Source code for autogluon.core.models.ensemble.bagged_ensemble_model
import copy
import logging
import os
import platform
import time
from collections import Counter
from statistics import mean
from typing import Union
import numpy as np
import pandas as pd
from autogluon.common.utils.log_utils import DuplicateFilter
from .fold_fitting_strategy import AbstractFoldFittingStrategy, SequentialLocalFoldFittingStrategy, ParallelLocalFoldFittingStrategy
from ..abstract.abstract_model import AbstractModel
from ...constants import MULTICLASS, REGRESSION, SOFTCLASS, QUANTILE, REFIT_FULL_SUFFIX
from ...utils.exceptions import TimeLimitExceeded
from ...utils.loaders import load_pkl
from ...utils.savers import save_pkl
from ...utils.try_import import try_import_ray
from ...utils.utils import CVSplitter, _compute_fi_with_stddev
logger = logging.getLogger(__name__)
dup_filter = DuplicateFilter()
logger.addFilter(dup_filter)
# TODO: Add metadata object with info like score on each model, train time on each model, etc.
[docs]class BaggedEnsembleModel(AbstractModel):
"""
Bagged ensemble meta-model which fits a given model multiple times across different splits of the training data.
For certain child models such as KNN, this may only train a single model and instead rely on the child model to generate out-of-fold predictions.
"""
_oof_filename = 'oof.pkl'
def __init__(self, model_base: AbstractModel, random_state=0, **kwargs):
self.model_base = model_base
self._child_type = type(self.model_base)
self.models = []
self._oof_pred_proba = None
self._oof_pred_model_repeats = None
self._n_repeats = 0 # Number of n_repeats with at least 1 model fit, if kfold=5 and 8 models have been fit, _n_repeats is 2
self._n_repeats_finished = 0 # Number of n_repeats finished, if kfold=5 and 8 models have been fit, _n_repeats_finished is 1
self._k_fold_end = 0 # Number of models fit in current n_repeat (0 if completed), if kfold=5 and 8 models have been fit, _k_fold_end is 3
self._k = None # k models per n_repeat, equivalent to kfold value
self._k_per_n_repeat = [] # k-fold used for each n_repeat. == [5, 10, 3] if first kfold was 5, second was 10, and third was 3
self._random_state = random_state
self.low_memory = True
self._bagged_mode = None
# _child_oof currently is only set to True for KNN models, that are capable of LOO prediction generation to avoid needing bagging.
# TODO: Consider moving `_child_oof` logic to a separate class / refactor OOF logic.
# FIXME: Avoid unnecessary refit during refit_full on `_child_oof=True` models, just re-use the original model.
self._child_oof = False # Whether the OOF preds were taken from a single child model (Assumes child can produce OOF preds without bagging).
self._cv_splitters = [] # Keeps track of the CV splitter used for each bagged repeat.
self._params_aux_child = None # aux params of child model
super().__init__(problem_type=self.model_base.problem_type, eval_metric=self.model_base.eval_metric, **kwargs)
def _set_default_params(self):
default_params = {
# 'use_child_oof': False, # [Advanced] Whether to defer to child model for OOF preds and only train a single child.
'save_bag_folds': True,
# 'refit_folds': False, # [Advanced, Experimental] Whether to refit bags immediately to a refit_full model in a single .fit call.
}
for param, val in default_params.items():
self._set_default_param_value(param, val)
super()._set_default_params()
def _get_default_auxiliary_params(self) -> dict:
default_auxiliary_params = super()._get_default_auxiliary_params()
extra_auxiliary_params = dict(
drop_unique=False, # TODO: Get the value from child instead
)
default_auxiliary_params.update(extra_auxiliary_params)
return default_auxiliary_params
def is_valid(self):
return self.is_fit() and (self._n_repeats == self._n_repeats_finished)
def can_infer(self):
return self.is_fit() and self.params.get('save_bag_folds', True)
def is_stratified(self):
if self.problem_type in [REGRESSION, QUANTILE, SOFTCLASS]:
return False
else:
return True
def is_fit(self):
return len(self.models) != 0
def can_fit(self) -> bool:
return not self.is_fit() or self._bagged_mode
def is_valid_oof(self):
return self.is_fit() and (self._child_oof or self._bagged_mode)
def get_oof_pred_proba(self, **kwargs):
# TODO: Require is_valid == True (add option param to ignore is_valid)
return self._oof_pred_proba_func(self._oof_pred_proba, self._oof_pred_model_repeats)
@staticmethod
def _oof_pred_proba_func(oof_pred_proba, oof_pred_model_repeats):
oof_pred_model_repeats_without_0 = np.where(oof_pred_model_repeats == 0, 1, oof_pred_model_repeats)
if oof_pred_proba.ndim == 2:
oof_pred_model_repeats_without_0 = oof_pred_model_repeats_without_0[:, None]
return oof_pred_proba / oof_pred_model_repeats_without_0
def _init_misc(self, **kwargs):
child = self._get_model_base().convert_to_template()
child.initialize(**kwargs)
self.eval_metric = child.eval_metric
self.stopping_metric = child.stopping_metric
self.quantile_levels = child.quantile_levels
self.normalize_pred_probas = child.normalize_pred_probas
self._params_aux_child = child.params_aux
def preprocess(self, X, preprocess_nonadaptive=True, model=None, **kwargs):
if preprocess_nonadaptive:
if model is None:
if not self.models:
return X
model = self.models[0]
model = self.load_child(model)
return model.preprocess(X, preprocess_stateful=False)
else:
return X
def _get_cv_splitter(self, n_splits, n_repeats, groups=None):
return CVSplitter(n_splits=n_splits, n_repeats=n_repeats, groups=groups, stratified=self.is_stratified(), random_state=self._random_state)
def _fit(self,
X,
y,
X_val=None,
y_val=None,
X_pseudo=None,
y_pseudo=None,
k_fold=None,
k_fold_start=0,
k_fold_end=None,
n_repeats=1,
n_repeat_start=0,
groups=None,
**kwargs):
use_child_oof = self.params.get('use_child_oof', False)
if use_child_oof:
if self.is_fit():
# TODO: We may want to throw an exception instead and avoid calling fit more than once
return self
k_fold = 1
k_fold_end = None
groups = None
if k_fold is None and groups is None:
k_fold = 5
if k_fold is not None and k_fold < 1:
k_fold = 1
if k_fold is None or k_fold > 1:
k_fold = self._get_cv_splitter(n_splits=k_fold, n_repeats=n_repeats, groups=groups).n_splits
self._validate_bag_kwargs(
k_fold=k_fold,
k_fold_start=k_fold_start,
k_fold_end=k_fold_end,
n_repeats=n_repeats,
n_repeat_start=n_repeat_start,
groups=groups,
)
if k_fold_end is None:
k_fold_end = k_fold
model_base = self._get_model_base()
model_base.rename(name='')
kwargs['feature_metadata'] = self.feature_metadata
kwargs['num_classes'] = self.num_classes # TODO: maybe don't pass num_classes to children
if self.model_base is not None:
self.save_model_base(self.model_base)
self.model_base = None
if self._oof_pred_proba is None and self.is_fit():
self._load_oof()
if (not self._get_tags_child().get('can_refit_full', False) or k_fold == 1) and not self.params.get('save_bag_folds', True):
# TODO: This is a hack to avoid a very challenging situation:
# in high_quality preset we don't save fold models, but for models that don't support refit_full,
# they must copy the first fold model instead of fitting again.
# Therefore we must override save_bag_folds for these unsupported models so that the refit versions have a fold model to copy.
# This could be implemented better by only keeping the first fold model artifact and avoid saving the other fold model artifacts (lower disk usage)
# However, this is complex to code accounting for the fitting strategies and would be prone to difficult to diagnose bugs.
self.params['save_bag_folds'] = True
if k_fold != 1:
# Only log in the situation where functionality is currently suboptimal
logger.log(20, '\tForcing `save_bag_folds=True` because child model does not support `refit_full`.')
save_bag_folds = self.params.get('save_bag_folds', True)
if k_fold == 1:
self._fit_single(X=X, y=y, model_base=model_base, use_child_oof=use_child_oof, **kwargs)
return self
else:
refit_folds = self.params.get('refit_folds', False)
if refit_folds:
save_bag_folds = False
if kwargs.get('time_limit', None) is not None:
fold_start = n_repeat_start * k_fold + k_fold_start
fold_end = (n_repeats - 1) * k_fold + k_fold_end
folds_to_fit = fold_end - fold_start
# Reserve time for final refit model
kwargs['time_limit'] = kwargs['time_limit'] * folds_to_fit / (folds_to_fit + 1.2)
self._fit_folds(X=X, y=y, model_base=model_base, X_pseudo=X_pseudo, y_pseudo=y_pseudo,
k_fold=k_fold, k_fold_start=k_fold_start, k_fold_end=k_fold_end,
n_repeats=n_repeats, n_repeat_start=n_repeat_start, save_folds=save_bag_folds, groups=groups, **kwargs)
# FIXME: Don't save folds except for refit
# FIXME: Cleanup self
# FIXME: Don't add `_FULL` to name
# FIXME: Support `can_refit_full=False` models
if refit_folds:
refit_template = self.convert_to_refit_full_template()
refit_template.params['use_child_oof'] = False
kwargs['time_limit'] = None
refit_template.fit(X=X, y=y, k_fold=1, **kwargs)
refit_template._oof_pred_proba = self._oof_pred_proba
refit_template._oof_pred_model_repeats = self._oof_pred_model_repeats
refit_template._child_oof = True
refit_template.fit_time += self.fit_time + self.predict_time
return refit_template
else:
return self
def _get_child_aux_val(self, key: str, default=None):
return self._params_aux_child.get(key, default)
def _validate_bag_kwargs(self, *,
k_fold,
k_fold_start,
k_fold_end,
n_repeats,
n_repeat_start,
groups):
if groups is not None:
if self._n_repeats_finished != 0:
raise AssertionError('Bagged models cannot call fit with `groups` specified when a full k-fold set has already been fit.')
if n_repeats > 1:
raise AssertionError('Cannot perform repeated bagging with `groups` specified.')
return
if k_fold_end is None:
k_fold_end = k_fold
if k_fold is None:
raise ValueError('k_fold cannot be None.')
if k_fold < 1:
raise ValueError(f'k_fold must be equal or greater than 1, value: ({k_fold})')
if n_repeat_start != self._n_repeats_finished:
raise ValueError(f'n_repeat_start must equal self._n_repeats_finished, values: ({n_repeat_start}, {self._n_repeats_finished})')
if n_repeats <= n_repeat_start:
raise ValueError(f'n_repeats must be greater than n_repeat_start, values: ({n_repeats}, {n_repeat_start})')
if k_fold_start != self._k_fold_end:
raise ValueError(f'k_fold_start must equal previous k_fold_end, values: ({k_fold_start}, {self._k_fold_end})')
if k_fold_start >= k_fold_end:
# TODO: Remove this limitation if n_repeats > 1
raise ValueError(f'k_fold_end must be greater than k_fold_start, values: ({k_fold_end}, {k_fold_start})')
if (n_repeats - n_repeat_start) > 1 and k_fold_end != k_fold:
# TODO: Remove this limitation
raise ValueError(f'k_fold_end must equal k_fold when (n_repeats - n_repeat_start) > 1, values: ({k_fold_end}, {k_fold})')
if self._k is not None and self._k != k_fold:
raise ValueError(f'k_fold must equal previously fit k_fold value for the current n_repeat, values: (({k_fold}, {self._k})')
def predict_proba(self, X, normalize=None, **kwargs):
model = self.load_child(self.models[0])
X = self.preprocess(X, model=model, **kwargs)
pred_proba = model.predict_proba(X=X, preprocess_nonadaptive=False, normalize=normalize)
for model in self.models[1:]:
model = self.load_child(model)
pred_proba += model.predict_proba(X=X, preprocess_nonadaptive=False, normalize=normalize)
pred_proba = pred_proba / len(self.models)
if self.temperature_scalar is not None:
pred_proba = self._apply_temperature_scaling(pred_proba)
elif self.conformalize is not None:
pred_proba = self._apply_conformalization(pred_proba)
return pred_proba
def _predict_proba(self, X, normalize=False, **kwargs):
return self.predict_proba(X=X, normalize=normalize, **kwargs)
def score_with_oof(self, y, sample_weight=None):
self._load_oof()
valid_indices = self._oof_pred_model_repeats > 0
y = y[valid_indices]
y_pred_proba = self.get_oof_pred_proba()[valid_indices]
if sample_weight is not None:
sample_weight = sample_weight[valid_indices]
return self.score_with_y_pred_proba(y=y, y_pred_proba=y_pred_proba, sample_weight=sample_weight)
def _fit_single(self, X, y, model_base, use_child_oof, time_limit=None, **kwargs):
if self.is_fit():
raise AssertionError('Model is already fit.')
if self._n_repeats != 0:
raise ValueError(f'n_repeats must equal 0 when fitting a single model with k_fold == 1, value: {self._n_repeats}')
model_base.name = f'{model_base.name}S1F1'
model_base.set_contexts(path_context=self.path + model_base.name + os.path.sep)
time_start_fit = time.time()
model_base.fit(X=X, y=y, time_limit=time_limit, **kwargs)
model_base.fit_time = time.time() - time_start_fit
model_base.predict_time = None
X_len = len(X)
# Check if pred_proba is going to take too long
if time_limit is not None and X_len >= 10000:
max_allowed_time = time_limit * 1.3 # allow some buffer
time_left = max(
max_allowed_time - model_base.fit_time,
time_limit * 0.1, # At least 10% of time_limit
10, # At least 10 seconds
)
# Sample at most 500 rows to estimate prediction time of all rows
# TODO: Consider moving this into end of abstract model fit for all models.
# Currently this only fixes problem when in bagged mode, if not bagging, then inference could still be problamatic
n_sample = min(500, round(X_len * 0.1))
frac = n_sample / X_len
X_sample = X.sample(n=n_sample)
time_start_predict = time.time()
model_base.predict_proba(X_sample)
time_predict_frac = time.time() - time_start_predict
time_predict_estimate = time_predict_frac / frac
logger.log(15, f'\t{round(time_predict_estimate, 2)}s\t= Estimated out-of-fold prediction time...')
if time_predict_estimate > time_left:
logger.warning(f'\tNot enough time to generate out-of-fold predictions for model. Estimated time required was {round(time_predict_estimate, 2)}s compared to {round(time_left, 2)}s of available time.')
raise TimeLimitExceeded
if use_child_oof:
logger.log(15, '\t`use_child_oof` was specified for this model. It will function similarly to a bagged model, but will only fit one child model.')
time_start_predict = time.time()
if model_base._get_tags().get('valid_oof', False):
self._oof_pred_proba = model_base.get_oof_pred_proba(X=X, y=y)
else:
logger.warning('\tWARNING: `use_child_oof` was specified but child model does not have a dedicated `get_oof_pred_proba` method. This model may have heavily overfit validation scores.')
self._oof_pred_proba = model_base.predict_proba(X=X)
self._child_oof = True
model_base.predict_time = time.time() - time_start_predict
model_base.val_score = model_base.score_with_y_pred_proba(y=y, y_pred_proba=self._oof_pred_proba)
else:
self._oof_pred_proba = model_base.predict_proba(X=X) # TODO: Cheater value, will be overfit to valid set
self._oof_pred_model_repeats = np.ones(shape=len(X), dtype=np.uint8)
model_base.reduce_memory_size(remove_fit=True, remove_info=False, requires_save=True)
if not self.params.get('save_bag_folds', True):
model_base.model = None
if self.low_memory:
self.save_child(model_base)
self.add_child(model=model_base, add_child_times=True)
self._set_n_repeat_single()
def _set_n_repeat_single(self):
"""Sets variables that track `n_repeats` to values that represent having only 1 child in the bag."""
self._n_repeats = 1
self._n_repeats_finished = 1
self._k_per_n_repeat = [1]
self._bagged_mode = False
def _get_default_fold_fitting_strategy(self):
# ray not working properly on macos: https://github.com/ray-project/ray/issues/20084
# TODO: re-enable macos once this issue is addressed
os_fitting_strategy_map = dict(
Darwin='sequential_local',
Windows='parallel_local',
Linux='parallel_local',
)
current_os = platform.system()
fold_fitting_strategy = os_fitting_strategy_map.get(current_os, 'sequential_local')
if fold_fitting_strategy == 'sequential_local':
warning_msg = f'\tWill use sequential fold fitting strategy because {current_os} OS does not yet support parallel folding.'
dup_filter.attach_filter_targets(warning_msg)
logger.warning(warning_msg)
else:
try:
try_import_ray()
except Exception:
warning_msg = 'Will use sequential fold fitting strategy because ray>=1.7.0,<1.8.0 is not installed.'
dup_filter.attach_filter_targets(warning_msg)
logger.warning(warning_msg)
fold_fitting_strategy = 'sequential_local'
assert fold_fitting_strategy in ['parallel_local', 'sequential_local']
return fold_fitting_strategy
def _fit_folds(self,
X,
y,
model_base,
X_pseudo=None,
y_pseudo=None,
k_fold=None,
k_fold_start=0,
k_fold_end=None,
n_repeats=1,
n_repeat_start=0,
time_limit=None,
sample_weight=None,
save_folds=True,
groups=None,
**kwargs):
fold_fitting_strategy = self.params.get('fold_fitting_strategy', 'auto')
if fold_fitting_strategy == 'auto':
fold_fitting_strategy = self._get_default_fold_fitting_strategy()
num_folds_parallel = self.params.get('num_folds_parallel', 'auto')
disable_parallel_fitting = self.params.get('_disable_parallel_fitting', False)
if fold_fitting_strategy == 'parallel_local':
if disable_parallel_fitting:
fold_fitting_strategy = SequentialLocalFoldFittingStrategy
logger.log(20, f'\t{model_base.__class__.__name__} does not support parallel folding yet. Will use sequential folding instead')
else:
fold_fitting_strategy = ParallelLocalFoldFittingStrategy
elif fold_fitting_strategy == 'sequential_local':
fold_fitting_strategy = SequentialLocalFoldFittingStrategy
else:
raise ValueError(
f'{fold_fitting_strategy} is not a valid option for fold_fitting_strategy'
'Valid options are: parallel_local and sequential_local'
)
# TODO: Preprocess data here instead of repeatedly
# FIXME: Raise exception if multiclass/binary and a single val fold contains all instances of a class. (Can happen if custom groups is specified)
time_start = time.time()
if k_fold_start != 0:
cv_splitter = self._cv_splitters[n_repeat_start]
else:
cv_splitter = self._get_cv_splitter(n_splits=k_fold, n_repeats=n_repeats, groups=groups)
if k_fold != cv_splitter.n_splits:
k_fold = cv_splitter.n_splits
if k_fold_end is None:
k_fold_end = k_fold
if cv_splitter.n_repeats < n_repeats:
# If current cv_splitter doesn't have enough n_repeats for all folds, then create a new one.
cv_splitter = self._get_cv_splitter(n_splits=k_fold, n_repeats=n_repeats, groups=groups)
fold_fit_args_list, n_repeats_started, n_repeats_finished = self._generate_fold_configs(
X=X,
y=y,
cv_splitter=cv_splitter,
k_fold_start=k_fold_start,
k_fold_end=k_fold_end,
n_repeat_start=n_repeat_start,
n_repeat_end=n_repeats,
)
fold_fit_args_list = [dict(fold_ctx=fold_ctx) for fold_ctx in fold_fit_args_list]
oof_pred_proba, oof_pred_model_repeats = self._construct_empty_oof(X=X, y=y)
models = []
if num_folds_parallel == 'auto':
num_folds_parallel = len(fold_fit_args_list)
fold_fitting_strategy_args = dict(
model_base=model_base, model_base_kwargs=kwargs,
bagged_ensemble_model=self, X=X, y=y, X_pseudo=X_pseudo, y_pseudo=y_pseudo, sample_weight=sample_weight,
time_limit=time_limit, time_start=time_start, models=models,
oof_pred_proba=oof_pred_proba, oof_pred_model_repeats=oof_pred_model_repeats,
save_folds=save_folds
)
# noinspection PyCallingNonCallable
if fold_fitting_strategy == ParallelLocalFoldFittingStrategy:
fold_fitting_strategy_args['num_folds_parallel'] = num_folds_parallel
fold_fitting_strategy = fold_fitting_strategy(**fold_fitting_strategy_args)
if type(fold_fitting_strategy) == ParallelLocalFoldFittingStrategy and not fold_fitting_strategy.is_mem_sufficient(num_folds_parallel):
# If memory is not sufficient, fall back to sequential fold strategy
fold_fitting_strategy_args.pop('num_folds_parallel', None)
fold_fitting_strategy: AbstractFoldFittingStrategy = SequentialLocalFoldFittingStrategy(**fold_fitting_strategy_args)
logger.log(30, f'\tMemory not enough to fit {model_base.__class__.__name__} folds in parallel. Will do sequential fitting instead. '
f'\tConsider decreasing folds trained in parallel by passing num_folds_parallel to ag_args_ensemble when calling predictor.fit')
logger.log(20, f'\tFitting {len(fold_fit_args_list)} child models '
f'({fold_fit_args_list[0]["fold_ctx"]["model_name_suffix"]} - {fold_fit_args_list[-1]["fold_ctx"]["model_name_suffix"]}) | '
f'Fitting with {fold_fitting_strategy.__class__.__name__}')
# noinspection PyCallingNonCallable
for fold_fit_args in fold_fit_args_list:
fold_fitting_strategy.schedule_fold_model_fit(**fold_fit_args)
fold_fitting_strategy.after_all_folds_scheduled()
for model in models:
# No need to add child times or save child here as this already occurred in the fold_fitting_strategy
self.add_child(model=model, add_child_times=False)
self._bagged_mode = True
if self._oof_pred_proba is None:
self._oof_pred_proba = oof_pred_proba
self._oof_pred_model_repeats = oof_pred_model_repeats
else:
self._oof_pred_proba += oof_pred_proba
self._oof_pred_model_repeats += oof_pred_model_repeats
self._cv_splitters += [cv_splitter for _ in range(n_repeats_started)]
self._k_per_n_repeat += [k_fold for _ in range(n_repeats_finished)]
self._n_repeats = n_repeats
if k_fold == k_fold_end:
self._k = None
self._k_fold_end = 0
self._n_repeats_finished = self._n_repeats
else:
self._k = k_fold
self._k_fold_end = k_fold_end
self._n_repeats_finished = self._n_repeats - 1
@staticmethod
def _generate_fold_configs(*,
X,
y,
cv_splitter,
k_fold_start,
k_fold_end,
n_repeat_start,
n_repeat_end) -> (list, int, int):
"""
Generates fold configs given a cv_splitter, k_fold start-end and n_repeat start-end.
Fold configs are used by inheritors of AbstractFoldFittingStrategy when fitting fold models.
Returns a list of fold configs, the number of started repeats, and the number of finished repeats.
"""
k_fold = cv_splitter.n_splits
kfolds = cv_splitter.split(X=X, y=y)
fold_start = n_repeat_start * k_fold + k_fold_start
fold_end = (n_repeat_end - 1) * k_fold + k_fold_end
folds_to_fit = fold_end - fold_start
fold_fit_args_list = []
n_repeats_started = 0
n_repeats_finished = 0
for repeat in range(n_repeat_start, n_repeat_end): # For each repeat
is_first_set = repeat == n_repeat_start
is_last_set = repeat == (n_repeat_end - 1)
if (not is_first_set) or (k_fold_start == 0):
n_repeats_started += 1
fold_in_set_start = k_fold_start if repeat == n_repeat_start else 0
fold_in_set_end = k_fold_end if is_last_set else k_fold
for fold_in_set in range(fold_in_set_start, fold_in_set_end): # For each fold
fold = fold_in_set + (repeat * k_fold)
fold_ctx = dict(
model_name_suffix=f'S{repeat + 1}F{fold_in_set + 1}', # S5F3 = 3rd fold of the 5th repeat set
fold=kfolds[fold],
is_last_fold=fold == (fold_end - 1),
folds_to_fit=folds_to_fit,
folds_finished=fold - fold_start,
folds_left=fold_end - fold,
)
fold_fit_args_list.append(fold_ctx)
if fold_in_set_end == k_fold:
n_repeats_finished += 1
assert len(fold_fit_args_list) == folds_to_fit, "fold_fit_args_list is not the expected length!"
return fold_fit_args_list, n_repeats_started, n_repeats_finished
# TODO: Augment to generate OOF after shuffling each column in X (Batching), this is the fastest way.
# TODO: Reduce logging clutter during OOF importance calculation (Currently logs separately for each child)
# Generates OOF predictions from pre-trained bagged models, assuming X and y are in the same row order as used in .fit(X, y)
def compute_feature_importance(self,
X,
y,
features=None,
silent=False,
time_limit=None,
is_oof=False,
**kwargs) -> pd.DataFrame:
if features is None:
# FIXME: use FULL features (children can have different features)
features = self.load_child(model=self.models[0]).features
if not is_oof:
return super().compute_feature_importance(X, y, features=features, time_limit=time_limit, silent=silent, **kwargs)
fi_fold_list = []
model_index = 0
num_children = len(self.models)
if time_limit is not None:
time_limit_per_child = time_limit / num_children
else:
time_limit_per_child = None
if not silent:
logging_message = f'Computing feature importance via permutation shuffling for {len(features)} features using out-of-fold (OOF) data aggregated across {num_children} child models...'
if time_limit is not None:
logging_message = f'{logging_message} Time limit: {time_limit}s...'
logger.log(20, logging_message)
time_start = time.time()
early_stop = False
children_completed = 0
log_final_suffix = ''
for n_repeat, k in enumerate(self._k_per_n_repeat):
if is_oof:
if self._child_oof or not self._bagged_mode:
raise AssertionError('Model trained with no validation data cannot get feature importances on training data, please specify new test data to compute feature importances (model=%s)' % self.name)
kfolds = self._cv_splitters[n_repeat].split(X=X, y=y)
cur_kfolds = kfolds[n_repeat * k:(n_repeat + 1) * k]
else:
cur_kfolds = [(None, list(range(len(X))))] * k
for i, fold in enumerate(cur_kfolds):
_, test_index = fold
model = self.load_child(self.models[model_index + i])
fi_fold = model.compute_feature_importance(X=X.iloc[test_index, :], y=y.iloc[test_index], features=features, time_limit=time_limit_per_child,
silent=silent, log_prefix='\t', importance_as_list=True, **kwargs)
fi_fold_list.append(fi_fold)
children_completed += 1
if time_limit is not None and children_completed != num_children:
time_now = time.time()
time_left = time_limit - (time_now - time_start)
time_child_average = (time_now - time_start) / children_completed
if time_left < (time_child_average * 1.1):
log_final_suffix = f' (Early stopping due to lack of time...)'
early_stop = True
break
if early_stop:
break
model_index += k
# TODO: DON'T THROW AWAY SAMPLES! USE LARGER N
fi_list_dict = dict()
for val in fi_fold_list:
val = val['importance'].to_dict() # TODO: Don't throw away stddev information of children
for key in val:
if key not in fi_list_dict:
fi_list_dict[key] = []
fi_list_dict[key] += val[key]
fi_df = _compute_fi_with_stddev(fi_list_dict)
if not silent:
logger.log(20, f'\t{round(time.time() - time_start, 2)}s\t= Actual runtime (Completed {children_completed} of {num_children} children){log_final_suffix}')
return fi_df
def get_features(self):
assert self.is_fit(), "The model must be fit before calling the get_features method."
return self.load_child(self.models[0]).get_features()
def load_child(self, model: Union[AbstractModel, str], verbose=False) -> AbstractModel:
if isinstance(model, str):
child_path = self.create_contexts(self.path + model + os.path.sep)
return self._child_type.load(path=child_path, verbose=verbose)
else:
return model
def add_child(self, model: Union[AbstractModel, str], add_child_times=False):
"""
Add a new fit child model to `self.models`
Parameters
----------
model : Union[AbstractModel, str]
The child model to add. If str, it is the name of the model.
add_child_times : bool, default = False
Whether to add child metadata on times to the bag times.
This includes fit_time, predict_time, and predict_1_time.
"""
if self.models is None:
self.models = []
if isinstance(model, str):
model_name = model
model = None
else:
model_name = model.name
if self.low_memory:
self.models.append(model_name)
else:
if model is None:
model = self.load_child(model=model_name, verbose=False)
self.models.append(model)
if add_child_times:
if model is None:
model = self.load_child(model=model_name, verbose=False)
self._add_child_times_to_bag(model=model)
def save_child(self, model: Union[AbstractModel, str], verbose=False):
"""Save child model to disk."""
child = self.load_child(model)
child.set_contexts(self.path + child.name + os.path.sep)
child.save(verbose=verbose)
# TODO: Multiply epochs/n_iterations by some value (such as 1.1) to account for having more training data than bagged models
def convert_to_refit_full_template(self):
init_args = self.get_params()
init_args['hyperparameters']['save_bag_folds'] = True # refit full models must save folds
init_args['model_base'] = self.convert_to_refit_full_template_child()
init_args['name'] = init_args['name'] + REFIT_FULL_SUFFIX
model_full_template = self.__class__(**init_args)
return model_full_template
def convert_to_refit_full_template_child(self):
refit_params_trained = self._get_compressed_params_trained()
refit_params = copy.deepcopy(self._get_model_base().get_params())
refit_params['hyperparameters'].update(refit_params_trained)
refit_child_template = self._child_type(**refit_params)
return refit_child_template
def convert_to_refit_full_via_copy(self) -> AbstractModel:
"""
Creates a new refit_full variant of the model, but instead of training it simply copies `self` while keeping only the first fold model.
This method is for compatibility with models that have not implemented refit_full support as a fallback.
"""
if not self.params.get('save_bag_folds', True):
raise AssertionError('Cannot perform copy-based refit_full when save_bag_folds is False!')
__models = self.models
self.models = []
model_full = copy.deepcopy(self)
self.models = __models
child_0 = self.load_child(self.models[0])
model_full.fit_time = None
model_full.predict_time = None
model_full.predict_1_time = None
model_full.val_score = None
model_full.rename(model_full.name + REFIT_FULL_SUFFIX)
if model_full.low_memory:
model_full.save_child(child_0)
model_full.add_child(model=child_0, add_child_times=True)
model_full._set_n_repeat_single()
return model_full
def get_params(self):
init_args = dict(
model_base=self._get_model_base(),
random_state=self._random_state,
)
init_args.update(super().get_params())
init_args.pop('eval_metric')
init_args.pop('problem_type')
return init_args
def convert_to_template_child(self):
return self._get_model_base().convert_to_template()
def _get_compressed_params(self, model_params_list=None):
if model_params_list is None:
model_params_list = [
self.load_child(child).get_trained_params()
for child in self.models
]
model_params_compressed = dict()
for param in model_params_list[0].keys():
model_param_vals = [model_params[param] for model_params in model_params_list]
if all(isinstance(val, bool) for val in model_param_vals):
counter = Counter(model_param_vals)
compressed_val = counter.most_common(1)[0][0]
elif all(isinstance(val, int) for val in model_param_vals):
compressed_val = round(mean(model_param_vals))
elif all(isinstance(val, float) for val in model_param_vals):
compressed_val = mean(model_param_vals)
else:
try:
counter = Counter(model_param_vals)
compressed_val = counter.most_common(1)[0][0]
except TypeError:
compressed_val = model_param_vals[0]
model_params_compressed[param] = compressed_val
return model_params_compressed
def _get_compressed_params_trained(self):
model_params_list = [
self.load_child(child).params_trained
for child in self.models
]
return self._get_compressed_params(model_params_list=model_params_list)
def _get_model_base(self):
if self.model_base is None:
return self.load_model_base()
else:
return self.model_base
def _add_child_times_to_bag(self, model):
if self.fit_time is None:
self.fit_time = model.fit_time
else:
self.fit_time += model.fit_time
if self.predict_time is None:
self.predict_time = model.predict_time
else:
self.predict_time += model.predict_time
if self.predict_1_time is None:
self.predict_1_time = model.predict_1_time
else:
self.predict_1_time += model.predict_1_time
def _add_parallel_child_times(self, fit_time, predict_time, predict_1_time):
if self.fit_time is None:
self.fit_time = fit_time
else:
self.fit_time += fit_time
if self.predict_time is None:
self.predict_time = predict_time
else:
self.predict_time += predict_time
if self.predict_1_time is None:
self.predict_1_time = predict_1_time
else:
self.predict_1_time += predict_1_time
@classmethod
def load(cls, path: str, reset_paths=True, low_memory=True, load_oof=False, verbose=True):
model = super().load(path=path, reset_paths=reset_paths, verbose=verbose)
if not low_memory:
model.persist_child_models(reset_paths=reset_paths)
if load_oof:
model._load_oof()
return model
@classmethod
def load_oof(cls, path, verbose=True):
try:
oof = load_pkl.load(path=path + 'utils' + os.path.sep + cls._oof_filename, verbose=verbose)
oof_pred_proba = oof['_oof_pred_proba']
oof_pred_model_repeats = oof['_oof_pred_model_repeats']
except FileNotFoundError:
model = cls.load(path=path, reset_paths=True, verbose=verbose)
model._load_oof()
oof_pred_proba = model._oof_pred_proba
oof_pred_model_repeats = model._oof_pred_model_repeats
return cls._oof_pred_proba_func(oof_pred_proba=oof_pred_proba, oof_pred_model_repeats=oof_pred_model_repeats)
def _load_oof(self):
if self._oof_pred_proba is not None:
pass
else:
oof = load_pkl.load(path=self.path + 'utils' + os.path.sep + self._oof_filename)
self._oof_pred_proba = oof['_oof_pred_proba']
self._oof_pred_model_repeats = oof['_oof_pred_model_repeats']
def persist_child_models(self, reset_paths=True):
for i, model_name in enumerate(self.models):
if isinstance(model_name, str):
child_path = self.create_contexts(self.path + model_name + os.path.sep)
child_model = self._child_type.load(path=child_path, reset_paths=reset_paths, verbose=True)
self.models[i] = child_model
def load_model_base(self):
return load_pkl.load(path=self.path + 'utils' + os.path.sep + 'model_template.pkl')
def save_model_base(self, model_base):
save_pkl.save(path=self.path + 'utils' + os.path.sep + 'model_template.pkl', object=model_base)
def save(self, path=None, verbose=True, save_oof=True, save_children=False) -> str:
if path is None:
path = self.path
if save_children:
model_names = []
for child in self.models:
child = self.load_child(child)
child.set_contexts(path + child.name + os.path.sep)
child.save(verbose=False)
model_names.append(child.name)
self.models = model_names
if save_oof and self._oof_pred_proba is not None:
save_pkl.save(path=path + 'utils' + os.path.sep + self._oof_filename, object={
'_oof_pred_proba': self._oof_pred_proba,
'_oof_pred_model_repeats': self._oof_pred_model_repeats,
})
self._oof_pred_proba = None
self._oof_pred_model_repeats = None
return super().save(path=path, verbose=verbose)
# If `remove_fit_stack=True`, variables will be removed that are required to fit more folds and to fit new stacker models which use this model as a base model.
# This includes OOF variables.
def reduce_memory_size(self, remove_fit_stack=False, remove_fit=True, remove_info=False, requires_save=True, reduce_children=False, **kwargs):
super().reduce_memory_size(remove_fit=remove_fit, remove_info=remove_info, requires_save=requires_save, **kwargs)
if remove_fit_stack:
try:
os.remove(self.path + 'utils' + os.path.sep + self._oof_filename)
except FileNotFoundError:
pass
if requires_save:
self._oof_pred_proba = None
self._oof_pred_model_repeats = None
try:
os.remove(self.path + 'utils' + os.path.sep + 'model_template.pkl')
except FileNotFoundError:
pass
if requires_save:
self.model_base = None
try:
os.rmdir(self.path + 'utils')
except OSError:
pass
if reduce_children:
for model in self.models:
model = self.load_child(model)
model.reduce_memory_size(remove_fit=remove_fit, remove_info=remove_info, requires_save=requires_save, **kwargs)
if requires_save and self.low_memory:
self.save_child(model=model)
def _get_model_names(self):
model_names = []
for model in self.models:
if isinstance(model, str):
model_names.append(model)
else:
model_names.append(model.name)
return model_names
def get_info(self):
info = super().get_info()
children_info = self._get_child_info()
child_memory_sizes = [child['memory_size'] for child in children_info.values()]
sum_memory_size_child = sum(child_memory_sizes)
if child_memory_sizes:
max_memory_size_child = max(child_memory_sizes)
else:
max_memory_size_child = 0
if self.low_memory:
max_memory_size = info['memory_size'] + sum_memory_size_child
min_memory_size = info['memory_size'] + max_memory_size_child
else:
max_memory_size = info['memory_size']
min_memory_size = info['memory_size'] - sum_memory_size_child + max_memory_size_child
# Necessary if save_space is used as save_space deletes model_base.
if len(self.models) > 0:
child_model = self.load_child(self.models[0])
else:
child_model = self._get_model_base()
child_hyperparameters = child_model.params
child_ag_args_fit = child_model.params_aux
bagged_info = dict(
child_model_type=self._child_type.__name__,
num_child_models=len(self.models),
child_model_names=self._get_model_names(),
_n_repeats=self._n_repeats,
# _n_repeats_finished=self._n_repeats_finished, # commented out because these are too technical
# _k_fold_end=self._k_fold_end,
# _k=self._k,
_k_per_n_repeat=self._k_per_n_repeat,
_random_state=self._random_state,
low_memory=self.low_memory, # If True, then model will attempt to use at most min_memory_size memory by having at most one child in memory. If False, model will use max_memory_size memory.
bagged_mode=self._bagged_mode,
max_memory_size=max_memory_size, # Memory used when all children are loaded into memory at once.
min_memory_size=min_memory_size, # Memory used when only the largest child is loaded into memory.
child_hyperparameters=child_hyperparameters,
child_hyperparameters_fit=self._get_compressed_params_trained(),
child_ag_args_fit=child_ag_args_fit,
)
info['bagged_info'] = bagged_info
info['children_info'] = children_info
child_features_full = list(set().union(*[child['features'] for child in children_info.values()]))
info['features'] = child_features_full
info['num_features'] = len(child_features_full)
return info
def get_memory_size(self):
models = self.models
self.models = None
memory_size = super().get_memory_size()
self.models = models
return memory_size
def _validate_fit_memory_usage(self, **kwargs):
# memory is checked downstream on the child model
pass
def _get_child_info(self):
child_info_dict = dict()
for model in self.models:
if isinstance(model, str):
child_path = self.create_contexts(self.path + model + os.path.sep)
child_info_dict[model] = self._child_type.load_info(child_path)
else:
child_info_dict[model.name] = model.get_info()
return child_info_dict
def _construct_empty_oof(self, X, y):
if self.problem_type == MULTICLASS:
oof_pred_proba = np.zeros(shape=(len(X), len(y.unique())), dtype=np.float32)
elif self.problem_type == SOFTCLASS:
oof_pred_proba = np.zeros(shape=y.shape, dtype=np.float32)
elif self.problem_type == QUANTILE:
oof_pred_proba = np.zeros(shape=(len(X), len(self.quantile_levels)), dtype=np.float32)
else:
oof_pred_proba = np.zeros(shape=len(X), dtype=np.float32)
oof_pred_model_repeats = np.zeros(shape=len(X), dtype=np.uint8)
return oof_pred_proba, oof_pred_model_repeats
def _preprocess_fit_resources(self, silent=False, **kwargs):
"""Pass along to child models to avoid altering up-front"""
return kwargs
# TODO: Currently double disk usage, saving model in HPO and also saving model in bag
# FIXME: with use_bag_holdout=True, the fold-1 scores that are logged are of the inner validation score, not the holdout score.
# Fix this by passing X_val, y_val into this method
def _hyperparameter_tune(self, X, y, k_fold, scheduler_options, preprocess_kwargs=None, groups=None, **kwargs):
if len(self.models) != 0:
raise ValueError('self.models must be empty to call hyperparameter_tune, value: %s' % self.models)
kwargs['feature_metadata'] = self.feature_metadata
kwargs['num_classes'] = self.num_classes # TODO: maybe don't pass num_classes to children
self.model_base.set_contexts(self.path + 'hpo' + os.path.sep)
# TODO: Preprocess data here instead of repeatedly
if preprocess_kwargs is None:
preprocess_kwargs = dict()
use_child_oof = self.params.get('use_child_oof', False)
X = self.preprocess(X=X, preprocess=False, fit=True, **preprocess_kwargs)
if use_child_oof:
k_fold = 1
X_fold = X
y_fold = y
X_val_fold = None
y_val_fold = None
train_index = list(range(len(X)))
test_index = train_index
cv_splitter = None
else:
cv_splitter = self._get_cv_splitter(n_splits=k_fold, n_repeats=1, groups=groups)
if k_fold != cv_splitter.n_splits:
k_fold = cv_splitter.n_splits
kfolds = cv_splitter.split(X=X, y=y)
train_index, test_index = kfolds[0]
X_fold, X_val_fold = X.iloc[train_index, :], X.iloc[test_index, :]
y_fold, y_val_fold = y.iloc[train_index], y.iloc[test_index]
orig_time = scheduler_options[1]['time_out']
if orig_time:
scheduler_options[1]['time_out'] = orig_time * 0.8 # TODO: Scheduler doesn't early stop on final model, this is a safety net. Scheduler should be updated to early stop
hpo_models, hpo_model_performances, hpo_results = self.model_base.hyperparameter_tune(X=X_fold, y=y_fold, X_val=X_val_fold, y_val=y_val_fold, scheduler_options=scheduler_options, **kwargs)
scheduler_options[1]['time_out'] = orig_time
bags = {}
bags_performance = {}
for i, (model_name, model_path) in enumerate(hpo_models.items()):
child: AbstractModel = self._child_type.load(path=model_path)
# TODO: Create new Ensemble Here
bag = copy.deepcopy(self)
bag.rename(f"{bag.name}{os.path.sep}T{i+1}")
bag.set_contexts(self.path_root + bag.name + os.path.sep)
oof_pred_proba, oof_pred_model_repeats = self._construct_empty_oof(X=X, y=y)
if child._get_tags().get('valid_oof', False):
y_pred_proba = child.get_oof_pred_proba(X=X, y=y)
bag._n_repeats_finished = 1
bag._k_per_n_repeat = [1]
bag._bagged_mode = False
bag._child_oof = True # TODO: Consider a separate tag for refit_folds vs efficient OOF
else:
y_pred_proba = child.predict_proba(X_val_fold)
oof_pred_proba[test_index] += y_pred_proba
oof_pred_model_repeats[test_index] += 1
bag.model_base = None
child.rename('')
child.set_contexts(bag.path + child.name + os.path.sep)
bag.save_model_base(child.convert_to_template())
bag._k = k_fold
bag._k_fold_end = 1
bag._n_repeats = 1
bag._oof_pred_proba = oof_pred_proba
bag._oof_pred_model_repeats = oof_pred_model_repeats
child.rename('S1F1')
child.set_contexts(bag.path + child.name + os.path.sep)
if not self.params.get('save_bag_folds', True):
child.model = None
if bag.low_memory:
bag.save_child(child, verbose=False)
bag.models.append(child.name)
else:
bag.models.append(child)
bag.val_score = child.val_score
bag._add_child_times_to_bag(model=child)
if cv_splitter is not None:
bag._cv_splitters = [cv_splitter]
bag.save()
bags[bag.name] = bag.path
bags_performance[bag.name] = bag.val_score
# TODO: hpo_results likely not correct because no renames
return bags, bags_performance, hpo_results
def _more_tags(self):
return {
'valid_oof': True,
'can_refit_full': True,
}
def _get_tags_child(self):
"""Gets the tags of the child model."""
return self._get_model_base()._get_tags()