def run_experiment():
pattern = re.compile("lda_([0-9]+)\.pb")
data_dir = "data"
files = [
(re.search(pattern, f).group(1), join(data_dir, f))
for f in listdir(data_dir)
if isfile(join(data_dir, f)) and re.match(pattern, f)
]
cmd_str = "peircebayes {} -n 100 -m lda -t -s {}"
cmd_str2 = "peircebayes {} -n 100 -m lda -t -s {} -a cgs"
np.random.seed(1234)
start = time.time()
for i, f in files:
print i
# sample 10 times
for j, seed in enumerate(np.random.choice(5000, 10, replace=False) + 1):
call_cmd(cmd_str.format(f, seed))
phi = np.load("/tmp/peircebayes/avg_samples.npz")["arr_1"]
np.savez(join(data_dir, "phi_{}_{}".format(i, j)), **{"phi": phi})
call_cmd("cp /tmp/peircebayes/lls.npz data/lls_{}_{}.npz".format(i, j))
call_cmd(cmd_str2.format(f, seed))
call_cmd("cp /tmp/peircebayes/lls.npz data/lls_cgs_{}_{}.npz".format(i, j))
end = time.time()
with open("data/time_pb", "w") as f:
f.write(str(end - start))
cmd_str_r = "Rscript run_lda.R"
start = time.time()
call_cmd(cmd_str_r)
end = time.time()
with open("data/time_r", "w") as f:
f.write(str(end - start))
def do_pb(data_dir, j, seed, topics, alpha, beta, D, W):
print 'Doing PB.'
pb_file = join(data_dir,'lda_0.pb')
new_pb_file = join(data_dir,'new_lda_0.pb')
# change this if you're not me
path_to_pb_out = '/home/rares/p/peircebayes_experiments/lda_ll_topics/data/peircebayes'
cmd_str = 'peircebayes {} -n {} -m lda -d -t -s {} -o '+path_to_pb_out
it = 200
metric_pb = []
for T in topics:
print '\t{}'.format(T)
with open(pb_file, 'r') as fin, open(new_pb_file, 'w') as fout:
fout.write('''pb_dirichlet({}, mu, {}, {}).
pb_dirichlet({}, phi, {}, {}).
generate(Doc, Token) :-
Topic in 1..{},
mu(Topic,Doc),
phi(Token,Topic).
'''.format(alpha, T, D, beta, W, T, T))
fout.write(fin.read())
start = time.time()
call_cmd(cmd_str.format(new_pb_file, it, seed))
#time_pb.append(time.time()-start)
lls = np.load(join(path_to_pb_out, 'lls.npz'))['lls']
ll = np.average(lls[-10:])
metric_pb.append(ll)
return metric_pb
def do_stan(data_dir, j, seed, T, counts):
print 'Doing Stan.'
time_stan = []
metric_stan = []
for i in [5,10,15,20]:
print '\t{}'.format(i)
stan_file = join(data_dir, 'lda_stan_kwargs.py')
out_file = join(data_dir, 'stan_ll_{}.npz'.format(j))
phi_file = join(data_dir, 'stan_phi_{}.npz'.format(j))
theta_file = join(data_dir, 'stan_theta_{}.npz'.format(j))
with open(join(data_dir, 'lda_stan_0.py'), 'r') as fin, open(
stan_file, 'w') as fout:
fout.write("kwargs = {{'seed': {}, 'iter':{} }}\n".format(seed, i))
fout.write("out_file = '{}'\n".format(out_file))
fout.write("phi_file = '{}'\n".format(phi_file))
fout.write("theta_file = '{}'\n".format(theta_file))
fout.write(fin.read())
start = time.time()
call_cmd('python3 {}'.format(stan_file))
time_stan.append(time.time()-start)
mu = np.load(theta_file)['arr_0']
phi = np.load(phi_file)['arr_0']
ll = ull(mu, phi, T, counts)
metric_stan.append(ll)
return time_stan, metric_stan
def do_tm_vem(data_dir, j, seed):
print 'Doing topicmodels-VEM.'
vem_file = join(data_dir, 'vem_lda.R')
final_vem = join(data_dir, 'vem_lda_{}.R'.format(j))
vem_ll = join(data_dir, 'vem_ll_{}.R'.format(j))
time_vem = []
metric_vem = []
for i in [20,30,40,50]:
print '\t{}'.format(i)
with open(vem_file, 'r') as fin, open(final_vem, 'w') as fout:
fout.write('''
iter = {}
seed = {}
'''.format(i, seed))
fout.write(fin.read())
fout.write('''
vem_lls = lapply(list.files("{}", pattern='lda_0.txt', full.names=T), run_vem)
write.table(vem_lls, "{}", sep=" ", row.names=F, col.names=F)
'''.format(data_dir, vem_ll))
start = time.time()
call_cmd('Rscript {}'.format(final_vem))
time_vem.append(time.time()-start)
with open(vem_ll, 'r') as fin:
lls = [float(line.strip()) for line in fin]
ll = lls[-1]
metric_vem.append(ll)
return time_vem, metric_vem
def do_pb(data_dir, j, seed, T, K):
print 'Doing PB.'
times_pb, metrics_pb = [], []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
pb_file = 'lda_0_{}.pb'.format(k)
# change this if you're not me
path_to_pb_out = '/home/rares/p/peircebayes_experiments/lda_p_time/data/peircebayes'
cmd_str = 'peircebayes {} -n {} -m lda -d -t -s {} -o '+path_to_pb_out
time_pb = []
metric_pb = []
for i in [10,20,30,40,200]:
print '\t\t{}'.format(i)
start = time.time()
call_cmd(cmd_str.format(join(data_dir, pb_file), i, seed))
time_pb.append(time.time()-start)
# get mu and phi
theta = np.load(join(path_to_pb_out, 'avg_samples.npz'))
mu = theta['arr_0']
phi = theta['arr_1']
# call ull
ll = perplexity(mu, phi, T, counts)
metric_pb.append(ll)
times_pb.append(time_pb)
metrics_pb.append(metric_pb)
return list(np.average(times_pb, axis=0)), list(np.average(metrics_pb, axis=0))
def do_pb(data_dir, j, seed, T, counts):
print 'Doing PB.'
pb_file = 'lda_0.pb'
# change this if you're not me
path_to_pb_out = '/home/rares/p/peircebayes_experiments/lda_ull_time/data/peircebayes'
cmd_str = 'peircebayes {} -n {} -m lda -d -t -s {} -o '+path_to_pb_out
time_pb = []
metric_pb = []
for i in [50,100,150,200]:
print '\t{}'.format(i)
start = time.time()
call_cmd(cmd_str.format(join(data_dir, pb_file), i, seed))
time_pb.append(time.time()-start)
# get mu and phi
theta = np.load(join(path_to_pb_out, 'avg_samples.npz'))
mu = theta['arr_0']
phi = theta['arr_1']
# call ull
ll = ull(mu, phi, T, counts)
metric_pb.append(ll)
return time_pb, metric_pb
def do_tm_gibbs(data_dir, j, seed):
print 'Doing topicmodels-Gibbs.'
gibbs_file = join(data_dir, 'gibbs_lda.R')
final_gibbs = join(data_dir, 'gibbs_lda_{}.R'.format(j))
gibbs_ll = join(data_dir, 'gibbs_ll_{}.R'.format(j))
time_gibbs = []
metric_gibbs = []
for i in [25,50,75,100]:
print '\t{}'.format(i)
with open(gibbs_file, 'r') as fin, open(final_gibbs, 'w') as fout:
fout.write('''
iter = {}
seed = {}
'''.format(i, seed))
fout.write(fin.read())
fout.write('''
gibbs_lls = lapply(list.files("{}", pattern='lda_0.txt', full.names=T), run_gibbs)
write.table(gibbs_lls, "{}", sep=" ", row.names=F, col.names=F)
'''.format(data_dir, gibbs_ll))
start = time.time()
call_cmd('Rscript {}'.format(final_gibbs))
time_gibbs.append(time.time()-start)
with open(gibbs_ll, 'r') as fin:
lls = [float(line.strip()) for line in fin]
ll = np.average(lls[-10:])
metric_gibbs.append(ll)
return time_gibbs, metric_gibbs
def main():
use_seeds = False
if len(sys.argv)==2 and sys.argv[1] == 'seeds':
use_seeds = True
if use_seeds:
data_dir = 'data'
cmd_str = 'peircebayes data/news20comp_c.pb -n 400 -d -t -o $PWD/data/peircebayes'
#call_cmd(cmd_str)
#call_cmd('cp data/peircebayes/avg_samples.npz data/avg_samples.npz')
#call_cmd('upprism clda.psm')
else:
data_dir = 'data'
cmd_str = 'peircebayes data/news20comp.pb -n 400 -d -t -o $PWD/data/peircebayes'
seed = 1234
n_stan_samples = 20
# 1 tm
#TODO tm
start = time.time()
#call_cmd('Rscript data/news20_tm.R')
tm_time = time.time()-start
# 2 pb
start = time.time()
#call_cmd(cmd_str)
#call_cmd('cp data/peircebayes/avg_samples.npz data/avg_samples.npz')
pb_time = time.time()-start
# 3 prism
start = time.time()
call_cmd('upprism data/news20_prism.psm')
prism_time = time.time()-start
# 4 stan
stan_file = 'data/lda_stan.py'
with open(os.path.join(data_dir, 'news20_stan.py'), 'r') as fin, open(
stan_file, 'w') as fout:
fout.write("kwargs = {{'seed': {}, 'iter':{} }}\n".format(seed, n_stan_samples))
fout.write(fin.read())
start = time.time()
#call_cmd('python3 {}'.format(stan_file))
stan_time = time.time()-start
with open('data/times', 'w') as fout:
fout.write('PB: {} seconds\n'.format(pb_time))
fout.write('Prism: {} seconds\n'.format(prism_time))
fout.write('Stan: {} seconds\n'.format(stan_time))
fout.write('Topicmodels: {} seconds\n'.format(tm_time))
def do_tm_vem(data_dir, j, seed, topics, alpha, beta, D, W, K):
print 'Doing topicmodels-VEM.'
vem_file = join(data_dir, 'vem_lda.R')
final_vem = join(data_dir, 'vem_lda_{}.R'.format(j))
vem_theta = join(data_dir, 'vem_theta_{}.csv'.format(j))
vem_phi = join(data_dir, 'vem_phi_{}.csv'.format(j))
metrics = []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
metric_gibbs = []
metric_vem = []
for T in topics:
print '\t\t{}'.format(T)
with open(vem_file, 'r') as fin, open(final_vem, 'w') as fout:
fout.write('''
K = {}
alpha = {}
beta = {}
iter = {}
seed = {}
'''.format(T, alpha, beta, 500, seed))
fout.write(fin.read())
fout.write('''
vem_models = lapply(list.files("{}", pattern='lda_0_{}.txt', full.names=T), run_vem)
write.table(vem_models[[1]][[1]]@gamma, "{}", sep=" ", row.names=F, col.names=F)
write.table(exp(vem_models[[1]][[1]]@beta), "{}", sep=" ", row.names=F, col.names=F)
'''.format(data_dir, k, vem_theta, vem_phi))
start = time.time()
call_cmd('Rscript {}'.format(final_vem))
#time_vem.append(time.time()-start)
with open(vem_theta, 'r') as fin:
mu = []
for line in fin:
mu.append([float(i) for i in line.strip().split()])
mu = np.array(mu)
with open(vem_phi, 'r') as fin:
phi = []
for line in fin:
phi.append([float(i) for i in line.strip().split()])
phi = np.array(phi)
ll = perplexity(mu, phi, T, counts)
metric_vem.append(ll)
metrics.append(metric_vem)
return list(np.average(metrics, axis=0))
def data_gen():
K = 6
beta = 50./float(K)
gamma = 0.1
fin_name = 'data/sushi3/sushi3a.5000.10.order'
fout_name = 'data/sushi3/sushi3.pb'
rewrite_dir('data')
call_cmd('sh get_data.sh')
N, data = read_data(fin_name)
write_pb(fout_name, N, data, K, beta, gamma)
def do_tm_gibbs(data_dir, j, seed, T, K):
print 'Doing topicmodels-Gibbs.'
gibbs_file = join(data_dir, 'gibbs_lda.R')
final_gibbs = join(data_dir, 'gibbs_lda_{}.R'.format(j))
gibbs_theta = join(data_dir, 'gibbs_theta_{}.csv'.format(j))
gibbs_phi = join(data_dir, 'gibbs_phi_{}.csv'.format(j))
times, metrics = [], []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
#for doc in counts.toarray():
# print list(doc)
time_gibbs = []
metric_gibbs = []
for i in [10,20,30,40,200]:
print '\t\t{}'.format(i)
with open(gibbs_file, 'r') as fin, open(final_gibbs, 'w') as fout:
fout.write('''
iter = {}
seed = {}
'''.format(i, seed))
fout.write(fin.read())
fout.write('''
gibbs_models = lapply(list.files("{}", pattern='lda_0_{}.txt', full.names=T), run_gibbs)
write.table(gibbs_models[[1]][[1]]@gamma, "{}", sep=" ", row.names=F, col.names=F)
write.table(exp(gibbs_models[[1]][[1]]@beta), "{}", sep=" ", row.names=F, col.names=F)
'''.format(data_dir, k, gibbs_theta, gibbs_phi))
start = time.time()
call_cmd('Rscript {}'.format(final_gibbs))
time_gibbs.append(time.time()-start)
with open(gibbs_theta, 'r') as fin:
mu = []
for line in fin:
mu.append([float(i) for i in line.strip().split()])
mu = np.array(mu)
with open(gibbs_phi, 'r') as fin:
phi = []
for line in fin:
phi.append([float(i) for i in line.strip().split()])
phi = np.array(phi)
ll = perplexity(mu, phi, T, counts)
metric_gibbs.append(ll)
times.append(time_gibbs)
metrics.append(metric_gibbs)
return list(np.average(times, axis=0)), list(np.average(metrics, axis=0))
def do_tm_gibbs(data_dir, j, seed, topics, alpha, beta, D, W, counts):
print 'Doing topicmodels-Gibbs.'
gibbs_file = join(data_dir, 'gibbs_lda.R')
final_gibbs = join(data_dir, 'gibbs_lda_{}.R'.format(j))
gibbs_theta = join(data_dir, 'gibbs_theta_{}.csv'.format(j))
gibbs_phi = join(data_dir, 'gibbs_phi_{}.csv'.format(j))
it = 200
metric_gibbs = []
for T in topics:
print '\t{}'.format(T)
with open(gibbs_file, 'r') as fin, open(final_gibbs, 'w') as fout:
fout.write('''
K = {}
alpha = {}
beta = {}
iter = {}
seed = {}
'''.format(T, alpha, beta, it, seed))
fout.write(fin.read())
fout.write('''
gibbs_models = lapply(list.files("{}", pattern='lda_0.txt', full.names=T), run_gibbs)
write.table(gibbs_models[[1]][[1]]@gamma, "{}", sep=" ", row.names=F, col.names=F)
write.table(exp(gibbs_models[[1]][[1]]@beta), "{}", sep=" ", row.names=F, col.names=F)
'''.format(data_dir, gibbs_theta, gibbs_phi))
start = time.time()
call_cmd('Rscript {}'.format(final_gibbs))
#time_gibbs.append(time.time()-start)
with open(gibbs_theta, 'r') as fin:
mu = []
for line in fin:
mu.append([float(i) for i in line.strip().split()])
mu = np.array(mu)
with open(gibbs_phi, 'r') as fin:
phi = []
for line in fin:
phi.append([float(i) for i in line.strip().split()])
phi = np.array(phi)
ll = ull(mu, phi, T, counts)
metric_gibbs.append(ll)
return metric_gibbs
def main():
cmd_str = 'peircebayes data/lda2_arxiv.pb -d -t -n 50 -b 100'
call_cmd('cat data/pb_hlda3.pb data/arxiv_obs.pb',
open('data/lda2_arxiv.pb', 'w'))
call_cmd(cmd_str)
call_cmd('cp /tmp/peircebayes/avg_samples.npz data/avg_samples.npz')
call_cmd('rm data/lda2_arxiv.pb')
def do_stan(data_dir, j, seed, topics, alpha, beta, D, W, K):
print 'Doing Stan.'
it = 20
metrics = []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
metric_stan = []
for T in topics:
print '\t\t{}'.format(T)
stan_file = join(data_dir, 'lda_stan_kwargs.py')
out_file = join(data_dir, 'stan_ll_{}.npz'.format(j))
phi_file = join(data_dir, 'stan_phi_{}.npz'.format(j))
theta_file = join(data_dir, 'stan_theta_{}.npz'.format(j))
with open(join(data_dir, 'lda_stan_0_{}.py'.format(k)), 'r') as fin, open(
stan_file, 'w') as fout:
fout.write("kwargs = {{'seed': {}, 'iter':{} }}\n".format(seed, it))
fout.write("out_file = '{}'\n".format(out_file))
fout.write("phi_file = '{}'\n".format(phi_file))
fout.write("theta_file = '{}'\n".format(theta_file))
for line in fin:
if 'lda_dat = {' in line:
fout.write(line)
alpha_l = [alpha]*T
beta_l = [beta]*W
fout.write(''' 'K' : {},
'alpha' : {},
'beta' : {},
'''.format(T, alpha_l, beta_l))
else:
fout.write(line)
start = time.time()
call_cmd('python3 {}'.format(stan_file))
#time_stan.append(time.time()-start)
mu = np.load(theta_file)['arr_0']
phi = np.load(phi_file)['arr_0']
ll = perplexity(mu, phi, T, counts)
metric_stan.append(ll)
metrics.append(metric_stan)
return list(np.average(metrics, axis=0))
def do_pb(data_dir, j, seed, topics, alpha, beta, D, W, K):
print 'Doing PB.'
new_pb_file = join(data_dir,'new_lda_0.pb')
# change this if you're not me
path_to_pb_out = '/home/rares/p/peircebayes_experiments/lda_p_topics/data/peircebayes'
cmd_str = 'peircebayes {} -n {} -m lda -d -t -s {} -o '+path_to_pb_out
it = 200
metrics = []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
pb_file = join(data_dir,'lda_0_{}.pb'.format(k))
metric_pb = []
for T in topics:
print '\t\t{}'.format(T)
with open(pb_file, 'r') as fin, open(new_pb_file, 'w') as fout:
fout.write('''pb_dirichlet({}, mu, {}, {}).
pb_dirichlet({}, phi, {}, {}).
generate(Doc, Token) :-
Topic in 1..{},
mu(Topic,Doc),
phi(Token,Topic).
'''.format(alpha, T, D, beta, W, T, T))
fout.write(fin.read())
start = time.time()
call_cmd(cmd_str.format(new_pb_file, it, seed))
#time_pb.append(time.time()-start)
# get mu and phi
theta = np.load(join(path_to_pb_out, 'avg_samples.npz'))
mu = theta['arr_0']
phi = theta['arr_1']
# call ull
ll = perplexity(mu, phi, T, counts)
metric_pb.append(ll)
metrics.append(metric_pb)
return list(np.average(metrics, axis=0))
def do_prism(data_dir, j, seed, topics, alpha, beta, D, W):
print 'Doing Prism.'
prism_file = join(data_dir, 'lda_prism_0.psm')
in_prism = join(data_dir, 'in_prism_{}'.format(j))
out_prism = join(data_dir, 'out_prism_{}'.format(j))
vfe_prism = join(data_dir, 'vfe_prism_{}'.format(j))
metric_prism = []
for T in topics:
print '\t{}'.format(T)
theta_str = 'values(theta(_), [1-{}], a@{}).'.format(T,alpha)
phi_str = 'values(phi(_), [1-{}], a@{}).'.format(W,beta)
with open(prism_file, 'r') as fin, open(in_prism, 'w') as fout:
fout.write('''
{}
{}
'''.format(theta_str, phi_str))
fout.write(fin.read())
fout.write('''
prism_main :-
random_set_seed({}),
set_prism_flag(learn_mode,both),
go,
learn_statistics(free_energy, V),
open('{}',write, Stream), write(Stream,V), close(Stream),
save_phi.
save_phi :-
findall(Param, get_sw(phi(_), [_,_,Param]), Params),
open('{}',write, Stream), forall(member(Param, Params), (write(Stream,Param), nl(Stream))), close(Stream).
'''.format(seed, vfe_prism, out_prism))
start = time.time()
call_cmd('upprism {}'.format(in_prism))
#time_prism.append(time.time()-start)
with open(vfe_prism, 'r') as fin:
vfe = float(fin.read().strip())
metric_prism.append(vfe)
return metric_prism
def do_tm_vem(data_dir, j, seed, T, counts):
print 'Doing topicmodels-VEM.'
vem_file = join(data_dir, 'vem_lda.R')
final_vem = join(data_dir, 'vem_lda_{}.R'.format(j))
vem_theta = join(data_dir, 'vem_theta_{}.csv'.format(j))
vem_phi = join(data_dir, 'vem_phi_{}.csv'.format(j))
time_vem = []
metric_vem = []
for i in [20,30,40,50]:
print '\t{}'.format(i)
with open(vem_file, 'r') as fin, open(final_vem, 'w') as fout:
fout.write('''
iter = {}
seed = {}
'''.format(i, seed))
fout.write(fin.read())
fout.write('''
vem_models = lapply(list.files("{}", pattern='lda_0.txt', full.names=T), run_vem)
write.table(vem_models[[1]][[1]]@gamma, "{}", sep=" ", row.names=F, col.names=F)
write.table(exp(vem_models[[1]][[1]]@beta), "{}", sep=" ", row.names=F, col.names=F)
'''.format(data_dir, vem_theta, vem_phi))
start = time.time()
call_cmd('Rscript {}'.format(final_vem))
time_vem.append(time.time()-start)
with open(vem_theta, 'r') as fin:
mu = []
for line in fin:
mu.append([float(i) for i in line.strip().split()])
mu = np.array(mu)
with open(vem_phi, 'r') as fin:
phi = []
for line in fin:
phi.append([float(i) for i in line.strip().split()])
phi = np.array(phi)
ll = ull(mu, phi, T, counts)
metric_vem.append(ll)
return time_vem, metric_vem
def _ls_file_list(self):
cmd = 'ssh %s ls %s' % (self._remote_ip, self._remote_dir)
#self._logger.debug('excute cmd:%s', cmd)
sta, result = call_cmd(cmd)
#print sta, result
if sta == 0:
#self._logger.debug('success get filelist:\n%s', result)
return result.split()
else:
return None
def do_stan(data_dir, j, seed, topics, alpha, beta, D, W, counts):
print 'Doing Stan.'
it = 20
metric_stan = []
for T in topics:
print '\t{}'.format(T)
stan_file = join(data_dir, 'lda_stan_kwargs.py')
out_file = join(data_dir, 'stan_ll_{}.npz'.format(j))
phi_file = join(data_dir, 'stan_phi_{}.npz'.format(j))
theta_file = join(data_dir, 'stan_theta_{}.npz'.format(j))
with open(join(data_dir, 'lda_stan_0.py'), 'r') as fin, open(
stan_file, 'w') as fout:
fout.write("kwargs = {{'seed': {}, 'iter':{} }}\n".format(seed, it))
fout.write("out_file = '{}'\n".format(out_file))
fout.write("phi_file = '{}'\n".format(phi_file))
fout.write("theta_file = '{}'\n".format(theta_file))
for line in fin:
if 'lda_dat = {' in line:
fout.write(line)
alpha_l = [alpha]*T
beta_l = [beta]*W
fout.write(''' 'K' : {},
'alpha' : {},
'beta' : {},
'''.format(T, alpha_l, beta_l))
else:
fout.write(line)
start = time.time()
call_cmd('python3 {}'.format(stan_file))
#time_stan.append(time.time()-start)
mu = np.load(theta_file)['arr_0']
phi = np.load(phi_file)['arr_0']
ll = ull(mu, phi, T, counts)
metric_stan.append(ll)
return metric_stan
def do_pb(data_dir, j, seed):
print 'Doing PB.'
pb_file = 'lda_0.pb'
# change this if you're not me
path_to_pb_out = '/home/rares/p/peircebayes_experiments/lda_ll_time/data/peircebayes'
cmd_str = 'peircebayes {} -n {} -m lda -d -t -s {} -o '+path_to_pb_out
time_pb = []
metric_pb = []
for i in [50,100,150,200]:
print '\t{}'.format(i)
start = time.time()
call_cmd(cmd_str.format(join(data_dir, pb_file), i, seed))
time_pb.append(time.time()-start)
lls = np.load(join(path_to_pb_out, 'lls.npz'))['lls']
ll = np.average(lls[-10:])
metric_pb.append(ll)
return time_pb, metric_pb
def do_prism(data_dir, j, seed):
print 'Doing Prism.'
prism_file = join(data_dir, 'lda_prism_0.psm')
in_prism = join(data_dir, 'in_prism_{}'.format(j))
out_prism = join(data_dir, 'out_prism_{}'.format(j))
vfe_prism = join(data_dir, 'vfe_prism_{}'.format(j))
time_prism = []
metric_prism = []
for i in [50,100,150,200]:
print '\t{}'.format(i)
with open(prism_file, 'r') as fin, open(in_prism, 'w') as fout:
fout.write(fin.read())
fout.write('''
prism_main :-
random_set_seed({}),
set_prism_flag(learn_mode,both),
set_prism_flag(max_iterate,{}),
go,
learn_statistics(free_energy, V),
open('{}',write, Stream), write(Stream,V), close(Stream),
save_phi.
save_phi :-
findall(Param, get_sw(phi(_), [_,_,Param]), Params),
open('{}',write, Stream), forall(member(Param, Params), (write(Stream,Param), nl(Stream))), close(Stream).
'''.format(seed, i, vfe_prism, out_prism))
start = time.time()
call_cmd('upprism {}'.format(in_prism))
time_prism.append(time.time()-start)
with open(vfe_prism, 'r') as fin:
vfe = float(fin.read().strip())
metric_prism.append(vfe)
return time_prism, metric_prism
def run_experiment():
pattern = re.compile('lda_([0-9]+)\.pb')
data_dir = 'data'
files = [ (re.search(pattern, f).group(1), join(data_dir,f) )
for f in listdir(data_dir)
if isfile(join(data_dir,f)) and re.match(pattern, f)]
cmd_str = 'peircebayes {} -n 200 -m lda_ll -t -s {}'
#cmd_str2 = 'peircebayes {} -n 200 -m lda_ll -t -s {} -a amcmc'
np.random.seed(1234)
start = time.time()
for i,f in files:
# sample 10 times
for j,seed in enumerate(np.random.choice(5000, 10, replace=False)+1):
call_cmd(cmd_str.format(f, seed))
phi = np.load('/tmp/peircebayes/avg_samples.npz')['arr_1']
np.savez(join(data_dir, 'phi_{}_{}'.format(i,j)), **{'phi':phi})
call_cmd('cp /tmp/peircebayes/lls.npz data/lls_{}_{}.npz'.format(i,j))
#call_cmd(cmd_str2.format(f, seed))
#call_cmd('cp /tmp/peircebayes/lls.npz data/lls_amcmc_{}_{}.npz'.format(i,j))
end = time.time()
with open('data/time_pb', 'w') as f:
f.write(str(end-start))
cmd_str_r = 'Rscript run_lda.R'
start = time.time()
call_cmd(cmd_str_r)
end = time.time()
with open('data/time_r', 'w') as f:
f.write(str(end-start))
def do_stan(data_dir, j, seed, T, K):
print 'Doing Stan.'
times, metrics = [], []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
time_stan = []
metric_stan = []
for i in [2,4,6,8,20]:
print '\t\t{}'.format(i)
stan_file = join(data_dir, 'lda_stan_kwargs.py')
out_file = join(data_dir, 'stan_ll_{}.npz'.format(j))
phi_file = join(data_dir, 'stan_phi_{}.npz'.format(j))
theta_file = join(data_dir, 'stan_theta_{}.npz'.format(j))
with open(join(data_dir, 'lda_stan_0_{}.py'.format(k)), 'r'
) as fin, open(stan_file, 'w') as fout:
fout.write("kwargs = {{'seed': {}, 'iter':{} }}\n".format(seed, i))
fout.write("out_file = '{}'\n".format(out_file))
fout.write("phi_file = '{}'\n".format(phi_file))
fout.write("theta_file = '{}'\n".format(theta_file))
fout.write(fin.read())
start = time.time()
call_cmd('python3 {}'.format(stan_file))
time_stan.append(time.time()-start)
mu = np.load(theta_file)['arr_0']
phi = np.load(phi_file)['arr_0']
ll = perplexity(mu, phi, T, counts)
metric_stan.append(ll)
times.append(time_stan)
metrics.append(metric_stan)
return list(np.average(times, axis=0)), list(np.average(metrics, axis=0))
def run_experiment():
data_dir = 'data/sushi3'
pb_file = 'sushi3.pb'
cmd_str = 'peircebayes {} -n 100 -t -s {}'
np.random.seed(1234)
start = time.time()
for j,seed in enumerate(np.random.choice(1000, 10, replace=False)+1):
call_cmd(cmd_str.format(join(data_dir, pb_file), seed))
call_cmd('cp /tmp/peircebayes/avg_samples.npz data/avg_samples_{}.npz'.format(j))
call_cmd('cp /tmp/peircebayes/lls.npz data/lls_{}.npz'.format(j))
end = time.time()
with open('data/rim_time', 'w') as f:
f.write(str(end-start))
def do_prism(data_dir, j, seed, topics, alpha, beta, D, W, K):
print 'Doing Prism.'
metrics = []
for k in range(K):
print '\tfold {}'.format(k+1)
counts = pickle.load(open(join(data_dir, 'counts_{}.pkl'.format(k)), 'r'))
prism_file = join(data_dir, 'lda_prism_0_{}.psm'.format(k))
in_prism = join(data_dir, 'in_prism_{}'.format(j))
phi_prism = join(data_dir, 'phi_prism_{}'.format(j))
theta_prism = join(data_dir, 'theta_prism_{}'.format(j))
vfe_prism = join(data_dir, 'vfe_prism_{}'.format(j))
metric_prism = []
for T in topics:
print '\t\t{}'.format(T)
theta_str = 'values(theta(_), [1-{}], a@{}).'.format(T,alpha)
phi_str = 'values(phi(_), [1-{}], a@{}).'.format(W,beta)
with open(prism_file, 'r') as fin, open(in_prism, 'w') as fout:
fout.write('''
{}
{}
'''.format(theta_str, phi_str))
fout.write(fin.read())
fout.write('''
prism_main :-
random_set_seed({}),
set_prism_flag(learn_mode,both),
go,
learn_statistics(free_energy, V),
open('{}',write, Stream), write(Stream,V), close(Stream),
save_phi,
save_theta.
save_phi :-
findall((V,Param), get_sw(phi(V), [_,_,Param]), Params),
open('{}',write, Stream), forall(member((V,Param), Params), (write(Stream,V), write(Stream,'|'), write(Stream,Param), nl(Stream))), close(Stream).
save_theta :-
findall((V,Param), get_sw(theta(V), [_,_,Param]), Params),
open('{}',write, Stream), forall(member((V,Param), Params), (write(Stream,V), write(Stream,'|'), write(Stream,Param), nl(Stream))), close(Stream).
'''.format(seed, vfe_prism, phi_prism, theta_prism))
start = time.time()
call_cmd('upprism {}'.format(in_prism))
#time_prism.append(time.time()-start)
with open(phi_prism, 'r') as fin:
phi_idx = []
for line in fin:
idx, rest = line.strip().split('|')
idx = int(idx)-1
topic = np.array(ast.literal_eval(rest))
phi_idx.append((idx, topic))
phi = [0 for i in range(len(phi_idx))]
for idx, topic in phi_idx:
phi[idx] = topic
phi = np.array(phi)
with open(theta_prism, 'r') as fin:
theta_idx = []
for line in fin:
idx, rest = line.strip().split('|')
idx = int(idx)-1
doc_mix = np.array(ast.literal_eval(rest))
theta_idx.append((idx, doc_mix))
mu = [0 for i in range(len(theta_idx))]
for idx, doc_mix in theta_idx:
mu[idx] = doc_mix
mu = np.array(mu)
ll = perplexity(mu, phi, T, counts)
metric_prism.append(ll)
metrics.append(metric_prism)
return list(np.average(metrics, axis=0))
def run_experiment():
data_dir = 'data'
pb_file = 'lda_0.pb'
cmd_str = 'peircebayes {} -n 300 -m lda_ll -d -t -s {}'
np.random.seed(1234)
times_pb = []
times_church = []
times_church2 = []
for j,seed in enumerate(np.random.choice(5000, 10, replace=False)+1):
start = time.time()
call_cmd(cmd_str.format(join(data_dir, pb_file), seed))
end = time.time()
times_pb.append(end-start)
call_cmd('cp /tmp/peircebayes/last_sample.npz data/last_sample_{}.npz'.format(j))
call_cmd('cp /tmp/peircebayes/lls.npz data/lls_{}.npz'.format(j))
church_str = 'church -s {} data/lda_church1_0.md'.format(seed)
start = time.time()
call_cmd(church_str)
end = time.time()
times_church.append(end-start)
call_cmd('mv ll_church1.csv data/ll_church1_{}.csv'.format(j))
church2_str = 'church -s {} data/lda_church2_0.md'.format(seed)
start = time.time()
call_cmd(church2_str)
end = time.time()
times_church2.append(end-start)
call_cmd('mv ll_church2.csv data/ll_church2_{}.csv'.format(j))
with open('data/times', 'w') as f:
f.write('pb: {}\n'.format(np.average(times_pb)))
f.write('church: {}\n'.format(np.average(times_church)))
f.write('church2: {}\n'.format(np.average(times_church2)))
def generate_seed(project, bugnumber):
""" generates a file that contains json info to run d4j and lithium """
initial_projects = ["Chart", "Lang", "Closure", "Math", "Mockito", "Time"]
if project not in initial_projects:
raise Exception("Project {} invalid. Please select one of {}".format(
project, initial_projects))
project_path = os.path.join(os.getcwd(), "data", project)
if not os.path.isdir(project_path):
print("FAILED") # should print to stop the main script
raise Exception("Project {} directory not found".format(project_path))
# Solves the issue of different source paths for the same project
if project == 'Lang' and int(bugnumber) < 36:
source_path = get_source_path(project + '2')
elif project == 'Math' and int(bugnumber) > 84:
source_path = get_source_path(project + '2')
else:
source_path = get_source_path(project)
# get only bugs choosen by user
bugnumber = bugnumber.split(",")
if not is_input_number_valid(bugnumber, project_path):
print("FAILED") # should print to stop the main script
raise Exception(
"one or more json files({}) are not found in path {}".format(
bugnumber, project_path))
bugnumbers = ['{}.json'.format(bug) for bug in bugnumber]
if '0' in bugnumber: # 0 similar to "all" bugs
bugnumbers = os.listdir(project_path)
else:
bugnumbers = [
doc for doc in os.listdir(project_path) if doc in bugnumbers
]
# for each bug
for bug in bugnumbers:
data = json_to_dict(os.path.join(project_path, bug))
bug_number = bug.replace(".json", "")
# getting the expected message
expected_dir = 'oracle/' + project_name + '/'
if not os.path.exists(expected_dir):
os.makedirs(expected_dir)
expected_msg_path = expected_dir + bug_number
project_dir = tempfile.mkdtemp(prefix="lithium-slicer_")
output_filepath = project_dir + '/failing_tests'
print('output_filepath=', output_filepath)
expected_msg = []
failing = ''
runtest_script = "bash run_input_test.sh {PROJECTDIR} {PROJECT} {BUG}"
cmd_str = runtest_script.format(PROJECTDIR=project_dir,
PROJECT=project_name,
BUG=bug_number + 'b')
output = call_cmd(cmd_str) # call shell script
if os.path.isfile(output_filepath):
with open(output_filepath) as out_fail:
failing = out_fail.readlines()
with open(expected_msg_path, "w+") as expected:
expected.write("{}".format(''.join(failing)))
def do_prism(data_dir, j, seed, T, counts):
print 'Doing Prism.'
prism_file = join(data_dir, 'lda_prism_0.psm')
in_prism = join(data_dir, 'in_prism_{}'.format(j))
phi_prism = join(data_dir, 'phi_prism_{}'.format(j))
theta_prism = join(data_dir, 'theta_prism_{}'.format(j))
vfe_prism = join(data_dir, 'vfe_prism_{}'.format(j))
time_prism = []
metric_prism = []
for i in [50,100,150,200]:
print '\t{}'.format(i)
with open(prism_file, 'r') as fin, open(in_prism, 'w') as fout:
fout.write(fin.read())
fout.write('''
prism_main :-
random_set_seed({}),
set_prism_flag(learn_mode,both),
set_prism_flag(max_iterate,{}),
go,
learn_statistics(free_energy, V),
open('{}',write, Stream), write(Stream,V), close(Stream),
save_phi,
save_theta.
save_phi :-
findall((V,Param), get_sw(phi(V), [_,_,Param]), Params),
open('{}',write, Stream), forall(member((V,Param), Params), (write(Stream,V), write(Stream,'|'), write(Stream,Param), nl(Stream))), close(Stream).
save_theta :-
findall((V,Param), get_sw(theta(V), [_,_,Param]), Params),
open('{}',write, Stream), forall(member((V,Param), Params), (write(Stream,V), write(Stream,'|'), write(Stream,Param), nl(Stream))), close(Stream).
'''.format(seed, i, vfe_prism, phi_prism, theta_prism))
start = time.time()
call_cmd('upprism {}'.format(in_prism))
time_prism.append(time.time()-start)
with open(phi_prism, 'r') as fin:
phi_idx = []
for line in fin:
idx, rest = line.strip().split('|')
idx = int(idx)-1
topic = np.array(ast.literal_eval(rest))
phi_idx.append((idx, topic))
phi = [0 for i in range(len(phi_idx))]
for idx, topic in phi_idx:
phi[idx] = topic
phi = np.array(phi)
with open(theta_prism, 'r') as fin:
theta_idx = []
for line in fin:
idx, rest = line.strip().split('|')
idx = int(idx)-1
doc_mix = np.array(ast.literal_eval(rest))
theta_idx.append((idx, doc_mix))
mu = [0 for i in range(len(theta_idx))]
for idx, doc_mix in theta_idx:
mu[idx] = doc_mix
mu = np.array(mu)
ll = ull(mu, phi, T, counts)
metric_prism.append(ll)
return time_prism, metric_prism
def _delete_file_remote(self, filename):
cmd = 'ssh search@%s rm %s/%s' % (self._remote_ip, self._remote_dir, filename)
#self._logger.debug('excute cmd:%s', cmd)
sta, result = call_cmd(cmd)
return True if sta == 0 else False
def _scp_file(self, filename, filename_tmp):
cmd = 'scp search@%s:%s/%s %s/%s' % (self._remote_ip, self._remote_dir, filename, self._local_dir, filename_tmp)
#self._logger.debug('excute cmd:%s', cmd)
sta, result = call_cmd(cmd)
return True if sta==0 else False