class ComputeSeriation(object):
"""Seriation algorithm.
Re-order words to improve promote the legibility of multi-word
phrases and reveal the clustering of related terms.
As output, the algorithm produces a list of seriated terms and its 'ranking'
(i.e., the iteration in which a term was seriated).
"""
DEFAULT_NUM_SERIATED_TERMS = 100
def __init__(self, logging_level):
self.logger = logging.getLogger('ComputeSeriation')
self.logger.setLevel(logging_level)
handler = logging.StreamHandler(sys.stderr)
handler.setLevel(logging_level)
self.logger.addHandler(handler)
def execute(self, data_path, numSeriatedTerms=None):
assert data_path is not None
if numSeriatedTerms is None:
numSeriatedTerms = ComputeSeriation.DEFAULT_NUM_SERIATED_TERMS
self.logger.info(
'--------------------------------------------------------------------------------'
)
self.logger.info('Computing term seriation...')
self.logger.info(' data_path = %s', data_path)
self.logger.info(' number_of_seriated_terms = %d', numSeriatedTerms)
self.logger.info('Connecting to data...')
self.saliency = SaliencyAPI(data_path)
self.similarity = SimilarityAPI(data_path)
self.seriation = SeriationAPI(data_path)
self.logger.info('Reading data from disk...')
self.saliency.read()
self.similarity.read()
self.logger.info('Reshaping saliency data...')
self.reshape()
self.logger.info('Computing seriation...')
self.compute(numSeriatedTerms)
self.logger.info('Writing data to disk...')
self.seriation.write()
self.logger.info(
'--------------------------------------------------------------------------------'
)
def reshape(self):
self.candidateSize = 100
self.orderedTermList = []
self.termSaliency = {}
self.termFreqs = {}
self.termDistinct = {}
self.termRank = {}
self.termVisibility = {}
for element in self.saliency.term_info:
term = element['term']
self.orderedTermList.append(term)
self.termSaliency[term] = element['saliency']
self.termFreqs[term] = element['frequency']
self.termDistinct[term] = element['distinctiveness']
self.termRank[term] = element['rank']
self.termVisibility[term] = element['visibility']
def compute(self, numSeriatedTerms):
# Elicit from user (1) the number of terms to output and (2) a list of terms that should be included in the output...
# set in init (i.e. read from config file)
# Seriate!
start_time = time.time()
candidateTerms = self.orderedTermList
self.seriation.term_ordering = []
self.seriation.term_iter_index = []
self.buffers = [0, 0]
preBest = []
postBest = []
for iteration in range(numSeriatedTerms) and candidateTerms:
print "Iteration no. ", iteration
addedTerm = 0
if len(self.seriation.term_iter_index) > 0:
addedTerm = self.seriation.term_iter_index[-1]
if iteration == 1:
(preBest,
postBest) = self.initBestEnergies(addedTerm, candidateTerms)
(preBest, postBest,
self.bestEnergies) = self.getBestEnergies(preBest, postBest,
addedTerm)
(candidateTerms, self.seriation.term_ordering,
self.seriation.term_iter_index, self.buffers) = self.iterate_eff(
candidateTerms, self.seriation.term_ordering,
self.seriation.term_iter_index, self.buffers,
self.bestEnergies, iteration)
print "---------------"
seriation_time = time.time() - start_time
# Output consists of (1) a list of ordered terms, and (2) the iteration index in which a term was ordered
#print "term_ordering: ", self.seriation.term_ordering
#print "term_iter_index: ", self.seriation.term_iter_index # Feel free to pick a less confusing variable name
#print "similarity matrix generation time: ", compute_sim_time
#print "seriation time: ", seriation_time
self.logger.debug("seriation time: " + str(seriation_time))
#-------------------------------------------------------------------------------#
# Helper Functions
def initBestEnergies(self, firstTerm, candidateTerms):
preBest = []
postBest = []
for candidate in candidateTerms:
pre_score = 0
post_score = 0
# preBest
if (candidate, firstTerm) in self.similarity.combined_g2:
pre_score = self.similarity.combined_g2[(candidate, firstTerm)]
# postBest
if (firstTerm, candidate) in self.similarity.combined_g2:
post_score = self.similarity.combined_g2[(firstTerm,
candidate)]
preBest.append((candidate, pre_score))
postBest.append((candidate, post_score))
return (preBest, postBest)
def getBestEnergies(self, preBest, postBest, addedTerm):
if addedTerm == 0:
return (preBest, postBest, [])
term_order = [x[0] for x in preBest]
# compare candidate terms' bests against newly added term
remove_index = -1
for existingIndex in range(len(preBest)):
term = term_order[existingIndex]
if term == addedTerm:
remove_index = existingIndex
# check pre energies
if (term, addedTerm) in self.similarity.combined_g2:
if self.similarity.combined_g2[(
term, addedTerm)] > preBest[existingIndex][1]:
preBest[existingIndex] = (
term, self.similarity.combined_g2[(term, addedTerm)])
# check post energies
if (addedTerm, term) in self.similarity.combined_g2:
if self.similarity.combined_g2[(
addedTerm, term)] > postBest[existingIndex][1]:
postBest[existingIndex] = (
term, self.similarity.combined_g2[(addedTerm, term)])
# remove the added term's preBest and postBest scores
if remove_index != -1:
del preBest[remove_index]
del postBest[remove_index]
#create and sort the bestEnergies list
energyMax = [
sum(pair)
for pair in zip([x[1] for x in preBest], [y[1] for y in postBest])
]
bestEnergies = zip([x[0] for x in preBest], energyMax)
return (preBest, postBest,
sorted(bestEnergies, key=itemgetter(1), reverse=True))
def iterate_eff(self, candidateTerms, term_ordering, term_iter_index,
buffers, bestEnergies, iteration_no):
maxEnergyChange = -9999999999999999
maxTerm = ""
maxPosition = 0
if len(bestEnergies) != 0:
bestEnergy_terms = [x[0] for x in bestEnergies]
else:
bestEnergy_terms = candidateTerms
breakout_counter = 0
for candidate_index in range(len(bestEnergy_terms)):
breakout_counter += 1
candidate = bestEnergy_terms[candidate_index]
for position in range(len(term_ordering) + 1):
current_buffer = buffers[position]
candidateRank = self.termRank[candidate]
if candidateRank <= (len(term_ordering) + self.candidateSize):
current_energy_change = self.getEnergyChange(
candidate, position, term_ordering, current_buffer,
iteration_no)
if current_energy_change > maxEnergyChange:
maxEnergyChange = current_energy_change
maxTerm = candidate
maxPosition = position
# check for early termination
if candidate_index < len(bestEnergy_terms) - 1 and len(
bestEnergies) != 0:
if maxEnergyChange >= (
2 *
(bestEnergies[candidate_index][1] + current_buffer)):
print "#-------- breaking out early ---------#"
print "candidates checked: ", breakout_counter
break
print "change in energy: ", maxEnergyChange
print "maxTerm: ", maxTerm
print "maxPosition: ", maxPosition
candidateTerms.remove(maxTerm)
# update buffers
buf_score = 0
if len(term_ordering) == 0:
buffers = buffers
elif maxPosition >= len(term_ordering):
if (term_ordering[-1], maxTerm) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(term_ordering[-1],
maxTerm)]
buffers.insert(len(buffers) - 1, buf_score)
elif maxPosition == 0:
if (maxTerm, term_ordering[0]) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(maxTerm,
term_ordering[0])]
buffers.insert(1, buf_score)
else:
if (term_ordering[maxPosition - 1],
maxTerm) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(
term_ordering[maxPosition - 1], maxTerm)]
buffers[maxPosition] = buf_score
buf_score = 0
if (maxTerm,
term_ordering[maxPosition]) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(
maxTerm, term_ordering[maxPosition])]
buffers.insert(maxPosition + 1, buf_score)
# update term ordering and ranking
if maxPosition >= len(term_ordering):
term_ordering.append(maxTerm)
else:
term_ordering.insert(maxPosition, maxTerm)
term_iter_index.append(maxTerm)
return (candidateTerms, term_ordering, term_iter_index, buffers)
def getEnergyChange(self, candidateTerm, position, term_list,
currentBuffer, iteration_no):
prevBond = 0.0
postBond = 0.0
# first iteration only
if iteration_no == 0:
current_freq = 0.0
current_saliency = 0.0
if candidateTerm in self.termFreqs:
current_freq = self.termFreqs[candidateTerm]
if candidateTerm in self.termSaliency:
current_saliency = self.termSaliency[candidateTerm]
return 0.001 * current_freq * current_saliency
# get previous term
if position > 0:
prev_term = term_list[position - 1]
if (prev_term, candidateTerm) in self.similarity.combined_g2:
prevBond = self.similarity.combined_g2[(prev_term,
candidateTerm)]
# get next term
if position < len(term_list):
next_term = term_list[position]
if (next_term, candidateTerm) in self.similarity.combined_g2:
postBond = self.similarity.combined_g2[(candidateTerm,
next_term)]
return 2 * (prevBond + postBond - currentBuffer)
class ComputeSeriation( object ):
"""Seriation algorithm.
Re-order words to improve promote the legibility of multi-word
phrases and reveal the clustering of related terms.
As output, the algorithm produces a list of seriated terms and its 'ranking'
(i.e., the iteration in which a term was seriated).
"""
DEFAULT_NUM_SERIATED_TERMS = 100
def __init__( self, logging_level ):
self.logger = logging.getLogger( 'ComputeSeriation' )
self.logger.setLevel( logging_level )
handler = logging.StreamHandler( sys.stderr )
handler.setLevel( logging_level )
self.logger.addHandler( handler )
def execute( self, data_path, numSeriatedTerms = None ):
assert data_path is not None
if numSeriatedTerms is None:
numSeriatedTerms = ComputeSeriation.DEFAULT_NUM_SERIATED_TERMS
self.logger.info( '--------------------------------------------------------------------------------' )
self.logger.info( 'Computing term seriation...' )
self.logger.info( ' data_path = %s', data_path )
self.logger.info( ' number_of_seriated_terms = %d', numSeriatedTerms )
self.logger.info( 'Connecting to data...' )
self.saliency = SaliencyAPI( data_path )
self.similarity = SimilarityAPI( data_path )
self.seriation = SeriationAPI( data_path )
self.logger.info( 'Reading data from disk...' )
self.saliency.read()
self.similarity.read()
self.logger.info( 'Reshaping saliency data...' )
self.reshape()
self.logger.info( 'Computing seriation...' )
self.compute( numSeriatedTerms )
self.logger.info( 'Writing data to disk...' )
self.seriation.write()
self.logger.info( '--------------------------------------------------------------------------------' )
def reshape( self ):
self.candidateSize = 100
self.orderedTermList = []
self.termSaliency = {}
self.termFreqs = {}
self.termDistinct = {}
self.termRank = {}
self.termVisibility = {}
for element in self.saliency.term_info:
term = element['term']
self.orderedTermList.append( term )
self.termSaliency[term] = element['saliency']
self.termFreqs[term] = element['frequency']
self.termDistinct[term] = element['distinctiveness']
self.termRank[term] = element['rank']
self.termVisibility[term] = element['visibility']
def compute( self, numSeriatedTerms ):
# Elicit from user (1) the number of terms to output and (2) a list of terms that should be included in the output...
# set in init (i.e. read from config file)
# Seriate!
start_time = time.time()
candidateTerms = self.orderedTermList
self.seriation.term_ordering = []
self.seriation.term_iter_index = []
self.buffers = [0,0]
preBest = []
postBest = []
for iteration in range(numSeriatedTerms):
print "Iteration no. ", iteration
addedTerm = 0
if len(self.seriation.term_iter_index) > 0:
addedTerm = self.seriation.term_iter_index[-1]
if iteration == 1:
(preBest, postBest) = self.initBestEnergies(addedTerm, candidateTerms)
(preBest, postBest, self.bestEnergies) = self.getBestEnergies(preBest, postBest, addedTerm)
(candidateTerms, self.seriation.term_ordering, self.seriation.term_iter_index, self.buffers) = self.iterate_eff(candidateTerms, self.seriation.term_ordering, self.seriation.term_iter_index, self.buffers, self.bestEnergies, iteration)
print "---------------"
seriation_time = time.time() - start_time
# Output consists of (1) a list of ordered terms, and (2) the iteration index in which a term was ordered
#print "term_ordering: ", self.seriation.term_ordering
#print "term_iter_index: ", self.seriation.term_iter_index # Feel free to pick a less confusing variable name
#print "similarity matrix generation time: ", compute_sim_time
#print "seriation time: ", seriation_time
self.logger.debug("seriation time: " + str(seriation_time))
#-------------------------------------------------------------------------------#
# Helper Functions
def initBestEnergies(self, firstTerm, candidateTerms):
preBest = []
postBest = []
for candidate in candidateTerms:
pre_score = 0
post_score = 0
# preBest
if (candidate, firstTerm) in self.similarity.combined_g2:
pre_score = self.similarity.combined_g2[(candidate, firstTerm)]
# postBest
if (firstTerm, candidate) in self.similarity.combined_g2:
post_score = self.similarity.combined_g2[(firstTerm, candidate)]
preBest.append((candidate, pre_score))
postBest.append((candidate, post_score))
return (preBest, postBest)
def getBestEnergies(self, preBest, postBest, addedTerm):
if addedTerm == 0:
return (preBest, postBest, [])
term_order = [x[0] for x in preBest]
# compare candidate terms' bests against newly added term
remove_index = -1
for existingIndex in range(len(preBest)):
term = term_order[existingIndex]
if term == addedTerm:
remove_index = existingIndex
# check pre energies
if (term, addedTerm) in self.similarity.combined_g2:
if self.similarity.combined_g2[(term, addedTerm)] > preBest[existingIndex][1]:
preBest[existingIndex] = (term, self.similarity.combined_g2[(term, addedTerm)])
# check post energies
if (addedTerm, term) in self.similarity.combined_g2:
if self.similarity.combined_g2[(addedTerm, term)] > postBest[existingIndex][1]:
postBest[existingIndex] = (term, self.similarity.combined_g2[(addedTerm, term)])
# remove the added term's preBest and postBest scores
if remove_index != -1:
del preBest[remove_index]
del postBest[remove_index]
#create and sort the bestEnergies list
energyMax = [sum(pair) for pair in zip([x[1] for x in preBest], [y[1] for y in postBest])]
bestEnergies = zip([x[0] for x in preBest], energyMax)
return (preBest, postBest, sorted(bestEnergies, key=itemgetter(1), reverse=True))
def iterate_eff( self, candidateTerms, term_ordering, term_iter_index, buffers, bestEnergies, iteration_no ):
maxEnergyChange = 0.0;
maxTerm = "";
maxPosition = 0;
if len(bestEnergies) != 0:
bestEnergy_terms = [x[0] for x in bestEnergies]
else:
bestEnergy_terms = candidateTerms
breakout_counter = 0
for candidate_index in range(len(bestEnergy_terms)):
breakout_counter += 1
candidate = bestEnergy_terms[candidate_index]
for position in range(len(term_ordering)+1):
current_buffer = buffers[position]
candidateRank = self.termRank[candidate]
if candidateRank <= (len(term_ordering) + self.candidateSize):
current_energy_change = self.getEnergyChange(candidate, position, term_ordering, current_buffer, iteration_no)
if current_energy_change > maxEnergyChange:
maxEnergyChange = current_energy_change
maxTerm = candidate
maxPosition = position
# check for early termination
if candidate_index < len(bestEnergy_terms)-1 and len(bestEnergies) != 0:
if maxEnergyChange >= (2*(bestEnergies[candidate_index][1] + current_buffer)):
print "#-------- breaking out early ---------#"
print "candidates checked: ", breakout_counter
break;
print "change in energy: ", maxEnergyChange
print "maxTerm: ", maxTerm
print "maxPosition: ", maxPosition
candidateTerms.remove(maxTerm)
# update buffers
buf_score = 0
if len(term_ordering) == 0:
buffers = buffers
elif maxPosition >= len(term_ordering):
if (term_ordering[-1], maxTerm) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(term_ordering[-1], maxTerm)]
buffers.insert(len(buffers)-1, buf_score)
elif maxPosition == 0:
if (maxTerm, term_ordering[0]) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(maxTerm, term_ordering[0])]
buffers.insert(1, buf_score)
else:
if (term_ordering[maxPosition-1], maxTerm) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(term_ordering[maxPosition-1], maxTerm)]
buffers[maxPosition] = buf_score
buf_score = 0
if (maxTerm, term_ordering[maxPosition]) in self.similarity.combined_g2:
buf_score = self.similarity.combined_g2[(maxTerm, term_ordering[maxPosition])]
buffers.insert(maxPosition+1, buf_score)
# update term ordering and ranking
if maxPosition >= len(term_ordering):
term_ordering.append(maxTerm)
else:
term_ordering.insert(maxPosition, maxTerm)
term_iter_index.append(maxTerm)
return (candidateTerms, term_ordering, term_iter_index, buffers)
def getEnergyChange(self, candidateTerm, position, term_list, currentBuffer, iteration_no):
prevBond = 0.0
postBond = 0.0
# first iteration only
if iteration_no == 0:
current_freq = 0.0
current_saliency = 0.0
if candidateTerm in self.termFreqs:
current_freq = self.termFreqs[candidateTerm]
if candidateTerm in self.termSaliency:
current_saliency = self.termSaliency[candidateTerm]
return 0.001 * current_freq * current_saliency
# get previous term
if position > 0:
prev_term = term_list[position-1]
if (prev_term, candidateTerm) in self.similarity.combined_g2:
prevBond = self.similarity.combined_g2[(prev_term, candidateTerm)]
# get next term
if position < len(term_list):
next_term = term_list[position]
if (next_term, candidateTerm) in self.similarity.combined_g2:
postBond = self.similarity.combined_g2[(candidateTerm, next_term)]
return 2*(prevBond + postBond - currentBuffer)
