kubapok/biological-lms
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

names in/not in train splits

Browse Source
This commit is contained in:
kubapok 2024-08-08 17:05:41 +02:00
parent 77a1e13c8f
commit bdb188e609
1 changed files with 51 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
1.py
View File

@ -11,22 +11,27 @@ import pandas as pd
# PREDICTED_COLUMN_NAME = 'query_annot' # PREDICTED_COLUMN_NAME = 'query_annot'
# LABEL_COLUMN_NAME = 'target_annot' # LABEL_COLUMN_NAME = 'target_annot'
# COLUMN_SEPARATOR = '\t' # COLUMN_SEPARATOR = '\t'
# NAMES_IN_TRAIN_COLUMN_NAME = 'annot_present_in_target' # or leave empty NAMES_IN_TRAIN_COLUMN_NAME = '' if no such column
PREDICTED_COLUMN_NAME = 'plm_names' PREDICTED_COLUMN_NAME = 'plm_names'
LABEL_COLUMN_NAME = 'targets' LABEL_COLUMN_NAME = 'targets'
COLUMN_SEPARATOR = ',' COLUMN_SEPARATOR = ','
NAMES_IN_TRAIN_COLUMN_NAME = '' # or leave empty NAMES_IN_TRAIN_COLUMN_NAME = '' if no such column
predicted_all_splits = list()
label_all_splits = list()
bleu = BLEU() bleu = BLEU()
bleu_one_sentence = BLEU(effective_order=True) bleu_one_sentence = BLEU(effective_order=True)
chrf = CHRF() chrf = CHRF()
def get_statistics(r): def get_statistics(r):
metrics = dict() metrics = dict()
r['score_bleu'] = r.apply( r['score_bleu'] = r.apply(
lambda row: round(bleu_one_sentence.sentence_score(row[PREDICTED_COLUMN_NAME], [row[LABEL_COLUMN_NAME]]).score, 2), axis=1) lambda row: round(bleu_one_sentence.sentence_score(row[PREDICTED_COLUMN_NAME], [row[LABEL_COLUMN_NAME]]).score,
2), axis=1)
r['score_chrf'] = r.apply( r['score_chrf'] = r.apply(
lambda row: round(chrf.sentence_score(row[PREDICTED_COLUMN_NAME], [row[LABEL_COLUMN_NAME]]).score, 2), axis=1) lambda row: round(chrf.sentence_score(row[PREDICTED_COLUMN_NAME], [row[LABEL_COLUMN_NAME]]).score, 2), axis=1)
r['score_exact_match'] = r.apply(lambda row: 1 if row[PREDICTED_COLUMN_NAME] == row[LABEL_COLUMN_NAME] else 0, r['score_exact_match'] = r.apply(lambda row: 1 if row[PREDICTED_COLUMN_NAME] == row[LABEL_COLUMN_NAME] else 0,
@ -42,8 +47,18 @@ def get_statistics(r):
return r, metrics return r, metrics
def main(names_in_train = None):
assert names_in_train in (True, False, None)
predicted_all_splits = list()
label_all_splits = list()
for FILE_PATH in sys.argv[1:]: for FILE_PATH in sys.argv[1:]:
r = pd.read_csv(FILE_PATH,sep = COLUMN_SEPARATOR) r = pd.read_csv(FILE_PATH,sep = COLUMN_SEPARATOR)
if names_in_train == True:
r= r[r[NAMES_IN_TRAIN_COLUMN_NAME] == True]
elif names_in_train == False:
r = r[r[NAMES_IN_TRAIN_COLUMN_NAME] == False]
print(FILE_PATH + ':') print(FILE_PATH + ':')
report_with_metrics, metrics = get_statistics(r) report_with_metrics, metrics = get_statistics(r)
@ -51,6 +66,7 @@ for FILE_PATH in sys.argv[1:]:
predicted_all_splits.extend(r[PREDICTED_COLUMN_NAME].to_list()) predicted_all_splits.extend(r[PREDICTED_COLUMN_NAME].to_list())
label_all_splits.extend(r[LABEL_COLUMN_NAME].to_list()) label_all_splits.extend(r[LABEL_COLUMN_NAME].to_list())
print('samples:', len(r))
print(metrics) print(metrics)
report_with_metrics = report_with_metrics.sort_values(by='score_chrf', ascending=False)[ report_with_metrics = report_with_metrics.sort_values(by='score_chrf', ascending=False)[
@ -61,7 +77,21 @@ if len(sys.argv) > 2:
print('ALL SPLITS:') print('ALL SPLITS:')
label_all_splits = [label_all_splits, ] label_all_splits = [label_all_splits, ]
metrics = dict() metrics = dict()
print('samples:', len(label_all_splits))
metrics['bleu'] = round(bleu.corpus_score(predicted_all_splits, label_all_splits).score, 2) metrics['bleu'] = round(bleu.corpus_score(predicted_all_splits, label_all_splits).score, 2)
metrics['chrf'] = round(chrf.corpus_score(predicted_all_splits, label_all_splits).score, 2) metrics['chrf'] = round(chrf.corpus_score(predicted_all_splits, label_all_splits).score, 2)
metrics['exact'] = round(float(100 * r['score_exact_match'].mean()), 2) metrics['exact'] = round(float(100 * r['score_exact_match'].mean()), 2)
print(metrics) print(metrics)
print('WHOLE DATASET:')
main()
print()
if len(NAMES_IN_TRAIN_COLUMN_NAME) > 0:
print('NAMES IN TRAIN:')
main(names_in_train=True)
print()
print('NAMES NOT IN TRAIN:')
main(names_in_train=False)
print()