sklearn_sample_generator: search_model

comparison search_model_validation.py @ 26:ebf295f2faf6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty

author	bgruening
date	Fri, 09 Aug 2019 07:20:20 -0400
parents	97b467e06354
children	52ea044c667f

comparison

equal deleted inserted replaced

-:86a086d2bbed
+:ebf295f2faf6
 import argparse
 import collections
 import imblearn
+import joblib
 import json
 import numpy as np
-import pandas
+import pandas as pd
 import pickle
 import skrebate
 import sklearn
 import sys
 import xgboost
 import warnings
-import iraps_classifier
-import model_validations
-import preprocessors
-import feature_selectors
 from imblearn import under_sampling, over_sampling, combine
 from scipy.io import mmread
 from mlxtend import classifier, regressor
+from sklearn.base import clone
 from sklearn import (cluster, compose, decomposition, ensemble,
 feature_extraction, feature_selection,
 gaussian_process, kernel_approximation, metrics,
 model_selection, naive_bayes, neighbors,
 pipeline, preprocessing, svm, linear_model,
 tree, discriminant_analysis)
 from sklearn.exceptions import FitFailedWarning
-from sklearn.externals import joblib
+from sklearn.model_selection._validation import _score, cross_validate
-from sklearn.model_selection._validation import _score
+from sklearn.model_selection import _search, _validation
-from utils import (SafeEval, get_cv, get_scoring, get_X_y,
+from galaxy_ml.utils import (SafeEval, get_cv, get_scoring, load_model,
-load_model, read_columns)
+read_columns, try_get_attr, get_module)
-from model_validations import train_test_split
+_fit_and_score = try_get_attr('galaxy_ml.model_validations', '_fit_and_score')
+setattr(_search, '_fit_and_score', _fit_and_score)
+setattr(_validation, '_fit_and_score', _fit_and_score)
 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
 CACHE_DIR = './cached'
-NON_SEARCHABLE = ('n_jobs', 'pre_dispatch', 'memory', 'steps',
+NON_SEARCHABLE = ('n_jobs', 'pre_dispatch', 'memory', '_path',
-'nthread', 'verbose')
+'nthread', 'callbacks')
+ALLOWED_CALLBACKS = ('EarlyStopping', 'TerminateOnNaN', 'ReduceLROnPlateau',
+'CSVLogger', 'None')
 def _eval_search_params(params_builder):
 search_params = {}
 # Have `:` before search list, asks for estimator evaluatio
 safe_eval_es = SafeEval(load_estimators=True)
 search_list = search_list[1:].strip()
 # TODO maybe add regular express check
 ev = safe_eval_es(search_list)
-preprocessors = (
+preprocessings = (
 preprocessing.StandardScaler(), preprocessing.Binarizer(),
-preprocessing.Imputer(), preprocessing.MaxAbsScaler(),
+preprocessing.MaxAbsScaler(),
 preprocessing.Normalizer(), preprocessing.MinMaxScaler(),
 preprocessing.PolynomialFeatures(),
 preprocessing.RobustScaler(), feature_selection.SelectKBest(),
 feature_selection.GenericUnivariateSelect(),
 feature_selection.SelectPercentile(),
 newlist = []
 for obj in ev:
 if obj is None:
 newlist.append(None)
 elif obj == 'all_0':
-newlist.extend(preprocessors[0:36])
+newlist.extend(preprocessings[0:35])
 elif obj == 'sk_prep_all':      # no KernalCenter()
-newlist.extend(preprocessors[0:8])
+newlist.extend(preprocessings[0:7])
 elif obj == 'fs_all':
-newlist.extend(preprocessors[8:15])
+newlist.extend(preprocessings[7:14])
 elif obj == 'decomp_all':
-newlist.extend(preprocessors[15:26])
+newlist.extend(preprocessings[14:25])
 elif obj == 'k_appr_all':
-newlist.extend(preprocessors[26:30])
+newlist.extend(preprocessings[25:29])
 elif obj == 'reb_all':
-newlist.extend(preprocessors[31:36])
+newlist.extend(preprocessings[30:35])
 elif obj == 'imb_all':
-newlist.extend(preprocessors[36:55])
+newlist.extend(preprocessings[35:54])
-elif type(obj) is int and -1 < obj < len(preprocessors):
+elif type(obj) is int and -1 < obj < len(preprocessings):
-newlist.append(preprocessors[obj])
+newlist.append(preprocessings[obj])
 elif hasattr(obj, 'get_params'):       # user uploaded object
 if 'n_jobs' in obj.get_params():
 newlist.append(obj.set_params(n_jobs=N_JOBS))
 else:
 newlist.append(obj)
 return search_params
 def main(inputs, infile_estimator, infile1, infile2,
-outfile_result, outfile_object=None, groups=None):
+outfile_result, outfile_object=None,
+outfile_weights=None, groups=None,
+ref_seq=None, intervals=None, targets=None,
+fasta_path=None):
 """
 Parameter
 ---------
 inputs : str
 File path to galaxy tool parameter
 File path to save the results, either cv_results or test result
 outfile_object : str, optional
 File path to save searchCV object
+outfile_weights : str, optional
+File path to save model weights
 groups : str
 File path to dataset containing groups labels
+ref_seq : str
+File path to dataset containing genome sequence file
+intervals : str
+File path to dataset containing interval file
+targets : str
+File path to dataset compressed target bed file
+fasta_path : str
+File path to dataset containing fasta file
 """
 warnings.simplefilter('ignore')
 with open(inputs, 'r') as param_handler:
 params = json.load(param_handler)
-if groups:
-(params['search_schemes']['options']['cv_selector']
-['groups_selector']['infile_g']) = groups
 params_builder = params['search_schemes']['search_params_builder']
+with open(infile_estimator, 'rb') as estimator_handler:
+estimator = load_model(estimator_handler)
+estimator_params = estimator.get_params()
+# store read dataframe object
+loaded_df = {}
 input_type = params['input_options']['selected_input']
+# tabular input
 if input_type == 'tabular':
 header = 'infer' if params['input_options']['header1'] else None
 column_option = (params['input_options']['column_selector_options_1']
 ['selected_column_selector_option'])
 if column_option in ['by_index_number', 'all_but_by_index_number',
 'by_header_name', 'all_but_by_header_name']:
 c = params['input_options']['column_selector_options_1']['col1']
 else:
 c = None
-X = read_columns(
-infile1,
+df_key = infile1 + repr(header)
-c=c,
+df = pd.read_csv(infile1, sep='\t', header=header,
-c_option=column_option,
+parse_dates=True)
-sep='\t',
+loaded_df[df_key] = df
-header=header,
-parse_dates=True).astype(float)
+X = read_columns(df, c=c, c_option=column_option).astype(float)
-else:
+# sparse input
+elif input_type == 'sparse':
 X = mmread(open(infile1, 'r'))
+# fasta_file input
+elif input_type == 'seq_fasta':
+pyfaidx = get_module('pyfaidx')
+sequences = pyfaidx.Fasta(fasta_path)
+n_seqs = len(sequences.keys())
+X = np.arange(n_seqs)[:, np.newaxis]
+for param in estimator_params.keys():
+if param.endswith('fasta_path'):
+estimator.set_params(
+**{param: fasta_path})
+break
+else:
+raise ValueError(
+"The selected estimator doesn't support "
+"fasta file input! Please consider using "
+"KerasGBatchClassifier with "
+"FastaDNABatchGenerator/FastaProteinBatchGenerator "
+"or having GenomeOneHotEncoder/ProteinOneHotEncoder "
+"in pipeline!")
+elif input_type == 'refseq_and_interval':
+path_params = {
+'data_batch_generator__ref_genome_path': ref_seq,
+'data_batch_generator__intervals_path': intervals,
+'data_batch_generator__target_path': targets
+}
+estimator.set_params(**path_params)
+n_intervals = sum(1 for line in open(intervals))
+X = np.arange(n_intervals)[:, np.newaxis]
+# Get target y
 header = 'infer' if params['input_options']['header2'] else None
 column_option = (params['input_options']['column_selector_options_2']
 ['selected_column_selector_option2'])
 if column_option in ['by_index_number', 'all_but_by_index_number',
 'by_header_name', 'all_but_by_header_name']:
 c = params['input_options']['column_selector_options_2']['col2']
 else:
 c = None
+df_key = infile2 + repr(header)
+if df_key in loaded_df:
+infile2 = loaded_df[df_key]
+else:
+infile2 = pd.read_csv(infile2, sep='\t',
+header=header, parse_dates=True)
+loaded_df[df_key] = infile2
 y = read_columns(
 infile2,
 c=c,
 c_option=column_option,
 sep='\t',
 header=header,
 parse_dates=True)
-y = y.ravel()
+if len(y.shape) == 2 and y.shape[1] == 1:
+y = y.ravel()
+if input_type == 'refseq_and_interval':
+estimator.set_params(
+data_batch_generator__features=y.ravel().tolist())
+y = None
+# end y
 optimizer = params['search_schemes']['selected_search_scheme']
 optimizer = getattr(model_selection, optimizer)
+# handle gridsearchcv options
 options = params['search_schemes']['options']
+if groups:
+header = 'infer' if (options['cv_selector']['groups_selector']
+['header_g']) else None
+column_option = (options['cv_selector']['groups_selector']
+['column_selector_options_g']
+['selected_column_selector_option_g'])
+if column_option in ['by_index_number', 'all_but_by_index_number',
+'by_header_name', 'all_but_by_header_name']:
+c = (options['cv_selector']['groups_selector']
+['column_selector_options_g']['col_g'])
+else:
+c = None
+df_key = groups + repr(header)
+if df_key in loaded_df:
+groups = loaded_df[df_key]
+groups = read_columns(
+groups,
+c=c,
+c_option=column_option,
+sep='\t',
+header=header,
+parse_dates=True)
+groups = groups.ravel()
+options['cv_selector']['groups_selector'] = groups
 splitter, groups = get_cv(options.pop('cv_selector'))
 options['cv'] = splitter
 options['n_jobs'] = N_JOBS
 primary_scoring = options['scoring']['primary_scoring']
 if options['refit'] and isinstance(options['scoring'], dict):
 options['refit'] = primary_scoring
 if 'pre_dispatch' in options and options['pre_dispatch'] == '':
 options['pre_dispatch'] = None
-with open(infile_estimator, 'rb') as estimator_handler:
+# del loaded_df
-estimator = load_model(estimator_handler)
+del loaded_df
+# handle memory
 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
 # cache iraps_core fits could increase search speed significantly
 if estimator.__class__.__name__ == 'IRAPSClassifier':
 estimator.set_params(memory=memory)
 else:
-for p, v in estimator.get_params().items():
+# For iraps buried in pipeline
+for p, v in estimator_params.items():
 if p.endswith('memory'):
+# for case of `__irapsclassifier__memory`
 if len(p) > 8 and p[:-8].endswith('irapsclassifier'):
 # cache iraps_core fits could increase search
 # speed significantly
 new_params = {p: memory}
 estimator.set_params(**new_params)
+# security reason, we don't want memory being
+# modified unexpectedly
 elif v:
 new_params = {p, None}
 estimator.set_params(**new_params)
+# For now, 1 CPU is suggested for iprasclassifier
 elif p.endswith('n_jobs'):
 new_params = {p: 1}
 estimator.set_params(**new_params)
+# for security reason, types of callbacks are limited
+elif p.endswith('callbacks'):
+for cb in v:
+cb_type = cb['callback_selection']['callback_type']
+if cb_type not in ALLOWED_CALLBACKS:
+raise ValueError(
+"Prohibited callback type: %s!" % cb_type)
 param_grid = _eval_search_params(params_builder)
 searcher = optimizer(estimator, param_grid, **options)
-# do train_test_split
+# do nested split
-do_train_test_split = params['train_test_split'].pop('do_split')
+split_mode = params['outer_split'].pop('split_mode')
-if do_train_test_split == 'yes':
+# nested CV, outer cv using cross_validate
-# make sure refit is choosen
+if split_mode == 'nested_cv':
-if not options['refit']:
+outer_cv, _ = get_cv(params['outer_split']['cv_selector'])
-raise ValueError("Refit must be `True` for shuffle splitting!")
-split_options = params['train_test_split']
+if options['error_score'] == 'raise':
+rval = cross_validate(
-# splits
+searcher, X, y, scoring=options['scoring'],
-if split_options['shuffle'] == 'stratified':
+cv=outer_cv, n_jobs=N_JOBS, verbose=0,
-split_options['labels'] = y
+error_score=options['error_score'])
-X, X_test, y, y_test = train_test_split(X, y, **split_options)
+else:
-elif split_options['shuffle'] == 'group':
+warnings.simplefilter('always', FitFailedWarning)
-if not groups:
+with warnings.catch_warnings(record=True) as w:
-raise ValueError("No group based CV option was "
+try:
-"choosen for group shuffle!")
+rval = cross_validate(
-split_options['labels'] = groups
+searcher, X, y,
-X, X_test, y, y_test, groups, _ =\
+scoring=options['scoring'],
-train_test_split(X, y, **split_options)
+cv=outer_cv, n_jobs=N_JOBS,
-else:
+verbose=0,
-if split_options['shuffle'] == 'None':
+error_score=options['error_score'])
-split_options['shuffle'] = None
+except ValueError:
-X, X_test, y, y_test =\
+pass
-train_test_split(X, y, **split_options)
+for warning in w:
-# end train_test_split
+print(repr(warning.message))
-if options['error_score'] == 'raise':
+keys = list(rval.keys())
-searcher.fit(X, y, groups=groups)
+for k in keys:
+if k.startswith('test'):
+rval['mean_' + k] = np.mean(rval[k])
+rval['std_' + k] = np.std(rval[k])
+if k.endswith('time'):
+rval.pop(k)
+rval = pd.DataFrame(rval)
+rval = rval[sorted(rval.columns)]
+rval.to_csv(path_or_buf=outfile_result, sep='\t',
+header=True, index=False)
 else:
-warnings.simplefilter('always', FitFailedWarning)
+if split_mode == 'train_test_split':
-with warnings.catch_warnings(record=True) as w:
+train_test_split = try_get_attr(
-try:
+'galaxy_ml.model_validations', 'train_test_split')
-searcher.fit(X, y, groups=groups)
+# make sure refit is choosen
-except ValueError:
+# this could be True for sklearn models, but not the case for
-pass
+# deep learning models
-for warning in w:
+if not options['refit'] and \
-print(repr(warning.message))
+not all(hasattr(estimator, attr)
+for attr in ('config', 'model_type')):
-if do_train_test_split == 'no':
+warnings.warn("Refit is change to `True` for nested "
-# save results
+"validation!")
-cv_results = pandas.DataFrame(searcher.cv_results_)
+setattr(searcher, 'refit', True)
-cv_results = cv_results[sorted(cv_results.columns)]
+split_options = params['outer_split']
-cv_results.to_csv(path_or_buf=outfile_result, sep='\t',
-header=True, index=False)
+# splits
+if split_options['shuffle'] == 'stratified':
-# output test result using best_estimator_
+split_options['labels'] = y
-else:
+X, X_test, y, y_test = train_test_split(X, y, **split_options)
-best_estimator_ = searcher.best_estimator_
+elif split_options['shuffle'] == 'group':
-if isinstance(options['scoring'], collections.Mapping):
+if groups is None:
-is_multimetric = True
+raise ValueError("No group based CV option was "
-else:
+"choosen for group shuffle!")
-is_multimetric = False
+split_options['labels'] = groups
+if y is None:
-test_score = _score(best_estimator_, X_test,
+X, X_test, groups, _ =\
-y_test, options['scoring'],
+train_test_split(X, groups, **split_options)
-is_multimetric=is_multimetric)
+else:
-if not is_multimetric:
+X, X_test, y, y_test, groups, _ =\
-test_score = {primary_scoring: test_score}
+train_test_split(X, y, groups, **split_options)
-for key, value in test_score.items():
+else:
-test_score[key] = [value]
+if split_options['shuffle'] == 'None':
-result_df = pandas.DataFrame(test_score)
+split_options['shuffle'] = None
-result_df.to_csv(path_or_buf=outfile_result, sep='\t',
+X, X_test, y, y_test =\
-header=True, index=False)
+train_test_split(X, y, **split_options)
+# end train_test_split
+# shared by both train_test_split and non-split
+if options['error_score'] == 'raise':
+searcher.fit(X, y, groups=groups)
+else:
+warnings.simplefilter('always', FitFailedWarning)
+with warnings.catch_warnings(record=True) as w:
+try:
+searcher.fit(X, y, groups=groups)
+except ValueError:
+pass
+for warning in w:
+print(repr(warning.message))
+# no outer split
+if split_mode == 'no':
+# save results
+cv_results = pd.DataFrame(searcher.cv_results_)
+cv_results = cv_results[sorted(cv_results.columns)]
+cv_results.to_csv(path_or_buf=outfile_result, sep='\t',
+header=True, index=False)
+# train_test_split, output test result using best_estimator_
+# or rebuild the trained estimator using weights if applicable.
+else:
+scorer_ = searcher.scorer_
+if isinstance(scorer_, collections.Mapping):
+is_multimetric = True
+else:
+is_multimetric = False
+best_estimator_ = getattr(searcher, 'best_estimator_', None)
+if not best_estimator_:
+raise ValueError("GridSearchCV object has no "
+"`best_estimator_` when `refit`=False!")
+if best_estimator_.__class__.__name__ == 'KerasGBatchClassifier' \
+and hasattr(estimator.data_batch_generator, 'target_path'):
+test_score = best_estimator_.evaluate(
+X_test, scorer=scorer_, is_multimetric=is_multimetric)
+else:
+test_score = _score(best_estimator_, X_test,
+y_test, scorer_,
+is_multimetric=is_multimetric)
+if not is_multimetric:
+test_score = {primary_scoring: test_score}
+for key, value in test_score.items():
+test_score[key] = [value]
+result_df = pd.DataFrame(test_score)
+result_df.to_csv(path_or_buf=outfile_result, sep='\t',
+header=True, index=False)
 memory.clear(warn=False)
 if outfile_object:
+best_estimator_ = getattr(searcher, 'best_estimator_', None)
+if not best_estimator_:
+warnings.warn("GridSearchCV object has no attribute "
+"'best_estimator_', because either it's "
+"nested gridsearch or `refit` is False!")
+return
+main_est = best_estimator_
+if isinstance(best_estimator_, pipeline.Pipeline):
+main_est = best_estimator_.steps[-1][-1]
+if hasattr(main_est, 'model_') \
+and hasattr(main_est, 'save_weights'):
+if outfile_weights:
+main_est.save_weights(outfile_weights)
+del main_est.model_
+del main_est.fit_params
+del main_est.model_class_
+del main_est.validation_data
+if getattr(main_est, 'data_generator_', None):
+del main_est.data_generator_
+del main_est.data_batch_generator
 with open(outfile_object, 'wb') as output_handler:
-pickle.dump(searcher, output_handler, pickle.HIGHEST_PROTOCOL)
+pickle.dump(best_estimator_, output_handler,
+pickle.HIGHEST_PROTOCOL)
 if __name__ == '__main__':
 aparser = argparse.ArgumentParser()
 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
 aparser.add_argument("-X", "--infile1", dest="infile1")
 aparser.add_argument("-y", "--infile2", dest="infile2")
-aparser.add_argument("-r", "--outfile_result", dest="outfile_result")
+aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
+aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights")
 aparser.add_argument("-g", "--groups", dest="groups")
+aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
+aparser.add_argument("-b", "--intervals", dest="intervals")
+aparser.add_argument("-t", "--targets", dest="targets")
+aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
 args = aparser.parse_args()
 main(args.inputs, args.infile_estimator, args.infile1, args.infile2,
 args.outfile_result, outfile_object=args.outfile_object,
-groups=args.groups)
+outfile_weights=args.outfile_weights, groups=args.groups,
+ref_seq=args.ref_seq, intervals=args.intervals,
+targets=args.targets, fasta_path=args.fasta_path)

Mercurial > repos > bgruening > sklearn_sample_generator

comparison search_model_validation.py @ 26:ebf295f2faf6 draft