def __init__(self, gpu=False, device=0):
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, gpu, device), {"m3"}), # Any
"page_rank":
FeatureMeta(PageRankCalculator,
{"pr"}), # Directed (but works for any)
"motif4":
FeatureMeta(nth_nodes_motif(4, gpu, device), {"m4"}), # Any
}
self.MOTIFS = {
"motif3": FeatureMeta(nth_nodes_motif(3, gpu, device), {"m3"}),
"motif4": FeatureMeta(nth_nodes_motif(4, gpu, device), {"m4"})
}
"""
def __init__(self, params, graph, dir_path, gpu, device):
self._params = params
self._graph = graph
self._dir_path = dir_path
self._mp = MotifProbability(self._params["vertices"],
self._params["probability"],
self._params["clique_size"],
self._params["directed"])
self._motif_mat = None
self._motif_features = {
"motif3":
FeatureMeta(nth_nodes_motif(3, gpu=gpu, device=device), {"m3"}),
"motif4":
FeatureMeta(nth_nodes_motif(4, gpu=gpu, device=device), {"m4"})
}
def __init__(self, gpu=False):
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, gpu), {"m3"}),
"page_rank":
FeatureMeta(PageRankCalculator, {"pr"}),
"motif4":
FeatureMeta(nth_nodes_motif(4, gpu), {"m4"}),
}
self.MOTIFS = {
"motif3": FeatureMeta(nth_nodes_motif(3, gpu), {"m3"}),
"motif4": FeatureMeta(nth_nodes_motif(4, gpu), {"m4"})
}
def _calc_motif3(self):
raw_ftr = GraphFeatures(self._graph, {
"motif3":
FeatureMeta(nth_nodes_motif(3, gpu=self._gpu, device=self._device),
{"m3"})
},
dir_path=self._dir_path)
raw_ftr.build(should_dump=self._dump)
feature = raw_ftr['motif3']._features
if type(feature) == dict:
motif_matrix = self._to_matrix(feature)
else:
motif_matrix = feature
return self._log_norm(motif_matrix)
def _calc_motif4(self):
# FOR NOW, NO GPU FOR US
if os.path.exists(os.path.join(self._dir_path, "motif4.pkl")):
pkl4 = pickle.load(
open(os.path.join(self._dir_path, "motif4.pkl"), "rb"))
if type(pkl4) == dict:
motif4 = self._to_matrix(pkl4)
elif type(pkl4) == MotifsNodeCalculator:
motif4 = np.array(pkl4._features)
else:
motif4 = np.array(pkl4)
if self._motif_choice == "All_Motifs":
mp = MotifProbability(self._params['vertices'],
self._params['probability'],
self._params['clique_size'],
self._params['directed'])
motif3_count = 1 + mp.get_3_clique_motifs(3)[
-1] # The full 3 clique is the last motif 3.
clique_motifs = [
m - motif3_count for m in mp.get_3_clique_motifs(4)
]
return motif4[:, clique_motifs]
else:
return motif4
raw_ftr = GraphFeatures(self._graph, {
"motif4":
FeatureMeta(nth_nodes_motif(4, gpu=self._gpu, device=self._device),
{"m4"})
},
dir_path=self._dir_path)
raw_ftr.build(should_dump=True)
feature = raw_ftr['motif4']._features
if type(feature) == dict:
motif_matrix = self._to_matrix(feature)
else:
motif_matrix = feature
normed_matrix = self._log_norm(motif_matrix)
if self._motif_choice == "All_Motifs":
mp = MotifProbability(self._params['vertices'],
self._params['probability'],
self._params['clique_size'],
self._params['directed'])
motif3_count = 1 + mp.get_3_clique_motifs(3)[
-1] # The full 3 clique is the last motif 3.
clique_motifs = [
m - motif3_count for m in mp.get_3_clique_motifs(4)
]
return normed_matrix[:, clique_motifs]
else:
return normed_matrix
def _calc_motif4(self):
raw_ftr = GraphFeatures(self._graph, {
"motif4":
FeatureMeta(nth_nodes_motif(4, gpu=self._gpu, device=self._device),
{"m4"})
},
dir_path="")
raw_ftr.build(should_dump=False)
feature = raw_ftr['motif4']._features
if type(feature) == dict:
motif_matrix = self._to_matrix(feature)
else:
motif_matrix = feature
normed_matrix = self._log_norm(motif_matrix)
return normed_matrix
def _calc_motif3(self):
raw_ftr = GraphFeatures(self._graph,
{"motif3": FeatureMeta(nth_nodes_motif(3, gpu=self._gpu, device=self._device), {"m3"})},
dir_path=self._dir_path)
raw_ftr.build(should_dump=True)
feature = raw_ftr['motif3']._features
if type(feature) == dict:
motif_matrix = self._to_matrix(feature)
else:
motif_matrix = feature
normed_matrix = self._log_norm(motif_matrix)
if self._motif_choice == "All_Motifs":
mp = MotifProbability(self._params['vertices'], self._params['probability'],
self._params['subgraph_size'], self._params['directed'])
clique_motifs = mp.get_3_clique_motifs(3)
return normed_matrix[:, clique_motifs]
else:
return normed_matrix
def _calc_motif4(self):
raw_ftr = GraphFeatures(self._graph,
{"motif4": FeatureMeta(nth_nodes_motif(4, gpu=self._gpu, device=self._device), {"m4"})},
dir_path=self._dir_path)
raw_ftr.build(should_dump=True)
feature = raw_ftr['motif4']._features
if type(feature) == dict:
motif_matrix = self._to_matrix(feature)
else:
motif_matrix = feature
normed_matrix = self._log_norm(motif_matrix)
if self._motif_choice == "All_Motifs":
mp = MotifProbability(self._params['vertices'], self._params['probability'],
self._params['subgraph_size'], self._params['directed'])
motif3_count = 1 + mp.get_3_clique_motifs(3)[-1] # The full 3 clique is the last motif 3.
clique_motifs = [m - motif3_count for m in mp.get_3_clique_motifs(4)]
return normed_matrix[:, clique_motifs]
else:
return normed_matrix
def _calc_motif3(self):
# FOR NOW, NO GPU FOR US
if os.path.exists(os.path.join(self._dir_path, "motif3.pkl")):
pkl3 = pickle.load(
open(os.path.join(self._dir_path, "motif3.pkl"), "rb"))
if type(pkl3) == dict:
motif3 = self._to_matrix(pkl3)
elif type(pkl3) == MotifsNodeCalculator:
motif3 = np.array(pkl3._features)
else:
motif3 = np.array(pkl3)
if self._motif_choice == "All_Motifs":
mp = MotifProbability(self._params['vertices'],
self._params['probability'],
self._params['clique_size'],
self._params['directed'])
clique_motifs = mp.get_3_clique_motifs(3)
return motif3[:, clique_motifs]
else:
return motif3
raw_ftr = GraphFeatures(self._graph, {
"motif3":
FeatureMeta(nth_nodes_motif(3, gpu=self._gpu, device=self._device),
{"m3"})
},
dir_path=self._dir_path)
raw_ftr.build(should_dump=True)
feature = raw_ftr['motif3']._features
if type(feature) == dict:
motif_matrix = self._to_matrix(feature)
else:
motif_matrix = feature
normed_matrix = self._log_norm(motif_matrix)
if self._motif_choice == "All_Motifs":
mp = MotifProbability(self._params['vertices'],
self._params['probability'],
self._params['clique_size'],
self._params['directed'])
clique_motifs = mp.get_3_clique_motifs(3)
return normed_matrix[:, clique_motifs]
else:
return normed_matrix