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@@ -59,7 +59,7 @@ class Marginalized(GraphKernel): |
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from itertools import combinations_with_replacement |
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itr = combinations_with_replacement(range(0, len(self._graphs)), 2) |
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if self._verbose >= 2: |
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iterator = tqdm(itr, desc='calculating kernels', file=sys.stdout) |
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iterator = tqdm(itr, desc='Computing kernels', file=sys.stdout) |
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else: |
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iterator = itr |
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for i, j in iterator: |
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@@ -119,7 +119,7 @@ class Marginalized(GraphKernel): |
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# compute kernel list. |
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kernel_list = [None] * len(g_list) |
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if self._verbose >= 2: |
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iterator = tqdm(range(len(g_list)), desc='calculating kernels', file=sys.stdout) |
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iterator = tqdm(range(len(g_list)), desc='Computing kernels', file=sys.stdout) |
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else: |
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iterator = range(len(g_list)) |
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for i in iterator: |
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@@ -165,7 +165,7 @@ class Marginalized(GraphKernel): |
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len_itr = len(g_list) |
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parallel_me(do_fun, func_assign, kernel_list, itr, len_itr=len_itr, |
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init_worker=init_worker, glbv=(g1, g_list), method='imap_unordered', |
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n_jobs=self._n_jobs, itr_desc='calculating kernels', verbose=self._verbose) |
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n_jobs=self._n_jobs, itr_desc='Computing kernels', verbose=self._verbose) |
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return kernel_list |
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@@ -184,12 +184,12 @@ class Marginalized(GraphKernel): |
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def __kernel_do(self, g1, g2): |
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"""Calculate marginalized graph kernel between 2 graphs. |
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"""Compute marginalized graph kernel between 2 graphs. |
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Parameters |
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---------- |
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g1, g2 : NetworkX graphs |
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2 graphs between which the kernel is calculated. |
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2 graphs between which the kernel is computed. |
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Return |
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------ |
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@@ -212,12 +212,12 @@ class Marginalized(GraphKernel): |
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# # matrix to save all the R_inf for all pairs of nodes |
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# R_inf = np.zeros([num_nodes_G1, num_nodes_G2]) |
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# |
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# # calculate R_inf with a simple interative method |
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# # Compute R_inf with a simple interative method |
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# for i in range(1, n_iteration): |
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# R_inf_new = np.zeros([num_nodes_G1, num_nodes_G2]) |
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# R_inf_new.fill(r1) |
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# |
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# # calculate R_inf for each pair of nodes |
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# # Compute R_inf for each pair of nodes |
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# for node1 in g1.nodes(data=True): |
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# neighbor_n1 = g1[node1[0]] |
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# # the transition probability distribution in the random walks |
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@@ -243,7 +243,7 @@ class Marginalized(GraphKernel): |
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# neighbor2] # ref [1] equation (8) |
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# R_inf[:] = R_inf_new |
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# |
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# # add elements of R_inf up and calculate kernel |
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# # add elements of R_inf up and compute kernel |
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# for node1 in g1.nodes(data=True): |
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# for node2 in g2.nodes(data=True): |
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# s = p_init_G1 * p_init_G2 * deltakernel( |
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@@ -288,11 +288,11 @@ class Marginalized(GraphKernel): |
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deltakernel(tuple(g1.nodes[neighbor1][nl] for nl in self.__node_labels), tuple(g2.nodes[neighbor2][nl] for nl in self.__node_labels)) * \ |
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deltakernel(tuple(neighbor_n1[neighbor1][el] for el in self.__edge_labels), tuple(neighbor_n2[neighbor2][el] for el in self.__edge_labels)) |
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# calculate R_inf with a simple interative method |
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# Compute R_inf with a simple interative method |
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for i in range(2, self.__n_iteration + 1): |
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R_inf_old = R_inf.copy() |
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# calculate R_inf for each pair of nodes |
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# Compute R_inf for each pair of nodes |
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for node1 in g1.nodes(): |
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neighbor_n1 = g1[node1] |
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# the transition probability distribution in the random walks |
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@@ -309,7 +309,7 @@ class Marginalized(GraphKernel): |
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(t_dict[(node1, node2, neighbor1, neighbor2)] * \ |
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R_inf_old[(neighbor1, neighbor2)]) # ref [1] equation (8) |
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# add elements of R_inf up and calculate kernel |
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# add elements of R_inf up and compute kernel. |
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for (n1, n2), value in R_inf.items(): |
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s = p_init_G1 * p_init_G2 * deltakernel(tuple(g1.nodes[n1][nl] for nl in self.__node_labels), tuple(g2.nodes[n2][nl] for nl in self.__node_labels)) |
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kernel += s * value # ref [1] equation (6) |
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