def kernelFunction(Data, rowInd, colInd, gamma=0.1, _type_="rbf"):
# a kernel generator: outputs the submatrix of the associated kernel
# with variance parameter.
# input:
#
# Data: Data matrix with n points and d features
# rowInd, colInd: List of indices between [1,n] for each row & col
# gamma: kernel variance parameter
#
# output:
#
# Ksub = Let K(i,j) = e^-(-1/(2*gamma)*||X(i,:)-X(j,:)||^2). Then Ksub =
# K(rowInd,colInd). Or if colInd = [] then Ksub = diag(K)(rowInd).
if _type_ == "rbf":
if len(colInd) <= 0:
Ksub = np.ones((len(rowInd)))
else:
Ksub = compute_kernel(Data, rowInd, colInd, kernel_type=_type_, sigma=gamma)
else:
pass
return Ksub
def median_on_k_closest_graphs(Gn, node_label, edge_label, gkernel, k, fit_method,
graph_dir='/media/ljia/DATA/research-repo/codes/Linlin/py-graph/datasets/monoterpenoides/',
edit_costs=None, group_min=None, dataset='monoterpenoides',
cost='CONSTANT', parallel=True):
dataset = dataset.lower()
# # compute distances in kernel space.
# dis_mat, _, _, _ = kernel_distance_matrix(Gn, node_label, edge_label,
# Kmatrix=None, gkernel=gkernel)
# # ged.
# gmfile = np.load('results/test_k_closest_graphs/ged_mat.fit_on_whole_dataset.with_medians.gm.npz')
# ged_mat = gmfile['ged_mat']
# dis_mat = ged_mat[0:len(Gn), 0:len(Gn)]
# # choose k closest graphs
# time0 = time.time()
# sod_ks_min, group_min = get_closest_k_graphs(dis_mat, k, parallel)
# time_spent = time.time() - time0
# print('closest graphs:', sod_ks_min, group_min)
# print('time spent:', time_spent)
# group_min = (12, 13, 22, 29) # closest w.r.t path kernel
# group_min = (77, 85, 160, 171) # closest w.r.t ged
# group_min = (0,1,2,3,4,5,6,7,8,9,10,11) # closest w.r.t treelet kernel
Gn_median = [Gn[g].copy() for g in group_min]
# fit edit costs.
if fit_method == 'random': # random
if cost == 'LETTER':
edit_cost_constant = random.sample(range(1, 10), 3)
edit_cost_constant = [item * 0.1 for item in edit_cost_constant]
elif cost == 'LETTER2':
random.seed(time.time())
edit_cost_constant = random.sample(range(1, 10), 5)
# edit_cost_constant = [item * 0.1 for item in edit_cost_constant]
else:
edit_cost_constant = random.sample(range(1, 10), 6)
print('edit costs used:', edit_cost_constant)
elif fit_method == 'expert': # expert
edit_cost_constant = [3, 3, 1, 3, 3, 1]
elif fit_method == 'k-graphs':
itr_max = 6
if cost == 'LETTER':
init_costs = [0.9, 1.7, 0.75]
elif cost == 'LETTER2':
init_costs = [0.675, 0.675, 0.75, 0.425, 0.425]
else:
init_costs = [3, 3, 1, 3, 3, 1]
algo_options = '--threads 1 --initial-solutions 40 --ratio-runs-from-initial-solutions 1'
params_ged = {'lib': 'gedlibpy', 'cost': cost, 'method': 'IPFP',
'algo_options': algo_options, 'stabilizer': None}
# fit on k-graph subset
edit_cost_constant, _, _, _, _, _, _ = fit_GED_to_kernel_distance(Gn_median,
node_label, edge_label, gkernel, itr_max, params_ged=params_ged,
init_costs=init_costs, dataset=dataset, parallel=True)
elif fit_method == 'whole-dataset':
itr_max = 6
if cost == 'LETTER':
init_costs = [0.9, 1.7, 0.75]
elif cost == 'LETTER2':
init_costs = [0.675, 0.675, 0.75, 0.425, 0.425]
else:
init_costs = [3, 3, 1, 3, 3, 1]
algo_options = '--threads 1 --initial-solutions 40 --ratio-runs-from-initial-solutions 1'
params_ged = {'lib': 'gedlibpy', 'cost': cost, 'method': 'IPFP',
'algo_options': algo_options, 'stabilizer': None}
# fit on all subset
edit_cost_constant, _, _, _, _, _, _ = fit_GED_to_kernel_distance(Gn,
node_label, edge_label, gkernel, itr_max, params_ged=params_ged,
init_costs=init_costs, dataset=dataset, parallel=True)
elif fit_method == 'precomputed':
edit_cost_constant = edit_costs
# compute set median and gen median using IAM (C++ through bash).
group_fnames = [Gn[g].graph['filename'] for g in group_min]
sod_sm, sod_gm, fname_sm, fname_gm = iam_bash(group_fnames, edit_cost_constant,
cost=cost, graph_dir=graph_dir,
dataset=dataset)
# compute distances in kernel space.
Gn_median = [Gn[g].copy() for g in group_min]
set_median = loadGXL(fname_sm)
gen_median = loadGXL(fname_gm)
# print(gen_median.nodes(data=True))
# print(gen_median.edges(data=True))
if dataset == 'letter':
for g in Gn_median:
reform_attributes(g)
reform_attributes(set_median)
reform_attributes(gen_median)
# compute distance in kernel space for set median.
Kmatrix_sm = compute_kernel([set_median] + Gn_median, gkernel,
None if dataset == 'letter' else 'chem',
None if dataset == 'letter' else 'valence',
False)
dis_k_sm = dis_gstar(0, range(1, 1+len(Gn_median)),
[1 / len(Gn_median)] * len(Gn_median), Kmatrix_sm, withterm3=False)
# print(gen_median.nodes(data=True))
# print(gen_median.edges(data=True))
# print(set_median.nodes(data=True))
# print(set_median.edges(data=True))
# compute distance in kernel space for generalized median.
Kmatrix_gm = compute_kernel([gen_median] + Gn_median, gkernel,
None if dataset == 'letter' else 'chem',
None if dataset == 'letter' else 'valence',
False)
dis_k_gm = dis_gstar(0, range(1, 1+len(Gn_median)),
[1 / len(Gn_median)] * len(Gn_median), Kmatrix_gm, withterm3=False)
# compute distance in kernel space for each graph in median set.
dis_k_gi = []
for idx in range(len(Gn_median)):
dis_k_gi.append(dis_gstar(idx+1, range(1, 1+len(Gn_median)),
[1 / len(Gn_median)] * len(Gn_median), Kmatrix_gm, withterm3=False))
print('sod_sm:', sod_sm)
print('sod_gm:', sod_gm)
print('dis_k_sm:', dis_k_sm)
print('dis_k_gm:', dis_k_gm)
print('dis_k_gi:', dis_k_gi)
idx_dis_k_gi_min = np.argmin(dis_k_gi)
dis_k_gi_min = dis_k_gi[idx_dis_k_gi_min]
print('index min dis_k_gi:', group_min[idx_dis_k_gi_min])
print('min dis_k_gi:', dis_k_gi_min)
return sod_sm, sod_gm, dis_k_sm, dis_k_gm, dis_k_gi, dis_k_gi_min, group_min[idx_dis_k_gi_min]
def preimage_iam(Gn_init, Gn_median, alpha, idx_gi, Kmatrix, k, r_max,
gkernel, epsilon=0.001, InitIAMWithAllDk=False,
params_iam={'c_ei': 1, 'c_er': 1, 'c_es': 1,
'ite_max': 50, 'epsilon': 0.001,
'removeNodes': True, 'connected': False},
params_ged={'lib': 'gedlibpy', 'cost': 'CHEM_1', 'method': 'IPFP',
'edit_cost_constant': [], 'stabilizer': 'min',
'repeat': 50}):
"""This function constructs graph pre-image by the iterative pre-image
framework in reference [1], algorithm 1, where the step of generating new
graphs randomly is replaced by the IAM algorithm in reference [2].
notes
-----
Every time a set of n better graphs is acquired, their distances in kernel space are
compared with the k nearest ones, and the k nearest distances from the k+n
distances will be used as the new ones.
"""
# compute k nearest neighbors of phi in DN.
dis_all = [] # distance between g_star and each graph.
term3 = 0
for i1, a1 in enumerate(alpha):
for i2, a2 in enumerate(alpha):
term3 += a1 * a2 * Kmatrix[idx_gi[i1], idx_gi[i2]]
for ig, g in tqdm(enumerate(Gn_init), desc='computing distances', file=sys.stdout):
dtemp = dis_gstar(ig, idx_gi, alpha, Kmatrix, term3=term3)
dis_all.append(dtemp)
# sort
sort_idx = np.argsort(dis_all)
dis_k = [dis_all[idis] for idis in sort_idx[0:k]] # the k shortest distances
nb_best = len(np.argwhere(dis_k == dis_k[0]).flatten().tolist())
ghat_list = [Gn_init[idx].copy() for idx in sort_idx[0:nb_best]] # the nearest neighbors of phi in DN
if dis_k[0] == 0: # the exact pre-image.
print('The exact pre-image is found from the input dataset.')
return 0, ghat_list, 0, 0
dhat = dis_k[0] # the nearest distance
# for g in ghat_list:
# draw_Letter_graph(g)
# nx.draw_networkx(g)
# plt.show()
# print(g.nodes(data=True))
# print(g.edges(data=True))
Gk = [Gn_init[ig].copy() for ig in sort_idx[0:k]] # the k nearest neighbors
# for gi in Gk:
# nx.draw(gi, labels=nx.get_node_attributes(gi, 'atom'), with_labels=True)
## nx.draw_networkx(gi)
# plt.show()
## draw_Letter_graph(g)
# print(gi.nodes(data=True))
# print(gi.edges(data=True))
# i = 1
r = 0
itr_total = 0
dis_of_each_itr = [dhat]
found = False
nb_updated = 0
nb_updated_k = 0
while r < r_max:# and not found: # @todo: if not found?# and np.abs(old_dis - cur_dis) > epsilon:
print('\n-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-')
print('Current preimage iteration =', r)
print('Total preimage iteration =', itr_total, '\n')
found = False
Gn_nearest_median = [g.copy() for g in Gk]
if InitIAMWithAllDk: # each graph in D_k is used to initialize IAM.
ghat_new_list = []
for g_tmp in Gk:
Gn_nearest_init = [g_tmp.copy()]
ghat_new_list_tmp, _, _ = iam_upgraded(Gn_nearest_median,
Gn_nearest_init, params_ged=params_ged, **params_iam)
ghat_new_list += ghat_new_list_tmp
else: # only the best graph in D_k is used to initialize IAM.
Gn_nearest_init = [g.copy() for g in Gk]
ghat_new_list, _, _ = iam_upgraded(Gn_nearest_median, Gn_nearest_init,
params_ged=params_ged, **params_iam)
# for g in g_tmp_list:
# nx.draw_networkx(g)
# plt.show()
# draw_Letter_graph(g)
# print(g.nodes(data=True))
# print(g.edges(data=True))
# compute distance between \psi and the new generated graphs.
knew = compute_kernel(ghat_new_list + Gn_median, gkernel, False)
dhat_new_list = []
for idx, g_tmp in enumerate(ghat_new_list):
# @todo: the term3 below could use the one at the beginning of the function.
dhat_new_list.append(dis_gstar(idx, range(len(ghat_new_list),
len(ghat_new_list) + len(Gn_median) + 1),
alpha, knew, withterm3=False))
for idx_g, ghat_new in enumerate(ghat_new_list):
dhat_new = dhat_new_list[idx_g]
# if the new distance is smaller than the max of D_k.
if dhat_new < dis_k[-1] and np.abs(dhat_new - dis_k[-1]) >= epsilon:
# check if the new distance is the same as one in D_k.
is_duplicate = False
for dis_tmp in dis_k[1:-1]:
if np.abs(dhat_new - dis_tmp) < epsilon:
is_duplicate = True
print('IAM: duplicate k nearest graph generated.')
break
if not is_duplicate:
if np.abs(dhat_new - dhat) < epsilon:
print('IAM: I am equal!')
# dhat = dhat_new
# ghat_list = [ghat_new.copy()]
else:
print('IAM: we got better k nearest neighbors!')
nb_updated_k += 1
print('the k nearest neighbors are updated',
nb_updated_k, 'times.')
dis_k = [dhat_new] + dis_k[0:k-1] # add the new nearest distance.
Gk = [ghat_new.copy()] + Gk[0:k-1] # add the corresponding graph.
sort_idx = np.argsort(dis_k)
dis_k = [dis_k[idx] for idx in sort_idx[0:k]] # the new k nearest distances.
Gk = [Gk[idx] for idx in sort_idx[0:k]]
if dhat_new < dhat:
print('IAM: I have smaller distance!')
print(str(dhat) + '->' + str(dhat_new))
dhat = dhat_new
ghat_list = [Gk[0].copy()]
r = 0
nb_updated += 1
print('the graph is updated', nb_updated, 'times.')
nx.draw(Gk[0], labels=nx.get_node_attributes(Gk[0], 'atom'),
with_labels=True)
## plt.savefig("results/gk_iam/simple_two/xx" + str(i) + ".png", format="PNG")
plt.show()
found = True
if not found:
r += 1
dis_of_each_itr.append(dhat)
itr_total += 1
print('\nthe k shortest distances are', dis_k)
print('the shortest distances for previous iterations are', dis_of_each_itr)
print('\n\nthe graph is updated', nb_updated, 'times.')
print('\nthe k nearest neighbors are updated', nb_updated_k, 'times.')
print('distances in kernel space:', dis_of_each_itr, '\n')
return dhat, ghat_list, dis_of_each_itr[-1], nb_updated, nb_updated_k
def preimage_iam_random_mix(Gn_init, Gn_median, alpha, idx_gi, Kmatrix, k, r_max,
l_max, gkernel, epsilon=0.001,
InitIAMWithAllDk=False, InitRandomWithAllDk=True,
params_iam={'c_ei': 1, 'c_er': 1, 'c_es': 1,
'ite_max': 50, 'epsilon': 0.001,
'removeNodes': True, 'connected': False},
params_ged={'lib': 'gedlibpy', 'cost': 'CHEM_1',
'method': 'IPFP', 'edit_cost_constant': [],
'stabilizer': 'min', 'repeat': 50}):
"""This function constructs graph pre-image by the iterative pre-image
framework in reference [1], algorithm 1, where new graphs are generated
randomly and by the IAM algorithm in reference [2].
notes
-----
Every time a set of n better graphs is acquired, their distances in kernel space are
compared with the k nearest ones, and the k nearest distances from the k+n
distances will be used as the new ones.
"""
Gn_init = [nx.convert_node_labels_to_integers(g) for g in Gn_init]
# compute k nearest neighbors of phi in DN.
dis_all = [] # distance between g_star and each graph.
term3 = 0
for i1, a1 in enumerate(alpha):
for i2, a2 in enumerate(alpha):
term3 += a1 * a2 * Kmatrix[idx_gi[i1], idx_gi[i2]]
for ig, g in tqdm(enumerate(Gn_init), desc='computing distances', file=sys.stdout):
dtemp = dis_gstar(ig, idx_gi, alpha, Kmatrix, term3=term3)
dis_all.append(dtemp)
# sort
sort_idx = np.argsort(dis_all)
dis_k = [dis_all[idis] for idis in sort_idx[0:k]] # the k shortest distances
nb_best = len(np.argwhere(dis_k == dis_k[0]).flatten().tolist())
ghat_list = [Gn_init[idx].copy() for idx in sort_idx[0:nb_best]] # the nearest neighbors of psi in DN
if dis_k[0] == 0: # the exact pre-image.
print('The exact pre-image is found from the input dataset.')
return 0, ghat_list, 0, 0
dhat = dis_k[0] # the nearest distance
# for g in ghat_list:
# draw_Letter_graph(g)
# nx.draw_networkx(g)
# plt.show()
# print(g.nodes(data=True))
# print(g.edges(data=True))
Gk = [Gn_init[ig].copy() for ig in sort_idx[0:k]] # the k nearest neighbors
# for gi in Gk:
# nx.draw(gi, labels=nx.get_node_attributes(gi, 'atom'), with_labels=True)
## nx.draw_networkx(gi)
# plt.show()
## draw_Letter_graph(g)
# print(gi.nodes(data=True))
# print(gi.edges(data=True))
r = 0
itr_total = 0
dis_of_each_itr = [dhat]
nb_updated_iam = 0
nb_updated_k_iam = 0
nb_updated_random = 0
nb_updated_k_random = 0
# is_iam_duplicate = False
while r < r_max: # and not found: # @todo: if not found?# and np.abs(old_dis - cur_dis) > epsilon:
print('\n-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-')
print('Current preimage iteration =', r)
print('Total preimage iteration =', itr_total, '\n')
found_iam = False
Gn_nearest_median = [g.copy() for g in Gk]
if InitIAMWithAllDk: # each graph in D_k is used to initialize IAM.
ghat_new_list = []
for g_tmp in Gk:
Gn_nearest_init = [g_tmp.copy()]
ghat_new_list_tmp, _ = iam_upgraded(Gn_nearest_median,
Gn_nearest_init, params_ged=params_ged, **params_iam)
ghat_new_list += ghat_new_list_tmp
else: # only the best graph in D_k is used to initialize IAM.
Gn_nearest_init = [g.copy() for g in Gk]
ghat_new_list, _ = iam_upgraded(Gn_nearest_median, Gn_nearest_init,
params_ged=params_ged, **params_iam)
# for g in g_tmp_list:
# nx.draw_networkx(g)
# plt.show()
# draw_Letter_graph(g)
# print(g.nodes(data=True))
# print(g.edges(data=True))
# compute distance between \psi and the new generated graphs.
knew = compute_kernel(ghat_new_list + Gn_median, gkernel, False)
dhat_new_list = []
for idx, g_tmp in enumerate(ghat_new_list):
# @todo: the term3 below could use the one at the beginning of the function.
dhat_new_list.append(dis_gstar(idx, range(len(ghat_new_list),
len(ghat_new_list) + len(Gn_median) + 1),
alpha, knew, withterm3=False))
# find the new k nearest graphs.
for idx_g, ghat_new in enumerate(ghat_new_list):
dhat_new = dhat_new_list[idx_g]
# if the new distance is smaller than the max of D_k.
if dhat_new < dis_k[-1] and np.abs(dhat_new - dis_k[-1]) >= epsilon:
# check if the new distance is the same as one in D_k.
is_duplicate = False
for dis_tmp in dis_k[1:-1]:
if np.abs(dhat_new - dis_tmp) < epsilon:
is_duplicate = True
print('IAM: duplicate k nearest graph generated.')
break
if not is_duplicate:
if np.abs(dhat_new - dhat) < epsilon:
print('IAM: I am equal!')
# dhat = dhat_new
# ghat_list = [ghat_new.copy()]
else:
print('IAM: we got better k nearest neighbors!')
nb_updated_k_iam += 1
print('the k nearest neighbors are updated',
nb_updated_k_iam, 'times.')
dis_k = [dhat_new] + dis_k[0:k-1] # add the new nearest distance.
Gk = [ghat_new.copy()] + Gk[0:k-1] # add the corresponding graph.
sort_idx = np.argsort(dis_k)
dis_k = [dis_k[idx] for idx in sort_idx[0:k]] # the new k nearest distances.
Gk = [Gk[idx] for idx in sort_idx[0:k]]
if dhat_new < dhat:
print('IAM: I have smaller distance!')
print(str(dhat) + '->' + str(dhat_new))
dhat = dhat_new
ghat_list = [Gk[0].copy()]
r = 0
nb_updated_iam += 1
print('the graph is updated by IAM', nb_updated_iam,
'times.')
nx.draw(Gk[0], labels=nx.get_node_attributes(Gk[0], 'atom'),
with_labels=True)
## plt.savefig("results/gk_iam/simple_two/xx" + str(i) + ".png", format="PNG")
plt.show()
found_iam = True
# when new distance is not smaller than the max of D_k, use random generation.
if not found_iam:
print('Distance not better, switching to random generation now.')
print(str(dhat) + '->' + str(dhat_new))
if InitRandomWithAllDk: # use all k nearest graphs as the initials.
init_list = [g_init.copy() for g_init in Gk]
else: # use just the nearest graph as the initial.
init_list = [Gk[0].copy()]
# number of edges to be changed.
if len(init_list) == 1:
# @todo what if the log is negetive? how to choose alpha (scalar)? seems fdgs is always 1.
# fdgs = dhat_new
fdgs = nb_updated_random + 1
if fdgs < 1:
fdgs = 1
fdgs = int(np.ceil(np.log(fdgs)))
if fdgs < 1:
fdgs += 1
# fdgs = nb_updated_random + 1 # @todo:
fdgs_list = [fdgs]
else:
# @todo what if the log is negetive? how to choose alpha (scalar)?
fdgs_list = np.array(dis_k[:])
if np.min(fdgs_list) < 1:
fdgs_list /= dis_k[0]
fdgs_list = [int(item) for item in np.ceil(np.log(fdgs_list))]
if np.min(fdgs_list) < 1:
fdgs_list = np.array(fdgs_list) + 1
l = 0
found_random = False
while l < l_max and not found_random:
for idx_g, g_tmp in enumerate(init_list):
# add and delete edges.
ghat_new = nx.convert_node_labels_to_integers(g_tmp.copy())
# @todo: should we use just half of the adjacency matrix for undirected graphs?
nb_vpairs = nx.number_of_nodes(ghat_new) * (nx.number_of_nodes(ghat_new) - 1)
np.random.seed()
# which edges to change.
# @todo: what if fdgs is bigger than nb_vpairs?
idx_change = random.sample(range(nb_vpairs), fdgs_list[idx_g] if
fdgs_list[idx_g] < nb_vpairs else nb_vpairs)
# idx_change = np.random.randint(0, nx.number_of_nodes(gs) *
# (nx.number_of_nodes(gs) - 1), fdgs)
for item in idx_change:
node1 = int(item / (nx.number_of_nodes(ghat_new) - 1))
node2 = (item - node1 * (nx.number_of_nodes(ghat_new) - 1))
if node2 >= node1: # skip the self pair.
node2 += 1
# @todo: is the randomness correct?
if not ghat_new.has_edge(node1, node2):
ghat_new.add_edge(node1, node2)
# nx.draw_networkx(gs)
# plt.show()
# nx.draw_networkx(ghat_new)
# plt.show()
else:
ghat_new.remove_edge(node1, node2)
# nx.draw_networkx(gs)
# plt.show()
# nx.draw_networkx(ghat_new)
# plt.show()
# nx.draw_networkx(ghat_new)
# plt.show()
# compute distance between \psi and the new generated graph.
knew = compute_kernel([ghat_new] + Gn_median, gkernel, verbose=False)
dhat_new = dis_gstar(0, range(1, len(Gn_median) + 1),
alpha, knew, withterm3=False)
# @todo: the new distance is smaller or also equal?
if dhat_new < dis_k[-1] and np.abs(dhat_new - dis_k[-1]) >= epsilon:
# check if the new distance is the same as one in D_k.
is_duplicate = False
for dis_tmp in dis_k[1:-1]:
if np.abs(dhat_new - dis_tmp) < epsilon:
is_duplicate = True
print('Random: duplicate k nearest graph generated.')
break
if not is_duplicate:
if np.abs(dhat_new - dhat) < epsilon:
print('Random: I am equal!')
# dhat = dhat_new
# ghat_list = [ghat_new.copy()]
else:
print('Random: we got better k nearest neighbors!')
print('l =', str(l))
nb_updated_k_random += 1
print('the k nearest neighbors are updated by random generation',
nb_updated_k_random, 'times.')
dis_k = [dhat_new] + dis_k # add the new nearest distances.
Gk = [ghat_new.copy()] + Gk # add the corresponding graphs.
sort_idx = np.argsort(dis_k)
dis_k = [dis_k[idx] for idx in sort_idx[0:k]] # the new k nearest distances.
Gk = [Gk[idx] for idx in sort_idx[0:k]]
if dhat_new < dhat:
print('\nRandom: I am smaller!')
print('l =', str(l))
print(dhat, '->', dhat_new)
dhat = dhat_new
ghat_list = [ghat_new.copy()]
r = 0
nb_updated_random += 1
print('the graph is updated by random generation',
nb_updated_random, 'times.')
nx.draw(ghat_new, labels=nx.get_node_attributes(ghat_new, 'atom'),
with_labels=True)
## plt.savefig("results/gk_iam/simple_two/xx" + str(i) + ".png", format="PNG")
plt.show()
found_random = True
break
l += 1
if not found_random: # l == l_max:
r += 1
dis_of_each_itr.append(dhat)
itr_total += 1
print('\nthe k shortest distances are', dis_k)
print('the shortest distances for previous iterations are', dis_of_each_itr)
print('\n\nthe graph is updated by IAM', nb_updated_iam, 'times, and by random generation',
nb_updated_random, 'times.')
print('\nthe k nearest neighbors are updated by IAM', nb_updated_k_iam,
'times, and by random generation', nb_updated_k_random, 'times.')
print('distances in kernel space:', dis_of_each_itr, '\n')
return dhat, ghat_list, dis_of_each_itr[-1], \
nb_updated_iam, nb_updated_random, nb_updated_k_iam, nb_updated_k_random
###############################################################################
# Old implementations.
#def gk_iam(Gn, alpha):
# """This function constructs graph pre-image by the iterative pre-image
# framework in reference [1], algorithm 1, where the step of generating new
# graphs randomly is replaced by the IAM algorithm in reference [2].
#
# notes
# -----
# Every time a better graph is acquired, the older one is replaced by it.
# """
# pass
# # compute k nearest neighbors of phi in DN.
# dis_list = [] # distance between g_star and each graph.
# for ig, g in tqdm(enumerate(Gn), desc='computing distances', file=sys.stdout):
# dtemp = k_list[ig] - 2 * (alpha * k_g1_list[ig] + (1 - alpha) *
# k_g2_list[ig]) + (alpha * alpha * k_list[idx1] + alpha *
# (1 - alpha) * k_g2_list[idx1] + (1 - alpha) * alpha *
# k_g1_list[idx2] + (1 - alpha) * (1 - alpha) * k_list[idx2])
# dis_list.append(dtemp)
#
# # sort
# sort_idx = np.argsort(dis_list)
# dis_gs = [dis_list[idis] for idis in sort_idx[0:k]]
# g0hat = Gn[sort_idx[0]] # the nearest neighbor of phi in DN
# if dis_gs[0] == 0: # the exact pre-image.
# print('The exact pre-image is found from the input dataset.')
# return 0, g0hat
# dhat = dis_gs[0] # the nearest distance
# Gk = [Gn[ig] for ig in sort_idx[0:k]] # the k nearest neighbors
# gihat_list = []
#
## i = 1
# r = 1
# while r < r_max:
# print('r =', r)
## found = False
# Gs_nearest = Gk + gihat_list
# g_tmp = iam(Gs_nearest)
#
# # compute distance between \psi and the new generated graph.
# knew = marginalizedkernel([g_tmp, g1, g2], node_label='atom', edge_label=None,
# p_quit=lmbda, n_iteration=20, remove_totters=False,
# n_jobs=multiprocessing.cpu_count(), verbose=False)
# dnew = knew[0][0, 0] - 2 * (alpha * knew[0][0, 1] + (1 - alpha) *
# knew[0][0, 2]) + (alpha * alpha * k_list[idx1] + alpha *
# (1 - alpha) * k_g2_list[idx1] + (1 - alpha) * alpha *
# k_g1_list[idx2] + (1 - alpha) * (1 - alpha) * k_list[idx2])
# if dnew <= dhat: # the new distance is smaller
# print('I am smaller!')
# dhat = dnew
# g_new = g_tmp.copy() # found better graph.
# gihat_list = [g_new]
# dis_gs.append(dhat)
# r = 0
# else:
# r += 1
#
# ghat = ([g0hat] if len(gihat_list) == 0 else gihat_list)
#
# return dhat, ghat
#def gk_iam_nearest(Gn, alpha, idx_gi, Kmatrix, k, r_max):
# """This function constructs graph pre-image by the iterative pre-image
# framework in reference [1], algorithm 1, where the step of generating new
# graphs randomly is replaced by the IAM algorithm in reference [2].
#
# notes
# -----
# Every time a better graph is acquired, its distance in kernel space is
# compared with the k nearest ones, and the k nearest distances from the k+1
# distances will be used as the new ones.
# """
# # compute k nearest neighbors of phi in DN.
# dis_list = [] # distance between g_star and each graph.
# for ig, g in tqdm(enumerate(Gn), desc='computing distances', file=sys.stdout):
# dtemp = dis_gstar(ig, idx_gi, alpha, Kmatrix)
## dtemp = k_list[ig] - 2 * (alpha * k_g1_list[ig] + (1 - alpha) *
## k_g2_list[ig]) + (alpha * alpha * k_list[0] + alpha *
## (1 - alpha) * k_g2_list[0] + (1 - alpha) * alpha *
## k_g1_list[6] + (1 - alpha) * (1 - alpha) * k_list[6])
# dis_list.append(dtemp)
#
# # sort
# sort_idx = np.argsort(dis_list)
# dis_gs = [dis_list[idis] for idis in sort_idx[0:k]] # the k shortest distances
# g0hat = Gn[sort_idx[0]] # the nearest neighbor of phi in DN
# if dis_gs[0] == 0: # the exact pre-image.
# print('The exact pre-image is found from the input dataset.')
# return 0, g0hat
# dhat = dis_gs[0] # the nearest distance
# ghat = g0hat.copy()
# Gk = [Gn[ig].copy() for ig in sort_idx[0:k]] # the k nearest neighbors
# for gi in Gk:
# nx.draw_networkx(gi)
# plt.show()
# print(gi.nodes(data=True))
# print(gi.edges(data=True))
# Gs_nearest = Gk.copy()
## gihat_list = []
#
## i = 1
# r = 1
# while r < r_max:
# print('r =', r)
## found = False
## Gs_nearest = Gk + gihat_list
## g_tmp = iam(Gs_nearest)
# g_tmp = test_iam_with_more_graphs_as_init(Gs_nearest, Gs_nearest, c_ei=1, c_er=1, c_es=1)
# nx.draw_networkx(g_tmp)
# plt.show()
# print(g_tmp.nodes(data=True))
# print(g_tmp.edges(data=True))
#
# # compute distance between \psi and the new generated graph.
# gi_list = [Gn[i] for i in idx_gi]
# knew = compute_kernel([g_tmp] + gi_list, 'untilhpathkernel', False)
# dnew = dis_gstar(0, range(1, len(gi_list) + 1), alpha, knew)
#
## dnew = knew[0, 0] - 2 * (alpha[0] * knew[0, 1] + alpha[1] *
## knew[0, 2]) + (alpha[0] * alpha[0] * k_list[0] + alpha[0] *
## alpha[1] * k_g2_list[0] + alpha[1] * alpha[0] *
## k_g1_list[1] + alpha[1] * alpha[1] * k_list[1])
# if dnew <= dhat and g_tmp != ghat: # the new distance is smaller
# print('I am smaller!')
# print(str(dhat) + '->' + str(dnew))
## nx.draw_networkx(ghat)
## plt.show()
## print('->')
## nx.draw_networkx(g_tmp)
## plt.show()
#
# dhat = dnew
# g_new = g_tmp.copy() # found better graph.
# ghat = g_tmp.copy()
# dis_gs.append(dhat) # add the new nearest distance.
# Gs_nearest.append(g_new) # add the corresponding graph.
# sort_idx = np.argsort(dis_gs)
# dis_gs = [dis_gs[idx] for idx in sort_idx[0:k]] # the new k nearest distances.
# Gs_nearest = [Gs_nearest[idx] for idx in sort_idx[0:k]]
# r = 0
# else:
# r += 1
#
# return dhat, ghat
#def gk_iam_nearest_multi(Gn, alpha, idx_gi, Kmatrix, k, r_max):
# """This function constructs graph pre-image by the iterative pre-image
# framework in reference [1], algorithm 1, where the step of generating new
# graphs randomly is replaced by the IAM algorithm in reference [2].
#
# notes
# -----
# Every time a set of n better graphs is acquired, their distances in kernel space are
# compared with the k nearest ones, and the k nearest distances from the k+n
# distances will be used as the new ones.
# """
# Gn_median = [Gn[idx].copy() for idx in idx_gi]
# # compute k nearest neighbors of phi in DN.
# dis_list = [] # distance between g_star and each graph.
# for ig, g in tqdm(enumerate(Gn), desc='computing distances', file=sys.stdout):
# dtemp = dis_gstar(ig, idx_gi, alpha, Kmatrix)
## dtemp = k_list[ig] - 2 * (alpha * k_g1_list[ig] + (1 - alpha) *
## k_g2_list[ig]) + (alpha * alpha * k_list[0] + alpha *
## (1 - alpha) * k_g2_list[0] + (1 - alpha) * alpha *
## k_g1_list[6] + (1 - alpha) * (1 - alpha) * k_list[6])
# dis_list.append(dtemp)
#
# # sort
# sort_idx = np.argsort(dis_list)
# dis_gs = [dis_list[idis] for idis in sort_idx[0:k]] # the k shortest distances
# nb_best = len(np.argwhere(dis_gs == dis_gs[0]).flatten().tolist())
# g0hat_list = [Gn[idx] for idx in sort_idx[0:nb_best]] # the nearest neighbors of phi in DN
# if dis_gs[0] == 0: # the exact pre-image.
# print('The exact pre-image is found from the input dataset.')
# return 0, g0hat_list
# dhat = dis_gs[0] # the nearest distance
# ghat_list = [g.copy() for g in g0hat_list]
# for g in ghat_list:
# nx.draw_networkx(g)
# plt.show()
# print(g.nodes(data=True))
# print(g.edges(data=True))
# Gk = [Gn[ig].copy() for ig in sort_idx[0:k]] # the k nearest neighbors
# for gi in Gk:
# nx.draw_networkx(gi)
# plt.show()
# print(gi.nodes(data=True))
# print(gi.edges(data=True))
# Gs_nearest = Gk.copy()
## gihat_list = []
#
## i = 1
# r = 1
# while r < r_max:
# print('r =', r)
## found = False
## Gs_nearest = Gk + gihat_list
## g_tmp = iam(Gs_nearest)
# g_tmp_list = test_iam_moreGraphsAsInit_tryAllPossibleBestGraphs_deleteNodesInIterations(
# Gn_median, Gs_nearest, c_ei=1, c_er=1, c_es=1)
# for g in g_tmp_list:
# nx.draw_networkx(g)
# plt.show()
# print(g.nodes(data=True))
# print(g.edges(data=True))
#
# # compute distance between \psi and the new generated graphs.
# gi_list = [Gn[i] for i in idx_gi]
# knew = compute_kernel(g_tmp_list + gi_list, 'marginalizedkernel', False)
# dnew_list = []
# for idx, g_tmp in enumerate(g_tmp_list):
# dnew_list.append(dis_gstar(idx, range(len(g_tmp_list),
# len(g_tmp_list) + len(gi_list) + 1), alpha, knew))
#
## dnew = knew[0, 0] - 2 * (alpha[0] * knew[0, 1] + alpha[1] *
## knew[0, 2]) + (alpha[0] * alpha[0] * k_list[0] + alpha[0] *
## alpha[1] * k_g2_list[0] + alpha[1] * alpha[0] *
## k_g1_list[1] + alpha[1] * alpha[1] * k_list[1])
#
# # find the new k nearest graphs.
# dis_gs = dnew_list + dis_gs # add the new nearest distances.
# Gs_nearest = [g.copy() for g in g_tmp_list] + Gs_nearest # add the corresponding graphs.
# sort_idx = np.argsort(dis_gs)
# if len([i for i in sort_idx[0:k] if i < len(dnew_list)]) > 0:
# print('We got better k nearest neighbors! Hurray!')
# dis_gs = [dis_gs[idx] for idx in sort_idx[0:k]] # the new k nearest distances.
# print(dis_gs[-1])
# Gs_nearest = [Gs_nearest[idx] for idx in sort_idx[0:k]]
# nb_best = len(np.argwhere(dis_gs == dis_gs[0]).flatten().tolist())
# if len([i for i in sort_idx[0:nb_best] if i < len(dnew_list)]) > 0:
# print('I have smaller or equal distance!')
# dhat = dis_gs[0]
# print(str(dhat) + '->' + str(dhat))
# idx_best_list = np.argwhere(dnew_list == dhat).flatten().tolist()
# ghat_list = [g_tmp_list[idx].copy() for idx in idx_best_list]
# for g in ghat_list:
# nx.draw_networkx(g)
# plt.show()
# print(g.nodes(data=True))
# print(g.edges(data=True))
# r = 0
# else:
# r += 1
#
# return dhat, ghat_list
def preimage_random(Gn_init, Gn_median, alpha, idx_gi, Kmatrix, k, r_max, l,
gkernel):
Gn_init = [nx.convert_node_labels_to_integers(g) for g in Gn_init]
# compute k nearest neighbors of phi in DN.
dis_list = [] # distance between g_star and each graph.
term3 = 0
for i1, a1 in enumerate(alpha):
for i2, a2 in enumerate(alpha):
term3 += a1 * a2 * Kmatrix[idx_gi[i1], idx_gi[i2]]
for ig, g in tqdm(enumerate(Gn_init),
desc='computing distances',
file=sys.stdout):
dtemp = dis_gstar(ig, idx_gi, alpha, Kmatrix, term3=term3)
dis_list.append(dtemp)
# print(np.max(dis_list))
# print(np.min(dis_list))
# print(np.min([item for item in dis_list if item != 0]))
# print(np.mean(dis_list))
# sort
sort_idx = np.argsort(dis_list)
dis_gs = [dis_list[idis]
for idis in sort_idx[0:k]] # the k shortest distances
nb_best = len(np.argwhere(dis_gs == dis_gs[0]).flatten().tolist())
g0hat_list = [Gn_init[idx] for idx in sort_idx[0:nb_best]
] # the nearest neighbors of phi in DN
if dis_gs[0] == 0: # the exact pre-image.
print('The exact pre-image is found from the input dataset.')
return 0, g0hat_list[0], 0
dhat = dis_gs[0] # the nearest distance
# ghat_list = [g.copy() for g in g0hat_list]
# for g in ghat_list:
# draw_Letter_graph(g)
# nx.draw_networkx(g)
# plt.show()
# print(g.nodes(data=True))
# print(g.edges(data=True))
Gk = [Gn_init[ig].copy()
for ig in sort_idx[0:k]] # the k nearest neighbors
# for gi in Gk:
## nx.draw_networkx(gi)
## plt.show()
# draw_Letter_graph(g)
# print(gi.nodes(data=True))
# print(gi.edges(data=True))
Gs_nearest = [g.copy() for g in Gk]
gihat_list = []
dihat_list = []
# i = 1
r = 0
# sod_list = [dhat]
# found = False
dis_of_each_itr = [dhat]
nb_updated = 0
g_best = []
while r < r_max:
print('\nr =', r)
print('itr for gk =', nb_updated, '\n')
found = False
dis_bests = dis_gs + dihat_list
# @todo what if the log is negetive? how to choose alpha (scalar)?
fdgs_list = np.array(dis_bests)
if np.min(fdgs_list) < 1:
fdgs_list /= np.min(dis_bests)
fdgs_list = [int(item) for item in np.ceil(np.log(fdgs_list))]
if np.min(fdgs_list) < 1:
fdgs_list = np.array(fdgs_list) + 1
for ig, gs in enumerate(Gs_nearest + gihat_list):
# nx.draw_networkx(gs)
# plt.show()
for trail in range(0, l):
# for trail in tqdm(range(0, l), desc='l loops', file=sys.stdout):
# add and delete edges.
gtemp = gs.copy()
np.random.seed()
# which edges to change.
# @todo: should we use just half of the adjacency matrix for undirected graphs?
nb_vpairs = nx.number_of_nodes(gs) * (nx.number_of_nodes(gs) -
1)
# @todo: what if fdgs is bigger than nb_vpairs?
idx_change = random.sample(
range(nb_vpairs),
fdgs_list[ig] if fdgs_list[ig] < nb_vpairs else nb_vpairs)
# idx_change = np.random.randint(0, nx.number_of_nodes(gs) *
# (nx.number_of_nodes(gs) - 1), fdgs)
for item in idx_change:
node1 = int(item / (nx.number_of_nodes(gs) - 1))
node2 = (item - node1 * (nx.number_of_nodes(gs) - 1))
if node2 >= node1: # skip the self pair.
node2 += 1
# @todo: is the randomness correct?
if not gtemp.has_edge(node1, node2):
gtemp.add_edge(node1, node2)
# nx.draw_networkx(gs)
# plt.show()
# nx.draw_networkx(gtemp)
# plt.show()
else:
gtemp.remove_edge(node1, node2)
# nx.draw_networkx(gs)
# plt.show()
# nx.draw_networkx(gtemp)
# plt.show()
# nx.draw_networkx(gtemp)
# plt.show()
# compute distance between \psi and the new generated graph.
# knew = marginalizedkernel([gtemp, g1, g2], node_label='atom', edge_label=None,
# p_quit=lmbda, n_iteration=20, remove_totters=False,
# n_jobs=multiprocessing.cpu_count(), verbose=False)
knew = compute_kernel([gtemp] + Gn_median,
gkernel,
verbose=False)
dnew = dis_gstar(0,
range(1,
len(Gn_median) + 1),
alpha,
knew,
withterm3=False)
if dnew <= dhat: # @todo: the new distance is smaller or also equal?
if dnew < dhat:
print('\nI am smaller!')
print('ig =', str(ig), ', l =', str(trail))
print(dhat, '->', dnew)
nb_updated += 1
elif dnew == dhat:
print('I am equal!')
# nx.draw_networkx(gtemp)
# plt.show()
# print(gtemp.nodes(data=True))
# print(gtemp.edges(data=True))
dhat = dnew
gnew = gtemp.copy()
found = True # found better graph.
if found:
r = 0
gihat_list = [gnew]
dihat_list = [dhat]
else:
r += 1
dis_of_each_itr.append(dhat)
print('the shortest distances for previous iterations are',
dis_of_each_itr)
# dis_best.append(dhat)
g_best = (g0hat_list[0] if len(gihat_list) == 0 else gihat_list[0])
print('distances in kernel space:', dis_of_each_itr, '\n')
return dhat, g_best, nb_updated
idx1 = 0
idx2 = 6
g1 = DN[idx1]
g2 = DN[idx2]
# compute
k_list = [] # kernel between each graph and itself.
k_g1_list = [] # kernel between each graph and g1
k_g2_list = [] # kernel between each graph and g2
for ig, g in tqdm(enumerate(DN),
desc='computing self kernels',
file=sys.stdout):
# ktemp = marginalizedkernel([g, g1, g2], node_label='atom', edge_label=None,
# p_quit=lmbda, n_iteration=20, remove_totters=False,
# n_jobs=multiprocessing.cpu_count(), verbose=False)
ktemp = compute_kernel([g, g1, g2], 'untilhpathkernel', verbose=False)
k_list.append(ktemp[0, 0])
k_g1_list.append(ktemp[0, 1])
k_g2_list.append(ktemp[0, 2])
g_best = []
dis_best = []
# for each alpha
for alpha in alpha_range:
print('alpha =', alpha)
# compute k nearest neighbors of phi in DN.
dis_list = [] # distance between g_star and each graph.
for ig, g in tqdm(enumerate(DN),
desc='computing distances',
file=sys.stdout):
dtemp = k_list[ig] - 2 * (
def test_iam_fitdistance():
ds = {
'name': 'MUTAG',
'dataset': '../datasets/MUTAG/MUTAG_A.txt',
'extra_params': {}
} # node/edge symb
Gn, y_all = loadDataset(ds['dataset'], extra_params=ds['extra_params'])
# Gn = Gn[0:50]
# remove_edges(Gn)
gkernel = 'marginalizedkernel'
node_label = 'atom'
edge_label = 'bond_type'
# lmbda = 0.03 # termination probalility
# # parameters for GED function
# c_vi = 0.037
# c_vr = 0.038
# c_vs = 0.075
# c_ei = 0.001
# c_er = 0.001
# c_es = 0.0
# ite_max_iam = 50
# epsilon_iam = 0.001
# removeNodes = False
# connected_iam = False
# # parameters for IAM function
# ged_cost = 'CONSTANT'
# ged_method = 'IPFP'
# edit_cost_constant = [c_vi, c_vr, c_vs, c_ei, c_er, c_es]
# ged_stabilizer = 'min'
# ged_repeat = 50
# params_ged = {'lib': 'gedlibpy', 'cost': ged_cost, 'method': ged_method,
# 'edit_cost_constant': edit_cost_constant,
# 'stabilizer': ged_stabilizer, 'repeat': ged_repeat}
# parameters for GED function
c_vi = 4
c_vr = 4
c_vs = 2
c_ei = 1
c_er = 1
c_es = 1
ite_max_iam = 50
epsilon_iam = 0.001
removeNodes = False
connected_iam = False
# parameters for IAM function
ged_cost = 'CHEM_1'
ged_method = 'IPFP'
edit_cost_constant = []
ged_stabilizer = 'min'
ged_repeat = 50
params_ged = {
'lib': 'gedlibpy',
'cost': ged_cost,
'method': ged_method,
'edit_cost_constant': edit_cost_constant,
'stabilizer': ged_stabilizer,
'repeat': ged_repeat
}
# find out all the graphs classified to positive group 1.
idx_dict = get_same_item_indices(y_all)
Gn = [Gn[i] for i in idx_dict[1]]
# number of graphs; we what to compute the median of these graphs.
# nb_median_range = [2, 3, 4, 5, 10, 20, 30, 40, 50, 100]
nb_median_range = [10]
# # compute Gram matrix.
# time0 = time.time()
# km = compute_kernel(Gn, gkernel, True)
# time_km = time.time() - time0
# # write Gram matrix to file.
# np.savez('results/gram_matrix_marg_itr10_pq0.03_mutag_positive.gm', gm=km, gmtime=time_km)
time_list = []
dis_ks_min_list = []
dis_ks_gen_median_list = []
sod_gs_list = []
# sod_gs_min_list = []
# nb_updated_list = []
# nb_updated_k_list = []
g_best = []
for nb_median in nb_median_range:
print('\n-------------------------------------------------------')
print('number of median graphs =', nb_median)
random.seed(1)
idx_rdm = random.sample(range(len(Gn)), nb_median)
print('graphs chosen:', idx_rdm)
Gn_median = [Gn[idx].copy() for idx in idx_rdm]
Gn_candidate = [g.copy() for g in Gn_median]
# for g in Gn_median:
# nx.draw(g, labels=nx.get_node_attributes(g, 'atom'), with_labels=True)
## plt.savefig("results/preimage_mix/mutag.png", format="PNG")
# plt.show()
# plt.clf()
###################################################################
# gmfile = np.load('results/gram_matrix_marg_itr10_pq0.03_mutag_positive.gm.npz')
# km_tmp = gmfile['gm']
# time_km = gmfile['gmtime']
# # modify mixed gram matrix.
# km = np.zeros((len(Gn) + nb_median, len(Gn) + nb_median))
# for i in range(len(Gn)):
# for j in range(i, len(Gn)):
# km[i, j] = km_tmp[i, j]
# km[j, i] = km[i, j]
# for i in range(len(Gn)):
# for j, idx in enumerate(idx_rdm):
# km[i, len(Gn) + j] = km[i, idx]
# km[len(Gn) + j, i] = km[i, idx]
# for i, idx1 in enumerate(idx_rdm):
# for j, idx2 in enumerate(idx_rdm):
# km[len(Gn) + i, len(Gn) + j] = km[idx1, idx2]
###################################################################
alpha_range = [1 / nb_median] * nb_median
time0 = time.time()
G_gen_median_list, sod_gen_median, sod_list, G_set_median_list, sod_set_median \
= iam_upgraded(Gn_median, Gn_candidate,
c_ei=c_ei, c_er=c_er, c_es=c_es, ite_max=ite_max_iam,
epsilon=epsilon_iam, connected=connected_iam, removeNodes=removeNodes,
params_ged=params_ged)
time_total = time.time() - time0
print('\ntime: ', time_total)
time_list.append(time_total)
# compute distance between \psi and the new generated graphs.
knew = compute_kernel(G_gen_median_list + Gn_median, gkernel,
node_label, edge_label, False)
dhat_new_list = []
for idx, g_tmp in enumerate(G_gen_median_list):
# @todo: the term3 below could use the one at the beginning of the function.
dhat_new_list.append(
dis_gstar(idx,
range(len(G_gen_median_list),
len(G_gen_median_list) + len(Gn_median) + 1),
alpha_range,
knew,
withterm3=False))
print('\nsmallest distance in kernel space: ', dhat_new_list[0])
dis_ks_min_list.append(dhat_new_list[0])
g_best.append(G_gen_median_list[0])
# show the best graph and save it to file.
# print('the shortest distance is', dhat)
print('one of the possible corresponding pre-images is')
nx.draw(G_gen_median_list[0],
labels=nx.get_node_attributes(G_gen_median_list[0], 'atom'),
with_labels=True)
plt.show()
# plt.savefig('results/iam/mutag_median.fit_costs2.001.nb' + str(nb_median) +
# plt.savefig('results/iam/mutag_median_unfit2.nb' + str(nb_median) +
# '.png', format="PNG")
plt.clf()
# print(ghat_list[0].nodes(data=True))
# print(ghat_list[0].edges(data=True))
sod_gs_list.append(sod_gen_median)
# sod_gs_min_list.append(np.min(sod_gen_median))
print('\nsmallest sod in graph space: ', sod_gen_median)
print('\nsmallest sod of set median in graph space: ', sod_set_median)
print('\nsods in graph space: ', sod_gs_list)
# print('\nsmallest sod in graph space for each set of median graphs: ', sod_gs_min_list)
print(
'\nsmallest distance in kernel space for each set of median graphs: ',
dis_ks_min_list)
# print('\nnumber of updates of the best graph for each set of median graphs by IAM: ',
# nb_updated_list)
# print('\nnumber of updates of k nearest graphs for each set of median graphs by IAM: ',
# nb_updated_k_list)
print('\ntimes:', time_list)
def test_iam_letter_h():
from median import draw_Letter_graph
ds = {
'name': 'Letter-high',
'dataset': '../datasets/Letter-high/Letter-high_A.txt',
'extra_params': {}
} # node nsymb
# ds = {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt',
# 'extra_params': {}} # node nsymb
# Gn = Gn[0:50]
Gn, y_all = loadDataset(ds['dataset'], extra_params=ds['extra_params'])
gkernel = 'structuralspkernel'
# parameters for GED function from the IAM paper.
c_vi = 3
c_vr = 3
c_vs = 1
c_ei = 3
c_er = 3
c_es = 1
ite_max_iam = 50
epsilon_iam = 0.001
removeNodes = False
connected_iam = False
# parameters for IAM function
# ged_cost = 'CONSTANT'
ged_cost = 'LETTER'
ged_method = 'IPFP'
# edit_cost_constant = [c_vi, c_vr, c_vs, c_ei, c_er, c_es]
edit_cost_constant = []
ged_stabilizer = 'min'
ged_repeat = 50
params_ged = {
'lib': 'gedlibpy',
'cost': ged_cost,
'method': ged_method,
'edit_cost_constant': edit_cost_constant,
'stabilizer': ged_stabilizer,
'repeat': ged_repeat
}
# classify graphs according to letters.
time_list = []
dis_ks_min_list = []
sod_gs_list = []
g_best = []
sod_set_median_list = []
idx_dict = get_same_item_indices(y_all)
for letter in idx_dict:
print('\n-------------------------------------------------------')
print('letter', letter)
Gn_let = [Gn[i].copy() for i in idx_dict[letter]]
time_list.append([])
dis_ks_min_list.append([])
sod_gs_list.append([])
g_best.append([])
sod_set_median_list.append([])
for repeat in range(50):
idx_rdm = random.sample(range(len(Gn_let)), 50)
print('graphs chosen:', idx_rdm)
Gn_median = [Gn_let[idx].copy() for idx in idx_rdm]
Gn_candidate = [g.copy() for g in Gn_median]
alpha_range = [1 / len(Gn_median)] * len(Gn_median)
time0 = time.time()
ghat_new_list, sod_min, sod_set_median = iam_upgraded(
Gn_median,
Gn_candidate,
c_ei=c_ei,
c_er=c_er,
c_es=c_es,
ite_max=ite_max_iam,
epsilon=epsilon_iam,
connected=connected_iam,
removeNodes=removeNodes,
params_ged=params_ged)
time_total = time.time() - time0
print('\ntime: ', time_total)
time_list[-1].append(time_total)
g_best[-1].append(ghat_new_list[0])
sod_set_median_list[-1].append(sod_set_median)
print('\nsmallest sod of the set median:', sod_set_median)
sod_gs_list[-1].append(sod_min)
print('\nsmallest sod in graph space:', sod_min)
# show the best graph and save it to file.
print('one of the possible corresponding pre-images is')
draw_Letter_graph(ghat_new_list[0],
savepath='results/iam/paper_compare/')
# compute distance between \psi and the new generated graphs.
knew = compute_kernel(ghat_new_list + Gn_median, gkernel, False)
dhat_new_list = []
for idx, g_tmp in enumerate(ghat_new_list):
# @todo: the term3 below could use the one at the beginning of the function.
dhat_new_list.append(
dis_gstar(idx,
range(len(ghat_new_list),
len(ghat_new_list) + len(Gn_median) + 1),
alpha_range,
knew,
withterm3=False))
print('\nsmallest distance in kernel space: ', dhat_new_list[0])
dis_ks_min_list[-1].append(dhat_new_list[0])
print('\nsods of the set median for this letter:',
sod_set_median_list[-1])
print('\nsods in graph space for this letter:', sod_gs_list[-1])
print('\nsmallest distances in kernel space for this letter:',
dis_ks_min_list[-1])
print('\ntimes for this letter:', time_list[-1])
sod_set_median_list[-1] = np.mean(sod_set_median_list[-1])
sod_gs_list[-1] = np.mean(sod_gs_list[-1])
dis_ks_min_list[-1] = np.mean(dis_ks_min_list[-1])
time_list[-1] = np.mean(time_list[-1])
print('\nmean sods of the set median for each letter:',
sod_set_median_list)
print('\nmean sods in graph space for each letter:', sod_gs_list)
print('\nmean smallest distances in kernel space for each letter:',
dis_ks_min_list)
print('\nmean times for each letter:', time_list)
print('\nmean sods of the set median of all:',
np.mean(sod_set_median_list))
print('\nmean sods in graph space of all:', np.mean(sod_gs_list))
print('\nmean smallest distances in kernel space of all:',
np.mean(dis_ks_min_list))
print('\nmean times of all:', np.mean(time_list))
def test_iam_mutag():
ds = {
'name': 'MUTAG',
'dataset': '../datasets/MUTAG/MUTAG_A.txt',
'extra_params': {}
} # node/edge symb
Gn, y_all = loadDataset(ds['dataset'], extra_params=ds['extra_params'])
# Gn = Gn[0:50]
gkernel = 'untilhpathkernel'
node_label = 'atom'
edge_label = 'bond_type'
# parameters for GED function from the IAM paper.
# fitted edit costs.
c_vi = 0.03523843108436513
c_vr = 0.03347339739350128
c_vs = 0.06871290673612238
c_ei = 0.08591999846720685
c_er = 0.07962086440894103
c_es = 0.08596855855478233
# unfitted edit costs.
# c_vi = 3
# c_vr = 3
# c_vs = 1
# c_ei = 3
# c_er = 3
# c_es = 1
ite_max_iam = 50
epsilon_iam = 0.001
removeNodes = False
connected_iam = False
# parameters for IAM function
# ged_cost = 'CONSTANT'
ged_cost = 'CONSTANT'
ged_method = 'IPFP'
edit_cost_constant = [c_vi, c_vr, c_vs, c_ei, c_er, c_es]
# edit_cost_constant = []
ged_stabilizer = 'min'
ged_repeat = 50
params_ged = {
'lib': 'gedlibpy',
'cost': ged_cost,
'method': ged_method,
'edit_cost_constant': edit_cost_constant,
'stabilizer': ged_stabilizer,
'repeat': ged_repeat
}
# classify graphs according to letters.
time_list = []
dis_ks_min_list = []
dis_ks_set_median_list = []
sod_gs_list = []
g_best = []
sod_set_median_list = []
sod_list_list = []
idx_dict = get_same_item_indices(y_all)
for y_class in idx_dict:
print('\n-------------------------------------------------------')
print('class of y:', y_class)
Gn_class = [Gn[i].copy() for i in idx_dict[y_class]]
time_list.append([])
dis_ks_min_list.append([])
dis_ks_set_median_list.append([])
sod_gs_list.append([])
g_best.append([])
sod_set_median_list.append([])
for repeat in range(50):
idx_rdm = random.sample(range(len(Gn_class)), 10)
print('graphs chosen:', idx_rdm)
Gn_median = [Gn_class[idx].copy() for idx in idx_rdm]
Gn_candidate = [g.copy() for g in Gn_median]
alpha_range = [1 / len(Gn_median)] * len(Gn_median)
time0 = time.time()
G_gen_median_list, sod_gen_median, sod_list, G_set_median_list, sod_set_median \
= iam_upgraded(Gn_median,
Gn_candidate, c_ei=c_ei, c_er=c_er, c_es=c_es, ite_max=ite_max_iam,
epsilon=epsilon_iam, connected=connected_iam, removeNodes=removeNodes,
params_ged=params_ged)
time_total = time.time() - time0
print('\ntime: ', time_total)
time_list[-1].append(time_total)
g_best[-1].append(G_gen_median_list[0])
sod_set_median_list[-1].append(sod_set_median)
print('\nsmallest sod of the set median:', sod_set_median)
sod_gs_list[-1].append(sod_gen_median)
print('\nsmallest sod in graph space:', sod_gen_median)
sod_list_list.append(sod_list)
# show the best graph and save it to file.
print('one of the possible corresponding pre-images is')
nx.draw(G_gen_median_list[0],
labels=nx.get_node_attributes(G_gen_median_list[0],
'atom'),
with_labels=True)
# plt.show()
# plt.savefig('results/iam/mutag_median.fit_costs2.001.nb' + str(nb_median) +
# plt.savefig('results/iam/paper_compare/mutag_y' + str(y_class) +
# '_repeat' + str(repeat) + '_' + str(time.time()) +
# '.png', format="PNG")
plt.clf()
# print(G_gen_median_list[0].nodes(data=True))
# print(G_gen_median_list[0].edges(data=True))
# compute distance between \psi and the set median graph.
knew_set_median = compute_kernel(G_set_median_list + Gn_median,
gkernel, node_label, edge_label,
False)
dhat_new_set_median_list = []
for idx, g_tmp in enumerate(G_set_median_list):
# @todo: the term3 below could use the one at the beginning of the function.
dhat_new_set_median_list.append(
dis_gstar(idx,
range(
len(G_set_median_list),
len(G_set_median_list) + len(Gn_median) + 1),
alpha_range,
knew_set_median,
withterm3=False))
print('\ndistance in kernel space of set median: ',
dhat_new_set_median_list[0])
dis_ks_set_median_list[-1].append(dhat_new_set_median_list[0])
# compute distance between \psi and the new generated graphs.
knew = compute_kernel(G_gen_median_list + Gn_median, gkernel,
node_label, edge_label, False)
dhat_new_list = []
for idx, g_tmp in enumerate(G_gen_median_list):
# @todo: the term3 below could use the one at the beginning of the function.
dhat_new_list.append(
dis_gstar(idx,
range(
len(G_gen_median_list),
len(G_gen_median_list) + len(Gn_median) + 1),
alpha_range,
knew,
withterm3=False))
print('\nsmallest distance in kernel space: ', dhat_new_list[0])
dis_ks_min_list[-1].append(dhat_new_list[0])
print('\nsods of the set median for this class:',
sod_set_median_list[-1])
print('\nsods in graph space for this class:', sod_gs_list[-1])
print('\ndistance in kernel space of set median for this class:',
dis_ks_set_median_list[-1])
print('\nsmallest distances in kernel space for this class:',
dis_ks_min_list[-1])
print('\ntimes for this class:', time_list[-1])
sod_set_median_list[-1] = np.mean(sod_set_median_list[-1])
sod_gs_list[-1] = np.mean(sod_gs_list[-1])
dis_ks_set_median_list[-1] = np.mean(dis_ks_set_median_list[-1])
dis_ks_min_list[-1] = np.mean(dis_ks_min_list[-1])
time_list[-1] = np.mean(time_list[-1])
print()
print('\nmean sods of the set median for each class:', sod_set_median_list)
print('\nmean sods in graph space for each class:', sod_gs_list)
print('\ndistances in kernel space of set median for each class:',
dis_ks_set_median_list)
print('\nmean smallest distances in kernel space for each class:',
dis_ks_min_list)
print('\nmean times for each class:', time_list)
print('\nmean sods of the set median of all:',
np.mean(sod_set_median_list))
print('\nmean sods in graph space of all:', np.mean(sod_gs_list))
print('\nmean distances in kernel space of set median of all:',
np.mean(dis_ks_set_median_list))
print('\nmean smallest distances in kernel space of all:',
np.mean(dis_ks_min_list))
print('\nmean times of all:', np.mean(time_list))
nb_better_sods = 0
nb_worse_sods = 0
nb_same_sods = 0
for sods in sod_list_list:
if sods[0] > sods[-1]:
nb_better_sods += 1
elif sods[0] < sods[-1]:
nb_worse_sods += 1
else:
nb_same_sods += 1
print('\n In', str(len(sod_list_list)), 'sod lists,', str(nb_better_sods),
'are getting better,', str(nb_worse_sods), 'are getting worse,',
str(nb_same_sods), 'are not changed; ',
str(nb_better_sods / len(sod_list_list)), 'sods are improved.')
