in_fpath = 'example/lastfm_our.dat'
size = sum(1 for _ in open(in_fpath))
nz = 50
#Intervent kernel with eccdf heuristic. Priors are for the beta distribution.
inter_event_kernel = kernels.names['eccdf']()
priors = np.array([1.0, nz - 1])
inter_event_kernel.build(size, nz, priors)
#Trace, num envs, alpha prior, beta prior, kernel, kernels priors as array
#num iter, burn in
rv = fit(in_fpath, nz, nz / 10, .001, inter_event_kernel, priors, 800, 300)
out_fpath = 'example/model.h5'
dataio.save_model(out_fpath, rv)
#Let's load the model so that we can get a feel of how to work with the pandas
#output
model = pd.HDFStore(out_fpath, 'r')
#Let's print the top 5 objects for each env.
Psi_sz = model["Psi_sz"].values
id2obj = dict((v, k) for k, v in model["source2id"].values)
for z in xrange(nz):
top = Psi_sz[:, z].argsort()[::-1][:5]
print(z)
for i in xrange(5):
print(id2obj[top[i]])
def main():
parser = argparse.ArgumentParser()
parser.add_argument('trace_fpath', help='The trace to learn topics from', \
type=str)
parser.add_argument('num_topics', help='The number of topics to learn', \
type=int)
parser.add_argument('model_fpath', \
help='The name of the model file (a h5 file)', type=str)
parser.add_argument('--num_iter', help='The number of iterations', \
type=int, default=1000)
parser.add_argument('--burn_in', \
help='The burn in (ignored if using mpi)', type=int, \
default=300)
parser.add_argument('--dynamic', \
help='If we should employ the dynamic strategy', \
type=bool, default=False)
parser.add_argument('--num_batches', \
help='Number of batches in dynamic case', type=int, default=10)
parser.add_argument('--alpha_zh', \
help='Value of alpha_zh (alpha) hyper. Defaults to 50 / nz', \
type=float, default=None)
parser.add_argument('--beta_zs', help='Value of beta_zs (beta) hyper', \
type=float, default=0.001)
parser.add_argument('--kernel',
choices=kernels.names,
help='The kernel to use',
type=str,
default='noop')
parser.add_argument('--residency_priors',
nargs='+',
help='Priors for the residency time dist',
type=float,
default=None)
parser.add_argument('--leaveout', \
help='The number of transitions to leave for test', type=float, \
default=0)
args = parser.parse_args()
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
try:
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
single_thread = size <= 1
except:
single_thread = True
if not single_thread and rank != plearn.MASTER:
plearn.work()
else:
started = time.mktime(time.localtime())
num_lines = 0
with open(args.trace_fpath) as trace_file:
num_lines = sum(1 for _ in trace_file)
if args.leaveout > 0:
leave_out = min(1, args.leaveout)
if leave_out == 1:
print('Leave out is 1 (100%), nothing todo')
return
from_ = 0
to = int(num_lines - num_lines * leave_out)
else:
from_ = 0
to = np.inf
if args.alpha_zh is None:
alpha_zh = 50.0 / args.num_topics
else:
alpha_zh = args.alpha_zh
kernel = kernels.names[args.kernel]()
if args.residency_priors:
residency_priors = np.array(args.residency_priors, dtype='d')
else:
residency_priors = np.zeros(shape=(0, ), dtype='d')
if np.isinf(to):
kernel.build(num_lines - from_, args.num_topics, residency_priors)
else:
kernel.build(to - from_, args.num_topics, residency_priors)
if single_thread:
print(
'Not on MPI mode or just one MPI proc, running single thread')
dyn = args.dynamic
if dyn:
num_iter = args.num_iter // args.num_batches
rv = dynamic.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, \
num_iter, args.num_batches, False, from_=from_, to=to)
else:
rv = learn.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, \
args.num_iter, args.burn_in, from_=from_, to=to)
else:
dyn = args.dynamic
if bool(dyn):
num_iter = args.num_iter // args.num_batches
rv = dynamic.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, num_iter, \
args.num_batches, True, from_=from_, to=to)
else:
rv = plearn.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, args.num_iter, \
from_=from_, to=to)
ended = time.mktime(time.localtime())
rv['training_time'] = np.array([ended - started])
dataio.save_model(args.model_fpath, rv)
print('Learning took', ended - started, 'seconds')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('trace_fpath', help='The trace to learn topics from', \
type=str)
parser.add_argument('num_topics', help='The number of topics to learn', \
type=int)
parser.add_argument('model_fpath', \
help='The name of the model file (a h5 file)', type=str)
parser.add_argument('--num_iter', help='The number of iterations', \
type=int, default=1000)
parser.add_argument('--burn_in', \
help='The burn in (ignored if using mpi)', type=int, \
default=300)
parser.add_argument('--dynamic', \
help='If we should employ the dynamic strategy', \
type=bool, default=False)
parser.add_argument('--num_batches', \
help='Number of batches in dynamic case', type=int, default=10)
parser.add_argument('--alpha_zh', \
help='Value of alpha_zh (alpha) hyper. Defaults to 50 / nz', \
type=float, default=None)
parser.add_argument('--beta_zs', help='Value of beta_zs (beta) hyper', \
type=float, default=0.001)
parser.add_argument('--kernel', choices=kernels.names,
help='The kernel to use', type=str, default='noop')
parser.add_argument('--residency_priors', nargs='+',
help='Priors for the residency time dist', type=float, default=None)
parser.add_argument('--leaveout', \
help='The number of transitions to leave for test', type=float, \
default=0)
args = parser.parse_args()
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
try:
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
single_thread = size <= 1
except:
single_thread = True
if not single_thread and rank != plearn.MASTER:
plearn.work()
else:
started = time.mktime(time.localtime())
num_lines = 0
with open(args.trace_fpath) as trace_file:
num_lines = sum(1 for _ in trace_file)
if args.leaveout > 0:
leave_out = min(1, args.leaveout)
if leave_out == 1:
print('Leave out is 1 (100%), nothing todo')
return
from_ = 0
to = int(num_lines - num_lines * leave_out)
else:
from_ = 0
to = np.inf
if args.alpha_zh is None:
alpha_zh = 50.0 / args.num_topics
else:
alpha_zh = args.alpha_zh
kernel = kernels.names[args.kernel]()
if args.residency_priors:
residency_priors = np.array(args.residency_priors, dtype='d')
else:
residency_priors = np.zeros(shape=(0, ), dtype='d')
if np.isinf(to):
kernel.build(num_lines - from_, args.num_topics, residency_priors)
else:
kernel.build(to - from_, args.num_topics, residency_priors)
if single_thread:
print('Not on MPI mode or just one MPI proc, running single thread')
dyn = args.dynamic
if dyn:
num_iter = args.num_iter // args.num_batches
rv = dynamic.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, \
num_iter, args.num_batches, False, from_=from_, to=to)
else:
rv = learn.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, \
args.num_iter, args.burn_in, from_=from_, to=to)
else:
dyn = args.dynamic
if bool(dyn):
num_iter = args.num_iter // args.num_batches
rv = dynamic.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, num_iter, \
args.num_batches, True, from_=from_, to=to)
else:
rv = plearn.fit(args.trace_fpath, args.num_topics, alpha_zh, \
args.beta_zs, kernel, residency_priors, args.num_iter, \
from_=from_, to=to)
ended = time.mktime(time.localtime())
rv['training_time'] = np.array([ended - started])
dataio.save_model(args.model_fpath, rv)
print('Learning took', ended - started, 'seconds')
