def include(self, patient): util_5353.assert_dict_key(patient, 'id', 'pt_filter') util_5353.assert_dict_key(patient, 'name', 'pt_filter') util_5353.assert_dict_key(patient, 'address', 'pt_filter') util_5353.assert_dict_key(patient, 'birthDate', 'pt_filter') util_5353.assert_dict_key(patient, 'gender', 'pt_filter') return True
print('::: Problem 6 :::')
six_ret = svm(dataset_id, train, test)
util_5353.assert_list(six_ret, len(test), '6')
print('::: Problem 7 :::')
seven_ret_dt = evaluate(dataset_id, test_out, three_ret)
seven_ret_kn = evaluate(dataset_id, test_out, four_ret)
seven_ret_nb = evaluate(dataset_id, test_out, five_ret)
seven_ret_sv = evaluate(dataset_id, test_out, six_ret)
for seven_ret in [
seven_ret_dt, seven_ret_kn, seven_ret_nb, seven_ret_sv
]:
util_5353.assert_dict(seven_ret, '7')
util_5353.assert_dict_key(seven_ret, 'accuracy', '7')
util_5353.assert_float(seven_ret['accuracy'], '7')
util_5353.assert_float_range((0.0, 1.0), seven_ret['accuracy'],
'7')
for target in targets[dataset_id]:
util_5353.assert_dict_key(seven_ret, target, '7')
util_5353.assert_dict(seven_ret[target], '7')
util_5353.assert_dict_key(seven_ret[target], 'precision', '7')
util_5353.assert_dict_key(seven_ret[target], 'recall', '7')
util_5353.assert_dict_key(seven_ret[target], 'f1', '7')
util_5353.assert_float(seven_ret[target]['precision'], '7')
util_5353.assert_float(seven_ret[target]['recall'], '7')
util_5353.assert_float(seven_ret[target]['f1'], '7')
util_5353.assert_float_range(
(0.0, 1.0), seven_ret[target]['precision'], '7')
util_5353.assert_float_range((0.0, 1.0),
GOLD = ['Adult', 'Aged', 'Chemoradiotherapy', 'Diffusion Magnetic Resonance Imaging', 'Female', 'Humans', 'Medical Oncology', 'Middle Aged', 'Reproducibility of Results', 'Time Factors', 'Treatment Outcome', 'Tumor Burden', 'Uterine Cervical Neoplasms']
util_5353.assert_list(three_ret, len(GOLD), '3', valid_values=GOLD)
print('::: Problem 4 :::')
mesh_list = ['Humans', 'Female', 'Male', 'Animals', 'Treatment Outcome',
'Neoplasms', 'Prognosis', 'Risk Factors', 'Breast Neoplasms', 'Lung Neoplasms']
mesh_set = set()
for pmid in pmids:
mesh_set.update(mesh(data, pmid))
for m in mesh_list:
if m not in mesh_set:
util_5353.die('4', 'Assertions assume MeSH term is present: %s', m)
four_ret = svm_predict_unigram(data, train, test, mesh_list)
util_5353.assert_dict(four_ret, '4')
for m in mesh_list:
util_5353.assert_dict_key(four_ret, m, '4')
util_5353.assert_list(four_ret[m], None, '4', valid_values=pmids)
util_5353.assert_int_range((0, len(test)), len(four_ret[m]), '4')
util_5353.assert_int_range((len(test)/2, len(test)), len(four_ret['Humans']), '4')
print('::: Problem 5 :::')
five_ret = svm_predict_tfidf(data, train, test, mesh_list)
util_5353.assert_dict(five_ret, '5')
for m in mesh_list:
util_5353.assert_dict_key(five_ret, m, '5')
util_5353.assert_list(five_ret[m], None, '5', valid_values=pmids)
util_5353.assert_int_range((0, len(test)), len(five_ret[m]), '5')
util_5353.assert_int_range((len(test)/2, len(test)), len(five_ret['Humans']), '5')
print('::: Problem 6 :::')
K = 10
if __name__ == '__main__':
# Include all patients
pt_filter = all_pass_filter()
print('::: Problem 1 :::')
one_ret = num_patients(pt_filter)
util_5353.assert_tuple(one_ret, 2, '1')
util_5353.assert_int_range((0, 10000000), one_ret[0], '1')
util_5353.assert_int_range((0, 10000000), one_ret[1], '1')
print('::: Problem 2 :::')
two_ret = patient_stats(pt_filter)
util_5353.assert_dict(two_ret, '2')
for key in ['gender', 'marital_status', 'race', 'ethnicity', 'age', 'with_address']:
util_5353.assert_dict_key(two_ret, key, '2')
util_5353.assert_dict(two_ret[key], '2')
for key2 in two_ret[key].keys():
util_5353.assert_str(key2, '2')
util_5353.assert_prob_dict(two_ret[key], '2')
for key2 in two_ret['age'].keys():
if not key2.isdigit():
util_5353.die('2', 'age key should be year: %s', key2)
print('::: Problem 3 :::')
three_ret = diabetes_quality_measure(pt_filter)
util_5353.assert_tuple(three_ret, 3, '3')
util_5353.assert_int_range((0, 1000000), three_ret[0], '3')
util_5353.assert_int_range((0, 1000000), three_ret[1], '3')
util_5353.assert_int_range((0, 1000000), three_ret[2], '3')
if three_ret[0] < three_ret[1] or three_ret[1] < three_ret[2]:
# encouraged to look at this code, however, especially if your code crashes.
if __name__ == '__main__':
# Include all patients
pt_filter = all_pass_filter()
print('::: Problem 1 :::')
one_ret = num_patients(pt_filter)
util_5353.assert_tuple(one_ret, 2, '1')
util_5353.assert_int_range((0, 10000000), one_ret[0], '1')
util_5353.assert_int_range((0, 10000000), one_ret[1], '1')
print('::: Problem 2 :::')
two_ret = patient_stats(pt_filter)
util_5353.assert_dict(two_ret, '2')
util_5353.assert_dict_key(two_ret, 'gender', '2')
util_5353.assert_dict_key(two_ret, 'marital_status', '2')
util_5353.assert_dict_key(two_ret, 'race', '2')
util_5353.assert_dict_key(two_ret, 'ethnicity', '2')
util_5353.assert_dict_key(two_ret, 'age', '2')
util_5353.assert_dict_key(two_ret, 'with_address', '2')
util_5353.assert_dict(two_ret['gender'], '2')
util_5353.assert_dict(two_ret['marital_status'], '2')
util_5353.assert_dict(two_ret['race'], '2')
util_5353.assert_dict(two_ret['ethnicity'], '2')
util_5353.assert_dict(two_ret['age'], '2')
util_5353.assert_dict(two_ret['with_address'], '2')
util_5353.assert_prob_dict(two_ret['gender'], '2')
util_5353.assert_prob_dict(two_ret['marital_status'], '2')
util_5353.assert_prob_dict(two_ret['race'], '2')
util_5353.assert_prob_dict(two_ret['ethnicity'], '2')