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Increase training and inference performance for GAK kernel #77

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Increase training and inference performance for GAK kernel #77

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48587e3
initial implementation of sparse sim matrix using support vectors
lejafar Oct 21, 2018
c86fef3
dataset2 should be set to None to trigger self_similarity
lejafar Oct 21, 2018
67b8bb3
remove comments
lejafar Oct 21, 2018
6ea1847
modified comment
lejafar Oct 21, 2018
bb75442
Made statement more compact
lejafar Oct 21, 2018
e8ca156
Changed to more logical order
lejafar Oct 21, 2018
0f2a5b0
Ommit introduction of new variable
lejafar Oct 22, 2018
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31 changes: 28 additions & 3 deletions tslearn/svm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,29 @@ def _kernel_func_gak(sz, d, gamma):
gamma = 1.
return lambda x, y: cdist_gak(x.reshape((-1, sz, d)), y.reshape((-1, sz, d)), sigma=numpy.sqrt(gamma / 2.))

def _sparse_kernel_func_gak(sz, d, gamma, slice_support_vectors=None):
if gamma == "auto":
gamma = 1.

def sparse_gak(X, X_fit):

if X_fit is X:
return cdist_gak(X.reshape((-1, sz, d)), None, sigma=numpy.sqrt(gamma / 2.))

if slice_support_vectors is not None:
# slice out support vectors
sliced_X_fit = X_fit[slice_support_vectors]
gak_sim_dense = cdist_gak(X.reshape((-1, sz, d)), sliced_X_fit.reshape((-1, sz, d)), sigma=numpy.sqrt(gamma / 2.))

# act like nothing has happend ...
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gak_sim = numpy.empty((len(X), len(X_fit)))
gak_sim[:, slice_support_vectors] = gak_sim_dense
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return gak_sim

return cdist_gak(X.reshape((-1, sz, d)), X_fit.reshape((-1, sz, d)), sigma=numpy.sqrt(gamma / 2.))

return sparse_gak

class TimeSeriesSVC(BaseSVC):
"""Time-series specific Support Vector Classifier.
Expand Down Expand Up @@ -148,7 +171,7 @@ def __init__(self, sz, d, C=1.0, kernel="gak", degree=3, gamma="auto", coef0=0.0
self.sz = sz
self.d = d
if kernel == "gak":
kernel = _kernel_func_gak(sz=sz, d=d, gamma=gamma)
kernel = _sparse_kernel_func_gak(sz=sz, d=d, gamma=gamma)
super(TimeSeriesSVC, self).__init__(C=C, kernel=kernel, degree=degree, gamma=gamma, coef0=coef0,
shrinking=shrinking, probability=probability, tol=tol,
cache_size=cache_size, class_weight=class_weight, verbose=verbose,
Expand All @@ -169,8 +192,10 @@ def fit(self, X, y, sample_weight=None):
sklearn_X = _prepare_ts_datasets_sklearn(X)
if self.kernel == "gak" and self.gamma == "auto":
self.gamma = gamma_soft_dtw(to_time_series_dataset(X))
self.kernel = _kernel_func_gak(sz=self.sz, d=self.d, gamma=self.gamma)
return super(TimeSeriesSVC, self).fit(sklearn_X, y, sample_weight=sample_weight)
self.kernel = _sparse_kernel_func_gak(sz=self.sz, d=self.d, gamma=self.gamma)
_self = super(TimeSeriesSVC, self).fit(sklearn_X, y, sample_weight=sample_weight)
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self.kernel = _sparse_kernel_func_gak(sz=self.sz, d=self.d, gamma=self.gamma, slice_support_vectors=self.support_)
return _self

def predict(self, X):
sklearn_X = _prepare_ts_datasets_sklearn(X)
Expand Down