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@@ -39,15 +39,15 @@ def marginalizedkernel(*args, |
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n_jobs=None, |
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chunksize=None, |
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verbose=True): |
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"""Calculate marginalized graph kernels between graphs. |
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"""Compute marginalized graph kernels between graphs. |
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Parameters |
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---------- |
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Gn : List of NetworkX graph |
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List of graphs between which the kernels are calculated. |
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List of graphs between which the kernels are computed. |
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G1, G2 : NetworkX graphs |
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Two graphs between which the kernel is calculated. |
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Two graphs between which the kernel is computed. |
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node_label : string |
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Node attribute used as symbolic label. The default node label is 'atom'. |
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@@ -59,7 +59,7 @@ def marginalizedkernel(*args, |
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The termination probability in the random walks generating step. |
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n_iteration : integer |
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Time of iterations to calculate R_inf. |
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Time of iterations to compute R_inf. |
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remove_totters : boolean |
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Whether to remove totterings by method introduced in [2]. The default |
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@@ -83,11 +83,11 @@ def marginalizedkernel(*args, |
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Gn, |
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attr_names=['node_labeled', 'edge_labeled', 'is_directed'], |
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node_label=node_label, edge_label=edge_label) |
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if not ds_attrs['node_labeled'] or node_label == None: |
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if not ds_attrs['node_labeled'] or node_label is None: |
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node_label = 'atom' |
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for G in Gn: |
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nx.set_node_attributes(G, '0', 'atom') |
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if not ds_attrs['edge_labeled'] or edge_label == None: |
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if not ds_attrs['edge_labeled'] or edge_label is None: |
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edge_label = 'bond_type' |
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for G in Gn: |
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nx.set_edge_attributes(G, '0', 'bond_type') |
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@@ -133,7 +133,7 @@ def marginalizedkernel(*args, |
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# # ---- direct running, normally use single CPU core. ---- |
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## pbar = tqdm( |
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## total=(1 + len(Gn)) * len(Gn) / 2, |
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## desc='calculating kernels', |
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## desc='Computing kernels', |
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## file=sys.stdout) |
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# for i in range(0, len(Gn)): |
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# for j in range(i, len(Gn)): |
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@@ -152,12 +152,12 @@ def marginalizedkernel(*args, |
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def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration): |
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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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node_label : string |
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node attribute used as label. |
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edge_label : string |
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@@ -165,7 +165,7 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration): |
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p_quit : integer |
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the termination probability in the random walks generating step. |
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n_iteration : integer |
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time of iterations to calculate R_inf. |
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time of iterations to compute R_inf. |
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Return |
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------ |
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@@ -188,12 +188,12 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration): |
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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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@@ -219,7 +219,7 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration): |
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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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@@ -267,11 +267,11 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration): |
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neighbor_n1[neighbor1][edge_label], |
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neighbor_n2[neighbor2][edge_label]) |
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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, 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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@@ -288,7 +288,7 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration): |
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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( |
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g1.nodes[n1][node_label], g2.nodes[n2][node_label]) |
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