Source code for pykeen.evaluation.evaluator

# -*- coding: utf-8 -*-

"""Basic structure of a evaluator."""

from __future__ import annotations

import logging
import timeit
import warnings
from abc import ABC, abstractmethod
from collections import ChainMap
from typing import (

import pandas
import torch
from torch_max_mem import maximize_memory_utilization
from tqdm.autonotebook import tqdm

from ..metrics.utils import Metric
from ..models import Model
from ..triples.triples_factory import restrict_triples
from ..triples.utils import get_entities, get_relations
from ..typing import LABEL_HEAD, LABEL_RELATION, LABEL_TAIL, InductiveMode, MappedTriples, Target
from ..utils import flatten_dictionary, format_relative_comparison, normalize_string, prepare_filter_triples

__all__ = [

logger = logging.getLogger(__name__)

# TODO: maybe move into separate module?
MetricKeyType = TypeVar("MetricKeyType", bound=Tuple)

[docs]class MetricResults(Generic[MetricKeyType]): """Results from computing metrics.""" metrics: ClassVar[Mapping[str, Type[Metric]]] data: Mapping[MetricKeyType, float] def __init__(self, data: Mapping[MetricKeyType | str, float]): """Initialize the result wrapper.""" = {self.string_or_key_to_key(key): value for key, value in data.items()}
[docs] @classmethod @abstractmethod def key_from_string(cls, s: str | None) -> MetricKeyType: """ Parse the metric key from a (un-normalized) string. :param s: the metric key, or `None` to get the default key. :return: the fully resolved key as a named tuple """ raise NotImplementedError
[docs] @classmethod def key_to_string(cls, s: str | MetricKeyType | None) -> str: """Convert a key to a normalized key.""" return ".".join(cls.string_or_key_to_key(s))
[docs] @classmethod def string_or_key_to_key(cls, s: str | MetricKeyType | None) -> MetricKeyType: """Convert a key to a named tuple.""" if s is None or isinstance(s, str): s = cls.key_from_string(s) return s
[docs] def get_metric(self, name: str | MetricKeyType) -> float: """Get the given metric from the results. :param name: The name of the metric :returns: The value for the metric """ return[self.string_or_key_to_key(name)]
[docs] def to_flat_dict(self) -> Mapping[str, Any]: """Get the results as a flattened dictionary.""" return {self.key_to_string(key): value for key, value in}
[docs] def to_dict(self) -> Mapping[str, Any]: """Extract a (potentially nested) JSON-compatible dictionary.""" # actual type: nested dictionary with string keys result: dict[str, Any] = {} for compound_key, metric_value in partial_result = result for key_part in compound_key[:-1]: partial_result.setdefault(str(key_part), {}) partial_result = partial_result[key_part] partial_result[str(compound_key[-1])] = metric_value return result
[docs] def to_df(self) -> pandas.DataFrame: """Output the metrics as a pandas dataframe.""" one_key = next(iter( # assert isinstance(one_key, NamedTuple) one_key_nt = cast(NamedTuple, one_key) columns = [field.capitalize() for field in one_key_nt._fields] + ["Value"] return pandas.DataFrame([(*key, value) for key, value in], columns=columns)
[docs]class Evaluator(ABC, Generic[MetricKeyType]): """An abstract evaluator for KGE models. The evaluator encapsulates the computation of evaluation metrics based on head and tail scores. To this end, it offers two methods to process a batch of triples together with the scores produced by some model. It maintains intermediate results in its state, and offers a method to obtain the final results once finished. """ metric_result_cls: Type[MetricResults[MetricKeyType]] def __init__( self, filtered: bool = False, requires_positive_mask: bool = False, batch_size: Optional[int] = None, slice_size: Optional[int] = None, automatic_memory_optimization: bool = True, mode: Optional[InductiveMode] = None, ): """Initialize the evaluator. :param filtered: Should filtered evaluation be performed? :param requires_positive_mask: Does the evaluator need access to the masks? :param batch_size: >0. Evaluation batch size. :param slice_size: >0. The divisor for the scoring function when using slicing :param automatic_memory_optimization: Whether to automatically optimize the sub-batch size during evaluation with regards to the hardware at hand. :param mode: the inductive mode, or None for transductive evaluation """ self.filtered = filtered self.requires_positive_mask = requires_positive_mask self.batch_size = batch_size self.slice_size = slice_size self.automatic_memory_optimization = automatic_memory_optimization self.mode = mode
[docs] @classmethod def get_normalized_name(cls) -> str: """Get the normalized name of the evaluator.""" return normalize_string(cls.__name__, suffix=Evaluator.__name__)
[docs] @abstractmethod def process_scores_( self, hrt_batch: MappedTriples, target: Target, scores: torch.FloatTensor, true_scores: Optional[torch.FloatTensor] = None, dense_positive_mask: Optional[torch.FloatTensor] = None, ) -> None: """Process a batch of triples with their computed scores for all entities. :param hrt_batch: shape: (batch_size, 3) :param target: the prediction target :param scores: shape: (batch_size, num_entities) :param true_scores: shape: (batch_size, 1) :param dense_positive_mask: shape: (batch_size, num_entities) An optional binary (0/1) tensor indicating other true entities. """ raise NotImplementedError
[docs] @abstractmethod def clear(self) -> None: """Clear buffers and intermediate results.""" raise NotImplementedError
[docs] @abstractmethod def finalize(self) -> MetricResults[MetricKeyType]: """Compute the final results, and clear buffers.""" raise NotImplementedError
[docs] def evaluate( self, model: Model, mapped_triples: MappedTriples, batch_size: Optional[int] = None, slice_size: Optional[int] = None, device: Optional[torch.device] = None, use_tqdm: bool = True, tqdm_kwargs: Optional[Mapping[str, Any]] = None, restrict_entities_to: Optional[Collection[int]] = None, restrict_relations_to: Optional[Collection[int]] = None, do_time_consuming_checks: bool = True, additional_filter_triples: Union[None, MappedTriples, List[MappedTriples]] = None, pre_filtered_triples: bool = True, targets: Collection[Target] = (LABEL_HEAD, LABEL_TAIL), ) -> MetricResults[MetricKeyType]: """Evaluate metrics for model on mapped triples. :param model: The model to evaluate. :param mapped_triples: The triples on which to evaluate. The mapped triples should *never* contain inverse triples - these are created by the model class on the fly. :param batch_size: >0 A positive integer used as batch size. Generally chosen as large as possible. Defaults to 1 if None. :param slice_size: >0 The divisor for the scoring function when using slicing. :param device: The device on which the evaluation shall be run. If None is given, use the model's device. :param use_tqdm: Should a progress bar be displayed? :param tqdm_kwargs: Additional keyword based arguments passed to the progress bar. :param restrict_entities_to: Optionally restrict the evaluation to the given entity IDs. This may be useful if one is only interested in a part of the entities, e.g. due to type constraints, but wants to train on all available data. For ranking the entities, we still compute all scores for all possible replacement entities to avoid irregular access patterns which might decrease performance, but the scores will afterward be filtered to only keep those of interest. If provided, we assume by default that the triples are already filtered, such that it only contains the entities of interest. To explicitly filter within this method, pass `pre_filtered_triples=False`. :param restrict_relations_to: Optionally restrict the evaluation to the given relation IDs. This may be useful if one is only interested in a part of the relations, e.g. due to relation types, but wants to train on all available data. If provided, we assume by default that the triples are already filtered, such that it only contains the relations of interest. To explicitly filter within this method, pass `pre_filtered_triples=False`. :param do_time_consuming_checks: Whether to perform some time-consuming checks on the provided arguments. Currently, this encompasses only: If `restrict_entities_to` or `restrict_relations_to` is not `None`, check whether the triples have been filtered. Disabling this option can accelerate the method. Only effective if `pre_filtered_triples` is set to `True`. :param pre_filtered_triples: Whether the triples have been pre-filtered to adhere to `restrict_entities_to` / `restrict_relations_to`. When set to `True`, and the triples have *not* been filtered, the results may be invalid. Pre-filtering the triples accelerates this method, and is recommended when evaluating multiple times on the same set of triples. :param additional_filter_triples: additional true triples to filter out during filtered evaluation. :param targets: the prediction targets :raises NotImplementedError: if relation prediction evaluation is requested :raises ValueError: if the pre_filtered_triples contain unwanted entities (can only be detected with the time-consuming checks). :raises MemoryError: if the evaluation fails on cpu :return: the evaluation results """ if LABEL_RELATION in targets: raise NotImplementedError("cf.") start = timeit.default_timer() # verify that the triples have been filtered if pre_filtered_triples and do_time_consuming_checks: if restrict_entities_to is not None: present_entity_ids = get_entities(triples=mapped_triples) unwanted = present_entity_ids.difference(restrict_entities_to) if len(unwanted) > 0: raise ValueError( f"mapped_triples contains IDs of entities which are not contained in restrict_entities_to:" f"{unwanted}. This will invalidate the evaluation results.", ) if restrict_relations_to is not None: present_relation_ids = get_relations(triples=mapped_triples) unwanted = present_relation_ids.difference(restrict_relations_to) if len(unwanted): raise ValueError( f"mapped_triples contains IDs of relations which are not contained in restrict_relations_to:" f"{unwanted}. This will invalidate the evaluation results.", ) # Filter triples if necessary if not pre_filtered_triples and (restrict_entities_to is not None or restrict_relations_to is not None): old_num_triples = mapped_triples.shape[0] mapped_triples = restrict_triples( mapped_triples=mapped_triples, entities=restrict_entities_to, relations=restrict_relations_to, )"keeping {format_relative_comparison(mapped_triples.shape[0], old_num_triples)} triples.") # Prepare for result filtering if self.filtered or self.requires_positive_mask: all_pos_triples = prepare_filter_triples( mapped_triples=mapped_triples, additional_filter_triples=additional_filter_triples, ) else: all_pos_triples = None device = device or model.device tqdm_kwargs = dict(tqdm_kwargs or {}) if not use_tqdm: tqdm_kwargs.update(dict(disable=False)) try: result = self._evaluate_on_device( model=model, mapped_triples=mapped_triples, batch_size=batch_size, slice_size=slice_size, device=device, all_pos_triples=all_pos_triples, restrict_entities_to=restrict_entities_to, targets=targets, tqdm_kwargs=tqdm_kwargs, ) except MemoryError as error: if device.type == "cpu": raise error logger.error( f"Memory error: {error}; falling back to evaluation on cpu. This will incur heavy runtime costs for " f"reasonably sized datasets and models." ) result = self._evaluate_on_device( model=model, mapped_triples=mapped_triples, batch_size=batch_size, slice_size=slice_size, device=torch.device("cpu"), all_pos_triples=all_pos_triples, restrict_entities_to=restrict_entities_to, targets=targets, tqdm_kwargs=tqdm_kwargs, ) stop = timeit.default_timer()"Evaluation took %.2fs seconds", stop - start) return result
def _evaluate_on_device( self, model: Model, mapped_triples: MappedTriples, batch_size: int | None, slice_size: int | None, device: torch.device, all_pos_triples: MappedTriples | None, targets: Collection[Target], tqdm_kwargs: Mapping[str, Any], **kwargs, ) -> MetricResults: """Evaluate the model on the given device.""" # Ensure evaluation mode model.eval() # Send model & tensors to device model = if all_pos_triples is not None: all_pos_triples = mapped_triples = num_triples = mapped_triples.shape[0] # no batch size -> automatic memory optimization if batch_size is None: batch_size = 32 if device.type == "cpu" else num_triples logger.debug(f"Automatically set maximum batch size to {batch_size=}") # no slice size -> automatic memory optimization if slice_size is None: nums: set[int] = set() if {LABEL_HEAD, LABEL_TAIL}.intersection(targets): nums.add(model.num_entities) if LABEL_RELATION in targets: nums.add(model.num_relations) slice_size = max(nums) logger.debug(f"Automatically set maximum slice size to {slice_size=}") # Show progressbar with tqdm( **ChainMap( dict(tqdm_kwargs), dict( desc=f"Evaluating on {model.device}", total=num_triples, unit="triple", unit_scale=True, ), ) ) as progress_bar: return evaluate( evaluator=self, mapped_triples=mapped_triples, # note: we provide the *maximum* batch and slice size here; it is reduced if necessary batch_size=num_triples, slice_size=slice_size, progress_bar=progress_bar, targets=targets, # kwargs all_pos_triples=all_pos_triples, model=model, mode=self.mode, **kwargs, ) @staticmethod def _check_slicing_availability(model: Model, batch_size: int, entities: bool, relations: bool) -> None: """ Raise an error if the necessary slicing operations are not supported. :param model: the model :param batch_size: the batch-size; only used for creating the error message :param entities: whether entities need to be scored :param relations: whether relations need to be scored :raises MemoryError: if the necessary slicing operations are not supported by the model """ reasons = [] if entities: # if inverse triples are used, we only do score_t (TODO: by default; can this be changed?) if not model.can_slice_t: reasons.append("score_t") # otherwise, i.e., without inverse triples, we also need score_h if not model.use_inverse_triples and not model.can_slice_t: reasons.append("score_h") # if relations are to be predicted, we need to slice score_r if relations and not model.can_slice_r: reasons.append("score_r") # raise an error, if any of the required methods cannot slice if reasons: raise MemoryError( f"The current model can't be evaluated on this hardware with these parameters, as " f"evaluation batch_size={batch_size} is too big and slicing is not implemented for this " f"model yet (missing support for: {reasons})" )
def _hasher(kwargs: Mapping[str, Any]) -> int: """Share optimal batch size whenever this hash matches.""" return hash((id(kwargs["evaluator"]), kwargs["mapped_triples"].shape[0], kwargs["targets"])) @maximize_memory_utilization(parameter_name=("batch_size", "slice_size"), hasher=_hasher) @torch.inference_mode() def evaluate( *, evaluator: Evaluator, mapped_triples: MappedTriples, batch_size: int, slice_size: int, progress_bar: tqdm, targets: Collection[Target], **kwargs, ) -> MetricResults: """ Evaluate a model with the given evaluator. .. note :: this method is wrapped into two memory utilization maximizer, which reduce the parameters `batch_size` and `slice_size`, if necessary due to memory constraints. :param evaluator: the evaluator instance that is used for evaluation :param mapped_triples: the evaluation triples :param batch_size: the (maximum) batch size. It will be reduced when (GPU) out-of-memory problems occur. :param slice_size: the (maximum) slice size. It will be reduced when (GPU) out-of-memory problems occur, and batch size reduction could not resolve the issue. :param progress_bar: whether to display a progress bar :param targets: the evaluation targets :param kwargs: additional keyword-based parameters are passed to :meth:`_evaluate_batch`. :return: the evaluation result """ # todo: maybe we want to have some more keys outside of kwargs for hashing / have more visibility about # what is passed around # clear evaluator and reset progress bar (necessary for size-probing / evaluation fallback) evaluator.clear() progress_bar.reset(total=mapped_triples.shape[0]) # batch-wise processing for batch in mapped_triples.split(split_size=batch_size): # the relation_filter can be re-used (per batch) when we evaluate head *and* tail predictions # (which is the standard setting), cf. create_sparse_positive_filter_ relation_filter = None for target in targets: relation_filter = _evaluate_batch( batch=batch, target=target, evaluator=evaluator, relation_filter=relation_filter, **kwargs, slice_size=slice_size, ) # update progress bar with actual batch size progress_bar.update(batch.shape[0]) return evaluator.finalize() def create_sparse_positive_filter_( hrt_batch: MappedTriples, all_pos_triples: torch.LongTensor, relation_filter: torch.BoolTensor | None = None, filter_col: int = 0, ) -> Tuple[torch.LongTensor, torch.BoolTensor]: """Compute indices of all positives. For simplicity, only the head-side is described, i.e. filter_col=0. The tail-side is processed alike. For each (h, r, t) triple in the batch, the entity identifiers are computed such that (h', r, t) exists in all positive triples. :param hrt_batch: shape: (batch_size, 3) A batch of triples. :param all_pos_triples: shape: (num_positive_triples, 3) All positive triples to base the filtering on. :param relation_filter: shape: (batch_size, num_positive_triples) A boolean mask R[i, j] which is True iff the j-th positive triple contains the same relation as the i-th triple in the batch. :param filter_col: The column along which to filter. Allowed are {0, 2}, where 0 corresponds to filtering head-based and 2 corresponds to filtering tail-based. :return: - positives, shape: (2, m) The indices of positives in format [(batch_index, entity_id)]. - the relation filter for re-usage. :raises NotImplementedError: if the `filter_col` is not in `{0, 2}` """ if filter_col not in {0, 2}: raise NotImplementedError( "This code has only been written for updating head (filter_col=0) or " f"tail (filter_col=2) mask, but filter_col={filter_col} was given.", ) if relation_filter is None: relations = hrt_batch[:, 1:2] relation_filter = (all_pos_triples[:, 1:2]).view(1, -1) == relations # Split batch other_col = 2 - filter_col entities = hrt_batch[:, other_col : other_col + 1] entity_filter_test = (all_pos_triples[:, other_col : other_col + 1]).view(1, -1) == entities filter_batch = (entity_filter_test & relation_filter).nonzero(as_tuple=False) filter_batch[:, 1] = all_pos_triples[:, filter_col : filter_col + 1].view(1, -1)[:, filter_batch[:, 1]] return filter_batch, relation_filter def create_dense_positive_mask_( zero_tensor: torch.FloatTensor, filter_batch: torch.LongTensor, ) -> torch.FloatTensor: """Construct dense positive mask. :param zero_tensor: shape: (batch_size, num_entities) A tensor of zeros of suitable shape. :param filter_batch: shape: (m, 2) The indices of all positives in format (batch_index, entity_id) :return: The dense positive mask with x[b, i] = 1 iff (b, i) in filter_batch. """ zero_tensor[filter_batch[:, 0], filter_batch[:, 1]] = 1 return zero_tensor def filter_scores_( scores: torch.FloatTensor, filter_batch: torch.LongTensor, ) -> torch.FloatTensor: """Filter scores by setting true scores to NaN. :param scores: shape: (batch_size, num_entities) The scores for all corrupted triples (including the currently considered true triple). Are modified *in-place*. :param filter_batch: (m, 2) The indices of all positives. :return: A reference to the scores, which have been updated in-place. """ # Bind shape batch_size, num_entities = scores.shape # Set all filtered triples to NaN to ensure their exclusion in subsequent calculations scores[filter_batch[:, 0], filter_batch[:, 1]] = float("nan") # Warn if all entities will be filtered # (scores != scores) yields true for all NaN instances (IEEE 754), thus allowing to count the filtered triples. if ((scores != scores).sum(dim=1) == num_entities).any(): logger.warning( "User selected filtered metric computation, but all corrupted triples exists also as positive " "triples", ) return scores def _evaluate_batch( batch: MappedTriples, model: Model, target: Target, evaluator: Evaluator, slice_size: Optional[int], all_pos_triples: Optional[MappedTriples], relation_filter: Optional[torch.BoolTensor], restrict_entities_to: Optional[torch.LongTensor], *, mode: Optional[InductiveMode], ) -> torch.BoolTensor: """ Evaluate ranking for batch. :param batch: shape: (batch_size, 3) The batch of currently evaluated triples. :param model: The model to evaluate. :param target: The prediction target. :param evaluator: The evaluator :param slice_size: An optional slice size for computing the scores. :param all_pos_triples: All positive triples (required if filtering is necessary). :param relation_filter: The relation filter. Can be re-used. :param restrict_entities_to: Restriction to evaluate only for these entities. :param mode: the inductive mode, or None for transductive evaluation :raises ValueError: if all positive triples are required (either due to filtered evaluation, or requiring dense masks). :return: The relation filter, which can be re-used for the same batch. """ scores = model.predict(hrt_batch=batch, target=target, slice_size=slice_size, mode=mode) if evaluator.filtered or evaluator.requires_positive_mask: column = TARGET_TO_INDEX[target] if all_pos_triples is None: raise ValueError( "If filtering_necessary of positive_masks_required is True, all_pos_triples has to be " "provided, but is None." ) # Create filter positive_filter, relation_filter = create_sparse_positive_filter_( hrt_batch=batch, all_pos_triples=all_pos_triples, relation_filter=relation_filter, filter_col=column, ) else: positive_filter = relation_filter = None if evaluator.filtered: assert positive_filter is not None # Select scores of true true_scores = scores[torch.arange(0, batch.shape[0]), batch[:, column]] # overwrite filtered scores scores = filter_scores_(scores=scores, filter_batch=positive_filter) # The scores for the true triples have to be rewritten to the scores tensor scores[torch.arange(0, batch.shape[0]), batch[:, column]] = true_scores # the rank-based evaluators needs the true scores with trailing 1-dim true_scores = true_scores.unsqueeze(dim=-1) else: true_scores = None # Create a positive mask with the size of the scores from the positive filter if evaluator.requires_positive_mask: assert positive_filter is not None positive_mask = create_dense_positive_mask_(zero_tensor=torch.zeros_like(scores), filter_batch=positive_filter) else: positive_mask = None # Restrict to entities of interest if restrict_entities_to is not None: scores = scores[:, restrict_entities_to] if positive_mask is not None: positive_mask = positive_mask[:, restrict_entities_to] # process scores evaluator.process_scores_( hrt_batch=batch, target=target, true_scores=true_scores, scores=scores, dense_positive_mask=positive_mask, ) return relation_filter def get_candidate_set_size( mapped_triples: MappedTriples, restrict_entities_to: Optional[Collection[int]] = None, restrict_relations_to: Optional[Collection[int]] = None, additional_filter_triples: Union[None, MappedTriples, List[MappedTriples]] = None, num_entities: Optional[int] = None, ) -> pandas.DataFrame: """ Calculate the candidate set sizes for head/tail prediction for the given triples. :param mapped_triples: shape: (n, 3) the evaluation triples :param restrict_entities_to: The entity IDs of interest. If None, defaults to all entities. cf. :func:`restrict_triples`. :param restrict_relations_to: The relations IDs of interest. If None, defaults to all relations. cf. :func:`restrict_triples`. :param additional_filter_triples: shape: (n, 3) additional filter triples besides the evaluation triples themselves. cf. `_prepare_filter_triples`. :param num_entities: the number of entities. If not given, this number is inferred from all triples :return: columns: "index" | "head" | "relation" | "tail" | "head_candidates" | "tail_candidates" a dataframe of all evaluation triples, with the number of head and tail candidates """ # optionally restrict triples (nop if no restriction) mapped_triples = restrict_triples( mapped_triples=mapped_triples, entities=restrict_entities_to, relations=restrict_relations_to, ) # evaluation triples as dataframe df_eval = pandas.DataFrame( data=mapped_triples.numpy(), columns=COLUMN_LABELS, ).reset_index() # determine filter triples filter_triples = prepare_filter_triples( mapped_triples=mapped_triples, additional_filter_triples=additional_filter_triples, ) # infer num_entities if not given if restrict_entities_to: num_entities = len(restrict_entities_to) else: # TODO: unique, or max ID + 1? num_entities = num_entities or filter_triples[:, [0, 2]].view(-1).unique().numel() # optionally restrict triples filter_triples = restrict_triples( mapped_triples=filter_triples, entities=restrict_entities_to, relations=restrict_relations_to, ) df_filter = pandas.DataFrame( data=filter_triples.numpy(), columns=COLUMN_LABELS, ) # compute candidate set sizes for different targets # TODO: extend to relations? for target in [LABEL_HEAD, LABEL_TAIL]: total = num_entities group_keys = TARGET_TO_KEY_LABELS[target] df_count = df_filter.groupby(by=group_keys).agg({target: "count"}) column = f"{target}_candidates" df_count[column] = total - df_count[target] df_count = df_count.drop(columns=target) df_eval = pandas.merge(df_eval, df_count, on=group_keys, how="left") df_eval[column] = df_eval[column].fillna(value=total) return df_eval def normalize_flattened_metric_results( result: Mapping[str, Any], metric_result_cls: Type[MetricResults] | None = None ) -> Mapping[str, Any]: """ Flatten metric result dictionary and normalize metric keys. :param result: the result dictionary. :param metric_result_cls: the metric result class providing metric name normalization :return: the flattened metric results with normalized metric names. """ # avoid cyclic imports from .rank_based_evaluator import RankBasedMetricResults # normalize keys if metric_result_cls is None: warnings.warn("Please explicitly provide a metric result class.", category=DeprecationWarning) metric_result_cls = RankBasedMetricResults # TODO: find a better way to handle this flat_result = flatten_dictionary(result) result = {} for key, value in flat_result.items(): try: normalized_key = metric_result_cls.key_from_string(key) except ValueError as error: new_key = key.replace("nondeterministic", "").replace("unknown", "").strip(".").replace("..", ".") logger.warning(f"Trying to fix malformed key={key} to key={new_key} (error: {error})") normalized_key = metric_result_cls.key_from_string(new_key) result[metric_result_cls.key_to_string(normalized_key)] = value return result