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New translations median_preimage_generator_cml.py (French)

l10n_v0.2.x
linlin 5 years ago
parent
d4d5e59905
commit
9005ceeb75
1 changed files with 221 additions and 221 deletions
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    -221
      lang/fr/gklearn/preimage/median_preimage_generator_cml.py

+ 221
- 221
lang/fr/gklearn/preimage/median_preimage_generator_cml.py View File

@@ -27,69 +27,69 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
def __init__(self, dataset=None): def __init__(self, dataset=None):
PreimageGenerator.__init__(self, dataset=dataset) PreimageGenerator.__init__(self, dataset=dataset)
### arguments to set. ### arguments to set.
self.__mge = None
self.__ged_options = {}
self.__mge_options = {}
# self.__fit_method = 'k-graphs'
self.__init_method = 'random'
self.__init_ecc = None
self.__parallel = True
self.__n_jobs = multiprocessing.cpu_count()
self.__ds_name = None
self._mge = None
self._ged_options = {}
self._mge_options = {}
# self._fit_method = 'k-graphs'
self._init_method = 'random'
self._init_ecc = None
self._parallel = True
self._n_jobs = multiprocessing.cpu_count()
self._ds_name = None
# for cml. # for cml.
self.__time_limit_in_sec = 0
self.__max_itrs = 100
self.__max_itrs_without_update = 3
self.__epsilon_residual = 0.01
self.__epsilon_ec = 0.1
self.__allow_zeros = True
# self.__triangle_rule = True
self._time_limit_in_sec = 0
self._max_itrs = 100
self._max_itrs_without_update = 3
self._epsilon_residual = 0.01
self._epsilon_ec = 0.1
self._allow_zeros = True
# self._triangle_rule = True
### values to compute. ### values to compute.
self.__runtime_optimize_ec = None
self.__runtime_generate_preimage = None
self.__runtime_total = None
self.__set_median = None
self.__gen_median = None
self.__best_from_dataset = None
self.__sod_set_median = None
self.__sod_gen_median = None
self.__k_dis_set_median = None
self.__k_dis_gen_median = None
self.__k_dis_dataset = None
self.__node_label_costs = None
self.__edge_label_costs = None
self._runtime_optimize_ec = None
self._runtime_generate_preimage = None
self._runtime_total = None
self._set_median = None
self._gen_median = None
self._best_from_dataset = None
self._sod_set_median = None
self._sod_gen_median = None
self._k_dis_set_median = None
self._k_dis_gen_median = None
self._k_dis_dataset = None
self._node_label_costs = None
self._edge_label_costs = None
# for cml. # for cml.
self.__itrs = 0
self.__converged = False
self.__num_updates_ecs = 0
self._itrs = 0
self._converged = False
self._num_updates_ecs = 0
### values that can be set or to be computed. ### values that can be set or to be computed.
self.__edit_cost_constants = []
self.__gram_matrix_unnorm = None
self.__runtime_precompute_gm = None
self._edit_cost_constants = []
self._gram_matrix_unnorm = None
self._runtime_precompute_gm = None


def set_options(self, **kwargs): def set_options(self, **kwargs):
self._kernel_options = kwargs.get('kernel_options', {}) self._kernel_options = kwargs.get('kernel_options', {})
self._graph_kernel = kwargs.get('graph_kernel', None) self._graph_kernel = kwargs.get('graph_kernel', None)
self._verbose = kwargs.get('verbose', 2) self._verbose = kwargs.get('verbose', 2)
self.__ged_options = kwargs.get('ged_options', {})
self.__mge_options = kwargs.get('mge_options', {})
# self.__fit_method = kwargs.get('fit_method', 'k-graphs')
self.__init_method = kwargs.get('init_method', 'random')
self.__init_ecc = kwargs.get('init_ecc', None)
self.__edit_cost_constants = kwargs.get('edit_cost_constants', [])
self.__parallel = kwargs.get('parallel', True)
self.__n_jobs = kwargs.get('n_jobs', multiprocessing.cpu_count())
self.__ds_name = kwargs.get('ds_name', None)
self.__time_limit_in_sec = kwargs.get('time_limit_in_sec', 0)
self.__max_itrs = kwargs.get('max_itrs', 100)
self.__max_itrs_without_update = kwargs.get('max_itrs_without_update', 3)
self.__epsilon_residual = kwargs.get('epsilon_residual', 0.01)
self.__epsilon_ec = kwargs.get('epsilon_ec', 0.1)
self.__gram_matrix_unnorm = kwargs.get('gram_matrix_unnorm', None)
self.__runtime_precompute_gm = kwargs.get('runtime_precompute_gm', None)
self.__allow_zeros = kwargs.get('allow_zeros', True)
# self.__triangle_rule = kwargs.get('triangle_rule', True)
self._ged_options = kwargs.get('ged_options', {})
self._mge_options = kwargs.get('mge_options', {})
# self._fit_method = kwargs.get('fit_method', 'k-graphs')
self._init_method = kwargs.get('init_method', 'random')
self._init_ecc = kwargs.get('init_ecc', None)
self._edit_cost_constants = kwargs.get('edit_cost_constants', [])
self._parallel = kwargs.get('parallel', True)
self._n_jobs = kwargs.get('n_jobs', multiprocessing.cpu_count())
self._ds_name = kwargs.get('ds_name', None)
self._time_limit_in_sec = kwargs.get('time_limit_in_sec', 0)
self._max_itrs = kwargs.get('max_itrs', 100)
self._max_itrs_without_update = kwargs.get('max_itrs_without_update', 3)
self._epsilon_residual = kwargs.get('epsilon_residual', 0.01)
self._epsilon_ec = kwargs.get('epsilon_ec', 0.1)
self._gram_matrix_unnorm = kwargs.get('gram_matrix_unnorm', None)
self._runtime_precompute_gm = kwargs.get('runtime_precompute_gm', None)
self._allow_zeros = kwargs.get('allow_zeros', True)
# self._triangle_rule = kwargs.get('triangle_rule', True)
def run(self): def run(self):
@@ -105,48 +105,48 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
start = time.time() start = time.time()
# 1. precompute gram matrix. # 1. precompute gram matrix.
if self.__gram_matrix_unnorm is None:
if self._gram_matrix_unnorm is None:
gram_matrix, run_time = self._graph_kernel.compute(self._dataset.graphs, **self._kernel_options) gram_matrix, run_time = self._graph_kernel.compute(self._dataset.graphs, **self._kernel_options)
self.__gram_matrix_unnorm = self._graph_kernel.gram_matrix_unnorm
self._gram_matrix_unnorm = self._graph_kernel.gram_matrix_unnorm
end_precompute_gm = time.time() end_precompute_gm = time.time()
self.__runtime_precompute_gm = end_precompute_gm - start
self._runtime_precompute_gm = end_precompute_gm - start
else: else:
if self.__runtime_precompute_gm is None:
if self._runtime_precompute_gm is None:
raise Exception('Parameter "runtime_precompute_gm" must be given when using pre-computed Gram matrix.') raise Exception('Parameter "runtime_precompute_gm" must be given when using pre-computed Gram matrix.')
self._graph_kernel.gram_matrix_unnorm = self.__gram_matrix_unnorm
self._graph_kernel.gram_matrix_unnorm = self._gram_matrix_unnorm
if self._kernel_options['normalize']: if self._kernel_options['normalize']:
self._graph_kernel.gram_matrix = self._graph_kernel.normalize_gm(np.copy(self.__gram_matrix_unnorm))
self._graph_kernel.gram_matrix = self._graph_kernel.normalize_gm(np.copy(self._gram_matrix_unnorm))
else: else:
self._graph_kernel.gram_matrix = np.copy(self.__gram_matrix_unnorm)
self._graph_kernel.gram_matrix = np.copy(self._gram_matrix_unnorm)
end_precompute_gm = time.time() end_precompute_gm = time.time()
start -= self.__runtime_precompute_gm
start -= self._runtime_precompute_gm
# if self.__fit_method != 'k-graphs' and self.__fit_method != 'whole-dataset':
# if self._fit_method != 'k-graphs' and self._fit_method != 'whole-dataset':
# start = time.time() # start = time.time()
# self.__runtime_precompute_gm = 0
# self._runtime_precompute_gm = 0
# end_precompute_gm = start # end_precompute_gm = start
# 2. optimize edit cost constants. # 2. optimize edit cost constants.
self.__optimize_edit_cost_vector()
self._optimize_edit_cost_vector()
end_optimize_ec = time.time() end_optimize_ec = time.time()
self.__runtime_optimize_ec = end_optimize_ec - end_precompute_gm
self._runtime_optimize_ec = end_optimize_ec - end_precompute_gm
# 3. compute set median and gen median using optimized edit costs. # 3. compute set median and gen median using optimized edit costs.
if self._verbose >= 2: if self._verbose >= 2:
print('\nstart computing set median and gen median using optimized edit costs...\n') print('\nstart computing set median and gen median using optimized edit costs...\n')
self.__gmg_bcu()
self._gmg_bcu()
end_generate_preimage = time.time() end_generate_preimage = time.time()
self.__runtime_generate_preimage = end_generate_preimage - end_optimize_ec
self.__runtime_total = end_generate_preimage - start
self._runtime_generate_preimage = end_generate_preimage - end_optimize_ec
self._runtime_total = end_generate_preimage - start
if self._verbose >= 2: if self._verbose >= 2:
print('medians computed.') print('medians computed.')
print('SOD of the set median: ', self.__sod_set_median)
print('SOD of the generalized median: ', self.__sod_gen_median)
print('SOD of the set median: ', self._sod_set_median)
print('SOD of the generalized median: ', self._sod_gen_median)
# 4. compute kernel distances to the true median. # 4. compute kernel distances to the true median.
if self._verbose >= 2: if self._verbose >= 2:
print('\nstart computing distances to true median....\n') print('\nstart computing distances to true median....\n')
self.__compute_distances_to_true_median()
self._compute_distances_to_true_median()


# 5. print out results. # 5. print out results.
if self._verbose: if self._verbose:
@@ -154,145 +154,145 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
print('================================================================================') print('================================================================================')
print('Finished generation of preimages.') print('Finished generation of preimages.')
print('--------------------------------------------------------------------------------') print('--------------------------------------------------------------------------------')
print('The optimized edit costs:', self.__edit_cost_constants)
print('SOD of the set median:', self.__sod_set_median)
print('SOD of the generalized median:', self.__sod_gen_median)
print('Distance in kernel space for set median:', self.__k_dis_set_median)
print('Distance in kernel space for generalized median:', self.__k_dis_gen_median)
print('Minimum distance in kernel space for each graph in median set:', self.__k_dis_dataset)
print('Time to pre-compute Gram matrix:', self.__runtime_precompute_gm)
print('Time to optimize edit costs:', self.__runtime_optimize_ec)
print('Time to generate pre-images:', self.__runtime_generate_preimage)
print('Total time:', self.__runtime_total)
print('Total number of iterations for optimizing:', self.__itrs)
print('Total number of updating edit costs:', self.__num_updates_ecs)
print('Is optimization of edit costs converged:', self.__converged)
print('The optimized edit costs:', self._edit_cost_constants)
print('SOD of the set median:', self._sod_set_median)
print('SOD of the generalized median:', self._sod_gen_median)
print('Distance in kernel space for set median:', self._k_dis_set_median)
print('Distance in kernel space for generalized median:', self._k_dis_gen_median)
print('Minimum distance in kernel space for each graph in median set:', self._k_dis_dataset)
print('Time to pre-compute Gram matrix:', self._runtime_precompute_gm)
print('Time to optimize edit costs:', self._runtime_optimize_ec)
print('Time to generate pre-images:', self._runtime_generate_preimage)
print('Total time:', self._runtime_total)
print('Total number of iterations for optimizing:', self._itrs)
print('Total number of updating edit costs:', self._num_updates_ecs)
print('Is optimization of edit costs converged:', self._converged)
print('================================================================================') print('================================================================================')
print() print()




def get_results(self): def get_results(self):
results = {} results = {}
results['edit_cost_constants'] = self.__edit_cost_constants
results['runtime_precompute_gm'] = self.__runtime_precompute_gm
results['runtime_optimize_ec'] = self.__runtime_optimize_ec
results['runtime_generate_preimage'] = self.__runtime_generate_preimage
results['runtime_total'] = self.__runtime_total
results['sod_set_median'] = self.__sod_set_median
results['sod_gen_median'] = self.__sod_gen_median
results['k_dis_set_median'] = self.__k_dis_set_median
results['k_dis_gen_median'] = self.__k_dis_gen_median
results['k_dis_dataset'] = self.__k_dis_dataset
results['itrs'] = self.__itrs
results['converged'] = self.__converged
results['num_updates_ecc'] = self.__num_updates_ecs
results['edit_cost_constants'] = self._edit_cost_constants
results['runtime_precompute_gm'] = self._runtime_precompute_gm
results['runtime_optimize_ec'] = self._runtime_optimize_ec
results['runtime_generate_preimage'] = self._runtime_generate_preimage
results['runtime_total'] = self._runtime_total
results['sod_set_median'] = self._sod_set_median
results['sod_gen_median'] = self._sod_gen_median
results['k_dis_set_median'] = self._k_dis_set_median
results['k_dis_gen_median'] = self._k_dis_gen_median
results['k_dis_dataset'] = self._k_dis_dataset
results['itrs'] = self._itrs
results['converged'] = self._converged
results['num_updates_ecc'] = self._num_updates_ecs
results['mge'] = {} results['mge'] = {}
results['mge']['num_decrease_order'] = self.__mge.get_num_times_order_decreased()
results['mge']['num_increase_order'] = self.__mge.get_num_times_order_increased()
results['mge']['num_converged_descents'] = self.__mge.get_num_converged_descents()
results['mge']['num_decrease_order'] = self._mge.get_num_times_order_decreased()
results['mge']['num_increase_order'] = self._mge.get_num_times_order_increased()
results['mge']['num_converged_descents'] = self._mge.get_num_converged_descents()
return results return results


def __optimize_edit_cost_vector(self):
def _optimize_edit_cost_vector(self):
"""Learn edit cost vector. """Learn edit cost vector.
""" """
# Initialize label costs randomly. # Initialize label costs randomly.
if self.__init_method == 'random':
if self._init_method == 'random':
# Initialize label costs. # Initialize label costs.
self.__initialize_label_costs()
self._initialize_label_costs()
# Optimize edit cost matrices. # Optimize edit cost matrices.
self.__optimize_ecm_by_kernel_distances()
self._optimize_ecm_by_kernel_distances()
# Initialize all label costs with the same value. # Initialize all label costs with the same value.
elif self.__init_method == 'uniform': # random
elif self._init_method == 'uniform': # random
pass pass
elif self.__fit_method == 'random': # random
if self.__ged_options['edit_cost'] == 'LETTER':
self.__edit_cost_constants = random.sample(range(1, 1000), 3)
self.__edit_cost_constants = [item * 0.001 for item in self.__edit_cost_constants]
elif self.__ged_options['edit_cost'] == 'LETTER2':
elif self._fit_method == 'random': # random
if self._ged_options['edit_cost'] == 'LETTER':
self._edit_cost_constants = random.sample(range(1, 1000), 3)
self._edit_cost_constants = [item * 0.001 for item in self._edit_cost_constants]
elif self._ged_options['edit_cost'] == 'LETTER2':
random.seed(time.time()) random.seed(time.time())
self.__edit_cost_constants = random.sample(range(1, 1000), 5)
self.__edit_cost_constants = [item * 0.01 for item in self.__edit_cost_constants]
elif self.__ged_options['edit_cost'] == 'NON_SYMBOLIC':
self.__edit_cost_constants = random.sample(range(1, 1000), 6)
self.__edit_cost_constants = [item * 0.01 for item in self.__edit_cost_constants]
self._edit_cost_constants = random.sample(range(1, 1000), 5)
self._edit_cost_constants = [item * 0.01 for item in self._edit_cost_constants]
elif self._ged_options['edit_cost'] == 'NON_SYMBOLIC':
self._edit_cost_constants = random.sample(range(1, 1000), 6)
self._edit_cost_constants = [item * 0.01 for item in self._edit_cost_constants]
if self._dataset.node_attrs == []: if self._dataset.node_attrs == []:
self.__edit_cost_constants[2] = 0
self._edit_cost_constants[2] = 0
if self._dataset.edge_attrs == []: if self._dataset.edge_attrs == []:
self.__edit_cost_constants[5] = 0
self._edit_cost_constants[5] = 0
else: else:
self.__edit_cost_constants = random.sample(range(1, 1000), 6)
self.__edit_cost_constants = [item * 0.01 for item in self.__edit_cost_constants]
self._edit_cost_constants = random.sample(range(1, 1000), 6)
self._edit_cost_constants = [item * 0.01 for item in self._edit_cost_constants]
if self._verbose >= 2: if self._verbose >= 2:
print('edit cost constants used:', self.__edit_cost_constants)
elif self.__fit_method == 'expert': # expert
if self.__init_ecc is None:
if self.__ged_options['edit_cost'] == 'LETTER':
self.__edit_cost_constants = [0.9, 1.7, 0.75]
elif self.__ged_options['edit_cost'] == 'LETTER2':
self.__edit_cost_constants = [0.675, 0.675, 0.75, 0.425, 0.425]
print('edit cost constants used:', self._edit_cost_constants)
elif self._fit_method == 'expert': # expert
if self._init_ecc is None:
if self._ged_options['edit_cost'] == 'LETTER':
self._edit_cost_constants = [0.9, 1.7, 0.75]
elif self._ged_options['edit_cost'] == 'LETTER2':
self._edit_cost_constants = [0.675, 0.675, 0.75, 0.425, 0.425]
else: else:
self.__edit_cost_constants = [3, 3, 1, 3, 3, 1]
self._edit_cost_constants = [3, 3, 1, 3, 3, 1]
else: else:
self.__edit_cost_constants = self.__init_ecc
elif self.__fit_method == 'k-graphs':
if self.__init_ecc is None:
if self.__ged_options['edit_cost'] == 'LETTER':
self.__init_ecc = [0.9, 1.7, 0.75]
elif self.__ged_options['edit_cost'] == 'LETTER2':
self.__init_ecc = [0.675, 0.675, 0.75, 0.425, 0.425]
elif self.__ged_options['edit_cost'] == 'NON_SYMBOLIC':
self.__init_ecc = [0, 0, 1, 1, 1, 0]
self._edit_cost_constants = self._init_ecc
elif self._fit_method == 'k-graphs':
if self._init_ecc is None:
if self._ged_options['edit_cost'] == 'LETTER':
self._init_ecc = [0.9, 1.7, 0.75]
elif self._ged_options['edit_cost'] == 'LETTER2':
self._init_ecc = [0.675, 0.675, 0.75, 0.425, 0.425]
elif self._ged_options['edit_cost'] == 'NON_SYMBOLIC':
self._init_ecc = [0, 0, 1, 1, 1, 0]
if self._dataset.node_attrs == []: if self._dataset.node_attrs == []:
self.__init_ecc[2] = 0
self._init_ecc[2] = 0
if self._dataset.edge_attrs == []: if self._dataset.edge_attrs == []:
self.__init_ecc[5] = 0
self._init_ecc[5] = 0
else: else:
self.__init_ecc = [3, 3, 1, 3, 3, 1]
self._init_ecc = [3, 3, 1, 3, 3, 1]
# optimize on the k-graph subset. # optimize on the k-graph subset.
self.__optimize_ecm_by_kernel_distances()
elif self.__fit_method == 'whole-dataset':
if self.__init_ecc is None:
if self.__ged_options['edit_cost'] == 'LETTER':
self.__init_ecc = [0.9, 1.7, 0.75]
elif self.__ged_options['edit_cost'] == 'LETTER2':
self.__init_ecc = [0.675, 0.675, 0.75, 0.425, 0.425]
self._optimize_ecm_by_kernel_distances()
elif self._fit_method == 'whole-dataset':
if self._init_ecc is None:
if self._ged_options['edit_cost'] == 'LETTER':
self._init_ecc = [0.9, 1.7, 0.75]
elif self._ged_options['edit_cost'] == 'LETTER2':
self._init_ecc = [0.675, 0.675, 0.75, 0.425, 0.425]
else: else:
self.__init_ecc = [3, 3, 1, 3, 3, 1]
self._init_ecc = [3, 3, 1, 3, 3, 1]
# optimizeon the whole set. # optimizeon the whole set.
self.__optimize_ecc_by_kernel_distances()
elif self.__fit_method == 'precomputed':
self._optimize_ecc_by_kernel_distances()
elif self._fit_method == 'precomputed':
pass pass
def __initialize_label_costs(self):
self.__initialize_node_label_costs()
self.__initialize_edge_label_costs()
def _initialize_label_costs(self):
self._initialize_node_label_costs()
self._initialize_edge_label_costs()
def __initialize_node_label_costs(self):
def _initialize_node_label_costs(self):
# Get list of node labels. # Get list of node labels.
nls = self._dataset.get_all_node_labels() nls = self._dataset.get_all_node_labels()
# Generate random costs. # Generate random costs.
nb_nl = int((len(nls) * (len(nls) - 1)) / 2 + 2 * len(nls)) nb_nl = int((len(nls) * (len(nls) - 1)) / 2 + 2 * len(nls))
rand_costs = random.sample(range(1, 10 * nb_nl + 1), nb_nl) rand_costs = random.sample(range(1, 10 * nb_nl + 1), nb_nl)
rand_costs /= np.max(rand_costs) # @todo: maybe not needed. rand_costs /= np.max(rand_costs) # @todo: maybe not needed.
self.__node_label_costs = rand_costs
self._node_label_costs = rand_costs




def __initialize_edge_label_costs(self):
def _initialize_edge_label_costs(self):
# Get list of edge labels. # Get list of edge labels.
els = self._dataset.get_all_edge_labels() els = self._dataset.get_all_edge_labels()
# Generate random costs. # Generate random costs.
nb_el = int((len(els) * (len(els) - 1)) / 2 + 2 * len(els)) nb_el = int((len(els) * (len(els) - 1)) / 2 + 2 * len(els))
rand_costs = random.sample(range(1, 10 * nb_el + 1), nb_el) rand_costs = random.sample(range(1, 10 * nb_el + 1), nb_el)
rand_costs /= np.max(rand_costs) # @todo: maybe not needed. rand_costs /= np.max(rand_costs) # @todo: maybe not needed.
self.__edge_label_costs = rand_costs
self._edge_label_costs = rand_costs
def __optimize_ecm_by_kernel_distances(self):
def _optimize_ecm_by_kernel_distances(self):
# compute distances in feature space. # compute distances in feature space.
dis_k_mat, _, _, _ = self._graph_kernel.compute_distance_matrix() dis_k_mat, _, _, _ = self._graph_kernel.compute_distance_matrix()
dis_k_vec = [] dis_k_vec = []
@@ -303,35 +303,35 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
dis_k_vec = np.array(dis_k_vec) dis_k_vec = np.array(dis_k_vec)
# Set GEDEnv options. # Set GEDEnv options.
# graphs = [self.__clean_graph(g) for g in self._dataset.graphs]
# self.__edit_cost_constants = self.__init_ecc
options = self.__ged_options.copy()
options['edit_cost_constants'] = self.__edit_cost_constants # @todo: not needed.
# graphs = [self._clean_graph(g) for g in self._dataset.graphs]
# self._edit_cost_constants = self._init_ecc
options = self._ged_options.copy()
options['edit_cost_constants'] = self._edit_cost_constants # @todo: not needed.
options['node_labels'] = self._dataset.node_labels options['node_labels'] = self._dataset.node_labels
options['edge_labels'] = self._dataset.edge_labels options['edge_labels'] = self._dataset.edge_labels
# options['node_attrs'] = self._dataset.node_attrs # options['node_attrs'] = self._dataset.node_attrs
# options['edge_attrs'] = self._dataset.edge_attrs # options['edge_attrs'] = self._dataset.edge_attrs
options['node_label_costs'] = self.__node_label_costs
options['edge_label_costs'] = self.__edge_label_costs
options['node_label_costs'] = self._node_label_costs
options['edge_label_costs'] = self._edge_label_costs
# Learner cost matrices. # Learner cost matrices.
# Initialize cost learner. # Initialize cost learner.
cml = CostMatricesLearner(edit_cost='CONSTANT', triangle_rule=False, allow_zeros=True, parallel=self.__parallel, verbose=self._verbose) # @todo
cml.set_update_params(time_limit_in_sec=self.__time_limit_in_sec, max_itrs=self.__max_itrs, max_itrs_without_update=self.__max_itrs_without_update, epsilon_residual=self.__epsilon_residual, epsilon_ec=self.__epsilon_ec)
cml = CostMatricesLearner(edit_cost='CONSTANT', triangle_rule=False, allow_zeros=True, parallel=self._parallel, verbose=self._verbose) # @todo
cml.set_update_params(time_limit_in_sec=self._time_limit_in_sec, max_itrs=self._max_itrs, max_itrs_without_update=self._max_itrs_without_update, epsilon_residual=self._epsilon_residual, epsilon_ec=self._epsilon_ec)
# Run cost learner. # Run cost learner.
cml.update(dis_k_vec, self._dataset.graphs, options) cml.update(dis_k_vec, self._dataset.graphs, options)
# Get results. # Get results.
results = cml.get_results() results = cml.get_results()
self.__converged = results['converged']
self.__itrs = results['itrs']
self.__num_updates_ecs = results['num_updates_ecs']
self._converged = results['converged']
self._itrs = results['itrs']
self._num_updates_ecs = results['num_updates_ecs']
cost_list = results['cost_list'] cost_list = results['cost_list']
self.__node_label_costs = cost_list[-1][0:len(self.__node_label_costs)]
self.__edge_label_costs = cost_list[-1][len(self.__node_label_costs):]
self._node_label_costs = cost_list[-1][0:len(self._node_label_costs)]
self._edge_label_costs = cost_list[-1][len(self._node_label_costs):]


def __gmg_bcu(self):
def _gmg_bcu(self):
""" """
The local search algorithm based on block coordinate update (BCU) for estimating a generalized median graph (GMG). The local search algorithm based on block coordinate update (BCU) for estimating a generalized median graph (GMG).


@@ -343,77 +343,77 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
# Set up the ged environment. # Set up the ged environment.
ged_env = GEDEnv() # @todo: maybe create a ged_env as a private varible. ged_env = GEDEnv() # @todo: maybe create a ged_env as a private varible.
# gedlibpy.restart_env() # gedlibpy.restart_env()
ged_env.set_edit_cost(self.__ged_options['edit_cost'], edit_cost_constants=self.__edit_cost_constants)
graphs = [self.__clean_graph(g) for g in self._dataset.graphs]
ged_env.set_edit_cost(self._ged_options['edit_cost'], edit_cost_constants=self._edit_cost_constants)
graphs = [self._clean_graph(g) for g in self._dataset.graphs]
for g in graphs: for g in graphs:
ged_env.add_nx_graph(g, '') ged_env.add_nx_graph(g, '')
graph_ids = ged_env.get_all_graph_ids() graph_ids = ged_env.get_all_graph_ids()
node_labels = ged_env.get_all_node_labels() node_labels = ged_env.get_all_node_labels()
edge_labels = ged_env.get_all_edge_labels() edge_labels = ged_env.get_all_edge_labels()
node_label_costs = label_costs_to_matrix(self.__node_label_costs, len(node_labels))
edge_label_costs = label_costs_to_matrix(self.__edge_label_costs, len(edge_labels))
node_label_costs = label_costs_to_matrix(self._node_label_costs, len(node_labels))
edge_label_costs = label_costs_to_matrix(self._edge_label_costs, len(edge_labels))
ged_env.set_label_costs(node_label_costs, edge_label_costs) ged_env.set_label_costs(node_label_costs, edge_label_costs)
set_median_id = ged_env.add_graph('set_median') set_median_id = ged_env.add_graph('set_median')
gen_median_id = ged_env.add_graph('gen_median') gen_median_id = ged_env.add_graph('gen_median')
ged_env.init(init_type=self.__ged_options['init_option'])
ged_env.init(init_type=self._ged_options['init_option'])
# Set up the madian graph estimator. # Set up the madian graph estimator.
self.__mge = MedianGraphEstimatorCML(ged_env, constant_node_costs(self.__ged_options['edit_cost']))
self.__mge.set_refine_method(self.__ged_options['method'], self.__ged_options)
options = self.__mge_options.copy()
self._mge = MedianGraphEstimatorCML(ged_env, constant_node_costs(self._ged_options['edit_cost']))
self._mge.set_refine_method(self._ged_options['method'], self._ged_options)
options = self._mge_options.copy()
if not 'seed' in options: if not 'seed' in options:
options['seed'] = int(round(time.time() * 1000)) # @todo: may not work correctly for possible parallel usage. options['seed'] = int(round(time.time() * 1000)) # @todo: may not work correctly for possible parallel usage.
options['parallel'] = self.__parallel
options['parallel'] = self._parallel
# Select the GED algorithm. # Select the GED algorithm.
self.__mge.set_options(mge_options_to_string(options))
self.__mge.set_label_names(node_labels=self._dataset.node_labels,
self._mge.set_options(mge_options_to_string(options))
self._mge.set_label_names(node_labels=self._dataset.node_labels,
edge_labels=self._dataset.edge_labels, edge_labels=self._dataset.edge_labels,
node_attrs=self._dataset.node_attrs, node_attrs=self._dataset.node_attrs,
edge_attrs=self._dataset.edge_attrs) edge_attrs=self._dataset.edge_attrs)
ged_options = self.__ged_options.copy()
if self.__parallel:
ged_options = self._ged_options.copy()
if self._parallel:
ged_options['threads'] = 1 ged_options['threads'] = 1
self.__mge.set_init_method(ged_options['method'], ged_options)
self.__mge.set_descent_method(ged_options['method'], ged_options)
self._mge.set_init_method(ged_options['method'], ged_options)
self._mge.set_descent_method(ged_options['method'], ged_options)
# Run the estimator. # Run the estimator.
self.__mge.run(graph_ids, set_median_id, gen_median_id)
self._mge.run(graph_ids, set_median_id, gen_median_id)
# Get SODs. # Get SODs.
self.__sod_set_median = self.__mge.get_sum_of_distances('initialized')
self.__sod_gen_median = self.__mge.get_sum_of_distances('converged')
self._sod_set_median = self._mge.get_sum_of_distances('initialized')
self._sod_gen_median = self._mge.get_sum_of_distances('converged')
# Get median graphs. # Get median graphs.
self.__set_median = ged_env.get_nx_graph(set_median_id)
self.__gen_median = ged_env.get_nx_graph(gen_median_id)
self._set_median = ged_env.get_nx_graph(set_median_id)
self._gen_median = ged_env.get_nx_graph(gen_median_id)
def __compute_distances_to_true_median(self):
def _compute_distances_to_true_median(self):
# compute distance in kernel space for set median. # compute distance in kernel space for set median.
kernels_to_sm, _ = self._graph_kernel.compute(self.__set_median, self._dataset.graphs, **self._kernel_options)
kernel_sm, _ = self._graph_kernel.compute(self.__set_median, self.__set_median, **self._kernel_options)
kernels_to_sm, _ = self._graph_kernel.compute(self._set_median, self._dataset.graphs, **self._kernel_options)
kernel_sm, _ = self._graph_kernel.compute(self._set_median, self._set_median, **self._kernel_options)
if self._kernel_options['normalize']: if self._kernel_options['normalize']:
kernels_to_sm = [kernels_to_sm[i] / np.sqrt(self.__gram_matrix_unnorm[i, i] * kernel_sm) for i in range(len(kernels_to_sm))] # normalize
kernels_to_sm = [kernels_to_sm[i] / np.sqrt(self._gram_matrix_unnorm[i, i] * kernel_sm) for i in range(len(kernels_to_sm))] # normalize
kernel_sm = 1 kernel_sm = 1
# @todo: not correct kernel value # @todo: not correct kernel value
gram_with_sm = np.concatenate((np.array([kernels_to_sm]), np.copy(self._graph_kernel.gram_matrix)), axis=0) gram_with_sm = np.concatenate((np.array([kernels_to_sm]), np.copy(self._graph_kernel.gram_matrix)), axis=0)
gram_with_sm = np.concatenate((np.array([[kernel_sm] + kernels_to_sm]).T, gram_with_sm), axis=1) gram_with_sm = np.concatenate((np.array([[kernel_sm] + kernels_to_sm]).T, gram_with_sm), axis=1)
self.__k_dis_set_median = compute_k_dis(0, range(1, 1+len(self._dataset.graphs)),
self._k_dis_set_median = compute_k_dis(0, range(1, 1+len(self._dataset.graphs)),
[1 / len(self._dataset.graphs)] * len(self._dataset.graphs), [1 / len(self._dataset.graphs)] * len(self._dataset.graphs),
gram_with_sm, withterm3=False) gram_with_sm, withterm3=False)
# compute distance in kernel space for generalized median. # compute distance in kernel space for generalized median.
kernels_to_gm, _ = self._graph_kernel.compute(self.__gen_median, self._dataset.graphs, **self._kernel_options)
kernel_gm, _ = self._graph_kernel.compute(self.__gen_median, self.__gen_median, **self._kernel_options)
kernels_to_gm, _ = self._graph_kernel.compute(self._gen_median, self._dataset.graphs, **self._kernel_options)
kernel_gm, _ = self._graph_kernel.compute(self._gen_median, self._gen_median, **self._kernel_options)
if self._kernel_options['normalize']: if self._kernel_options['normalize']:
kernels_to_gm = [kernels_to_gm[i] / np.sqrt(self.__gram_matrix_unnorm[i, i] * kernel_gm) for i in range(len(kernels_to_gm))] # normalize
kernels_to_gm = [kernels_to_gm[i] / np.sqrt(self._gram_matrix_unnorm[i, i] * kernel_gm) for i in range(len(kernels_to_gm))] # normalize
kernel_gm = 1 kernel_gm = 1
gram_with_gm = np.concatenate((np.array([kernels_to_gm]), np.copy(self._graph_kernel.gram_matrix)), axis=0) gram_with_gm = np.concatenate((np.array([kernels_to_gm]), np.copy(self._graph_kernel.gram_matrix)), axis=0)
gram_with_gm = np.concatenate((np.array([[kernel_gm] + kernels_to_gm]).T, gram_with_gm), axis=1) gram_with_gm = np.concatenate((np.array([[kernel_gm] + kernels_to_gm]).T, gram_with_gm), axis=1)
self.__k_dis_gen_median = compute_k_dis(0, range(1, 1+len(self._dataset.graphs)),
self._k_dis_gen_median = compute_k_dis(0, range(1, 1+len(self._dataset.graphs)),
[1 / len(self._dataset.graphs)] * len(self._dataset.graphs), [1 / len(self._dataset.graphs)] * len(self._dataset.graphs),
gram_with_gm, withterm3=False) gram_with_gm, withterm3=False)
@@ -424,19 +424,19 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
[1 / len(self._dataset.graphs)] * len(self._dataset.graphs), [1 / len(self._dataset.graphs)] * len(self._dataset.graphs),
gram_with_gm, withterm3=False)) gram_with_gm, withterm3=False))
idx_k_dis_median_set_min = np.argmin(k_dis_median_set) idx_k_dis_median_set_min = np.argmin(k_dis_median_set)
self.__k_dis_dataset = k_dis_median_set[idx_k_dis_median_set_min]
self.__best_from_dataset = self._dataset.graphs[idx_k_dis_median_set_min].copy()
self._k_dis_dataset = k_dis_median_set[idx_k_dis_median_set_min]
self._best_from_dataset = self._dataset.graphs[idx_k_dis_median_set_min].copy()
if self._verbose >= 2: if self._verbose >= 2:
print() print()
print('distance in kernel space for set median:', self.__k_dis_set_median)
print('distance in kernel space for generalized median:', self.__k_dis_gen_median)
print('minimum distance in kernel space for each graph in median set:', self.__k_dis_dataset)
print('distance in kernel space for set median:', self._k_dis_set_median)
print('distance in kernel space for generalized median:', self._k_dis_gen_median)
print('minimum distance in kernel space for each graph in median set:', self._k_dis_dataset)
print('distance in kernel space for each graph in median set:', k_dis_median_set) print('distance in kernel space for each graph in median set:', k_dis_median_set)
# def __clean_graph(self, G, node_labels=[], edge_labels=[], node_attrs=[], edge_attrs=[]):
def __clean_graph(self, G): # @todo: this may not be needed when datafile is updated.
# def _clean_graph(self, G, node_labels=[], edge_labels=[], node_attrs=[], edge_attrs=[]):
def _clean_graph(self, G): # @todo: this may not be needed when datafile is updated.
""" """
Cleans node and edge labels and attributes of the given graph. Cleans node and edge labels and attributes of the given graph.
""" """
@@ -458,63 +458,63 @@ class MedianPreimageGeneratorCML(PreimageGenerator):
@property @property
def mge(self): def mge(self):
return self.__mge
return self._mge
@property @property
def ged_options(self): def ged_options(self):
return self.__ged_options
return self._ged_options


@ged_options.setter @ged_options.setter
def ged_options(self, value): def ged_options(self, value):
self.__ged_options = value
self._ged_options = value


@property @property
def mge_options(self): def mge_options(self):
return self.__mge_options
return self._mge_options


@mge_options.setter @mge_options.setter
def mge_options(self, value): def mge_options(self, value):
self.__mge_options = value
self._mge_options = value




@property @property
def fit_method(self): def fit_method(self):
return self.__fit_method
return self._fit_method


@fit_method.setter @fit_method.setter
def fit_method(self, value): def fit_method(self, value):
self.__fit_method = value
self._fit_method = value
@property @property
def init_ecc(self): def init_ecc(self):
return self.__init_ecc
return self._init_ecc


@init_ecc.setter @init_ecc.setter
def init_ecc(self, value): def init_ecc(self, value):
self.__init_ecc = value
self._init_ecc = value
@property @property
def set_median(self): def set_median(self):
return self.__set_median
return self._set_median




@property @property
def gen_median(self): def gen_median(self):
return self.__gen_median
return self._gen_median
@property @property
def best_from_dataset(self): def best_from_dataset(self):
return self.__best_from_dataset
return self._best_from_dataset
@property @property
def gram_matrix_unnorm(self): def gram_matrix_unnorm(self):
return self.__gram_matrix_unnorm
return self._gram_matrix_unnorm
@gram_matrix_unnorm.setter @gram_matrix_unnorm.setter
def gram_matrix_unnorm(self, value): def gram_matrix_unnorm(self, value):
self.__gram_matrix_unnorm = value
self._gram_matrix_unnorm = value

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