def __init__(self):
self.NODE_LEVEL = {
"attractor_basin":
FeatureMeta(AttractorBasinCalculator, {"ab"}),
"average_neighbor_degree":
FeatureMeta(AverageNeighborDegreeCalculator, {"avg_nd"}),
"betweenness_centrality":
FeatureMeta(BetweennessCentralityCalculator, {"betweenness"}),
"bfs_moments":
FeatureMeta(BfsMomentsCalculator, {"bfs"}),
"closeness_centrality":
FeatureMeta(ClosenessCentralityCalculator, {"closeness"}),
"communicability_betweenness_centrality":
FeatureMeta(CommunicabilityBetweennessCentralityCalculator,
{"communicability"}),
"eccentricity":
FeatureMeta(EccentricityCalculator, {"ecc"}),
"fiedler_vector":
FeatureMeta(FiedlerVectorCalculator, {"fv"}),
"flow":
FeatureMeta(FlowCalculator, {}),
"general":
FeatureMeta(GeneralCalculator, {"gen"}),
"hierarchy_energy":
FeatureMeta(HierarchyEnergyCalculator, {"hierarchy"}),
"k_core":
FeatureMeta(KCoreCalculator, {"kc"}),
"load_centrality":
FeatureMeta(LoadCentralityCalculator, {"load_c"}),
"louvain":
FeatureMeta(LouvainCalculator, {"lov"}),
"motif3":
FeatureMeta(nth_nodes_motif(3), {"m3"}),
"page_rank":
FeatureMeta(PageRankCalculator, {"pr"}),
"motif4":
FeatureMeta(nth_nodes_motif(4), {"m4"}),
}
self.MOTIFS = {
"motif3": FeatureMeta(nth_nodes_motif(3), {"m3"}),
"motif4": FeatureMeta(nth_nodes_motif(4), {"m4"})
}
help='The dataset to use.')
parser.add_argument('--prefix',
type=str,
default="",
help='The prefix of the products dir name.')
args = parser.parse_args()
# args.cuda = not args.no_cuda and torch.cuda.is_available()
if not torch.cuda.is_available():
args.cuda = None
return args
NEIGHBOR_FEATURES = {
"first_neighbor_histogram":
FeatureMeta(nth_neighbor_calculator(1), {"fnh", "first_neighbor"}),
"second_neighbor_histogram":
FeatureMeta(nth_neighbor_calculator(2), {"snh", "second_neighbor"}),
}
def accuracy(output, labels):
preds = output.max(1)[1].type_as(labels)
correct = preds.eq(labels).double()
correct = correct.sum()
return correct / len(labels)
def get_features():
# if config["feat_type"] == "neighbors":
# feature_meta = NEIGHBOR_FEATURES
import networkx as nx
from features_infra.feature_calculators import NodeFeatureCalculator, FeatureMeta
class BetweennessCentralityCalculator(NodeFeatureCalculator):
def __init__(self, *args, normalized=False, **kwargs):
super(BetweennessCentralityCalculator, self).__init__(*args, **kwargs)
self._is_normalized = normalized
def _calculate(self, include: set):
self._features = nx.betweenness_centrality(
self._gnx, normalized=self._is_normalized)
def is_relevant(self):
return True
feature_entry = {
"betweenness_centrality":
FeatureMeta(BetweennessCentralityCalculator, {"betweenness"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(BetweennessCentralityCalculator,
is_max_connected=True)
}
max_b_u = float(max(b_u.values()))
for node in self._gnx:
# the delta determines whether this node is to be considered
if (b_u[node] / max_b_u) <= self._threshold:
self._features[node] = 0
continue
udists = undirected_dists[node]
dists = directed_dists[node]
# getting coordinated values from two dictionaries with the same keys
# saving the data as np.array type
num, denom = map(np.array,
zip(*((udists[n], dists[n]) for n in dists)))
num = num[denom != 0]
denom = denom[denom != 0]
self._features[node] = np.sum(num / denom) / float(b_u[node])
feature_entry = {
"flow": FeatureMeta(FlowCalculator, {}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(FlowCalculator, is_max_connected=True)
import networkx as nx
from features_infra.feature_calculators import NodeFeatureCalculator, FeatureMeta
class CommunicabilityBetweennessCentralityCalculator(NodeFeatureCalculator):
def _calculate(self, include: set):
self._features = nx.communicability_betweenness_centrality(self._gnx)
def is_relevant(self):
return not self._gnx.is_directed()
feature_entry = {
"communicability_betweenness_centrality":
FeatureMeta(CommunicabilityBetweennessCentralityCalculator,
{"communicability"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(CommunicabilityBetweennessCentralityCalculator,
is_max_connected=True)
def _calculate(self, include: set):
for node in self._gnx:
# calculate BFS distances
distances = nx.single_source_shortest_path_length(self._gnx, node)
# distances.pop(node)
# if not distances:
# self._features[node] = [0., 0.]
# continue
node_dist = Counter(distances.values())
dists, weights = zip(*node_dist.items())
# This was in the previous version
# instead of the above commented fix
adjusted_dists = np.asarray([x + 1 for x in dists])
weights = np.asarray(weights)
self._features[node] = [
self.weighted_avg_and_std(adjusted_dists, weights)
]
def _get_feature(self, element):
return list(self._features[element])
feature_entry = {
"bfs_moments": FeatureMeta(BfsMomentsCalculator, {"bfs"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(BfsMomentsCalculator, is_max_connected=True)
def _calculate_dep(self, include: set):
# Working on every connected component by itself
self._features = dict(
zip(self._gnx, alg_connectivity.fiedler_vector(self._gnx)))
def _calculate(self, include: set):
self._features = {}
for graph in nx.connected_component_subgraphs(self._gnx):
if len(graph) < 2:
self._features.update(zip(graph.nodes(), [0.] * len(graph)))
else:
self._features.update(
zip(graph.nodes(),
map(float, alg_connectivity.fiedler_vector(graph))))
def is_relevant(self):
# Fiedler vector also works only on connected undirected graphs
# so if gnx is not connected we shall expect an exception: networkx.exception.NetworkXError
# return (not self._gnx.is_directed()) and (nx.is_connected(self._gnx.to_undirected()))
return not self._gnx.is_directed()
feature_entry = {
"fiedler_vector": FeatureMeta(FiedlerVector, {"fv"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(FiedlerVector, is_max_connected=True)
from features_algorithms.vertices.eccentricity import EccentricityCalculator
from features_algorithms.vertices.fiedler_vector import FiedlerVector
from features_algorithms.vertices.flow import FlowCalculator
from features_algorithms.vertices.general import GeneralCalculator
from features_algorithms.vertices.hierarchy_energy import HierarchyEnergyCalculator
from features_algorithms.vertices.k_core import KCoreCalculator
from features_algorithms.vertices.load_centrality import LoadCentralityCalculator
from features_algorithms.vertices.louvain import LouvainCalculator
# from features_algorithms.vertices.neighbor_nodes_histogram import nth_neighbor_calculator
from features_algorithms.vertices.motifs import nth_nodes_motif
from features_algorithms.vertices.page_rank import PageRankCalculator
from features_infra.feature_calculators import FeatureMeta, FeatureCalculator
NODE_FEATURES = {
"attractor_basin":
FeatureMeta(AttractorBasinCalculator, {"ab"}),
"average_neighbor_degree":
FeatureMeta(AverageNeighborDegreeCalculator, {"avg_nd"}),
"betweenness_centrality":
FeatureMeta(BetweennessCentralityCalculator, {"betweenness"}),
"bfs_moments":
FeatureMeta(BfsMomentsCalculator, {"bfs"}),
"closeness_centrality":
FeatureMeta(ClosenessCentralityCalculator, {"closeness"}),
"communicability_betweenness_centrality":
FeatureMeta(CommunicabilityBetweennessCentralityCalculator,
{"communicability"}),
"eccentricity":
FeatureMeta(EccentricityCalculator, {"ecc"}),
"fiedler_vector":
FeatureMeta(FiedlerVector, {"fv"}),
import sys
sys.path.append(os.path.abspath('.'))
sys.path.append(os.path.abspath('..'))
sys.path.append(os.path.abspath('../..'))
sys.path.append(os.path.abspath('../../..'))
sys.path.append(os.path.abspath('src'))
sys.path.append(os.path.abspath('src/accelerated_graph_features'))
from features_infra.feature_calculators import NodeFeatureCalculator, FeatureMeta
from features_algorithms.accelerated_graph_features.src import node_page_rank
class PageRankCalculator(NodeFeatureCalculator):
def __init__(self, *args, alpha=0.9, **kwargs):
super(PageRankCalculator, self).__init__(*args, **kwargs)
self._alpha = alpha
def is_relevant(self):
# Undirected graphs will be converted to a directed
# graph with two directed edges for each undirected edge.
return True
def _calculate(self, include: set):
self._features = node_page_rank(self._gnx, dumping=self._alpha)
feature_entry = {
"page_rank": FeatureMeta(PageRankCalculator, {"pr"}),
}
from features_infra.feature_calculators import NodeFeatureCalculator, FeatureMeta
class GeneralCalculator(NodeFeatureCalculator):
def is_relevant(self):
return True
def _calculate(self, include: set):
if self._gnx.is_directed():
self._features = {
node: (in_deg, out_deg)
for (node, out_deg), (_, in_deg) in zip(
self._gnx.out_degree(), self._gnx.in_degree())
}
else:
self._features = {node: deg for node, deg in self._gnx.degree()}
feature_entry = {
"general": FeatureMeta(GeneralCalculator, {"gen"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(GeneralCalculator, is_max_connected=True)
import os
import sys
sys.path.append(os.path.abspath('.'))
sys.path.append(os.path.abspath('..'))
sys.path.append(os.path.abspath('../..'))
sys.path.append(os.path.abspath('../../..'))
sys.path.append(os.path.abspath('src'))
sys.path.append(os.path.abspath('src/accelerated_graph_features'))
from features_infra.feature_calculators import NodeFeatureCalculator, FeatureMeta
from features_algorithms.accelerated_graph_features.src import k_core
class KCoreCalculator(NodeFeatureCalculator):
def is_relevant(self):
return True
def _calculate(self, include: set):
self._features = k_core(self._gnx)
feature_entry = {
"k_core": FeatureMeta(KCoreCalculator, {"kc"}),
}
self._level = level
self._gpu = gpu
self._device = device
self._print_name += "_%d" % (self._level,)
def is_relevant(self):
return True
@classmethod
def print_name(cls, level=None):
print_name = super(MotifsNodeCalculator, cls).print_name()
if level is None:
return print_name
return "%s_%d_C_kernel" % (print_name, level)
def _calculate(self, include=None):
self._features = motif(self._gnx, level=self._level, gpu=self._gpu, cudaDevice=self._device)
def _get_feature(self, element):
return np.array(self._features[element])
def nth_nodes_motif(motif_level, gpu, device):
return partial(MotifsNodeCalculator, level=motif_level, gpu=gpu, device=device)
feature_node_entry = {
"motif3_c": FeatureMeta(nth_nodes_motif(3, gpu=False, device=2), {"m3_c"}),
"motif4_c": FeatureMeta(nth_nodes_motif(4, gpu=False, device=2), {"m4_c"}),
}
import networkx as nx
from features_infra.feature_calculators import NodeFeatureCalculator, FeatureMeta
class LoadCentralityCalculator(NodeFeatureCalculator):
def is_relevant(self):
return True
def _calculate(self, include: set):
self._features = nx.load_centrality(self._gnx)
feature_entry = {
"load_centrality": FeatureMeta(LoadCentralityCalculator, {"load_c"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(LoadCentralityCalculator, is_max_connected=True)
def __init__(self):
self.NODE_LEVEL = {
"attractor_basin":
FeatureMeta(AttractorBasinCalculator, {"ab"}), # Directed
"average_neighbor_degree":
FeatureMeta(AverageNeighborDegreeCalculator, {"avg_nd"}), # Any
"betweenness_centrality":
FeatureMeta(BetweennessCentralityCalculator,
{"betweenness"}), # Any
"bfs_moments":
FeatureMeta(BfsMomentsCalculator, {"bfs"}), # Any
"closeness_centrality":
FeatureMeta(ClosenessCentralityCalculator, {"closeness"}), # Any
"communicability_betweenness_centrality":
FeatureMeta(CommunicabilityBetweennessCentralityCalculator,
{"communicability"}), # Undirected
"eccentricity":
FeatureMeta(EccentricityCalculator, {"ecc"}), # Any
"fiedler_vector":
FeatureMeta(FiedlerVectorCalculator,
{"fv"}), # Undirected (due to a code limitation)
"flow":
FeatureMeta(FlowCalculator, {}), # Directed
# General - calculating degrees. Directed will get (in_deg, out_deg) and undirected will get degree only per vertex.
"general":
FeatureMeta(GeneralCalculator, {"gen"}), # Any
"hierarchy_energy":
FeatureMeta(HierarchyEnergyCalculator,
{"hierarchy"}), # Directed (but works for any)
"k_core":
FeatureMeta(KCoreCalculator, {"kc"}), # Any
"load_centrality":
FeatureMeta(LoadCentralityCalculator, {"load_c"}), # Any
"louvain":
FeatureMeta(LouvainCalculator, {"lov"}), # Undirected
"motif3":
FeatureMeta(nth_nodes_motif(3), {"m3"}), # Any
"page_rank":
FeatureMeta(PageRankCalculator,
{"pr"}), # Directed (but works for any)
"motif4":
FeatureMeta(nth_nodes_motif(4), {"m4"}), # Any
# new
"eigenvector_centrality":
FeatureMeta(EigenvectorCentralityCalculator, {"eigenvector"}),
"clustering_coefficient":
FeatureMeta(ClusteringCoefficientCalculator, {"clustering"}),
"square_clustering_coefficient":
FeatureMeta(SquareClusteringCoefficientCalculator,
{"square_clustering"}),
"generalized_degree":
FeatureMeta(GeneralizedDegreeCalculator, {"generalized_degree"}),
"all_pairs_shortest_path_length":
FeatureMeta(AllPairsShortestPathLengthCalculator,
{"all_pairs_shortest_path_length"}),
"all_pairs_shortest_path":
FeatureMeta(AllPairsShortestPathCalculator,
{"all_pairs_shortest_path"}),
}
self.MOTIFS = {
"motif3": FeatureMeta(nth_nodes_motif(3), {"m3"}),
"motif4": FeatureMeta(nth_nodes_motif(4), {"m4"})
}
import networkx as nx
from features_infra.feature_calculators import EdgeFeatureCalculator, FeatureMeta
class EdgeCurrentFlowCalculator(EdgeFeatureCalculator):
def _calculate(self, include: set):
self._features = nx.edge_current_flow_betweenness_centrality(self._gnx)
def is_relevant(self):
return True
feature_entry = {
"edge_current_flow": FeatureMeta(EdgeCurrentFlowCalculator, {"e_flow"}),
}
if __name__ == 'main':
pass
for node in self._gnx:
out_dist = ab_out_dist.get(node, {})
in_dist = ab_in_dist.get(node, {})
self._features[node] = self._default_val
denominator = sum((dist / avg_out[m]) * (self._alpha ** (-m)) for m, dist in out_dist.items())
if 0 != denominator:
numerator = sum((dist / avg_in[m]) * (self._alpha ** (-m)) for m, dist in in_dist.items())
self._features[node] = numerator / denominator
@staticmethod
def _calculate_average_per_dist(num_nodes, count_dist):
# rearrange the details in "count_dist" to be with unique distance in the array "all_dist_count"
all_dist_count = {}
for counter in count_dist.values():
for dist, occurrences in counter.items():
all_dist_count[dist] = all_dist_count.get(dist, 0) + occurrences
# calculating for each distance the average
return {dist: float(count) / num_nodes for dist, count in all_dist_count.items()}
feature_entry = {
"attractor_basin": FeatureMeta(AttractorBasinCalculator, {"ab"}),
}
if __name__ == "__main__":
from measure_tests.specific_feature_test import test_specific_feature
test_specific_feature(AttractorBasinCalculator, is_max_connected=True)