def run_confusion(clf, X, Y, Y_dist, sample_names, **kwargs):
#print X, Y
thres = kwargs['options'].get('confus_thres', 0.01)
random.seed(0)
if hasattr(clf, 'get_shape') and callable(getattr(X, 'get_shape')):
#sparse matrix
n_samples = X.get_shape()[0]
else:
#normal ndarray
n_samples = X.shape[0]
p = range(n_samples)
random.shuffle(p)
X, Y = X[p], Y[p]
half = int(n_samples / 2)
#Run classifier
sample_names = sample_names[half:]
y_ = clf.fit(X[:half], Y[:half]).predict(X[half:])
if hasattr(clf, 'predict_proba') and callable(getattr(clf, 'predict_proba')):
try:
y_prob= clf.predict_proba(X[half:])
valid_idx= []
invalid_idx = []
invalid_name = []
diff = y_prob-Y_dist
#for computing confusion matrix, we only pick
for i in xrange(len(diff)):
diff_sum = 0
for x in diff[i]:
diff_sum += abs(x)
if diff_sum > thres:
valid_idx.append(i)
else:
invalid_idx.append(i)
invalid_name.append(sample_names[i])
print "too close", y_prob[i], "\nversus\n", Y_dist
print "valid ", len(valid_idx), " invalid", len(invalid_idx)
for name in invalid_name:
logger.info("samples with class distribution: %s" % name)
except NotImplementedError:
valid_idx = range(len(y_))
else:
valid_idx = range(len(y_))
#Compute confusion matrix
Y_half = Y[half:]
corr = pearsonr(Y_half[valid_idx], y_[valid_idx])
print "Pearson correlation %f" %corr[0]
cm = metrics.confusion_matrix(Y_half[valid_idx], y_[valid_idx])
print cm
logger.info('confusion matrix : %s' % str(cm))
return (corr, cm, y_prob, sample_names)
def inner_pickler(*args, **kwargs):
name = build_pickle_name(func, *args, **kwargs)
print "name ", name
logger.info('name: %s' % name)
if os.path.exists(name+".pkl"):
tup = pickle.load(open(name+".pkl", 'rb'))
clf = tup[0]
scores = tup[1]
corr = tup[2]
cm = tup[3]
y_prob = tup[4]
sample_names = tup[5]
else:
clf = func(**kwargs)
logger.info('running confusion matrix')
(corr, cm, y_prob, sample_names) = run_confusion(clf, *args, **kwargs)
logger.info('running cross validation')
scores = run_cv(clf, *args[:2])
if kwargs['options'].get('train', True):
clf.fit(*args[:2])
pickle.dump((clf, scores,corr, cm,
y_prob, sample_names), open(name+".pkl", 'wb'))
logger.info('scores. %s' % str(scores))
return (name, scores, corr, cm, y_prob, sample_names)