Source code for skll.experiments

# License: BSD 3 clause
"""
Functions related to running experiments and parsing configuration files.

:author: Dan Blanchard (dblanchard@ets.org)
:author: Michael Heilman (mheilman@ets.org)
:author: Nitin Madnani (nmadnani@ets.org)
:author: Chee Wee Leong (cleong@ets.org)
"""

from __future__ import absolute_import, print_function, unicode_literals

import csv
import datetime
import json
import logging
import math
import numpy as np
import os
import sys

from collections import defaultdict
from io import open
from itertools import combinations
from os.path import basename, exists, isfile, join

import ruamel.yaml as yaml

from prettytable import PrettyTable, ALL
from six import iterkeys, iteritems  # Python 2/3
from six.moves import zip
from sklearn import __version__ as SCIKIT_VERSION

from skll import get_skll_logger
from skll.config import _munge_featureset_name, _parse_config_file
from skll.data.readers import Reader
from skll.learner import (Learner, MAX_CONCURRENT_PROCESSES,
                          _import_custom_learner)
from skll.version import __version__

# Check if gridmap is available
try:
    from gridmap import Job, process_jobs
except ImportError:
    _HAVE_GRIDMAP = False
else:
    _HAVE_GRIDMAP = True

# Check if pandas is available
try:
    import pandas as pd
except ImportError:
    _HAVE_PANDAS = False
else:
    _HAVE_PANDAS = True

# Check if seaborn (and matplotlib) are available
try:
    import matplotlib
    import seaborn as sns
except ImportError:
    _HAVE_SEABORN = False
else:
    import matplotlib.pyplot as plt
    plt.ioff()
    _HAVE_SEABORN = True

_VALID_TASKS = frozenset(['predict', 'train', 'evaluate', 'cross_validate'])
_VALID_SAMPLERS = frozenset(['Nystroem', 'RBFSampler', 'SkewedChi2Sampler',
                             'AdditiveChi2Sampler', ''])


[docs]class NumpyTypeEncoder(json.JSONEncoder): """ This class is used when serializing results, particularly the input label values if the input has int-valued labels. Numpy int64 objects can't be serialized by the json module, so we must convert them to int objects. A related issue where this was adapted from: http://stackoverflow.com/questions/11561932/why-does-json-dumpslistnp-arange5-fail-while-json-dumpsnp-arange5-tolis """ def default(self, obj): if isinstance(obj, np.int64): return int(obj) elif isinstance(obj, np.ndarray): return obj.tolist() return json.JSONEncoder.default(self, obj)
def _get_stat_float(label_result_dict, stat): """ A helper function to get output for the precision, recall, and f-score columns in the confusion matrix. Parameters ---------- label_result_dict : dict Dictionary containing the stat we'd like to retrieve for a particular label. stat : str The statistic we're looking for in the dictionary. Returns ------- stat_float : float The value of the stat if it's in the dictionary, and NaN otherwise. """ if stat in label_result_dict and label_result_dict[stat] is not None: return label_result_dict[stat] else: return float('nan') def _write_skll_folds(skll_fold_ids, skll_fold_ids_file): """ Function to take a dictionary of id->test-fold-number and write it to a file. Parameters ---------- skll_fold_ids : dict Dictionary with ids as keys and test-fold-numbers as values. skll_fold_ids_file : file buffer An open file handler to write to. """ f = csv.writer(skll_fold_ids_file) f.writerow(['id', 'cv_test_fold']) for example_id in skll_fold_ids: f.writerow([example_id, skll_fold_ids[example_id]]) skll_fold_ids_file.flush() def _write_summary_file(result_json_paths, output_file, ablation=0): """ Function to take a list of paths to individual result json files and returns a single file that summarizes all of them. Parameters ---------- result_json_paths : list of str A list of paths to the individual result JSON files. output_file : str The path to the output file (TSV format). ablation : int, optional The number of features to remove when doing ablation experiment. Defaults to 0. """ learner_result_dicts = [] # Map from feature set names to all features in them all_features = defaultdict(set) logger = get_skll_logger('experiment') for json_path in result_json_paths: if not exists(json_path): logger.error(('JSON results file %s not found. Skipping summary ' 'creation. You can manually create the summary file' ' after the fact by using the summarize_results ' 'script.'), json_path) return else: with open(json_path, 'r') as json_file: obj = json.load(json_file) featureset_name = obj[0]['featureset_name'] if ablation != 0 and '_minus_' in featureset_name: parent_set = featureset_name.split('_minus_', 1)[0] all_features[parent_set].update( yaml.safe_load(obj[0]['featureset'])) learner_result_dicts.extend(obj) # Build and write header header = set(learner_result_dicts[0].keys()) - {'result_table', 'descriptive'} if ablation != 0: header.add('ablated_features') header = sorted(header) writer = csv.DictWriter(output_file, header, extrasaction='ignore', dialect=csv.excel_tab) writer.writeheader() # Build "ablated_features" list and fix some backward compatible things for lrd in learner_result_dicts: featureset_name = lrd['featureset_name'] if ablation != 0: parent_set = featureset_name.split('_minus_', 1)[0] ablated_features = all_features[parent_set].difference( yaml.safe_load(lrd['featureset'])) lrd['ablated_features'] = '' if ablated_features: lrd['ablated_features'] = json.dumps(sorted(ablated_features)) # write out the new learner dict with the readable fields writer.writerow(lrd) output_file.flush() def _write_learning_curve_file(result_json_paths, output_file): """ Function to take a list of paths to individual learning curve results json files and writes out a single TSV file with the learning curve data. Parameters ---------- result_json_paths : list of str A list of paths to the individual result JSON files. output_file : str The path to the output file (TSV format). """ learner_result_dicts = [] # Map from feature set names to all features in them logger = get_skll_logger('experiment') for json_path in result_json_paths: if not exists(json_path): logger.error(('JSON results file %s not found. Skipping summary ' 'creation. You can manually create the summary file' ' after the fact by using the summarize_results ' 'script.'), json_path) return else: with open(json_path, 'r') as json_file: obj = json.load(json_file) learner_result_dicts.extend(obj) # Build and write header header = ['featureset_name', 'learner_name', 'metric', 'train_set_name', 'training_set_size', 'train_score_mean', 'test_score_mean', 'train_score_std', 'test_score_std', 'scikit_learn_version', 'version'] writer = csv.DictWriter(output_file, header, extrasaction='ignore', dialect=csv.excel_tab) writer.writeheader() # write out the fields we need for the learning curve file # specifically, we need to separate out the curve sizes # and scores into individual entries. for lrd in learner_result_dicts: training_set_sizes = lrd['computed_curve_train_sizes'] train_scores_means_by_size = lrd['learning_curve_train_scores_means'] test_scores_means_by_size = lrd['learning_curve_test_scores_means'] train_scores_stds_by_size = lrd['learning_curve_train_scores_stds'] test_scores_stds_by_size = lrd['learning_curve_test_scores_stds'] # rename `grid_objective` to `objective` since that can be confusing lrd['metric'] = lrd['grid_objective'] for (size, train_score_mean, test_score_mean, train_score_std, test_score_std) in zip(training_set_sizes, train_scores_means_by_size, test_scores_means_by_size, train_scores_stds_by_size, test_scores_stds_by_size): lrd['training_set_size'] = size lrd['train_score_mean'] = train_score_mean lrd['test_score_mean'] = test_score_mean lrd['train_score_std'] = train_score_std lrd['test_score_std'] = test_score_std writer.writerow(lrd) output_file.flush() def _print_fancy_output(learner_result_dicts, output_file=sys.stdout): """ Function to take all of the results from all of the folds and print nice tables with the results. Parameters ---------- learner_result_dicts : list of str A list of paths to the individual result JSON files. output_file : file buffer, optional The file buffer to print to. Defaults to ``sys.stdout``. """ if not learner_result_dicts: raise ValueError('Result dictionary list is empty!') lrd = learner_result_dicts[0] print('Experiment Name: {}'.format(lrd['experiment_name']), file=output_file) print('SKLL Version: {}'.format(lrd['version']), file=output_file) print('Training Set: {}'.format(lrd['train_set_name']), file=output_file) print('Training Set Size: {}'.format( lrd['train_set_size']), file=output_file) print('Test Set: {}'.format(lrd['test_set_name']), file=output_file) print('Test Set Size: {}'.format(lrd['test_set_size']), file=output_file) print('Shuffle: {}'.format(lrd['shuffle']), file=output_file) print('Feature Set: {}'.format(lrd['featureset']), file=output_file) print('Learner: {}'.format(lrd['learner_name']), file=output_file) print('Task: {}'.format(lrd['task']), file=output_file) if lrd['folds_file']: print('Specified Folds File: {}'.format(lrd['folds_file']), file=output_file) if lrd['task'] == 'cross_validate': print('Number of Folds: {}'.format(lrd['cv_folds']), file=output_file) if not lrd['cv_folds'].endswith('folds file'): print('Stratified Folds: {}'.format(lrd['stratified_folds']), file=output_file) print('Feature Scaling: {}'.format(lrd['feature_scaling']), file=output_file) print('Grid Search: {}'.format(lrd['grid_search']), file=output_file) if lrd['grid_search']: print('Grid Search Folds: {}'.format(lrd['grid_search_folds']), file=output_file) print('Grid Objective Function: {}'.format(lrd['grid_objective']), file=output_file) if (lrd['task'] == 'cross_validate' and lrd['grid_search'] and lrd['cv_folds'].endswith('folds file')): print('Using Folds File for Grid Search: {}'.format(lrd['use_folds_file_for_grid_search']), file=output_file) if lrd['task'] in ['evaluate', 'cross_validate'] and lrd['additional_scores']: print('Additional Evaluation Metrics: {}'.format(list(lrd['additional_scores'].keys())), file=output_file) print('Scikit-learn Version: {}'.format(lrd['scikit_learn_version']), file=output_file) print('Start Timestamp: {}'.format( lrd['start_timestamp']), file=output_file) print('End Timestamp: {}'.format(lrd['end_timestamp']), file=output_file) print('Total Time: {}'.format(lrd['total_time']), file=output_file) print('\n', file=output_file) for lrd in learner_result_dicts: print('Fold: {}'.format(lrd['fold']), file=output_file) print('Model Parameters: {}'.format(lrd.get('model_params', '')), file=output_file) print('Grid Objective Score (Train) = {}'.format(lrd.get('grid_score', '')), file=output_file) if 'result_table' in lrd: print(lrd['result_table'], file=output_file) print('Accuracy = {}'.format(lrd['accuracy']), file=output_file) if 'descriptive' in lrd: print('Descriptive statistics:', file=output_file) for desc_stat in ['min', 'max', 'avg', 'std']: actual = lrd['descriptive']['actual'][desc_stat] predicted = lrd['descriptive']['predicted'][desc_stat] print((' {} = {: .4f} (actual), {: .4f} ' '(predicted)').format(desc_stat.title(), actual, predicted), file=output_file) print('Pearson = {: f}'.format(lrd['pearson']), file=output_file) print('Objective Function Score (Test) = {}'.format(lrd['score']), file=output_file) # now print the additional metrics, if there were any if lrd['additional_scores']: print('', file=output_file) print('Additional Evaluation Metrics (Test):', file=output_file) for metric, score in lrd['additional_scores'].items(): score = '' if np.isnan(score) else score print(' {} = {}'.format(metric, score), file=output_file) print('', file=output_file) def _load_featureset(dir_path, feat_files, suffix, id_col='id', label_col='y', ids_to_floats=False, quiet=False, class_map=None, feature_hasher=False, num_features=None, logger=None): """ Load a list of feature files and merge them. Parameters ---------- dir_path : str Path to the directory that contains the feature files. feat_files : list of str A list of feature file prefixes. suffix : str The suffix to add to feature file prefixes to get the full filenames. id_col : str, optional Name of the column which contains the instance IDs. If no column with that name exists, or `None` is specified, example IDs will be automatically generated. Defaults to ``'id'``. label_col : str, optional Name of the column which contains the class labels. If no column with that name exists, or `None` is specified, the data is considered to be unlabeled. Defaults to ``'y'``. ids_to_floats : bool, optional Whether to convert the IDs to floats to save memory. Will raise error if we encounter non-numeric IDs. Defaults to ``False``. quiet : bool, optional Do not print "Loading..." status message to stderr. Defaults to ``False``. class_map : dict, optional Mapping from original class labels to new ones. This is mainly used for collapsing multiple labels into a single class. Anything not in the mapping will be kept the same. Defaults to ``None``. feature_hasher : bool, optional Should we use a FeatureHasher when vectorizing features? Defaults to ``False``. num_features : int, optional The number of features to use with the ``FeatureHasher``. This should always be set to the power of 2 greater than the actual number of features you're using. Defaults to ``None``. logger : logging.Logger, optional A logger instance to use to log messages instead of creating a new one by default. Defaults to ``None``. Returns ------- merged_set : skll.FeatureSet A ``FeatureSet`` instance containing the specified labels, IDs, features, and feature vectorizer. """ # if the training file is specified via train_file, then dir_path # actually contains the entire file name if isfile(dir_path): return Reader.for_path(dir_path, label_col=label_col, id_col=id_col, ids_to_floats=ids_to_floats, quiet=quiet, class_map=class_map, feature_hasher=feature_hasher, num_features=num_features, logger=logger).read() else: merged_set = None for file_name in sorted(join(dir_path, featfile + suffix) for featfile in feat_files): fs = Reader.for_path(file_name, label_col=label_col, id_col=id_col, ids_to_floats=ids_to_floats, quiet=quiet, class_map=class_map, feature_hasher=feature_hasher, num_features=num_features, logger=logger).read() if merged_set is None: merged_set = fs else: merged_set += fs return merged_set def _classify_featureset(args): """ Classification job to be submitted to grid. Parameters ---------- args : dict A dictionary with arguments for classifying the ``FeatureSet`` instance. Returns ------- res : list of dicts The results of the classification, in the format of a list of dictionaries. Raises ------ ValueError If extra unknown arguments are passed to the function. """ # Extract all the arguments. # (There doesn't seem to be a better way to do this since one can't specify # required keyword arguments.) experiment_name = args.pop("experiment_name") task = args.pop("task") sampler = args.pop("sampler") feature_hasher = args.pop("feature_hasher") hasher_features = args.pop("hasher_features") job_name = args.pop("job_name") featureset = args.pop("featureset") featureset_name = args.pop("featureset_name") learner_name = args.pop("learner_name") train_path = args.pop("train_path") test_path = args.pop("test_path") train_set_name = args.pop("train_set_name") test_set_name = args.pop("test_set_name") shuffle = args.pop('shuffle') model_path = args.pop("model_path") prediction_prefix = args.pop("prediction_prefix") grid_search = args.pop("grid_search") grid_objective = args.pop("grid_objective") output_metrics = args.pop("output_metrics") suffix = args.pop("suffix") job_log_file = args.pop("log_file") job_log_level = args.pop("log_level") probability = args.pop("probability") results_path = args.pop("results_path") fixed_parameters = args.pop("fixed_parameters") sampler_parameters = args.pop("sampler_parameters") param_grid = args.pop("param_grid") pos_label_str = args.pop("pos_label_str") overwrite = args.pop("overwrite") feature_scaling = args.pop("feature_scaling") min_feature_count = args.pop("min_feature_count") folds_file = args.pop("folds_file") grid_search_jobs = args.pop("grid_search_jobs") grid_search_folds = args.pop("grid_search_folds") cv_folds = args.pop("cv_folds") save_cv_folds = args.pop("save_cv_folds") use_folds_file_for_grid_search = args.pop("use_folds_file_for_grid_search") stratified_folds = args.pop("do_stratified_folds") label_col = args.pop("label_col") id_col = args.pop("id_col") ids_to_floats = args.pop("ids_to_floats") class_map = args.pop("class_map") custom_learner_path = args.pop("custom_learner_path") quiet = args.pop('quiet', False) learning_curve_cv_folds = args.pop("learning_curve_cv_folds") learning_curve_train_sizes = args.pop("learning_curve_train_sizes") if args: raise ValueError(("Extra arguments passed to _classify_featureset: " "{}").format(args.keys())) start_timestamp = datetime.datetime.now() # create a new SKLL logger for this specific job and # use the given log level logger = get_skll_logger(job_name, job_log_file, log_level=job_log_level) # log messages logger.info("Task: {}".format(task)) if task == 'cross_validate': if isinstance(cv_folds, int): num_folds = cv_folds else: # cv_folds_file was used, so count the unique fold ids. num_folds = len(set(cv_folds.values())) logger.info("Cross-validating ({} folds) on {}, feature " "set {} ...".format(num_folds, train_set_name, featureset)) elif task == 'evaluate': logger.info("Training on {}, Test on {}, " "feature set {} ...".format(train_set_name, test_set_name, featureset)) elif task == 'train': logger.info("Training on {}, feature set {} ...".format(train_set_name, featureset)) elif task == 'learning_curve': logger.info("Generating learning curve " "({} 80/20 folds, sizes={}, objective={}) on {}, " "feature set {} ...".format(learning_curve_cv_folds, learning_curve_train_sizes, grid_objective, train_set_name, featureset)) else: # predict logger.info("Training on {}, Making predictions about {}, " "feature set {} ...".format(train_set_name, test_set_name, featureset)) # check whether a trained model on the same data with the same # featureset already exists if so, load it and then use it on test data modelfile = join(model_path, '{}.model'.format(job_name)) if (task in ['cross_validate', 'learning_curve'] or not exists(modelfile) or overwrite): train_examples = _load_featureset(train_path, featureset, suffix, label_col=label_col, id_col=id_col, ids_to_floats=ids_to_floats, quiet=quiet, class_map=class_map, feature_hasher=feature_hasher, num_features=hasher_features, logger=logger) train_set_size = len(train_examples.ids) if not train_examples.has_labels: raise ValueError('Training examples do not have labels') # initialize a classifer object learner = Learner(learner_name, probability=probability, feature_scaling=feature_scaling, model_kwargs=fixed_parameters, pos_label_str=pos_label_str, min_feature_count=min_feature_count, sampler=sampler, sampler_kwargs=sampler_parameters, custom_learner_path=custom_learner_path, logger=logger) # load the model if it already exists else: # import the custom learner path here in case we are reusing a # saved model if custom_learner_path: _import_custom_learner(custom_learner_path, learner_name) train_set_size = 'unknown' if exists(modelfile) and not overwrite: logger.info("Loading pre-existing {} model: {}".format(learner_name, modelfile)) learner = Learner.from_file(modelfile) # attach the job logger to this learner learner.logger = logger # Load test set if there is one if task == 'evaluate' or task == 'predict': test_examples = _load_featureset(test_path, featureset, suffix, label_col=label_col, id_col=id_col, ids_to_floats=ids_to_floats, quiet=quiet, class_map=class_map, feature_hasher=feature_hasher, num_features=hasher_features) test_set_size = len(test_examples.ids) else: test_set_size = 'n/a' # compute information about xval and grid folds that can be put in results # in readable form if isinstance(cv_folds, dict): cv_folds_to_print = '{} via folds file'.format(len(set(cv_folds.values()))) else: cv_folds_to_print = str(cv_folds) if isinstance(grid_search_folds, dict): grid_search_folds_to_print = '{} via folds file'.format(len(set(grid_search_folds.values()))) else: grid_search_folds_to_print = str(grid_search_folds) # create a list of dictionaries of the results information learner_result_dict_base = {'experiment_name': experiment_name, 'train_set_name': train_set_name, 'train_set_size': train_set_size, 'test_set_name': test_set_name, 'test_set_size': test_set_size, 'featureset': json.dumps(featureset), 'featureset_name': featureset_name, 'shuffle': shuffle, 'learner_name': learner_name, 'task': task, 'start_timestamp': start_timestamp.strftime('%d %b %Y %H:%M:' '%S.%f'), 'version': __version__, 'feature_scaling': feature_scaling, 'folds_file': folds_file, 'grid_search': grid_search, 'grid_objective': grid_objective, 'grid_search_folds': grid_search_folds_to_print, 'min_feature_count': min_feature_count, 'cv_folds': cv_folds_to_print, 'using_folds_file': isinstance(cv_folds, dict) \ or isinstance(grid_search_folds, dict), 'save_cv_folds': save_cv_folds, 'use_folds_file_for_grid_search': use_folds_file_for_grid_search, 'stratified_folds': stratified_folds, 'scikit_learn_version': SCIKIT_VERSION} # check if we're doing cross-validation, because we only load/save # models when we're not. task_results = None if task == 'cross_validate': logger.info("Cross-validating") (task_results, grid_scores, skll_fold_ids) = learner.cross_validate(train_examples, shuffle=shuffle, stratified=stratified_folds, prediction_prefix=prediction_prefix, grid_search=grid_search, grid_search_folds=grid_search_folds, cv_folds=cv_folds, grid_objective=grid_objective, output_metrics=output_metrics, param_grid=param_grid, grid_jobs=grid_search_jobs, save_cv_folds=save_cv_folds, use_custom_folds_for_grid_search=use_folds_file_for_grid_search) elif task == 'learning_curve': logger.info("Generating learning curve(s)") (curve_train_scores, curve_test_scores, computed_curve_train_sizes) = learner.learning_curve(train_examples, cv_folds=learning_curve_cv_folds, train_sizes=learning_curve_train_sizes, metric=grid_objective) else: # if we have do not have a saved model, we need to train one. if not exists(modelfile) or overwrite: logger.info("Featurizing and training new {} model".format(learner_name)) best_score = learner.train(train_examples, shuffle=shuffle, grid_search=grid_search, grid_search_folds=grid_search_folds, grid_objective=grid_objective, param_grid=param_grid, grid_jobs=grid_search_jobs) grid_scores = [best_score] # save model if model_path: learner.save(modelfile) if grid_search: # note: bankers' rounding is used in python 3, # so these scores may be different between runs in # python 2 and 3 at the final decimal place. logger.info("Best {} grid search score: {}".format(grid_objective, round(best_score, 3))) else: grid_scores = [None] # print out the tuned parameters and best CV score param_out = ('{}: {}'.format(param_name, param_value) for param_name, param_value in iteritems(learner.model.get_params())) logger.info("Hyperparameters: {}".format(', '.join(param_out))) # run on test set or cross-validate on training data, # depending on what was asked for if task == 'evaluate': logger.info("Evaluating predictions") task_results = [learner.evaluate(test_examples, prediction_prefix=prediction_prefix, grid_objective=grid_objective, output_metrics=output_metrics)] elif task == 'predict': logger.info("Writing predictions") learner.predict(test_examples, prediction_prefix=prediction_prefix) # do nothing here for train end_timestamp = datetime.datetime.now() learner_result_dict_base['end_timestamp'] = end_timestamp.strftime( '%d %b %Y %H:%M:%S.%f') total_time = end_timestamp - start_timestamp learner_result_dict_base['total_time'] = str(total_time) if task == 'cross_validate' or task == 'evaluate': results_json_path = join(results_path, '{}.results.json'.format(job_name)) res = _create_learner_result_dicts(task_results, grid_scores, learner_result_dict_base) # write out the result dictionary to a json file file_mode = 'w' if sys.version_info >= (3, 0) else 'wb' with open(results_json_path, file_mode) as json_file: json.dump(res, json_file, cls=NumpyTypeEncoder) with open(join(results_path, '{}.results'.format(job_name)), 'w') as output_file: _print_fancy_output(res, output_file) elif task == 'learning_curve': results_json_path = join(results_path, '{}.results.json'.format(job_name)) res = {} res.update(learner_result_dict_base) res.update({'learning_curve_cv_folds': learning_curve_cv_folds, 'given_curve_train_sizes': learning_curve_train_sizes, 'learning_curve_train_scores_means': np.mean(curve_train_scores, axis=1), 'learning_curve_test_scores_means': np.mean(curve_test_scores, axis=1), 'learning_curve_train_scores_stds': np.std(curve_train_scores, axis=1, ddof=1), 'learning_curve_test_scores_stds': np.std(curve_test_scores, axis=1, ddof=1), 'computed_curve_train_sizes': computed_curve_train_sizes}) # we need to return and write out a list of dictionaries res = [res] # write out the result dictionary to a json file file_mode = 'w' if sys.version_info >= (3, 0) else 'wb' with open(results_json_path, file_mode) as json_file: json.dump(res, json_file, cls=NumpyTypeEncoder) else: res = [learner_result_dict_base] # write out the cv folds if required if task == 'cross_validate' and save_cv_folds: skll_fold_ids_file = experiment_name + '_skll_fold_ids.csv' file_mode = 'w' if sys.version_info >= (3, 0) else 'wb' with open(join(results_path, skll_fold_ids_file), file_mode) as output_file: _write_skll_folds(skll_fold_ids, output_file) return res def _create_learner_result_dicts(task_results, grid_scores, learner_result_dict_base): """ Create the learner result dictionaries that are used to create JSON and plain-text results files. Parameters ---------- task_results : list The task results list. grid_scores : list The grid scores list. learner_result_dict_base : dict Base dictionary for all learner results. Returns ------- res : list of dicts The results of the learners, as a list of dictionaries. """ res = [] num_folds = len(task_results) accuracy_sum = 0.0 pearson_sum = 0.0 additional_metric_score_sums = {} score_sum = None prec_sum_dict = defaultdict(float) recall_sum_dict = defaultdict(float) f_sum_dict = defaultdict(float) result_table = None for k, ((conf_matrix, fold_accuracy, result_dict, model_params, score, additional_scores), grid_score) in enumerate(zip(task_results, grid_scores), start=1): # create a new dict for this fold learner_result_dict = {} learner_result_dict.update(learner_result_dict_base) # initialize some variables to blanks so that the # set of columns is fixed. learner_result_dict['result_table'] = '' learner_result_dict['accuracy'] = '' learner_result_dict['pearson'] = '' learner_result_dict['score'] = '' learner_result_dict['fold'] = '' if learner_result_dict_base['task'] == 'cross_validate': learner_result_dict['fold'] = k learner_result_dict['model_params'] = json.dumps(model_params) if grid_score is not None: learner_result_dict['grid_score'] = grid_score if conf_matrix: labels = sorted(iterkeys(task_results[0][2])) result_table = PrettyTable([""] + labels + ["Precision", "Recall", "F-measure"], header=True, hrules=ALL) result_table.align = 'r' result_table.float_format = '.3' for i, actual_label in enumerate(labels): conf_matrix[i][i] = "[{}]".format(conf_matrix[i][i]) label_prec = _get_stat_float(result_dict[actual_label], "Precision") label_recall = _get_stat_float(result_dict[actual_label], "Recall") label_f = _get_stat_float(result_dict[actual_label], "F-measure") if not math.isnan(label_prec): prec_sum_dict[actual_label] += float(label_prec) if not math.isnan(label_recall): recall_sum_dict[actual_label] += float(label_recall) if not math.isnan(label_f): f_sum_dict[actual_label] += float(label_f) result_row = ([actual_label] + conf_matrix[i] + [label_prec, label_recall, label_f]) result_table.add_row(result_row) result_table_str = '{}'.format(result_table) result_table_str += '\n(row = reference; column = predicted)' learner_result_dict['result_table'] = result_table_str learner_result_dict['accuracy'] = fold_accuracy accuracy_sum += fold_accuracy # if there is no confusion matrix, then we must be dealing # with a regression model else: learner_result_dict.update(result_dict) pearson_sum += float(learner_result_dict['pearson']) # get the scores for all the metrics and compute the sums if score is not None: if score_sum is None: score_sum = score else: score_sum += score learner_result_dict['score'] = score learner_result_dict['additional_scores'] = additional_scores for metric, score in additional_scores.items(): if score is not None: additional_metric_score_sums[metric] = \ additional_metric_score_sums.get(metric, 0) + score res.append(learner_result_dict) if num_folds > 1: learner_result_dict = {} learner_result_dict.update(learner_result_dict_base) learner_result_dict['fold'] = 'average' if result_table: result_table = PrettyTable(["Label", "Precision", "Recall", "F-measure"], header=True) result_table.align = "r" result_table.align["Label"] = "l" result_table.float_format = '.3' for actual_label in labels: # Convert sums to means prec_mean = prec_sum_dict[actual_label] / num_folds recall_mean = recall_sum_dict[actual_label] / num_folds f_mean = f_sum_dict[actual_label] / num_folds result_table.add_row([actual_label] + [prec_mean, recall_mean, f_mean]) learner_result_dict['result_table'] = '{}'.format(result_table) learner_result_dict['accuracy'] = accuracy_sum / num_folds else: learner_result_dict['pearson'] = pearson_sum / num_folds if score_sum is not None: learner_result_dict['score'] = score_sum / num_folds scoredict = {} for metric, score_sum in additional_metric_score_sums.items(): scoredict[metric] = score_sum / num_folds learner_result_dict['additional_scores'] = scoredict res.append(learner_result_dict) return res
[docs]def run_configuration(config_file, local=False, overwrite=True, queue='all.q', hosts=None, write_summary=True, quiet=False, ablation=0, resume=False, log_level=logging.INFO): """ Takes a configuration file and runs the specified jobs on the grid. Parameters ---------- config_file : str Path to the configuration file we would like to use. local : bool, optional Should this be run locally instead of on the cluster? Defaults to ``False``. overwrite : bool, optional If the model files already exist, should we overwrite them instead of re-using them? Defaults to ``True``. queue : str, optional The DRMAA queue to use if we're running on the cluster. Defaults to ``'all.q'``. hosts : list of str, optional If running on the cluster, these are the machines we should use. Defaults to ``None``. write_summary : bool, optional Write a TSV file with a summary of the results. Defaults to ``True``. quite : bool, optional Suppress printing of "Loading..." messages. Defaults to ``False``. ablation : int, optional Number of features to remove when doing an ablation experiment. If positive, we will perform repeated ablation runs for all combinations of features removing the specified number at a time. If ``None``, we will use all combinations of all lengths. If 0, the default, no ablation is performed. If negative, a ``ValueError`` is raised. Defaults to 0. resume : bool, optional If result files already exist for an experiment, do not overwrite them. This is very useful when doing a large ablation experiment and part of it crashes. Defaults to ``False``. log_level : str, optional The level for logging messages. Defaults to ``logging.INFO``. Returns ------- result_json_paths : list of str A list of paths to .json results files for each variation in the experiment. Raises ------ ValueError If value for ``"ablation"`` is not a positive int or ``None``. OSError If the lenth of the ``FeatureSet`` name > 210. """ # Read configuration (experiment_name, task, sampler, fixed_sampler_parameters, feature_hasher, hasher_features, id_col, label_col, train_set_name, test_set_name, suffix, featuresets, do_shuffle, model_path, do_grid_search, grid_objectives, probability, results_path, pos_label_str, feature_scaling, min_feature_count, folds_file, grid_search_jobs, grid_search_folds, cv_folds, save_cv_folds, use_folds_file_for_grid_search, do_stratified_folds, fixed_parameter_list, param_grid_list, featureset_names, learners, prediction_dir, log_path, train_path, test_path, ids_to_floats, class_map, custom_learner_path, learning_curve_cv_folds_list, learning_curve_train_sizes, output_metrics) = _parse_config_file(config_file, log_level=log_level) # get the main experiment logger that will already have been # created by the configuration parser so we don't need anything # except the name `experiment`. logger = get_skll_logger('experiment') # Check if we have gridmap if not local and not _HAVE_GRIDMAP: local = True logger.warning('gridmap 0.10.1+ not available. Forcing local ' 'mode. To run things on a DRMAA-compatible ' 'cluster, install gridmap>=0.10.1 via pip.') # No grid search or ablation for learning curve generation if task == 'learning_curve': if do_grid_search: do_grid_search = False logger.warning("Grid search is not supported during " "learning curve generation. Ignoring.") if ablation is None or ablation > 0: ablation = 0 logger.warning("Ablating features is not supported during " "learning curve generation. Ignoring.") # if we just had a train file and a test file, there are no real featuresets # in which case there are no features to ablate if len(featuresets) == 1 and len(featuresets[0]) == 1: if ablation is None or ablation > 0: ablation = 0 logger.warning("Not enough featuresets for ablation. Ignoring.") # if performing ablation, expand featuresets to include combinations of # features within those sets if ablation is None or ablation > 0: # Make new feature set lists so that we can iterate without issue expanded_fs = [] expanded_fs_names = [] for features, featureset_name in zip(featuresets, featureset_names): features = sorted(features) featureset = set(features) # Expand to all feature combinations if ablation is None if ablation is None: for i in range(1, len(features)): for excluded_features in combinations(features, i): expanded_fs.append(sorted(featureset - set(excluded_features))) expanded_fs_names.append( featureset_name + '_minus_' + _munge_featureset_name(excluded_features)) # Otherwise, just expand removing the specified number at a time else: for excluded_features in combinations(features, ablation): expanded_fs.append(sorted(featureset - set(excluded_features))) expanded_fs_names.append( featureset_name + '_minus_' + _munge_featureset_name(excluded_features)) # Also add version with nothing removed as baseline expanded_fs.append(features) expanded_fs_names.append(featureset_name + '_all') # Replace original feature set lists featuresets = expanded_fs featureset_names = expanded_fs_names elif ablation < 0: raise ValueError('Value for "ablation" argument must be either ' 'positive integer or None.') # the list of jobs submitted (if running on grid) if not local: jobs = [] # the list to hold the paths to all the result json files result_json_paths = [] # check if the length of the featureset_name exceeds the maximum length # allowed for featureset_name in featureset_names: if len(featureset_name) > 210: raise OSError('System generated file length "{}" exceeds the ' 'maximum length supported. Please specify names of ' 'your datasets with "featureset_names". If you are ' 'running ablation experiment, please reduce the ' 'length of the features in "featuresets" because the' ' auto-generated name would be longer than the file ' 'system can handle'.format(featureset_name)) # if the task is learning curve, and ``metrics`` was specified, then # assign the value of ``metrics`` to ``grid_objectives`` - this lets # us piggyback on the parallelization of the objectives that is already # set up for us to use if task == 'learning_curve' and len(output_metrics) > 0: grid_objectives = output_metrics # Run each featureset-learner-objective combination for featureset, featureset_name in zip(featuresets, featureset_names): for learner_num, learner_name in enumerate(learners): for grid_objective in grid_objectives: # for the individual job name, we need to add the feature set name # and the learner name if len(grid_objectives) == 1: job_name_components = [experiment_name, featureset_name, learner_name] else: job_name_components = [experiment_name, featureset_name, learner_name, grid_objective] job_name = '_'.join(job_name_components) # change the prediction prefix to include the feature set prediction_prefix = join(prediction_dir, job_name) # the log file that stores the actual output of this script (e.g., # the tuned parameters, what kind of experiment was run, etc.) logfile = join(log_path, '{}.log'.format(job_name)) # Figure out result json file path result_json_path = join(results_path, '{}.results.json'.format(job_name)) # save the path to the results json file that will be written result_json_paths.append(result_json_path) # If result file already exists and we're resuming, move on if resume and (exists(result_json_path) and os.path.getsize(result_json_path)): logger.info('Running in resume mode and %s exists, ' 'so skipping job.', result_json_path) continue # create job if we're doing things on the grid job_args = {} job_args["experiment_name"] = experiment_name job_args["task"] = task job_args["sampler"] = sampler job_args["feature_hasher"] = feature_hasher job_args["hasher_features"] = hasher_features job_args["job_name"] = job_name job_args["featureset"] = featureset job_args["featureset_name"] = featureset_name job_args["learner_name"] = learner_name job_args["train_path"] = train_path job_args["test_path"] = test_path job_args["train_set_name"] = train_set_name job_args["test_set_name"] = test_set_name job_args["shuffle"] = do_shuffle job_args["model_path"] = model_path job_args["prediction_prefix"] = prediction_prefix job_args["grid_search"] = do_grid_search job_args["grid_objective"] = grid_objective job_args['output_metrics'] = output_metrics job_args["suffix"] = suffix job_args["log_file"] = logfile job_args["log_level"] = log_level job_args["probability"] = probability job_args["results_path"] = results_path job_args["sampler_parameters"] = (fixed_sampler_parameters if fixed_sampler_parameters else dict()) job_args["fixed_parameters"] = (fixed_parameter_list[learner_num] if fixed_parameter_list else dict()) job_args["param_grid"] = (param_grid_list[learner_num] if param_grid_list else None) job_args["pos_label_str"] = pos_label_str job_args["overwrite"] = overwrite job_args["feature_scaling"] = feature_scaling job_args["min_feature_count"] = min_feature_count job_args["grid_search_jobs"] = grid_search_jobs job_args["grid_search_folds"] = grid_search_folds job_args["folds_file"] = folds_file job_args["cv_folds"] = cv_folds job_args["save_cv_folds"] = save_cv_folds job_args["use_folds_file_for_grid_search"] = use_folds_file_for_grid_search job_args["do_stratified_folds"] = do_stratified_folds job_args["label_col"] = label_col job_args["id_col"] = id_col job_args["ids_to_floats"] = ids_to_floats job_args["quiet"] = quiet job_args["class_map"] = class_map job_args["custom_learner_path"] = custom_learner_path job_args["learning_curve_cv_folds"] = learning_curve_cv_folds_list[learner_num] job_args["learning_curve_train_sizes"] = learning_curve_train_sizes if not local: jobs.append(Job(_classify_featureset, [job_args], num_slots=(MAX_CONCURRENT_PROCESSES if (do_grid_search or task == 'learning_curve') else 1), name=job_name, queue=queue)) else: _classify_featureset(job_args) test_set_name = basename(test_path) # submit the jobs (if running on grid) if not local and _HAVE_GRIDMAP: if log_path: job_results = process_jobs(jobs, white_list=hosts, temp_dir=log_path) else: job_results = process_jobs(jobs, white_list=hosts) _check_job_results(job_results) # write out the summary results file if (task == 'cross_validate' or task == 'evaluate') and write_summary: summary_file_name = experiment_name + '_summary.tsv' file_mode = 'w' if sys.version_info >= (3, 0) else 'wb' with open(join(results_path, summary_file_name), file_mode) as output_file: _write_summary_file(result_json_paths, output_file, ablation=ablation) elif task == 'learning_curve': output_file_name = experiment_name + '_summary.tsv' file_mode = 'w' if sys.version_info >= (3, 0) else 'wb' output_file_path = join(results_path, output_file_name) with open(output_file_path, file_mode) as output_file: _write_learning_curve_file(result_json_paths, output_file) # generate the actual plot if we have the requirements installed if _HAVE_PANDAS and _HAVE_SEABORN: _generate_learning_curve_plots(experiment_name, results_path, output_file_path) else: logger.warning("Raw data for the learning curve saved in " "{}. No plots were generated since pandas and " "seaborn are not installed. ".format(output_file_path)) return result_json_paths
def _check_job_results(job_results): """ See if we have a complete results dictionary for every job. Parameters ---------- job_results : list of dicts A list of job result dictionaries. """ logger = get_skll_logger('experiment') logger.info('Checking job results') for result_dicts in job_results: if not result_dicts or 'task' not in result_dicts[0]: logger.error('There was an error running the experiment:\n%s', result_dicts) def _compute_ylimits_for_featureset(df, metrics): """ Compute the y-limits for learning curve plots. Parameters ---------- df : pd.DataFrame A data_frame with relevant metric information for train and test. metrics : list of str A list of metrics for learning curve plots. Returns ------- ylimits : dict A dictionary, with metric names as keys and a tuple of (lower_limit, upper_limit) as values. """ # set the y-limits of the curves depending on what kind # of values the metric produces ylimits = {} for metric in metrics: # get the real min and max for the values that will be plotted df_train = df[(df['variable'] == 'train_score_mean') & (df['metric'] == metric)] df_test = df[(df['variable'] == 'test_score_mean') & (df['metric'] == metric)] train_values_lower = df_train['value'].values - df_train['train_score_std'].values test_values_lower = df_test['value'].values - df_test['test_score_std'].values min_score = np.min(np.concatenate([train_values_lower, test_values_lower])) train_values_upper = df_train['value'].values + df_train['train_score_std'].values test_values_upper = df_test['value'].values + df_test['test_score_std'].values max_score = np.max(np.concatenate([train_values_upper, test_values_upper])) # squeeze the limits to hide unnecessary parts of the graph # set the limits with a little buffer on either side but not too much if min_score < 0: lower_limit = max(min_score - 0.1, math.floor(min_score) - 0.05) else: lower_limit = 0 if max_score > 0: upper_limit = min(max_score + 0.1, math.ceil(max_score) + 0.05) else: upper_limit = 0 ylimits[metric] = (lower_limit, upper_limit) return ylimits def _generate_learning_curve_plots(experiment_name, output_dir, learning_curve_tsv_file): """ Generate the learning curve plots given the TSV output file from a learning curve experiment. Parameters ---------- experiment_name : str The name of the experiment. output_dir : str Path to the output directory for the plots. learning_curve_tsv_file : str The path to the learning curve TSV file. """ # use pandas to read in the TSV file into a data frame # and massage it from wide to long format for plotting df = pd.read_csv(learning_curve_tsv_file, sep='\t') num_learners = len(df['learner_name'].unique()) num_metrics = len(df['metric'].unique()) df_melted = pd.melt(df, id_vars=[c for c in df.columns if c not in ['train_score_mean', 'test_score_mean']]) # if there are any training sizes greater than 1000, # then we should probably rotate the tick labels # since otherwise the labels are not clearly rendered rotate_labels = np.any([size >= 1000 for size in df['training_set_size'].unique()]) # set up and draw the actual learning curve figures, one for # each of the featuresets for fs_name, df_fs in df_melted.groupby('featureset_name'): fig = plt.figure(); fig.set_size_inches(2.5*num_learners, 2.5*num_metrics); # compute ylimits for this feature set for each objective with sns.axes_style('whitegrid', {"grid.linestyle": ':', "xtick.major.size": 3.0}): g = sns.FacetGrid(df_fs, row="metric", col="learner_name", hue="variable", size=2.5, aspect=1, margin_titles=True, despine=True, sharex=False, sharey=False, legend_out=False, palette="Set1") colors = train_color, test_color = sns.color_palette("Set1")[:2] g = g.map_dataframe(sns.pointplot, "training_set_size", "value", scale=.5, ci=None) ylimits = _compute_ylimits_for_featureset(df_fs, g.row_names) for ax in g.axes.flat: plt.setp(ax.texts, text="") g = (g.set_titles(row_template='', col_template='{col_name}') .set_axis_labels('Training Examples', 'Score')) if rotate_labels: g = g.set_xticklabels(rotation=60) for i, row_name in enumerate(g.row_names): for j, col_name in enumerate(g.col_names): ax = g.axes[i][j] ax.set(ylim=ylimits[row_name]) df_ax_train = df_fs[(df_fs['learner_name'] == col_name) & (df_fs['metric'] == row_name) & (df_fs['variable'] == 'train_score_mean')] df_ax_test = df_fs[(df_fs['learner_name'] == col_name) & (df_fs['metric'] == row_name) & (df_fs['variable'] == 'test_score_mean')] ax.fill_between(list(range(len(df_ax_train))), df_ax_train['value'] - df_ax_train['train_score_std'], df_ax_train['value'] + df_ax_train['train_score_std'], alpha=0.1, color=train_color) ax.fill_between(list(range(len(df_ax_test))), df_ax_test['value'] - df_ax_test['test_score_std'], df_ax_test['value'] + df_ax_test['test_score_std'], alpha=0.1, color=test_color) if j == 0: ax.set_ylabel(row_name) if i == 0: ax.legend(handles=[matplotlib.lines.Line2D([], [], color=c, label=l, linestyle='-') for c, l in zip(colors, ['Training', 'Cross-validation'])], loc=4, fancybox=True, fontsize='x-small', ncol=1, frameon=True) g.fig.tight_layout(w_pad=1) plt.savefig(join(output_dir,'{}_{}.png'.format(experiment_name, fs_name)), dpi=300);