Python eval_split Examples

Example #1

File: Feb7_tumor_vs_self.py Project: elkingtowa/oniumlabs

def run(x,y, f):
  x_test_true = f.transform(cancer_peptides)
  x_test_false = f.transform(self_peptides)
  x_test = np.vstack([x_test_true, x_test_false])
  y_test = np.ones(x_test.shape[0], dtype='bool')
  y_test[len(x_test_true):] = 0
  eval_dataset.eval_split(x,y,x_test,y_test)

Example #2

File: Jan31_bigram.py Project: hammerlab/immuno_research

print
print "---"
print "No HLA-A2 noisy = negative"
X_no_hla_a2_negtive, Y_no_hla_a2_negative = iedb.load_tcell_ngrams(
    noisy_labels="negative", human=True, max_ngram=2, mhc_class=1, exclude_hla_type=A2
)
eval_dataset.eval_cv(X_no_hla_a2_positive, Y_no_hla_a2_positive)


print
print "---"
print "Cross-accuracy for HLA-A2 data"
X_hla_a2, Y_hla_a2 = iedb.load_tcell_ngrams(noisy_labels="keep", human=True, max_ngram=2, mhc_class=1, hla_type=A2)
eval_dataset.eval_split(X_no_hla_a2, Y_no_hla_a2, X_hla_a2, Y_hla_a2)


print
print "---"
print "Cross-accuracy for HLA-A2 data filtered"
X_hla_a2_filtered, Y_hla_a2_filtered = iedb.load_tcell_ngrams(
    noisy_labels="drop", human=True, max_ngram=2, mhc_class=1, hla_type=A2
)
eval_dataset.eval_split(X_no_hla_a2_filter, Y_no_hla_a2_filter, X_hla_a2_filtered, Y_hla_a2_filtered)


print
print "---"
print "Cross-accuracy for HLA-A2 data noisy = positive"
X_hla_a2_positive, Y_hla_a2_positive = iedb.load_tcell_ngrams(

Example #3

File: Feb1_majority_label.py Project: elkingtowa/oniumlabs

                 noisy_labels = 'majority',
                 human = True,
                 mhc_class = 1,
                 exclude_hla_type = 'HLA-A2$|A-\*02')
eval_dataset.eval_cv(X_no_hla_a2, Y_no_hla_a2)


print
print "---"
print "Cross-accuracy for HLA-A2 data"
X_hla_a2, Y_hla_a2 = iedb.load_tcell_ngrams(
                 noisy_labels = 'majority',
                 human = True,
                 mhc_class = 1,
                 hla_type =  'HLA-A2$|A-\*02')
eval_dataset.eval_split(X_no_hla_a2, Y_no_hla_a2, X_hla_a2, Y_hla_a2)





print
print "---"
print "Cross-accuracy for HLA-A2 data filtered (assay_group = cytotoxity)"
X_no_hla_a2_cytotoxicity, Y_no_hla_a2_cytotoxicity = iedb.load_tcell_ngrams(
                 noisy_labels = 'majority',
                 assay_group = 'cytotoxicity',
                 human = True,
                 mhc_class = 1,
                 exclude_hla_type = 'HLA-A2$|A-\*02')
X_hla_a2_cytotoxicity, Y_hla_a2_cytotoxicity = iedb.load_tcell_ngrams(

Example #4

File: Feb7_tumor_specific_antigens.py Project: elkingtowa/oniumlabs

def run(x,y, f):
  x_test = f.transform(cancer_peptides)
  y_test = np.array([True] * len(cancer_peptides))
  eval_dataset.eval_split(x,y,x_test,y_test)