def confusion_matrix(pred: list,
label: list,
label_index: dict,
file_name: str = None,
output_dir='results'):
cm = ConfusionMatrix(pred, label)
cm.relabel(mapping=label_index)
cm_matrix = cm.matrix
cm_normalized_matrix = cm.normalized_matrix
if file_name is None:
file_name = 'confusion_matrix.json'
normalized_file_name = file_name.replace('.', '_normalized.')
if output_dir is not None:
if not os.path.exists(output_dir):
os.makedirs(output_dir)
with open(os.path.join(output_dir, file_name), 'w') as fp:
json.dump(cm_matrix, fp, indent=4)
# with open(os.path.join(output_dir, normalized_file_name), 'w') as fp:
# json.dump(cm_normalized_matrix, fp, indent=4)
return cm_matrix
def show_classification_metrics(pred,
label,
use_matric=None,
label_index=None,
matrics_list=None,
display=True):
"""calc metrics for classification model using PYCM
Args:
pred (numpy.array) : pred label for each batch (batch_size X number of pred classes)
label (numpy.array) : label for each batch (batch_size X number of classes)
label_index (dict) : class name (default=None)
matrics_list (list) : add matrics name (refer to the pycm metrics list) (defailt=None)
display (bool) : Whether to print the overall result (default=True)
Returns:
metrics (dict) : contain the 2-level result (overall_stat, class_stat)
"""
# pred = pred.reshape(-1)
# label = label.reshape(-1)
cm = ConfusionMatrix(pred, label)
if label_index is not None:
cm.relabel(mapping=label_index)
default_matrics_list = cm.recommended_list
if matrics_list is not None:
default_matrics_list.extend(matrics_list)
if display:
cm.stat(summary=True)
print("[Matrix]")
cm.print_matrix()
print("[Normalized Matrix]")
cm.print_normalized_matrix()
overall_stat = cm.overall_stat
class_stat = cm.class_stat
filter_overall_stat = {
k: v
for k, v in overall_stat.items() if k in default_matrics_list
}
filter_class_stat = {
k: v
for k, v in class_stat.items() if k in default_matrics_list
}
output = dict()
output["overall_stat"] = filter_overall_stat
output["class_stat"] = filter_class_stat
return output
def __call__(self):
confusion_matrix = ConfusionMatrix(
matrix=deepcopy(self._confusion_matrix))
confusion_matrix.relabel(
mapping={value - 1: key
for key, value in self._label_map.items()})
metrics = {
metric_name: getattr(confusion_matrix, metric_name)
for metric_name in self._metric_names
}
self.reset()
return metrics
x=np.array(x_train),
y=np.array(y_train),
validation_split=0.2, # 80/20 split
verbose=1,
epochs=50, # Notice that r-square is pretty low for the first 5 epochs
callbacks=[callback]) # Early stopping
tf_preds = model.predict(x=x_test)
dir(history)
# summarize history for R^2:
plt.plot(history.history['accuracy'])
plt.plot(history.history['val_accuracy'])
plt.title('Model Accuracy over Epochs')
plt.ylabel('Accuracy')
plt.xlabel('epoch')
plt.legend(['train', 'test'], loc='upper left')
plt.show()
#############################################################
# Model Performance #
#############################################################
from pycm import ConfusionMatrix
# Yes, both Sci-kit learn and PYCM give the same confusion matrix, thankfully.
cm = ConfusionMatrix(actual_vector=np.array(y_test),
predict_vector=np.array(RF_preds))
cm.relabel(mapping={0: "Non-graduate", 1: "Graduate"})
print(cm)
def _analyze_stats(results_dir, sf_lf_map, correct_str, errors_str, sf_confusion, id_map, experiment=None):
"""
:param results_dir: directory in which to write results
:param sf_lf_map: Map of SFs to candidate LFs (i.e. AA --> {amino acids, alcoholics anonymous, etc.})
:param correct_str: String containing prettified versions of all correctly predicted examples
:param errors_str: String containing prettified versions of all incorrectly predicted examples
:param sf_confusion: dictionary of confusion matrices for SFs
:param id_map: Dictionary with keys 'correct' and 'error'. Values are example ids. For generating inter-model
confusion matries
:param experiment: name of experiment in which to write results in side of results_dir/
:return:
"""
correct_fp = os.path.join(results_dir, 'correct.txt')
reports_fp = os.path.join(results_dir, 'reports.txt')
errors_fp = os.path.join(results_dir, 'errors.txt')
summary_fp = os.path.join(results_dir, 'summary.csv')
id_fp = os.path.join(results_dir, 'error_tracker.json')
df = defaultdict(list)
rare_lfs = get_rare_lfs()
rare_recalls = []
cols = [
'sf',
'experiment',
'support',
'num_targets',
'micro_precision',
'micro_recall',
'micro_f1',
'macro_precision',
'macro_recall',
'macro_f1',
'weighted_precision',
'weighted_recall',
'weighted_f1',
]
with open(id_fp, 'w') as fd:
json.dump(id_map, fd)
reports = []
with open(correct_fp, 'w') as fd:
for k in sorted(correct_str.keys()):
fd.write(correct_str[k])
with open(errors_fp, 'w') as fd:
for k in sorted(errors_str.keys()):
fd.write(errors_str[k])
for sf in sf_confusion:
labels = sf_lf_map[sf]
labels_trunc = list(map(lambda x: x.split(';')[0], labels))
y_true = sf_confusion[sf][0]
y_pred = sf_confusion[sf][1]
sf_results = classification_report(y_true, y_pred, labels=list(range(len(labels_trunc))),
target_names=labels_trunc, output_dict=True)
report = classification_report(y_true, y_pred, labels=list(range(len(labels_trunc))),
target_names=labels_trunc)
macro_nonzero = defaultdict(float)
num_nonzero = 0
for orig_lf, lf in zip(labels, labels_trunc):
if orig_lf in rare_lfs:
rare_recalls.append(sf_results[lf]['recall'])
d = sf_results[lf]
if d['support'] > 0:
macro_nonzero['precision'] += d['precision']
macro_nonzero['recall'] += d['recall']
macro_nonzero['f1-score'] += d['f1-score']
num_nonzero += 1
for suffix in ['precision', 'recall', 'f1-score']:
sf_results['macro avg'][suffix] = macro_nonzero[suffix] / float(num_nonzero)
reports.append(report)
reports.append('\n\n')
metrics = ['micro avg', 'macro avg', 'weighted avg']
for metric in metrics:
if metric in sf_results:
for k, v in sf_results[metric].items():
if not k == 'support':
metric_key = '{}_{}'.format(metric.split(' ')[0], k.split('-')[0])
df[metric_key].append(v)
else:
for suffix in ['precision', 'recall', 'f1']:
df['{}_{}'.format(metric.split(' ')[0], suffix)].append(None)
df['sf'].append(sf)
df['num_targets'].append(len(labels_trunc))
df['support'].append(sf_results['weighted avg']['support'])
try:
cm = ConfusionMatrix(actual_vector=y_true, predict_vector=y_pred)
label_idx_to_str = dict()
for idx in cm.classes:
label_idx_to_str[idx] = labels_trunc[int(idx)]
cm.relabel(mapping=label_idx_to_str)
cm_outpath = os.path.join(results_dir, 'confusion', sf)
cm.save_html(cm_outpath)
except:
print('Only 1 target class for test set SF={}'.format(sf))
df['experiment'] = [experiment] * len(df['sf'])
summary_df = pd.DataFrame(df, columns=cols)
summary_df.to_csv(summary_fp, index=False)
with open(reports_fp, 'w') as fd:
for report in reports:
fd.write(report)
suffixes = ['precision', 'recall', 'f1']
types = ['weighted', 'macro']
agg_metrics = {}
for t in types:
for suffix in suffixes:
key = '{}_{}'.format(t, suffix)
avg_val = summary_df[key].mean()
print('Global {} --> {}'.format(key, avg_val))
agg_metrics[key] = avg_val
num_targets = summary_df['num_targets'].unique().tolist()
print('Num Targets, Macro F1, Weighted F1')
for t in sorted(num_targets):
avg_macro_f1 = summary_df[summary_df['num_targets'] == t]['macro_f1'].mean()
avg_weighted_f1 = summary_df[summary_df['num_targets'] == t]['weighted_f1'].mean()
print('{},{},{}'.format(t, avg_macro_f1, avg_weighted_f1))
rare_recall = sum(rare_recalls) / float(len(rare_recalls))
num_rare = len(rare_recalls)
print('Recall on {} rare long forms: {}'.format(num_rare, rare_recall))
return agg_metrics
def showStats(true_labels,
predictions,
labels_dir,
showExtraStats,
writeToFile=''):
"""
Prints various statistics about model preformance.
Arguments:
true_labels: true labels of the predictions
predictions: predicted labels
labels_dir: directory to text file of labels to integers
Returns:
N/A
"""
#Print basic info
print("Labels:")
label_dict = fileToLabelDict(labels_dir)
print(label_dict)
print("\nPredictions:")
print(predictions)
print("\nActual:")
print(true_labels)
print("\n")
#Builds confusion matrix and additional stats
my_inverted_dict = {}
for elem in label_dict.keys():
my_inverted_dict[elem] = int(label_dict[elem])
my_inverted_dict = dict(
zip(my_inverted_dict.values(), my_inverted_dict.keys()))
cm = ConfusionMatrix(actual_vector=true_labels, predict_vector=predictions)
cm.relabel(mapping=my_inverted_dict)
cm.print_matrix()
if showExtraStats:
#print("Micro F1 Score: ",cm.overall_stat['F1 Micro'])
#print("Macro F1 Score: ",cm.overall_stat['F1 Macro'])
#print("Cross Entropy: ",cm.overall_stat['Cross Entropy'])
#print("95% CI: ",cm.overall_stat['95% CI'])
print("AUC: ", cm.AUC)
print("AUC quality:", cm.AUCI)
#Outputs to output.txt
if writeToFile == '':
pass
else:
with open(writeToFile, 'w') as f:
f.write("Labels:\n\n")
f.write(str(label_dict))
f.write("\n\nPredictions::\n\n")
f.write(str(predictions))
f.write("\n\nActual:\n\n")
f.write(str(true_labels))
f.write("\n\n")
f.write(dictToString(cm.matrix))
f.write("\n\n")
f.write("AUC: \n\n")
f.write(str(cm.AUC))
f.write("AUC Quality: \n\n")
f.write(str(cm.AUCI))
f.write("\n\n")