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Update the RPG experiment.

tags/v0.2.0
jajupmochi 5 years ago
parent
e66846f2a8
commit
924f028c0c
1 changed files with 163 additions and 28 deletions
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  1. +163
    -28
      gklearn/preimage/experiments/xp_random_preimage_generation.py

+ 163
- 28
gklearn/preimage/experiments/xp_random_preimage_generation.py View File

@@ -9,6 +9,7 @@ import multiprocessing
import numpy as np
import networkx as nx
import os
from gklearn.utils.graphfiles import saveGXL
from gklearn.preimage import RandomPreimageGenerator
from gklearn.utils import Dataset

@@ -16,7 +17,7 @@ from gklearn.utils import Dataset
dir_root = '../results/xp_random_preimage_generation/'


def xp_random_preimage_generation():
def xp_random_preimage_generation(kernel_name):
"""
Experiment similar to the one in Bakir's paper. A test to check if RandomPreimageGenerator class works correctly.

@@ -40,15 +41,26 @@ def xp_random_preimage_generation():
'alphas': None,
'parallel': True,
'verbose': 2}
kernel_options = {'name': 'PathUpToH',
'depth': 2, #
'k_func': 'MinMax', #
'compute_method': 'trie',
'parallel': 'imap_unordered',
# 'parallel': None,
'n_jobs': multiprocessing.cpu_count(),
'normalize': True,
'verbose': 0}
if kernel_name == 'PathUpToH':
kernel_options = {'name': 'PathUpToH',
'depth': 2, #
'k_func': 'MinMax', #
'compute_method': 'trie',
'parallel': 'imap_unordered',
# 'parallel': None,
'n_jobs': multiprocessing.cpu_count(),
'normalize': True,
'verbose': 0}
elif kernel_name == 'Marginalized':
kernel_options = {'name': 'Marginalized',
'p_quit': 0.8, #
'n_iteration': 7, #
'remove_totters': False,
'parallel': 'imap_unordered',
# 'parallel': None,
'n_jobs': multiprocessing.cpu_count(),
'normalize': True,
'verbose': 0}
edge_required = True
irrelevant_labels = {'edge_labels': ['label_0']}
cut_range = None
@@ -74,25 +86,30 @@ def xp_random_preimage_generation():
if cut_range is not None:
dataset_all.cut_graphs(cut_range)
# add two "random" graphs.
g1 = nx.Graph()
g1.add_nodes_from(range(0, 16), label_0='0')
g1.add_nodes_from(range(16, 25), label_0='1')
g1.add_node(25, label_0='2')
g1.add_nodes_from([26, 27], label_0='3')
g1.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 12), (5, 0), (4, 9), (12, 3), (10, 13), (13, 14), (14, 15), (15, 8), (0, 16), (1, 17), (2, 18), (12, 19), (11, 20), (13, 21), (15, 22), (7, 23), (6, 24), (14, 25), (25, 26), (25, 27)])
g2 = nx.Graph()
g2.add_nodes_from(range(0, 12), label_0='0')
g2.add_nodes_from(range(12, 19), label_0='1')
g2.add_nodes_from([19, 20, 21], label_0='2')
g2.add_nodes_from([22, 23], label_0='3')
g2.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 19), (19, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 20), (20, 7), (5, 0), (4, 8), (0, 12), (1, 13), (2, 14), (9, 15), (10, 16), (11, 17), (6, 18), (3, 21), (21, 22), (21, 23)])
dataset_all.load_graphs([g1, g2] + dataset_all.graphs, targets=None)
# # add two "random" graphs.
# g1 = nx.Graph()
# g1.add_nodes_from(range(0, 16), label_0='0')
# g1.add_nodes_from(range(16, 25), label_0='1')
# g1.add_node(25, label_0='2')
# g1.add_nodes_from([26, 27], label_0='3')
# g1.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 12), (5, 0), (4, 9), (12, 3), (10, 13), (13, 14), (14, 15), (15, 8), (0, 16), (1, 17), (2, 18), (12, 19), (11, 20), (13, 21), (15, 22), (7, 23), (6, 24), (14, 25), (25, 26), (25, 27)])
# g2 = nx.Graph()
# g2.add_nodes_from(range(0, 12), label_0='0')
# g2.add_nodes_from(range(12, 19), label_0='1')
# g2.add_nodes_from([19, 20, 21], label_0='2')
# g2.add_nodes_from([22, 23], label_0='3')
# g2.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 19), (19, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 20), (20, 7), (5, 0), (4, 8), (0, 12), (1, 13), (2, 14), (9, 15), (10, 16), (11, 17), (6, 18), (3, 21), (21, 22), (21, 23)])
# dataset_all.load_graphs([g1, g2] + dataset_all.graphs, targets=None)
# 2. initialize rpg and setting parameters.
print('2. initializing rpg and setting parameters...')
nb_graphs = len(dataset_all.graphs) - 2
rpg_options['alphas'] = [alpha1, 1 - alpha1] + [0] * nb_graphs
# nb_graphs = len(dataset_all.graphs) - 2
# rpg_options['alphas'] = [alpha1, 1 - alpha1] + [0] * nb_graphs
nb_graphs = len(dataset_all.graphs)
alphas = [0] * nb_graphs
alphas[1] = alpha1
alphas[6] = 1 - alpha1
rpg_options['alphas'] = alphas
if gmfile_exist:
rpg_options['gram_matrix_unnorm'] = gram_matrix_unnorm
rpg_options['runtime_precompute_gm'] = time_precompute_gm
@@ -114,11 +131,129 @@ def xp_random_preimage_generation():
# write Gram matrices to file.
if not gmfile_exist:
np.savez(dir_save + 'gram_matrix_unnorm.' + ds_name + '.' + kernel_options['name'] + '.gm', gram_matrix_unnorm=rpg.gram_matrix_unnorm, run_time=results['runtime_precompute_gm'])

# save graphs.
fn_best_dataset = dir_save + 'g_best_dataset.' + 'alpha1_' + str(alpha1)[0:3]
saveGXL(rpg.best_from_dataset, fn_best_dataset + '.gxl', method='default',
node_labels=dataset_all.node_labels, edge_labels=dataset_all.edge_labels,
node_attrs=dataset_all.node_attrs, edge_attrs=dataset_all.edge_attrs)
fn_preimage = dir_save + 'g_preimage.' + 'alpha1_' + str(alpha1)[0:3]
saveGXL(rpg.preimage, fn_preimage + '.gxl', method='default',
node_labels=dataset_all.node_labels, edge_labels=dataset_all.edge_labels,
node_attrs=dataset_all.node_attrs, edge_attrs=dataset_all.edge_attrs)
# draw graphs.
__draw_graph(rpg.best_from_dataset, fn_best_dataset)
__draw_graph(rpg.preimage, fn_preimage)
# plot results figure.
__plot_results(alpha1_list, k_dis_datasets, k_dis_preimages, dir_save)
print('\ncomplete.\n')
return k_dis_datasets, k_dis_preimages, bests_from_dataset, preimages


def __draw_graph(graph, file_prefix):
# import matplotlib
# matplotlib.use('agg')
import matplotlib.pyplot as plt
plt.figure()
pos = nx.spring_layout(graph)
nx.draw(graph, pos, node_size=500, labels=nx.get_node_attributes(graph, 'label_0'), font_color='w', width=3, with_labels=True)
plt.savefig(file_prefix + '.eps', format='eps', dpi=300)
# plt.show()
plt.clf()
plt.close()


def __plot_results(alpha1_list, k_dis_datasets, k_dis_preimages, dir_save):
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 1, figsize=(7, 4.5))

ind = np.arange(len(alpha1_list)) # the x locations for the groups
width = 0.35 # the width of the bars: can also be len(x) sequence
p1 = ax.bar(ind, k_dis_preimages, width, label='Reconstructed pre-image', zorder=3, color='#133AAC')
ax.set_xlabel(r'$\alpha \in [0,1]$')
ax.set_ylabel(r'$d(g_i,g^\star(\alpha))$')
#ax.set_title('Runtime of the shortest path kernel on all datasets')
plt.xticks(ind, [str(i)[0:3] for i in alpha1_list])
#ax.set_yticks(np.logspace(-16, -3, num=20, base=10))
#ax.set_ylim(bottom=1e-15)
ax.grid(axis='y', zorder=0)
ax.spines['top'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.xaxis.set_ticks_position('none')

p2 = ax.plot(ind, k_dis_datasets, 'b.-', label=r'Nearest neighbor in $D_N$', color='orange', zorder=4)
ax.yaxis.set_ticks_position('none')
fig.subplots_adjust(bottom=.2)
fig.legend(loc='lower center', ncol=2, frameon=False) # , ncol=5, labelspacing=0.1, handletextpad=0.4, columnspacing=0.6)
plt.savefig(dir_save + 'distances in kernel space.eps', format='eps', dpi=300,
transparent=True, bbox_inches='tight')
plt.show()
plt.clf()
plt.close()

if __name__ == '__main__':
k_dis_datasets, k_dis_preimages, bests_from_dataset, preimages = xp_random_preimage_generation()
# kernel_name = 'PathUpToH'
kernel_name = 'Marginalized'
k_dis_datasets, k_dis_preimages, bests_from_dataset, preimages = xp_random_preimage_generation(kernel_name)
# # save graphs.
# dir_save = dir_root + 'MUTAG.PathUpToH/'
# for i, alpha1 in enumerate(np.linspace(0, 1, 11)):
# fn_best_dataset = dir_save + 'g_best_dataset.' + 'alpha1_' + str(alpha1)[0:3]
# saveGXL(bests_from_dataset[i], fn_best_dataset + '.gxl', method='default',
# node_labels=['label_0'], edge_labels=[],
# node_attrs=[], edge_attrs=[])
# fn_preimage = dir_save + 'g_preimage.' + 'alpha1_' + str(alpha1)[0:3]
# saveGXL(preimages[i], fn_preimage + '.gxl', method='default',
# node_labels=['label_0'], edge_labels=[],
# node_attrs=[], edge_attrs=[])

# # draw graphs.
# dir_save = dir_root + 'MUTAG.PathUpToH/'
# for i, alpha1 in enumerate(np.linspace(0, 1, 11)):
# fn_best_dataset = dir_save + 'g_best_dataset.' + 'alpha1_' + str(alpha1)[0:3]
# __draw_graph(bests_from_dataset[i], fn_best_dataset)
# fn_preimage = dir_save + 'g_preimage.' + 'alpha1_' + str(alpha1)[0:3]
# __draw_graph(preimages[i], fn_preimage)

# # plot results figure.
# alpha1_list = np.linspace(0, 1, 11)
# dir_save = dir_root + 'MUTAG.PathUpToH/'
# __plot_results(alpha1_list, k_dis_datasets, k_dis_preimages, dir_save)

# k_dis_datasets = [0.0,
# 0.08882515554098754,
# 0.17765031108197632,
# 0.2664754666229643,
# 0.35530062216395264,
# 0.44412577770494066,
# 0.35530062216395236,
# 0.2664754666229643,
# 0.17765031108197632,
# 0.08882515554098878,
# 0.0]

# k_dis_preimages = [0.0,
# 0.08882515554098754,
# 0.17765031108197632,
# 0.2664754666229643,
# 0.35530062216395264,
# 0.44412577770494066,
# 0.35530062216395236,
# 0.2664754666229643,
# 0.17765031108197632,
# 0.08882515554098878,
# 0.0]

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