T = 16
lr = 0.5
its = 1500
fix_mix_its = int(its * 0.5)
logging_itv = 50
utils.set_log_potential_funs(
g.factors_list,
skip_existing=True) # g factors' lpot_fun should still be None
# above will also set the lpot_fun in all the (completely unobserved) factors in cond_g
if algo_name in ('OSI', 'NPVI'):
if cond: # TODO: ugly; fix
_g = cond_g
else:
_g = g
if algo_name == 'OSI':
vi = OneShot(g=_g, K=K, T=T, seed=seed)
else:
vi = NPVI(g=_g, K=K, T=T, isotropic_cov=False, seed=seed)
else:
if cond:
cg = CompressedGraphSorted(cond_g)
else:
# technically incorrect; currently we should run LOSI on the conditional MRF
cg = CompressedGraphSorted(g)
cg.run()
print('number of rvs in cg', len(cg.rvs))
print('number of factors in cg', len(cg.factors))
if algo_name == 'LOSI':
vi = LiftedOneShot(g=cg, K=K, T=T, seed=seed)
else:
vi = LiftedNPVI(g=cg, K=K, T=T, seed=seed)
def __init__(self, fileName, maxDuration, queue, prereqs = None):
OneShot.__init__(self, fileName, maxDuration, prereqs)
self.queue = queue
def stop(self, source, target, callbackFn):
OneShot.stop(self, source, target, callbackFn)
self.queue.put(self)
T = 10
# lr = 1e-1
lr = 5e-1
# its = 1000
its = 500
# fix_mix_its = int(its * 0.1)
fix_mix_its = int(its * 1.0)
# fix_mix_its = 500
logging_itv = 100
# cond = True
cond = True
if cond:
cond_g.init_nb(
) # this will make cond_g rvs' .nb attributes consistent (baseline didn't care so it was OK)
if cond:
osi = OneShot(g=cond_g, K=K, T=T, seed=seed)
else:
osi = OneShot(g=g, K=K, T=T, seed=seed)
if cond: # clearn up just in case someone need to uses rvs.nb in g later
for i, rv in enumerate(g.rvs_list):
rv.nb = g_rv_nbs[
i] # restore; undo possible mutation from cond_g.init_nb()
start_time = time.process_time()
osi.run(lr=lr, its=its, fix_mix_its=fix_mix_its, logging_itv=logging_itv)
# print('Mu =\n', osi.params['Mu'], '\nVar =\n', osi.params['Var'])
time_cost[name] = (time.process_time() -
start_time) / num_test + time_cost.get(name, 0)
print(name, f'time {time.process_time() - start_time}')
err = []
pred = {}
for key in key_list:
# time_cost[name] = (time.process_time() - start_time) / num_runs / num_tests + time_cost.get(name, 0)
# print(name, f'time {time.process_time() - start_time}')
for i, rv in enumerate(rvs):
mmap_res[algo, i] = bp.map(rv)
algo += 1
name = names[algo]
utils.set_log_potential_funs(
g.factors_list) # OSI assumes factors have callable .log_potential_fun
K = 2
T = 10
lr = 0.2
its = 10
fix_mix_its = int(its * 0.8)
osi = OneShot(
g, K,
T) # can be moved outside of all loops if the ground MRF doesn't change
osi.run(its, lr=lr)
for i, rv in enumerate(rvs):
mmap_res[algo, i] = osi.map(rv)
# ground truth
# first, need to convert factor.log_potential_funs to one of (LogTable, LogQuadratic, LogHybridQuadratic);
# this can be done by first converting the corresponding potentials to one of (TablePotential, QuadraticPotential,
# HybridQuadraticPotential), then calling the .to_log_potential method on the potential objects
# manual conversion here:
# factors[0].potential = HybridQuadraticPotential(
# A=-factors[0].potential.w * np.array([np.array([[1., 0], [0, 0]]), np.array([[1., 0.], [0., 0.]])]),
# b=-factors[0].potential.w * np.array([[-16., 0], [14., 0.]]),
# c=-factors[0].potential.w * np.array([64., 49.])
# )
rel_g = RelationalGraph()
rel_g.atoms = (atom_friend, atom_smoke_x, atom_cancer)
rel_g.param_factors = (f1, f2)
rel_g.init_nb()
rel_g.data = data
g, rvs_table = rel_g.grounded_graph()
print(rvs_table)
from OneShot import OneShot
utils.set_log_potential_funs(g.factors_list)
K = 4
T = 8
osi = OneShot(g=g, K=K, T=T, seed=seed)
res = osi.run(lr=1e-1, its=200)
for key, rv in sorted(rvs_table.items()):
if rv.value is None: # only test non-evidence nodes
print(key, osi.map(obs_rvs=[], query_rv=rv))
import matplotlib.pyplot as plt
record = res['record']
for key in record:
plt.plot(record[key], label=key)
plt.legend(loc='best')
save_name = __file__.split('.py')[0]
plt.savefig('%s.png' % save_name)
# EPBP inference
for i, key in enumerate(key_list):
res[i, :] -= ans[key]
avg_diff[name] = np.average(np.average(
abs(res), axis=1)) / num_test + avg_diff.get(name, 0)
err_var[name] = np.average(np.average(
res**2, axis=1)) / num_test + err_var.get(name, 0)
print(name, 'diff', np.average(np.average(abs(res), axis=1)))
print(
name, 'var',
np.average(np.average(res**2, axis=1)) -
np.average(np.average(abs(res), axis=1))**2)
name = 'OSI'
res = np.zeros((len(key_list), 5))
osi = OneShot(
g, num_mixtures=1, num_quadrature_points=2
) # can be moved outside of all loops, as the ground MRF doesn't change
for j in range(5):
start_time = time.process_time()
osi.run(200, lr=2)
time_cost[name] = (time.process_time() -
start_time) / 5 / num_test + time_cost.get(name, 0)
print(name, f'time {time.process_time() - start_time}')
for i, key in enumerate(key_list):
res[i, j] = osi.map(rvs_table[key])
for i, key in enumerate(key_list):
res[i, :] -= ans[key]
avg_diff[name] = np.average(np.average(
abs(res), axis=1)) / num_test + avg_diff.get(name, 0)
err_var[name] = np.average(np.average(
res**2, axis=1)) / num_test + err_var.get(name, 0)
for rv in g.rvs:
if rv.value is not None:
num_evidence += 1
print('number of evidence', num_evidence)
start_time = time.process_time()
bp.run(20, log_enable=False)
time_cost.append(time.process_time() - start_time)
print('time lapse', time.process_time() - start_time)
for idx, rv in enumerate(rvs_table[t - 1]):
result[idx, i] = bp.map(rv)
elif algo == 'OSI':
if cond:
osi = OneShot(g=cond_g, K=K, T=T, seed=seed)
else:
osi = OneShot(g=g, K=K, T=T, seed=seed)
start_time = time.process_time()
osi.run(lr=lr,
its=its,
fix_mix_its=fix_mix_its,
logging_itv=logging_itv)
time_cost.append(time.process_time() - start_time)
# print('Mu =\n', osi.params['Mu'], '\nVar =\n', osi.params['Var'])
print(algo, f'time {time_cost[-1]}')
for idx, rv in enumerate(rvs_table[t - 1]):
if cond:
result[idx, i] = osi.map(obs_rvs=[], query_rv=rv)
else:
T = 16
lr = 0.5
its = 1500
fix_mix_its = int(its * 0.2)
logging_itv = 500
utils.set_log_potential_funs(
g.factors_list,
skip_existing=True) # g factors' lpot_fun should still be None
# above will also set the lpot_fun in all the (completely unobserved) factors in cond_g
if algo_name in ('OSI', 'NPVI'):
if cond: # TODO: ugly; fix
_g = cond_g
else:
_g = g
if algo_name == 'OSI':
vi = OneShot(g=_g, K=K, T=T, seed=test_seed)
else:
vi = NPVI(g=_g,
K=K,
T=T,
isotropic_cov=False,
seed=test_seed)
else:
if cond:
cg = CompressedGraphSorted(cond_g)
else:
# technically incorrect; currently we should run LOSI on the conditional MRF
cg = CompressedGraphSorted(g)
cg.run()
print('number of rvs in cg', len(cg.rvs))
print('number of factors in cg', len(cg.factors))
print(params)
if 'pi' in params:
print(w @ params['pi'])
if 'mu' in params:
print(w @ params['mu'])
import matplotlib.pyplot as plt
record = res['record']
# for key in record:
# plt.plot(record[key], label=key)
plt.plot(record['bfe'], label='bfe (with lifting)')
print('no lifting')
osi = OneShot(g=g, K=K, T=T, seed=seed)
res = osi.run(lr=lr, its=its)
w = res['w']
for rv in sorted(g.rvs):
print(rv)
params = rv.belief_params
print(params)
if 'pi' in params:
print(w @ params['pi'])
if 'mu' in params:
print(w @ params['mu'])
import matplotlib.pyplot as plt
record = res['record']
# for key in record:
"""Unplugs any children that have terminated, and returns true if there are no
running child components left (ie. their microproceses have finished)
"""
for child in self.childComponents():
if child._isStopped():
self.removeChild(child) # deregisters linkages for us
return 0==len(self.childComponents())
__kamaelia_components__ = ( Seq, )
if __name__=="__main__":
from Kamaelia.Chassis.Pipeline import Pipeline
from OneShot import OneShot
from Kamaelia.Util.Console import ConsoleEchoer
Pipeline( Seq( "BEGIN SEQUENCE",
OneShot("Hello\n"),
OneShot("Doctor\n"),
OneShot("Name\n"),
OneShot("Continue\n"),
OneShot("Yesterday\n"),
OneShot("Tomorrow\n"),
"END SEQUENCE",
),
ConsoleEchoer(),
).run()
res**2, axis=1)) / num_tests + err_var.get(name, 0)
print(name, 'diff', np.average(np.average(abs(res), axis=1)))
print(
name, 'var',
np.average(np.average(res**2, axis=1)) -
np.average(np.average(abs(res), axis=1))**2)
name = 'OSI'
K = 5
T = 20
lr = 0.1
its = 200
fix_mix_its = int(its * 0.)
res = np.zeros((len(key_list), num_runs))
osi = OneShot(
g=g, K=K, T=T, seed=seed
) # can be moved outside of all loops if the ground MRF doesn't change
for j in range(num_runs):
start_time = time.process_time()
osi.run(lr=lr, its=its, fix_mix_its=fix_mix_its)
time_cost[name] = (time.process_time() -
start_time) / num_runs / num_tests + time_cost.get(
name, 0)
print(name, f'time {time.process_time() - start_time}')
for i, key in enumerate(key_list):
res[i, j] = osi.map(rvs_table[key])
print(res[:, j])
# print(osi.params)
print('Mu =\n', osi.params['Mu'], '\nVar =\n', osi.params['Var'])
for i, key in enumerate(key_list):
res[i, :] -= ans[key]
# time_cost[name] = (time.process_time() - start_time) / num_runs / num_tests + time_cost.get(name, 0)
# print(name, f'time {time.process_time() - start_time}')
for i, rv in enumerate(rvs):
mmap_res[algo, i] = bp.map(rv)
algo += 1
name = names[algo]
utils.set_log_potential_funs(
g.factors_list) # OSI assumes factors have callable .log_potential_fun
K = 2
T = 12
lr = 0.5
its = 200
fix_mix_its = int(its * 0.5)
osi = OneShot(
g=g, K=K, T=T, seed=seed
) # can be moved outside of all loops if the ground MRF doesn't change
osi.run(lr=lr, its=its, fix_mix_its=fix_mix_its)
# print('osi params', osi.params)
for i, rv in enumerate(rvs):
mmap_res[algo, i] = osi.map(obs_rvs=[], query_rv=rv)
# ground truth
# first, need to convert factor.log_potential_funs to one of (LogTable, LogQuadratic, LogHybridQuadratic);
# this can be done by first converting the corresponding potentials to one of (TablePotential, QuadraticPotential,
# HybridQuadraticPotential), then calling the .to_log_potential method on the potential objects
# manual conversion here:
factors[0].potential = HybridQuadraticPotential(
A=-factors[0].potential.w *
np.array([np.array([[1., 0], [0, 0]]),
np.array([[0., 0.], [0., 1.]])]),
rel_g.init_nb()
rel_g.data = data
g, rvs_table = rel_g.grounded_graph()
from OneShot import OneShot
utils.set_log_potential_funs(
g.factors_list) # OSI assumes factors have callable .log_potential_fun
grad_check = False
if not grad_check:
K = 3
T = 20
lr = 1e-2
its = 500
osi = OneShot(g=g, K=K, T=T, seed=seed)
res = osi.run(lr=lr, its=its)
record = res['record']
del res['record']
print(res)
for key, rv in rvs_table.items():
if rv.value is None: # only test non-evidence nodes
print(rv, key, osi.map(obs_rvs=[], query_rv=rv))
import matplotlib.pyplot as plt
for key in record:
plt.plot(record[key], label=key)
plt.legend(loc='best')
save_name = __file__.split('.py')[0]
plt.savefig('%s.png' % save_name)
def __init__(self, fileName, maxDuration, queue, prereqs=None):
OneShot.__init__(self, fileName, maxDuration, prereqs)
self.queue = queue
# marg_kls = np.zeros(len(query_rvs)) - 123
map_energy = -123
obj = -1
cpu_time = wall_time = -1 # don't care
if algo_name in ('OSI', 'LOSI', 'NPVI', 'LNPVI'):
# K = 1
T = 3
lr = 0.5
its = 1000
fix_mix_its = int(its * 0.5)
logging_itv = 100
if algo_name in ('OSI', 'NPVI'):
if algo_name == 'OSI':
vi = OneShot(g=cond_g, K=K, T=T, seed=test_seed)
else:
vi = NPVI(g=cond_g,
K=K,
T=T,
isotropic_cov=False,
seed=test_seed)
start_time = time.process_time()
start_wall_time = time.time()
res = vi.run(lr=lr,
its=its,
fix_mix_its=fix_mix_its,
logging_itv=logging_itv)
cpu_time = time.process_time() - start_time
wall_time = time.time() - start_wall_time
def stop(self, source, target, callbackFn):
OneShot.stop(self, source, target, callbackFn)
self.queue.put(self)
print('true -log Z =', -np.log(Z))
g = Graph()
g.rvs = rvs
g.factors = factors
g.init_nb()
g.init_rv_indices()
from OneShot import OneShot
grad_check = False
if not grad_check:
K = 4
T = 30
lr = 5e-1
osi = OneShot(g=g, K=K, T=T, seed=seed)
optimizer = tf.train.GradientDescentOptimizer(learning_rate=lr)
res = osi.run(lr=lr, optimizer=optimizer, its=1000)
w = res['w']
w_row = w[None, :]
for rv in sorted(g.rvs):
params = rv.belief_params
print(params)
if 'pi' in params:
print(w @ params['pi'])
if 'mu' in params:
print(w @ params['mu'])
import matplotlib.pyplot as plt
record = res['record']