def run(args):
"""
The command-line run script for LDA experiments.
"""
# scientific
import numpy as np
import scipy as sp
# display what run got in args
for tup in args.__dict__.iteritems():
print tup
# LOAD VOCAB
wlist = smart_list_reader( args.vocab_file )
if not wlist:
print "Vocab format not recognized"
sys.exit(-1)
# convert from list [term1, term2, ...] to dicts
# [term1:0, term2:1, ... ] and the inverse mapping
id2word = dict( enumerate(wlist) )
word2id = dict( [(word,id) for id,word in id2word.items()] )
vocab = word2id
# SETUP CORPUS (LAZY)
# doCounts -- not so lazy...
if args.docs_file[-3:]==".mm":
from liblda.newmmcorpus import NewMmCorpus
corpus = NewMmCorpus(args.docs_file)
corpus.setVocabFromDict( vocab )
corpus.doCounts()
elif args.docs_file[-4:]==".txt":
from liblda.low2corpus import Low2Corpus
corpus = Low2Corpus(args.docs_file)
corpus.setVocabFromDict( vocab )
corpus.doCounts()
else:
print "Corpus format not recognized"
sys.exit(-1)
# Create rundir
from socket import gethostname
from liblda.util import rungen
full_hostname = gethostname()
host_id = full_hostname.rstrip(".cs.mcgill.ca")
if not args.rundirs_root:
rundirs_root = RUNDIRS_ROOT
else:
rundirs_root = args.rundirs_root
if not os.path.exists(rundirs_root):
print "Error, rundirs_root %s doesn't exist" % rundirs_root
sys.exit(-1)
# create the host-specific rundir if necessary
host_rundirs_root = os.path.join(rundirs_root, host_id)
if not os.path.exists(host_rundirs_root):
os.mkdir( host_rundirs_root )
# create a new (sequential) rundir for this host
rundir = rungen.mk_next_rundir(host_rundirs_root)
logger.info("rundir: " + rundir )
# prepare a dict which will become input.json
input = {}
input["rundir"]=rundir
input["numT"]=args.numT
input["iter"]=args.iter
input["corpus"]=args.docs_file
input["vocab"]=args.vocab_file
input["alpha"]=args.alpha
input["beta"]= args.beta
input["seed"]=args.seed
input["host_id"]=host_id
# and write it to disk
f=open( os.path.join(rundir, "input.json"), "w" )
simplejson.dump( input, f, indent=0 )
f.close()
start_time = datetime.datetime.now()
# setup the lda model
lda = LdaModel( numT=args.numT, alpha=args.alpha, beta=args.beta, corpus=corpus, vocab=vocab )
# if not in seeded mode run as usual
if not args.seed_z_from:
lda.train(iter=args.iter, seed=args.seed )
# NEW: S
else:
logger.info("Using seeded z training ... ")
# training params
if not args.iter:
lda.iter = 50
else:
lda.iter = args.iter
if not args.seed:
seed = 777
lda.seed = 2*seed+1
else:
lda.seed = 2*args.seed + 1
# loadup the seed_z_from file into seed_z np array
seed_z = np.load( args.seed_z_from)
if args.expand_factors:
expand_factors_str = smart_list_reader( args.expand_factors )
expand_factors = np.array( [int(i) for i in expand_factors_str ] )
else:
expand_factors = None # let lda.seeded_initialize() handle it
# custom train sequence
lda.allocate_arrays()
lda.read_dw_alphabetical()
#self.random_initialize() # NO -- we want a seeded initialization!
lda.seeded_initialize(seed_z, expand_factors )
lda.gibbs_sample(iter=lda.iter, seed=lda.seed )
lda.wpdt_to_probs()
#self.deallocate_arrays()
# record how long it took
end_time = datetime.datetime.now()
duration = (end_time-start_time).seconds
# save word counts and topic assignment counts (these are sparse)
if args.save_counts: # TRUE by default
state = ["dp", "wp", "alpha", "beta" ]
for var_name in state:
f_name = os.path.join(rundir, RUN_FILENAMESS[var_name] )
np.save( f_name, lda.__getattribute__(var_name) )
logger.info("Done writing out Nwt+beta, Ndt+alpha")
# Gibbs sampler state, which consists of
# the full topic assignments "z.npy"
if args.save_z:
var_name="z"
f_name = os.path.join(rundir, RUN_FILENAMESS[var_name] )
np.save( f_name, lda.__getattribute__(var_name) )
logger.info("Done writing out z.npy")
# save probs
if args.save_probs:
probs = ["phi", "theta"]
for var_name in probs:
f_name = os.path.join(rundir, RUN_FILENAMESS[var_name] )
np.save( f_name, lda.__getattribute__(var_name) )
logger.info("Done writing out probabilities phi.npy and theta.npy")
# prepare a dict which will become output.json
output = {}
# run details
output["rundir"]=rundir
output["host_id"]=host_id
output["iter"]=lda.iter
output["seed"]=lda.seed
output["start_time"]=start_time.isoformat() # ISO format string
# to read ISO time stamps use dateutil
#>>> from dateutil import parser
#>>> parser.parse("2011-01-25T23:36:43.373248")
# datetime.datetime(2011, 1, 25, 23, 36, 43, 373247)
output["duration"]=int(duration)
# corpus info
output["corpus"]=args.docs_file
output["vocab"]=args.vocab_file
output["numDocs"] = lda.numDocs
output["numTerms"] = lda.numTerms
output["totalNterms"] = lda.corpus.totalNwords
# model parameters
output["numT"]=lda.numT
# the hyperparameters are too long to store in full here,
# use separate .npy files if alpha/beta non uniform
output["alpha"]= lda.alpha[0] #[np.average(lda.alpha), float(np.cov(lda.alpha)) ] # [avg, var]
output["beta"]= lda.beta[0] #[np.average(lda.beta), float(np.cov(lda.beta)) ] # [avg, var]
#
# calculate likelyhood
output["loglike"]=lda.loglike()
output["perplexity"]=lda.perplexity() # = np.exp( -1 * loglike() / totalNwords )
logger.info("Log likelyhood: %f" % output["loglike"] )
logger.info("Perplexity: %f" % output["perplexity"] )
#
# special seeding info
if args.seed_z_from:
output["seed_z_from"]= args.seed_z_from
if args.expand_factors:
output["expand_factors"]= args.expand_factors
# compute sparseness and write it out
sp = get_sparse_stats( lda.phi )
np.save( os.path.join(rundir, "phi_sparseness.npy"), sp)
# report on sparseness statisitcs (assume single mode)
nz = sp.nonzero()[0] # get the nonzero entries
sp_avg = sum([sp[i]*i for i in nz]) # where are non-zero they concentrated ?
sp_var = sum( [sp[i]*np.abs(i-sp_avg)**2 for i in nz] )
sp_stdev = np.sqrt( sp_var ) # how concentrated they are around sp_avg
output["phi_sparseness_avg"]=sp_avg
output["phi_sparseness_stdev"]=sp_stdev
logger.info("Phi sparseness. center=%d, width=%d" % (int(sp_avg),int(sp_stdev)) )
# same for theta
sp = get_sparse_stats( lda.theta )
np.save( os.path.join(rundir, "theta_sparseness.npy"), sp)
# report on sparseness statisitcs (assume single mode)
nz = sp.nonzero()[0] # get the nonzero entries
sp_avg = sum([sp[i]*i for i in nz]) # where are non-zero they concentrated ?
sp_var = sum( [sp[i]*np.abs(i-sp_avg)**2 for i in nz] )
sp_stdev = np.sqrt( sp_var ) # how concentrated they are around sp_avg
output["theta_sparseness_avg"]=sp_avg
output["theta_sparseness_stdev"]=sp_stdev
logger.info("Theta sparseness. center=%d, width=%d" % (int(sp_avg),int(sp_stdev)) )
# write all output data to disk
f=open( os.path.join(rundir, "output.json"), "w" )
simplejson.dump( output, f, indent=0 )
f.close()
logger.info("Done saving output.json")
if args.print_topics:
from liblda.topicviz.show_top import show_top
top_words_in_topics = show_top(lda.phi, num=args.print_topics, id2word=lda.corpus.id2word)
for topic in top_words_in_topics:
words = ", ".join(topic)
print words
logger.info("Done! --> thank you come again")
# get the topic list
top_words_in_topics = show_top(phi, num=args.num, id2word=id2word)
for topic in top_words_in_topics:
words = ", ".join(topic)
print words
print "phi sparsensess"
# compute sparseness and write it out
sp = get_sparse_stats( phi )
np.save("phi_sparseness.npy", sp)
# report on sparseness statisitcs (assume single mode)
nz = sp.nonzero()[0] # get the nonzero entries
sp_avg = sum([sp[i]*i for i in nz]) # where are non-zero they concentrated ?
sp_var = sum( [sp[i]*np.abs(i-sp_avg)**2 for i in nz] )
sp_stdev = np.sqrt( sp_var ) # how concentrated they are around sp_avg
logger.info("Phi sparseness. center=%d, width=%d" % (int(sp_avg),int(sp_stdev)) )
#print list(sp)
# exit with OK status
sys.exit(0)
# get the topic list
top_words_in_topics = show_top(phi, num=args.num, id2word=id2word)
for topic in top_words_in_topics:
words = ", ".join(topic)
print words
print "phi sparsensess"
# compute sparseness and write it out
sp = get_sparse_stats( phi )
np.save("phi_sparseness.npy", sp)
# report on sparseness statisitcs (assume single mode)
nz = sp.nonzero()[0] # get the nonzero entries
sp_avg = sum([sp[i]*i for i in nz]) # where are non-zero they concentrated ?
sp_var = sum( [sp[i]*np.abs(i-sp_avg)**2 for i in nz] )
sp_stdev = np.sqrt( sp_var ) # how concentrated they are around sp_avg
logger.info("Phi sparseness. center=%d, width=%d" % (int(sp_avg),int(sp_stdev)) )
#print list(sp)
# exit with OK status
sys.exit(0)
def run(args):
"""
The command-line run script for LDA experiments.
"""
# scientific
import numpy as np
import scipy as sp
# display what run got in args
for tup in args.__dict__.iteritems():
print tup
# LOAD VOCAB
wlist = smart_list_reader(args.vocab_file)
if not wlist:
print "Vocab format not recognized"
sys.exit(-1)
# convert from list [term1, term2, ...] to dicts
# [term1:0, term2:1, ... ] and the inverse mapping
id2word = dict(enumerate(wlist))
word2id = dict([(word, id) for id, word in id2word.items()])
vocab = word2id
# SETUP CORPUS (LAZY)
# doCounts -- not so lazy...
if args.docs_file[-3:] == ".mm":
from liblda.newmmcorpus import NewMmCorpus
corpus = NewMmCorpus(args.docs_file)
corpus.setVocabFromDict(vocab)
corpus.doCounts()
elif args.docs_file[-4:] == ".txt":
from liblda.low2corpus import Low2Corpus
corpus = Low2Corpus(args.docs_file)
corpus.setVocabFromDict(vocab)
corpus.doCounts()
else:
print "Corpus format not recognized"
sys.exit(-1)
# Create rundir
from socket import gethostname
from liblda.util import rungen
full_hostname = gethostname()
host_id = full_hostname.rstrip(".cs.mcgill.ca")
if not args.rundirs_root:
rundirs_root = RUNDIRS_ROOT
else:
rundirs_root = args.rundirs_root
if not os.path.exists(rundirs_root):
print "Error, rundirs_root %s doesn't exist" % rundirs_root
sys.exit(-1)
# create the host-specific rundir if necessary
host_rundirs_root = os.path.join(rundirs_root, host_id)
if not os.path.exists(host_rundirs_root):
os.mkdir(host_rundirs_root)
# create a new (sequential) rundir for this host
rundir = rungen.mk_next_rundir(host_rundirs_root)
logger.info("rundir: " + rundir)
# prepare a dict which will become input.json
input = {}
input["rundir"] = rundir
input["numT"] = args.numT
input["iter"] = args.iter
input["corpus"] = args.docs_file
input["vocab"] = args.vocab_file
input["alpha"] = args.alpha
input["beta"] = args.beta
input["seed"] = args.seed
input["host_id"] = host_id
# and write it to disk
f = open(os.path.join(rundir, "input.json"), "w")
simplejson.dump(input, f, indent=0)
f.close()
start_time = datetime.datetime.now()
# setup the lda model
lda = LdaModel(numT=args.numT,
alpha=args.alpha,
beta=args.beta,
corpus=corpus,
vocab=vocab)
# if not in seeded mode run as usual
if not args.seed_z_from:
if not args.save_perplexity_every:
lda.train(iter=args.iter, seed=args.seed)
else:
lda.allocate_arrays()
lda.read_dw_alphabetical()
lda.random_initialize()
cum = 0
perp_hist = []
while (cum < args.iter):
lda.gibbs_sample(iter=args.save_perplexity_every,
seed=args.seed + cum)
lda.wpdt_to_probs()
perp_hist.append(lda.perplexity()
) # = np.exp( -1 * loglike() / totalNwords )
cum += args.save_perplexity_every
# NEW: S
else:
logger.info("Using seeded z training ... ")
# training params
if not args.iter:
lda.iter = 50
else:
lda.iter = args.iter
if not args.seed:
seed = 777
lda.seed = 2 * seed + 1
else:
lda.seed = 2 * args.seed + 1
# loadup the seed_z_from file into seed_z np array
seed_z = np.load(args.seed_z_from)
if args.expand_factors:
expand_factors_str = smart_list_reader(args.expand_factors)
expand_factors = np.array([int(i) for i in expand_factors_str])
else:
expand_factors = None # let lda.seeded_initialize() handle it
# custom train sequence
lda.allocate_arrays()
lda.read_dw_alphabetical()
#self.random_initialize() # NO -- we want a seeded initialization!
lda.seeded_initialize(seed_z, expand_factors)
lda.gibbs_sample(iter=lda.iter, seed=lda.seed)
lda.wpdt_to_probs()
#self.deallocate_arrays()
# record how long it took
end_time = datetime.datetime.now()
duration = (end_time - start_time).seconds
# save word counts and topic assignment counts (these are sparse)
if args.save_counts: # TRUE by default
state = ["dp", "wp", "alpha", "beta"]
for var_name in state:
f_name = os.path.join(rundir, RUN_FILENAMESS[var_name])
np.save(f_name, lda.__getattribute__(var_name))
logger.info("Done writing out Nwt+beta, Ndt+alpha")
# Gibbs sampler state, which consists of
# the full topic assignments "z.npy"
if args.save_z:
var_name = "z"
f_name = os.path.join(rundir, RUN_FILENAMESS[var_name])
np.save(f_name, lda.__getattribute__(var_name))
logger.info("Done writing out z.npy")
# save probs
if args.save_probs:
probs = ["phi", "theta"]
for var_name in probs:
f_name = os.path.join(rundir, RUN_FILENAMESS[var_name])
np.save(f_name, lda.__getattribute__(var_name))
logger.info("Done writing out probabilities phi.npy and theta.npy")
# prepare a dict which will become output.json
output = {}
# run details
output["rundir"] = rundir
output["host_id"] = host_id
output["iter"] = args.iter
output["seed"] = args.seed
output["start_time"] = start_time.isoformat() # ISO format string
# to read ISO time stamps use dateutil
#>>> from dateutil import parser
#>>> parser.parse("2011-01-25T23:36:43.373248")
# datetime.datetime(2011, 1, 25, 23, 36, 43, 373247)
output["duration"] = int(duration)
# corpus info
output["corpus"] = args.docs_file
output["vocab"] = args.vocab_file
output["numDocs"] = lda.numDocs
output["numTerms"] = lda.numTerms
output["totalNterms"] = lda.corpus.totalNwords
# model parameters
output["numT"] = lda.numT
# the hyperparameters are too long to store in full here,
# use separate .npy files if alpha/beta non uniform
output["alpha"] = lda.alpha[
0] #[np.average(lda.alpha), float(np.cov(lda.alpha)) ] # [avg, var]
output["beta"] = lda.beta[
0] #[np.average(lda.beta), float(np.cov(lda.beta)) ] # [avg, var]
#
# calculate likelyhood
output["loglike"] = lda.loglike()
output["perplexity"] = lda.perplexity(
) # = np.exp( -1 * loglike() / totalNwords )
if args.save_perplexity_every:
output["perplexity_history"] = perp_hist
logger.info("Log likelyhood: %f" % output["loglike"])
logger.info("Perplexity: %f" % output["perplexity"])
#
# special seeding info
if args.seed_z_from:
output["seed_z_from"] = args.seed_z_from
if args.expand_factors:
output["expand_factors"] = args.expand_factors
# compute sparseness and write it out
sp = get_sparse_stats(lda.phi)
np.save(os.path.join(rundir, "phi_sparseness.npy"), sp)
# report on sparseness statisitcs (assume single mode)
nz = sp.nonzero()[0] # get the nonzero entries
sp_avg = sum([sp[i] * i
for i in nz]) # where are non-zero they concentrated ?
sp_var = sum([sp[i] * np.abs(i - sp_avg)**2 for i in nz])
sp_stdev = np.sqrt(sp_var) # how concentrated they are around sp_avg
output["phi_sparseness_avg"] = sp_avg
output["phi_sparseness_stdev"] = sp_stdev
logger.info("Phi sparseness. center=%d, width=%d" %
(int(sp_avg), int(sp_stdev)))
# same for theta
sp = get_sparse_stats(lda.theta)
np.save(os.path.join(rundir, "theta_sparseness.npy"), sp)
# report on sparseness statisitcs (assume single mode)
nz = sp.nonzero()[0] # get the nonzero entries
sp_avg = sum([sp[i] * i
for i in nz]) # where are non-zero they concentrated ?
sp_var = sum([sp[i] * np.abs(i - sp_avg)**2 for i in nz])
sp_stdev = np.sqrt(sp_var) # how concentrated they are around sp_avg
output["theta_sparseness_avg"] = sp_avg
output["theta_sparseness_stdev"] = sp_stdev
logger.info("Theta sparseness. center=%d, width=%d" %
(int(sp_avg), int(sp_stdev)))
# write all output data to disk
f = open(os.path.join(rundir, "output.json"), "w")
simplejson.dump(output, f, indent=0)
f.close()
logger.info("Done saving output.json")
if args.print_topics:
from liblda.topicviz.show_top import show_top
top_words_in_topics = show_top(lda.phi,
num=args.print_topics,
id2word=lda.corpus.id2word)
for topic in top_words_in_topics:
words = ", ".join(topic)
print words
logger.info("Done! --> thank you come again")
