def test_other_graphs(Gs, signals, lrn, data_state, models_state):
med_err = np.zeros((Gs['n_graphs'], N_EXPS))
mse = np.zeros((Gs['n_graphs'], N_EXPS))
for i in range(Gs['n_graphs']):
Gx, Gy = ds.perturbated_graphs(Gs['params'], Gs['create'], Gs['destroy'],
pct=Gs['pct'], seed=SEED)
data = ds.LinearDS2GSLinksPert(Gx, Gy, signals['samples'], signals['L'],
signals['deltas'], median=signals['median'],
same_coeffs=signals['same_coeffs'])
data.load_state_dict(data_state, unit_norm=True)
data.add_noise(signals['noise'], test_only=signals['test_only'])
sign_dist = np.median(np.linalg.norm(data.train_X-data.train_Y,
axis=1))
print('Distance signals:', sign_dist)
data.to_tensor()
# Create models
for j, exp in enumerate(EXPS):
model = create_model(Gx, Gy, exp, lrn)
model.load_state_dict(models_state[j])
_, med_err[i, j], mse[i, j] = model.test(data.test_X, data.test_Y)
print('Graph {}: {}-{} ({}): mse {} - MedianErr: {}'
.format(i, j, exp['type'], model.count_params(),
mse[i, j], med_err[i, j]))
return med_err, mse
def train_models(Gs, signals, lrn):
# Create data
Gx, Gy = ds.perturbated_graphs(Gs['params'], Gs['create'], Gs['destroy'],
pct=Gs['pct'], seed=SEED)
data = ds.LinearDS2GSLinksPert(Gx, Gy, signals['samples'], signals['L'],
signals['deltas'], median=signals['median'],
same_coeffs=signals['same_coeffs'])
data.to_unit_norm()
data.add_noise(signals['noise'], test_only=signals['test_only'])
sign_dist = np.median(np.linalg.norm(data.train_X-data.train_Y, axis=1))
print('Distance signals:', sign_dist)
data.to_tensor()
data_state = data.state_dict()
# med_err = np.zeros(N_EXPS)
# epochs = np.zeros(N_EXPS)
# mse = np.zeros(N_EXPS)
models_states = []
for i, exp in enumerate(EXPS):
model = create_model(Gx, Gy, exp, lrn)
# Fit models
epochs, _, _ = model.fit(data.train_X, data.train_Y, data.val_X,
data.val_Y)
_, med_error, mse_error = model.test(data.test_X, data.test_Y)
models_states.append(model.state_dict())
print('Original Graph {}-{} ({}): mse {} - MedianErr: {}'
.format(i, exp['type'], model.count_params(),
mse_error, med_error))
print()
return data_state, models_states, Gx, Gy
def test_model(id, signals, nn_params, model_params):
Gx, Gy = data_sets.perturbated_graphs(signals['g_params'], signals['eps1'], signals['eps2'],
pct=signals['pct'], perm=signals['perm'])
# Define the data model
data = data_sets.LinearDS2GSLinksPert(Gx, Gy,
signals['N_samples'],
signals['L_filter'], signals['g_params']['k'], # k is n_delts
median=signals['median'])
data.to_unit_norm()
data.add_noise(signals['noise'], test_only=signals['test_only'])
data.to_tensor()
Gx.compute_laplacian('normalized')
Gy.compute_laplacian('normalized')
archit = GIGOArch(Gx.L.todense(), Gy.L.todense(),
nn_params['Fi'], nn_params['Fo'], nn_params['Ki'], nn_params['Ko'], nn_params['C'],
nn_params['nonlin'], nn_params['last_act_fn'], nn_params['batch_norm'],
nn_params['arch_info'])
model_params['arch'] = archit
model = Model(**model_params)
t_init = time.time()
epochs, _, _ = model.fit(data.train_X, data.train_Y, data.val_X, data.val_Y)
t_conv = time.time() - t_init
mean_err, med_err, mse = model.test(data.test_X, data.test_Y)
print("DONE {}: MSE={} - Mean Err={} - Median Err={} - Params={} - t_conv={} - epochs={}".format(
id, mse, mean_err, med_err, model.count_params(), round(t_conv, 4), epochs
))
return mse, mean_err, med_err, model.count_params(), t_conv, epochs
def test_graph_reproducibility(self):
Gx, Gy = ds.perturbated_graphs(self.G_params, 10,
10, pct=True, seed=SEED)
print('Link x:', Gx.Ne)
print('Link y:', Gy.Ne)
self.assertEqual(1664, Gx.Ne)
self.assertEqual(1664, Gy.Ne)
print('Diff links:', np.sum(Gx.A != Gy.A)/2/Gx.Ne)
self.assertAlmostEqual(0.19951923076923078,
np.sum(Gx.A != Gy.A)/2/Gx.Ne)
def test_permute_graph(self):
Gx, Gy = ds.perturbated_graphs(self.G_params, 0, 0,
perm=True, pct=True, seed=SEED)
Ax = Gx.W.todense()
Ay = Gy.W.todense()
comm_X = Gx.info['node_com']
comm_Y = Gy.info['node_com']
P = Gy.info['perm_matrix']
self.assertFalse(np.array_equal(Ax, Ay))
self.assertFalse(np.array_equal(comm_X, comm_Y))
self.assertTrue(np.array_equal(np.eye(Gx.N), P.dot(P.T)))
self.assertTrue(np.array_equal(Ax, P.T.dot(Ay).dot(P)))
self.assertTrue(np.array_equal(comm_X, P.T.dot(comm_Y)))
def setUp(self):
np.random.seed(SEED)
self.G_params = {}
self.G_params['type'] = ds.SBM
self.G_params['N'] = 32
self.G_params['k'] = 4
self.G_params['p'] = 0.8
self.G_params['q'] = 0.1
self.G_params['type_z'] = ds.RAND
self.eps1 = 5
self.eps2 = 5
self.Gx, self.Gy = ds.perturbated_graphs(self.G_params, self.eps1,
self.eps2, seed=SEED)
def test_permutated_S(self):
n_samps = [50, 20, 20]
L = 6
n_delts = self.G_params['k']
Gx, Gy = ds.perturbated_graphs(self.G_params, 0, 0,
perm=True, seed=SEED)
data = ds.LinearDS2GSLinksPert(Gx, Gy, n_samps, L, n_delts)
P = data.Gy.info['perm_matrix']
self.assertFalse(np.array_equal(data.Hx, data.Hy))
self.assertFalse(np.array_equal(data.train_Sx, data.train_Sy))
self.assertFalse(np.array_equal(data.val_Sx, data.val_Sy))
self.assertFalse(np.array_equal(data.test_Sx, data.test_Sy))
self.assertTrue(np.array_equal(data.train_Sx, data.train_Sy.dot(P)))
self.assertTrue(np.array_equal(data.val_Sx, data.val_Sy.dot(P)))
self.assertTrue(np.array_equal(data.test_Sx, data.test_Sy.dot(P)))
def test_model(id, signals, nn_params, model_params):
Gx, Gy = data_sets.perturbated_graphs(signals['g_params'],
signals['eps1'],
signals['eps2'],
pct=signals['pct'],
perm=signals['perm'])
# Define the data model
data = data_sets.LinearDS2GSLinksPert(
Gx,
Gy,
signals['N_samples'],
signals['L_filter'],
signals['g_params']['k'], # k is n_delts
median=signals['median'])
data.to_unit_norm()
data.add_noise(signals['noise'], test_only=signals['test_only'])
data.to_tensor()
if nn_params['arch_type'] == "basic":
Gx.compute_laplacian('normalized')
archit = BasicArch(Gx.L.todense(), nn_params['F'], nn_params['K'],
nn_params['M'], nn_params['nonlin'], ARCH_INFO)
elif nn_params['arch_type'] == "mlp":
archit = MLP(nn_params['F'], nn_params['nonlin'], ARCH_INFO)
elif nn_params['arch_type'] == "conv":
archit = ConvNN(N, nn_params['F'], nn_params['K'], nn_params['nonlin'],
nn_params['M'], ARCH_INFO)
elif nn_params['arch_type'] == "linear":
archit = MLP(nn_params['F'], nn_params['nonlin'], ARCH_INFO)
else:
raise RuntimeError("arch_type has to be either basic, mlp or conv")
model_params['arch'] = archit
model = Model(**model_params)
t_init = time.time()
epochs, _, _ = model.fit(data.train_X, data.train_Y, data.val_X,
data.val_Y)
t_conv = time.time() - t_init
mean_err, med_err, mse = model.test(data.test_X, data.test_Y)
print(
"DONE {}: MSE={} - Mean Err={} - Median Err={} - Params={} - t_conv={} - epochs={}"
.format(id, mse, mean_err, med_err, model.count_params(),
round(t_conv, 4), epochs),
flush=True)
return mse, mean_err, med_err, model.count_params(), t_conv, epochs
def test_percentage_perturbation(self):
create = destroy = 5
up_err_margin = (create + destroy + 2)/100
bottom_err_margin = (create + destroy - 2)/100
for i in range(10):
Gx, Gy = ds.perturbated_graphs(self.G_params, create,
destroy, pct=True, seed=SEED)
Ax = Gx.W.todense()
Ay = Gy.W.todense()
print('diff:', np.sum(Ax != Ay)/Gx.Ne/2)
self.assertFalse(Gx.is_directed())
self.assertTrue(Gx.is_connected())
self.assertEqual(np.sum(np.diag(Ax)), 0)
self.assertFalse(Gy.is_directed())
self.assertTrue(Gy.is_connected())
self.assertEqual(np.sum(np.diag(Ay)), 0)
self.assertTrue(np.sum(Ax != Ay)/Gx.Ne/2 <= up_err_margin)
self.assertTrue(np.sum(Ax != Ay)/Gx.Ne/2 >= bottom_err_margin)
def test_S_ER(self):
n_samps = [50, 20, 20]
L = 6
n_delts = 6
self.G_params['type'] = ds.ER
Gx, Gy = ds.perturbated_graphs(self.G_params, self.eps1, self.eps2, seed=SEED)
data = ds.LinearDS2GS(Gx, Gy, n_samps, L, n_delts)
data.to_unit_norm()
self.assertFalse(np.array_equal(data.Hx, data.Hy))
for i in range(n_samps[0]):
self.assertLessEqual(np.sum(data.train_Sx[i,:][data.train_Sx[i,:]!=0]), n_delts)
self.assertLessEqual(np.sum(data.train_Sy[i,:][data.train_Sy[i,:]!=0]), n_delts)
for i in range(n_samps[1]):
self.assertLessEqual(np.sum(data.train_Sx[i,:][data.train_Sx[i,:]!=0]), n_delts)
self.assertLessEqual(np.sum(data.train_Sy[i,:][data.train_Sy[i,:]!=0]), n_delts)
for i in range(n_samps[2]):
self.assertLessEqual(np.sum(data.train_Sx[i,:][data.train_Sx[i,:]!=0]), n_delts)
self.assertLessEqual(np.sum(data.train_Sy[i,:][data.train_Sy[i,:]!=0]), n_delts)
def test_probability_perturbation(self):
create = 0.0005
destroy = 0.05
n_graphs = 10
diff_links = np.zeros(n_graphs)
exp_err = np.zeros(n_graphs)
margin = 6
for i in range(n_graphs):
Gx, Gy = ds.perturbated_graphs(self.G_params, create,
destroy, pct=False, seed=SEED)
Ax = Gx.W.todense()
Ay = Gy.W.todense()
self.assertFalse(Gx.is_directed())
self.assertTrue(Gx.is_connected())
self.assertEqual(np.sum(np.diag(Ax)), 0)
self.assertFalse(Gy.is_directed())
self.assertTrue(Gy.is_connected())
self.assertEqual(np.sum(np.diag(Ay)), 0)
diff_links[i] = np.sum(Ax != Ay)/Gx.Ne/2
exp_err[i] = (create*(Gx.N*(Gx.N-1)/2-Gx.Ne) + Gx.Ne*destroy)/Gx.N
self.assertTrue(np.mean(diff_links) <= (np.mean(exp_err)+margin)/100)
self.assertTrue(np.mean(diff_links) >= (np.mean(exp_err)-margin)/100)
def estimate_signals(i, G_params, eps_c, eps_d, n_samples, L, nodes_enc,
nodes_dec, ups, feat_enc, feat_dec, feat_only_conv):
# Create graphs
Gx, Gy = data_sets.perturbated_graphs(G_params, eps_c, eps_d, seed=SEED)
# Create graph signals
data = data_sets.LinearDS2GS(Gx,
Gy,
n_samples,
L,
3 * G_params['k'],
median=True)
data.to_unit_norm()
print('Median Diff between Y and X:',
np.median(np.linalg.norm((data.train_X - data.train_Y)**2, 1)))
X = data.train_X
Beta = np.linalg.pinv(X.T.dot(X)).dot(X.T).dot(data.train_Y)
test_Y = data.test_Y
est_Y_test = data.test_X.dot(Beta)
test_err = np.sum(
(est_Y_test - test_Y)**2, axis=1) / np.linalg.norm(data.test_Y)**2
print('Linear model: mean err: {} - median: {}'.format(
np.mean(test_err), np.median(test_err)))
data.to_tensor()
# Obtein clusters
cluster_x = gc.MultiResGraphClustering(Gx, nodes_enc, k=4, up_method=None)
cluster_y = gc.MultiResGraphClustering(Gy, nodes_dec, k=4, up_method=ups)
# Standar ConvAutoenc
net = architecture.GraphEncoderDecoder(feat_enc, [Gx.N] * 7,
cluster_x.Ds,
feat_dec, [Gx.N] * 7,
cluster_y.Us,
feat_only_conv,
As_dec=cluster_y.As,
last_act_fn=nn.Tanh(),
act_fn=nn.Tanh())
model = Model(net,
decay_rate=.9,
epochs=25,
batch_size=100,
learning_rate=0.05,
verbose=True,
eval_freq=1,
max_non_dec=5)
print('Model parameters: ', model.count_params())
model.fit(data.train_X, data.train_Y, data.val_X, data.val_Y)
mean_err, median_err, mse = model.test(data.test_X, data.test_Y)
print(
'Autoencoder: Graph {}: N: {} Mean MSE: {} - Mean Err: {} - Median Err: {}'
.format(i, Gx.N, mse, mean_err, median_err))
# Graph Autoenc
net = architecture.GraphEncoderDecoder(feat_enc,
cluster_x.sizes,
cluster_x.Ds,
feat_dec,
cluster_y.sizes,
cluster_y.Us,
feat_only_conv,
As_dec=cluster_y.As,
last_act_fn=nn.Tanh(),
act_fn=nn.Tanh())
model = Model(net,
decay_rate=.9,
epochs=25,
batch_size=100,
learning_rate=0.05,
verbose=True,
eval_freq=1,
max_non_dec=5)
print('Model parameters: ', model.count_params())
model.fit(data.train_X, data.train_Y, data.val_X, data.val_Y)
mean_err, median_err, mse = model.test(data.test_X, data.test_Y)
print(
'GRAPH ENC-DEC Graph {}: N: {} Mean MSE: {} - Mean Err: {} - Median Err: {}'
.format(i, Gx.N, mse, mean_err, median_err))
return mean_err, mse, model.count_params()
def estimate_signals(id, G_params, n_samples, L, nodes_enc, nodes_dec, ups,
feat_enc, feat_dec, feat_only_conv):
# Create graphs
Gx, Gy = data_sets.perturbated_graphs(G_params,
creat,
dest,
pct=pct,
seed=SEED)
diff_links = np.sum(Gx.A != Gy.A) / 2 / Gx.Ne * 100
print('Links different(%):', diff_links)
# Create graph signals
data = data_sets.NonLinearDS2GS(Gx,
Gy,
n_samples,
L,
deltas,
median=median,
same_coeffs=same_coeffs)
data.to_unit_norm()
data.add_noise(p_n, test_only=True)
mean_dist = np.median(np.linalg.norm(data.train_X - data.train_Y, axis=1))
print('Distance signals:', mean_dist)
data.to_tensor()
N = G_params['N']
k = G_params['k']
model = LinearModel(N)
model.fit(data.train_X, data.train_Y, data.val_X, data.val_Y)
mean_err, med_err, mse = model.test(data.test_X, data.test_Y)
print(
'LINEAR Graph {}: N: {} Mean MSE: {} - Mean Err: {} - Median Err: {}'.
format(id, Gx.N, mse, mean_err, med_err))
# Obtein clusters
cluster_x = gc.MultiResGraphClustering(Gx, nodes_enc, k=k, up_method=ups)
cluster_y = gc.MultiResGraphClustering(Gy, nodes_dec, k=k, up_method=ups)
# Graph Autoenc
net = architecture.GraphEncoderDecoder(feat_enc,
cluster_x.sizes,
cluster_x.Ds,
feat_dec,
cluster_y.sizes,
cluster_y.Us,
feat_only_conv,
As_dec=cluster_y.As,
As_enc=cluster_x.As,
ups=ups,
last_act_fn=nn.Tanh(),
downs=ups,
act_fn=nn.Tanh())
model = Model(net,
decay_rate=dr,
epochs=epochs,
batch_size=bs,
learning_rate=lr,
verbose=False,
eval_freq=1,
max_non_dec=10)
print('Model parameters: ', model.count_params())
iters, _, _ = model.fit(data.train_X, data.train_Y, data.val_X, data.val_Y)
mean_err, med_err, mse = model.test(data.test_X, data.test_Y)
print('G: {}, ({}): epochs {} - mse {} - MedianErr: {}'.format(
id, model.count_params(), iters, mse, med_err))
return mean_err, mse, med_err, diff_links, mean_dist, iters
def run(id, Gs, signals, lrn, p_n):
Gx, Gy = ds.perturbated_graphs(Gs['params'],
Gs['pct_val'][0],
Gs['pct_val'][1],
pct=Gs['pct'],
seed=SEED)
data = ds.LinearDS2GS(Gx,
Gy,
signals['samples'],
signals['L'],
signals['deltas'],
median=signals['median'],
same_coeffs=signals['same_coeffs'])
# data = ds.NonLinearDS2GS(Gx, Gy, signals['samples'], signals['L'],
# signals['deltas'], median=signals['median'],
# same_coeffs=signals['same_coeffs'])
data.to_unit_norm()
data.add_noise(p_n, test_only=signals['test_only'])
median_dist = np.median(np.linalg.norm(data.train_X - data.train_Y,
axis=1))
print('Signal {}: distance {}'.format(id, median_dist))
data.to_tensor()
med_err = np.zeros(N_EXPS)
mse = np.zeros(N_EXPS)
epochs = np.zeros(N_EXPS)
for i, exp in enumerate(EXPS):
clust_x = gc.MultiResGraphClustering(Gx,
exp['n_enc'],
k=exp['n_enc'][-1],
up_method=exp['downs'])
clust_y = gc.MultiResGraphClustering(Gy,
exp['n_dec'],
k=exp['n_enc'][-1],
up_method=exp['ups'])
net = GraphEncoderDecoder(exp['f_enc'],
clust_x.sizes,
clust_x.Ds,
exp['f_dec'],
clust_y.sizes,
clust_y.Us,
exp['f_conv'],
As_dec=clust_y.As,
As_enc=clust_x.As,
act_fn=lrn['af'],
last_act_fn=lrn['laf'],
ups=exp['ups'],
downs=exp['downs'])
model = Model(net,
learning_rate=lrn['lr'],
decay_rate=lrn['dr'],
batch_size=lrn['batch'],
epochs=lrn['epochs'],
eval_freq=EVAL_F,
max_non_dec=lrn['non_dec'],
verbose=VERBOSE)
epochs[i], _, _ = model.fit(data.train_X, data.train_Y, data.val_X,
data.val_Y)
_, med_err[i], mse[i] = model.test(data.test_X, data.test_Y)
print('G: {}, {}-{} ({}): epochs {} - mse {} - MedianErr: {}'.format(
id, i, exp['type'], model.count_params(), epochs[i], mse[i],
med_err[i]))
return med_err, mse, epochs
def run(id, Gs, Signals, lrn, samples):
Gx, Gy = ds.perturbated_graphs(Gs['params'],
Gs['pct_val'][0],
Gs['pct_val'][1],
pct=Gs['pct'],
perm=Gs['perm'],
seed=SEED)
data = ds.LinearDS2GSLinksPert(Gx,
Gy,
samples,
Signals['L'],
Signals['deltas'],
median=Signals['median'],
same_coeffs=Signals['same_coeffs'])
data.to_unit_norm()
data.add_noise(Signals['noise'], test_only=Signals['test_only'])
data.to_tensor()
params = np.zeros(N_EXPS)
epochs = np.zeros(N_EXPS)
med_err = np.zeros(N_EXPS)
mse = np.zeros(N_EXPS)
for i, exp in enumerate(EXPS):
if exp['type'] == 'Linear':
model = LinearModel(exp['N'])
elif exp['type'] == 'Enc_Dec':
clust_x = gc.MultiResGraphClustering(Gx,
exp['n_enc'],
k=exp['n_enc'][-1],
up_method=exp['downs'])
clust_y = gc.MultiResGraphClustering(Gy,
exp['n_dec'],
k=exp['n_enc'][-1],
up_method=exp['ups'])
net = GraphEncoderDecoder(exp['f_enc'],
clust_x.sizes,
clust_x.Ds,
exp['f_dec'],
clust_y.sizes,
clust_y.Us,
exp['f_conv'],
As_dec=clust_y.As,
As_enc=clust_x.As,
act_fn=lrn['af'],
K_dec=exp['K_dec'],
K_enc=exp['K_enc'],
last_act_fn=lrn['laf'],
ups=exp['ups'],
downs=exp['downs'])
elif exp['type'] == 'AutoConv':
net = ConvAutoencoder(exp['f_enc'], exp['kernel_enc'],
exp['f_dec'], exp['kernel_dec'])
elif exp['type'] == 'AutoFC':
net = FCAutoencoder(exp['n_enc'], exp['n_dec'], bias=exp['bias'])
else:
raise RuntimeError('Unknown experiment type')
if exp['type'] != 'Linear':
model = Model(net,
learning_rate=lrn['lr'],
decay_rate=lrn['dr'],
batch_size=lrn['batch'],
epochs=lrn['epochs'],
eval_freq=EVAL_F,
max_non_dec=lrn['non_dec'],
verbose=VERBOSE,
early_stop=exp['early_stop'])
epochs[i], _, _ = model.fit(data.train_X, data.train_Y, data.val_X,
data.val_Y)
_, med_err[i], mse[i] = model.test(data.test_X, data.test_Y)
params[i] = model.count_params()
print('G: {}, {}-{} ({}): epochs {} - mse {} - MedianErr: {}'.format(
id, i, exp['type'], params[i], epochs[i], mse[i], med_err[i]))
return params, med_err, mse