def findAnchorTopics_Orig(Data,
K=10,
loss='L2',
seed=0,
lowerDim=1000,
minDocPerWord=0,
eps=1e-4,
doRecover=1):
""" Estimate and return K topics using anchor word method
Returns
-------
topics : numpy 2D array, size K x V
"""
from Q_matrix import generate_Q_matrix
from fastRecover import do_recovery
params = Params(seed=seed,
lowerDim=lowerDim,
minDocPerWord=minDocPerWord,
eps=eps)
assert isinstance(Data, bnpy.data.DataObj)
DocWordMat = Data.getSparseDocTypeCountMatrix()
if not str(type(DocWordMat)).count('csr_matrix') > 0:
raise NotImplementedError('Need CSR matrix')
Q = generate_Q_matrix(DocWordMat.copy().T)
anchors = selectAnchorWords(DocWordMat.tocsc(), Q, K, params)
if doRecover:
topics, topic_likelihoods = do_recovery(Q, anchors, loss, params)
topics = topics.T
topics = topics / topics.sum(axis=1)[:, np.newaxis]
return topics
else:
return Q, anchors
var = np.zeros((M.shape))
row_sums = Q_emp.sum(1)
for i in xrange(len(Q_emp[:,0])):
Q_bar[i,:] = Q_emp[i,:]/float(row_sums[i])
var[i,:] = var_analytical[i,:]/(float(row_sums[i])**2)
# find anchors
(anchors, anchor_indices) = gs.Projection_Find(Q_bar, K, candidate_anchors, var)
anchor_indices = [int(a) for a in anchor_indices]
print "anchors are:"
for i, a in enumerate(anchors):
print i, vocab[int(a)]
# recover topics
A, topic_likelihoods, R = do_recovery(Q_emp, anchors, loss, params)
print "done recovering"
np.savetxt(outfile+".A", A)
np.savetxt(outfile+".topic_likelihoods", topic_likelihoods)
np.savetxt(outfile+".R", R)
# np.savetxt(outfile+".Q", Q)
#display
f = file(outfile+".topwords", 'w')
for k in xrange(K):
mask = A[:, k] > 0.01
topwords = [ x for x in np.argsort(A[:, k]) if mask[x] ][::-1]
# topwords = np.argsort(A[:, k])[-params.top_words:][::-1]
# print params.top_words
# print 'npargsort', A[:, k]
vocab = file(vocab_file).read().strip().split()
#check that Q sum is 1 or close to it
print "Q sum is", Q.sum()
V = Q.shape[0]
print "done reading documents"
#find anchors- this step uses a random projection
#into low dimensional space
anchors = findAnchors(Q, K, params, candidate_anchors)
print "anchors are:"
for i, a in enumerate(anchors):
print i, vocab[a]
#recover topics
A, topic_likelihoods = do_recovery(Q, anchors, loss, params)
print "done recovering"
np.savetxt(outfile+".A", A)
np.savetxt(outfile+".topic_likelihoods", topic_likelihoods)
#display
f = file(outfile+".topwords", 'w')
for k in xrange(K):
topwords = np.argsort(A[:, k])[-params.top_words:][::-1]
print vocab[anchors[k]], ':',
print >>f, vocab[anchors[k]], ':',
for w in topwords:
print vocab[w],
print >>f, vocab[w],
print ""
def anchor_words(D, loss='L2', params=config.default_config()):
Q = generate_Q_matrix(D * 100)
anchors = findAnchors(Q, params['T'], params)
W, topic_likelihoods = do_recovery(Q, anchors, loss, params)
return W
def run(self):
params = self.params
if isinstance(params.infile, basestr):
M = scipy.io.loadmat(params.infile)['M']
else:
M = params.infile
assert sparse.isspmatrix_csc(M), "Must provide a sparse CSC matrix"
print("Input matrix shape: {}".format(M.shape))
if isinstance(params.vocab_file, basestr):
with open(params.vocab_file) as f:
vocab = f.read().strip().split()
else:
vocab = params.vocab_file
assert np.iterable(vocab), "Must provide an iterable vocab"
assert M.shape[0] == len(vocab), \
"Number of rows must correspond to vocab size: {} rows vs {} vocab words" \
.format(M.shape[0], len(vocab))
#only accept anchors that appear in a significant number of docs
print("identifying candidate anchors")
candidate_anchors = []
for i in range(M.shape[0]):
if len(np.nonzero(M[i, :])[1]) > params.anchor_thresh:
candidate_anchors.append(i)
print(len(candidate_anchors), "candidates")
#forms Q matrix from document-word matrix
Q = generate_Q_matrix(M)
# Save copy of unnormalized Q, before any normalizations happen
self.Q_unnormalized = Q.copy()
#check that Q sum is 1 or close to it
print("Q sum is", Q.sum())
V = Q.shape[0]
print("done reading documents")
#find anchors- this step uses a random projection
#into low dimensional space
anchors = findAnchors(Q, params, candidate_anchors)
print("anchors are:")
for i, a in enumerate(anchors):
print(i, vocab[a])
#recover topics
A, topic_likelihoods = do_recovery(Q, anchors, params)
print("done recovering")
output_streams = [sys.stdout]
output_file_handle = None
if params.outfile is not None:
np.savetxt(params.outfile+".A", A)
np.savetxt(params.outfile+".topic_likelihoods", topic_likelihoods)
output_file_handle = open(params.outfile+".topwords", 'w')
output_streams.append(output_file_handle)
def print_multiple(*args, **kwargs):
# Print the same info to multiple output streams
for f in output_streams:
print(*args, file=f, **kwargs)
# Display top words per topic
all_topwords = []
for k in range(params.K):
topwords = np.argsort(A[:, k])[-params.top_words:][::-1]
print_multiple(vocab[anchors[k]], ':', end=' ')
for w in topwords:
print_multiple(vocab[w], end=' ')
print_multiple("")
all_topwords.append(TopWordsSummary(
topic_index = k,
anchor_word_index = anchors[k],
anchor_word = vocab[anchors[k]],
top_word_indices = topwords,
top_words = [vocab[w] for w in topwords]))
if params.outfile is not None:
output_file_handle.close()
# make some results available as attributes of "self"
self.Q = Q
self.M = M
self.A = A
self._R = None
self.topic_likelihoods = topic_likelihoods
self.candidate_anchors = candidate_anchors
self.anchors = anchors
self.vocab = vocab
self.all_topwords = all_topwords
print "done reading documents"
#find anchors- this step uses a random projection
#into low dimensional space
anchor_logfile = file(params.log_prefix + '.anchors', 'w')
anchors = findAnchors(Q, K, params, candidate_anchors, anchor_logfile)
print "anchors are:"
print >> anchor_logfile, "anchors are:"
for i, a in enumerate(anchors):
print i, vocab[a]
print >> anchor_logfile, i, vocab[a]
anchor_logfile.close()
#recover topics
A, topic_likelihoods, objective = do_recovery(Q, anchors, loss, params)
print "done recovering"
print "avg objective function during recovery using", K, "topics:", objective
np.savetxt(outfile + ".A", A)
np.savetxt(outfile + ".topic_likelihoods", topic_likelihoods)
#display
f = file(outfile + ".topwords", 'w')
for k in xrange(K):
topwords = np.argsort(A[:, k])[-params.top_words:][::-1]
print vocab[anchors[k]], ':',
print >> f, vocab[anchors[k]], ':',
for w in topwords:
print vocab[w],
print >> f, vocab[w],
print "done reading documents"
#find anchors- this step uses a random projection
#into low dimensional space
anchor_logfile = file(params.log_prefix+'.anchors', 'w')
anchors = findAnchors(Q, K, params, candidate_anchors, anchor_logfile)
print "anchors are:"
print >>anchor_logfile, "anchors are:"
for i, a in enumerate(anchors):
print i, vocab[a]
print >>anchor_logfile, i, vocab[a]
anchor_logfile.close()
#recover topics
A, topic_likelihoods,objective = do_recovery(Q, anchors, loss, params)
print "done recovering"
print "avg objective function during recovery using", K, "topics:", objective
np.savetxt(outfile+".A", A)
np.savetxt(outfile+".topic_likelihoods", topic_likelihoods)
#display
f = file(outfile+".topwords", 'w')
for k in xrange(K):
topwords = np.argsort(A[:, k])[-params.top_words:][::-1]
print vocab[anchors[k]], ':',
print >>f, vocab[anchors[k]], ':',
for w in topwords:
print vocab[w],
print >>f, vocab[w],
vocab = open(vocab_file).read().strip().split()
# check that Q sum is 1 or close to it
print("Q sum is", Q.sum())
V = Q.shape[0]
print("done reading documents")
# find anchors- this step uses a random projection
# into low dimensional space
anchors = findAnchors(Q, K, params, candidate_anchors)
print("anchors are:")
for i, a in enumerate(anchors):
print(i, vocab[a])
# recover topics
A, topic_likelihoods = do_recovery(Q, anchors, loss, params)
print("done recovering")
np.savetxt(outfile + ".A", A)
np.savetxt(outfile + ".topic_likelihoods", topic_likelihoods)
# display
with open(outfile + ".topwords", "w") as f:
for k in range(K):
topwords = np.argsort(A[:, k])[-params.top_words:][::-1]
print(vocab[anchors[k]], ":", end=" ")
print(vocab[anchors[k]], ":", end=" ", file=f)
for w in topwords:
print(vocab[w], end=" ")
print(vocab[w], end=" ", file=f)
print("")
