_func self.heuristic_func = heuristic_func self.nodes = dict() self.items_in_queue = PriorityQueue()
[docs] def add(self, n: LBLNode): """ Append a node into the search tree. Args: n: A Node object Returns: None """ self.items_in_queue.put((-n.heuristic, HeuristicOrderedNode(n))) # gets the smallest one. self.nodes[n.concept] = n
[docs] def add_root(self, node, kb_learning_problem): # pragma: no cover assert node.is_root assert not self.nodes self.quality_func.apply(node, node.individuals, kb_learning_problem) self.heuristic_func.apply(node, node.individuals, kb_learning_problem) self.items_in_queue.put((-node.heuristic, HeuristicOrderedNode(node))) # gets the smallest one. self.nodes[node.concept] = node
[docs] def add_node(self, *, node: LBLNode, parent_node: LBLNode, kb_learning_problem: EncodedLearningProblem) \ -> Optional[bool]: # pragma: no cover """ Add a node into the search tree after calculating heuristic value given its parent. Args: node: A Node object parent_node: A Node object kb_learning_problem: the encoded learning problem to compare the quality on Returns: True if node is a "goal node", i.e. quality_metric(node)=1.0 False if node is a "weak node", i.e. quality_metric(node)=0.0 None otherwise Notes: node is a refinement of refined_node """ if node.concept in self.nodes and node.parent_node != parent_node: old_heuristic = node.heuristic self.heuristic_func.apply(node, node.individuals, kb_learning_problem) new_heuristic = node.heuristic if new_heuristic > old_heuristic: node.parent_node.remove_child(node) node.parent_node = parent_node parent_node.add_child(node) self.items_in_queue.put((-node.heuristic, HeuristicOrderedNode(node))) # gets the smallest one. self.nodes[node.concept] = node else: # @todos reconsider it. self.quality_func.apply(node, node.individuals, kb_learning_problem) if node.quality == 0: return False self.heuristic_func.apply(node, node.individuals, kb_learning_problem) self.items_in_queue.put((-node.heuristic, HeuristicOrderedNode(node))) # gets the smallest one. self.nodes[node.concept] = node parent_node.add_child(node) if node.quality == 1: return True
[docs] def get_most_promising(self) -> LBLNode: # pragma: no cover """ Gets the current most promising node from Queue. Returns: node: A node object """ _, most_promising_str = self.items_in_queue.get() # get try: node = self.nodes[most_promising_str.node.concept] self.items_in_queue.put((-node.heuristic, HeuristicOrderedNode(node))) # put again into queue. return node except KeyError: print(most_promising_str, 'is not found') print('####') for k, v in self.nodes.items(): print(k) raise
[docs] def get_top_n(self, n: int, key='quality') -> List[LBLNode]: # pragma: no cover """ Gets the top n nodes determined by key from the search tree. Returns: top_n_predictions: A list of node objects """ if key == 'quality': top_n_predictions = sorted(self.nodes.values(), key=lambda node: node.quality, reverse=True)[:n] elif key == 'heuristic': top_n_predictions = sorted(self.nodes.values(), key=lambda node: node.heuristic, reverse=True)[:n] elif key == 'length': top_n_predictions = sorted(self.nodes.values(), key=lambda node: node.len, reverse=True)[:n] else: print('Wrong Key:{0}\tProgram exist.'.format(key)) raise KeyError return top_n_predictions
[docs] def clean(self): self.items_in_queue = PriorityQueue() self.nodes.clear()
[docs] def show_search_tree(self, root_concept: OWLClassExpression, heading_step: str): # pragma: no cover rdr = DLSyntaxObjectRenderer() print('######## ', heading_step, 'step Search Tree ###########') def node_as_length_ordered_concept(node: LBLNode): return LengthOrderedNode(node, node.len) def print_partial_tree_recursive(node: LBLNode, depth: int = 0): render_str = rdr.render(node.concept) depths = "`" * depth print("%s %s \t Q:%f Heur:%s" % (depths, render_str, node.quality, node.heuristic)) for c in sorted(node.children, key=node_as_length_ordered_concept): print_partial_tree_recursive(c, depth + 1) print_partial_tree_recursive(self.nodes[root_concept])
_TN = TypeVar('_TN', bound='TreeNode') #:
[docs] class TreeNode(Generic[_N]): """ Simple search tree node.""" __slots__ = 'children', 'node' node: Final[_N] children: Set['TreeNode[_N]'] def __init__(self: _TN, node: _N, parent_tree_node: Optional[_TN] = None, is_root: bool = False): self.node = node self.children = set() if not is_root: assert isinstance(parent_tree_node, TreeNode) parent_tree_node.children.add(self)
[docs] class DRILLSearchTreePriorityQueue(DRILLAbstractTree): """ #@TODO Move to learners/drill.py Search tree based on priority queue. Parameters ---------- quality_func : An instance of a subclass of AbstractScorer that measures the quality of a node. heuristic_func : An instance of a subclass of AbstractScorer that measures the promise of a node. Attributes ---------- quality_func : An instance of a subclass of AbstractScorer that measures the quality of a node. heuristic_func : An instance of a subclass of AbstractScorer that measures the promise of a node. items_in_queue: An instance of PriorityQueue Class. .nodes: A dictionary where keys are string representation of nodes and values are corresponding node objects. nodes: A property method for ._nodes. expressionTests: not being used . str_to_obj_instance_mapping: not being used. """ def __init__(self, verbose): super().__init__() self.verbose = verbose self.items_in_queue = PriorityQueue()
[docs] def add(self, node: RL_State): """ Append a node into the search tree. Parameters ---------- node : A RL_State object Returns ------- None """ assert node.quality > 0, f"{RL_State.concept} cannot be added into the search tree" assert node.heuristic is not None dl_representation = owl_expression_to_dl(node.concept.get_nnf()) if dl_representation in self.nodes: """Do nothing""" else: self.items_in_queue.put( (-node.heuristic, len(owl_expression_to_dl(node.concept)), dl_representation)) # gets the smallest one. self.nodes[dl_representation] = node
[docs] def show_current_search_tree(self, top_n=10): """ Show search tree.""" predictions = sorted( [(neg_heuristic, length, self.nodes[dl_representation]) for neg_heuristic, length, dl_representation in self.items_in_queue.queue])[:top_n] if self.verbose>0: print( f"\n######## Most Promising {top_n} Concepts out of {len(self.items_in_queue.queue)} Concepts ###########\n") for ith, (_, __, node) in enumerate(predictions): if self.verbose: print( f"{ith + 1}-\t{owl_expression_to_dl(node.concept)} | Quality:{node.quality:.3f}| Heuristic:{node.heuristic:.3f}") # print('\n######## Current Search Tree ###########\n') if self.verbose: print('\n') return predictions
[docs] def get_most_promising(self) -> RL_State: """ Gets the current most promising node from Queue. Returns ------- node: A node object """ assert len(self.items_in_queue.queue) > 0 ,("Search tree is empty. " "\nEnsure that there is at least one " "owl:Class or" "owl:ObjectProperty definitions") _, __, dl_representation = self.items_in_queue.get(timeout=1.0) # R node = self.nodes[dl_representation] return node
[docs] def get_top_n(self, n: int, key='quality') -> List[Node]: # pragma: no cover """ Gets the top n nodes determined by key from the search tree. Returns ------- top_n_predictions: A list of node objects """ all_nodes = self.refined_nodes + self.nodes.values() all_nodes.union(self.nodes) if key == 'quality': top_n_predictions = sorted(all_nodes, key=lambda node: node.quality, reverse=True)[:n] elif key == 'heuristic': top_n_predictions = sorted(all_nodes, key=lambda node: node.heuristic, reverse=True)[:n] elif key == 'length': top_n_predictions = sorted(self.nodes.values(), key=lambda node: len(node), reverse=True)[:n] else: print('Wrong Key:{0}\tProgram exist.'.format(key)) raise KeyError return top_n_predictions
[docs] def clean(self): self.items_in_queue = PriorityQueue() self._nodes.clear()
[docs] class EvaluatedConcept: """Explicitly declare the attributes that should be returned by the evaluate_concept method of a KnowledgeBase. This way, Python uses a more efficient way to store the instance attributes, which can significantly reduce the memory usage. """ __slots__ = 'q', 'inds', 'ic' pass
[docs] class SuperProp: # pragma: no cover """ Super wrapper which allows property setting & deletion. Super can't be subclassed with empty __init__ arguments. """ def __init__(self, super_obj): object.__setattr__(self, 'super_obj', super_obj) def _find_desc(self, name): super_obj = object.__getattribute__(self, 'super_obj') if name != '__class__': mro = iter(super_obj.__thisclass__.__mro__) for cls in mro: if cls == super_obj.__thisclass__: break for cls in mro: if isinstance(cls, type): try: # don't lookup further up the chain return object.__getattribute__(cls, name) except AttributeError: continue except KeyError: return None return None
[docs] def __getattr__(self, name): return getattr(object.__getattribute__(self, 'super_obj'), name)
[docs] def __setattr__(self, name, value): super_obj = object.__getattribute__(self, 'super_obj') desc = object.__getattribute__(self, '_find_desc')(name) if hasattr(desc, '__set__'): return desc.__set__(super_obj.__self__, value) return setattr(super_obj, name, value)
[docs] def __delattr__(self, name): super_obj = object.__getattribute__(self, 'super_obj') desc = object.__getattribute__(self, '_find_desc')(name) if hasattr(desc, '__delete__'): return desc.__delete__(super_obj.__self__) return delattr(super_obj, name)