def link_split_map (data, mdl, sample_model, train_plan, folds, model_dir = None):
'''
Train on all the words and half the links. Predict the remaining links.
Evaluate using mean average-precision.
Cross validation may be used, but note we're always evaluating on training
data.
:param data: the DataSet object with the data
:param mdl: the module with the train etc. functin
:param sample_model: a preconfigured model which is cloned at the start of each
cross-validation run
:param train_plan: the training plan (number of iterations etc.)
:param folds: the number of folds to cross validation
:param model_dir: if not none, and folds > 1, the models are stored in this
directory.
:return: the list of model files stored
'''
model_files = []
assert folds > 1, "Need at least two folds for this to make any sense whatsoever"
def prepareForTraining(data):
if mdl.is_undirected_link_predictor():
result = data.copy()
result.convert_to_undirected_graph()
result.convert_to_binary_link_matrix()
return result
else:
return data
for fold in range(folds):
model = mdl.newModelFromExisting(sample_model)
train_data, query_data = data.link_prediction_split(symmetric=False)
train_data = prepareForTraining(train_data) # make symmetric, if necessary, after split, so we
# can compare symmetric with non-symmetric models
train_tops = mdl.newQueryState(train_data, model)
model, train_tops, (train_itrs, train_vbs, train_likes) = \
mdl.train(train_data, model, train_tops, train_plan)
print("Training perplexity is %.2f " % perplexity_from_like(mdl.log_likelihood(train_data, model, train_tops), train_data.word_count))
min_link_probs = mdl.min_link_probs(model, train_tops, query_data.links)
predicted_link_probs = mdl.link_probs(model, train_tops, min_link_probs)
map = mean_average_prec (query_data.links, predicted_link_probs)
print ("Fold %2d: Mean-Average-Precision %6.3f" % (fold, map))
model_files = save_if_necessary(model_files, model_dir, model, data, fold, train_itrs, train_vbs, train_likes, train_tops, train_tops, mdl)
return model_files
def _testOnModelDerivedExample(self):
print("Cross-validated likelihoods on model-derived example")
useDiagonalPriorCov = True
rd.seed(0xBADB055) # Global init for repeatable test
D, T, K = 1000, 100, 7 # Document count, vocabularly size ("term count") and topic count
tpcs, vocab, docLens, W = self._sampleFromModel(D, T, K)
W = W.astype(DTYPE)
plt.imshow(vocab, interpolation="none", cmap = cm.Greys_r)
plt.show()
# Create the cross-validation folds
folds = 5
foldSize = ceil(D / 5)
querySize = foldSize
trainSize = D - querySize
for useDiagonalPriorCov in [False, True]:
trainLikely = []
trainWordCount = []
queryLikely = []
queryWordCount = []
for fold in range(folds):
# Split the datasets
start = fold * foldSize
end = start + trainSize
trainSet = np.arange(start,end) % D
querySet = np.arange(end, end + querySize) % D
W_train = W[trainSet,:]
W_query = W[querySet,:]
# Train the model
model = ctm.newModelAtRandom(W_train, K, dtype=DTYPE)
queryState = ctm.newQueryState(W_train, model)
plan = ctm.newTrainPlan(iterations=40, logFrequency=1, fastButInaccurate=useDiagonalPriorCov, debug=True)
model, queryState, (bndItrs, bndVals, likelies) = ctm.train (W_train, None, model, queryState, plan)
# Plot the evolution of the bound during training.
fig, ax1 = plt.subplots()
ax1.plot(bndItrs, bndVals, 'b-')
ax1.set_xlabel('Iterations')
ax1.set_ylabel('Bound', color='b')
ax2 = ax1.twinx()
ax2.plot(bndItrs, likelies, 'r-')
ax2.set_ylabel('Likelihood', color='r')
fig.show()
# Plot the topic covariance
self._plotCov(model)
# Plot the vocab
plt.imshow(model.vocab, interpolation="none", cmap = cm.Greys_r)
plt.show()
# Calculating the training set likelihood
trainLikely.append(ctm.log_likelihood(W_train, model, queryState))
trainWordCount.append(W_train.data.sum())
# Now query the model.
plan = ctm.newTrainPlan(iterations=10, fastButInaccurate=useDiagonalPriorCov)
queryState = ctm.newQueryState(W_query, model)
model, queryState = ctm.query(W_query, None, model, queryState, plan)
queryLikely.append(ctm.log_likelihood(W_query, model, queryState))
queryWordCount.append(W_query.data.sum())
# Print out the likelihood and perplexity for each fold.
print ("\n\n\nWith " + ("diagonal" if useDiagonalPriorCov else "full") + " covariances")
for fold in range(folds):
trainPerp = np.exp(-trainLikely[fold]/trainWordCount[fold])
queryPerp = np.exp(-queryLikely[fold]/queryWordCount[fold])
print("Fold %3d: Train-set Likelihood: %12f \t Query-set Likelihood: %12f" % (fold, trainLikely[fold], queryLikely[fold]))
print(" Perplexity: %12.2f \t Perplexity: %12.2f" % (trainPerp, queryPerp))
self.assertTrue(queryPerp < 60.0) # Maximum perplexity.
self.assertTrue(trainPerp < 60.0)
print ("\n\n")
print("End of Test")
def outsample_lro_style_prec_rec (data, mdl, sample_model, train_plan, feature_mask, model_dir=None, ldaModel=None, ldaTopics=None):
'''
Take a feature list. Train on all documents where none of those features
are set. Remove the first element from the feature list, query all documents
with that feature set, and then evaluate link prediction. Repeat until
feature-list is empty.
:param data: the DataSet object with the data
:param mdl: the module with the train etc. functin
:param sample_model: a preconfigured model which is cloned at the start of each
cross-validation run
:param train_plan: the training plan (number of iterations etc.)
:param feature_mask: the list of features used to separate training from query
This is a list of tuples, the left side is the feature label, the right side
is the
:param model_dir: if not none, the models are stored in this directory.
:param ldaModel: for those models that utilise and LDA component, a pre-trained
LDA model can be supplied.
:param ldaTopics: the topics of all documents in the corpus as given by the ldaModel
:return: the list of model files stored
'''
def prepareForTraining(data):
if mdl.is_undirected_link_predictor():
result = data.copy()
result.convert_to_undirected_graph()
result.convert_to_binary_link_matrix()
return result
else:
return data
ms = [10, 20, 30, 40, 50, 75, 100, 150, 250, 500]
model_files = []
combi_precs, combi_recs, combi_dcounts = None, None, None
mrr_sum, mrr_doc_count = 0, 0
map_sum, map_doc_count = 0, 0
while len(feature_mask) > 0:
# try:
# Prepare the training and query data
feature_mask_indices = [i for _,i in feature_mask]
train_data, query_data, train_indices = data.split_on_feature(feature_mask_indices)
(feat_label, feat_id) = feature_mask.pop(0)
print ("\n\nFeature: %s\n" % (feat_label,) + ("-" * 80))
train_data = prepareForTraining(train_data) # make symmetric, if necessary, after split, so we
# can compare symmetric with non-symmetric models
# Train the model
if model_uses_lda(sample_model):
ldaModelSubset, ldaTopicsSubset = subsetLda(ldaModel, ldaTopics, train_indices)
model = mdl.newModelFromExisting(sample_model, withLdaModel=ldaModelSubset)
train_tops = mdl.newQueryState(train_data, model, withLdaTopics=ldaTopicsSubset)
else:
model = mdl.newModelFromExisting(sample_model)
train_tops = mdl.newQueryState(train_data, model)
model, train_tops, (train_itrs, train_vbs, train_likes) = \
mdl.train(train_data, model, train_tops, train_plan)
print ("Training perplexity is %.2f " % perplexity_from_like(mdl.log_likelihood(train_data, model, train_tops), train_data.word_count))
# Infer the expected link probabilities
query_tops = mdl.newQueryState(query_data, model)
_, query_tops = mdl.query(query_data, model, query_tops, train_plan)
min_link_probs = mdl.min_link_probs(model, train_tops, query_tops, query_data.links)
predicted_link_probs = mdl.link_probs(model, train_tops, query_tops, min_link_probs)
expected_links = query_data.links
# Evaluation 1/3: Precision and Recall at M
precs, recs, doc_counts = mean_prec_rec_at (expected_links, predicted_link_probs, at=ms, groups=[(0,3), (3,5), (5,10), (10,1000)])
print (" Mean-Precisions for feature %s (#%d)" % (feat_label, feat_id), end="")
printTable("Precision", precs, doc_counts, ms)
printTable("Recall", recs, doc_counts, ms)
combi_precs, _ = combine_map(combi_precs, combi_dcounts, precs, doc_counts)
combi_recs, combi_dcounts = combine_map(combi_recs, combi_dcounts, recs, doc_counts)
# Evaluation 2/3: Mean Reciprocal-Rank
mrr = mean_reciprocal_rank(expected_links, predicted_link_probs)
print ("Mean reciprocal-rank : %f" % mrr)
mrr_sum += mrr * expected_links.shape[0]
mrr_doc_count += expected_links.shape[0]
# Evaluation 3/3: Mean Average-Precision
map = mean_average_prec (expected_links, predicted_link_probs)
print ("Mean Average Precision : %f" % map)
map_sum += map * expected_links.shape[0]
map_doc_count += expected_links.shape[0]
# Save the files if necessary and move onto the next fold if required
model_files = save_if_necessary(model_files, model_dir, model, data, feat_id, train_itrs, train_vbs, train_likes, train_tops, train_tops, mdl)
# except Exception as e:
# print("Fold " + str(fold) + " failed: " + str(e))
print ("-" * 80 + "\n\n Final Results\n\n")
printTable("Precision", combi_precs, combi_dcounts, ms)
printTable("Recall", combi_recs, combi_dcounts, ms)
print("Mean reciprocal-rank: %f" % (mrr_sum / mrr_doc_count))
print("Mean average-precision: %f" % (map_sum / map_doc_count))
return model_files
def insample_lro_style_prec_rec (data, mdl, sample_model, train_plan, folds, target_folds=None, model_dir=None, ldaModel=None, ldaTopics=None):
'''
For documents with > 5 links remove a portion. The portion is determined by
the number of folds (e.g. five-fold implied remove one fifth of links, three
fold implies remove a third, etc.)
Train on all documents and all remaining links.
Predict remaining links.
Evaluate using precision@m, recall@m, mean reciprocal-rank and
mean average-precision
Average all results.
:param data: the DataSet object with the data
:param mdl: the module with the train etc. functin
:param sample_model: a preconfigured model which is cloned at the start of each
cross-validation run
:param train_plan: the training plan (number of iterations etc.)
:param folds: the number of folds to cross validation
:param target_folds: the number of folds to complete before finishing. Set
to folds by default
:param model_dir: if not none, and folds > 1, the models are stored in this
directory.
:param ldaModel: for those models that utilise and LDA component, a pre-trained
LDA model can be supplied.
:param ldaTopics: the topics of all documents in the corpus as given by the ldaModel
:return: the list of model files stored
'''
ms = [10, 20, 30, 40, 50, 75, 100, 150, 250, 500]
model_files = []
assert folds > 1, "Need at least two folds for this to make any sense whatsoever"
def prepareForTraining(data):
if mdl.is_undirected_link_predictor():
result = data.copy()
result.convert_to_undirected_graph()
result.convert_to_binary_link_matrix()
return result
else:
return data
if target_folds is None:
target_folds = folds
combi_precs, combi_recs, combi_dcounts = None, None, None
mrr_sum, mrr_doc_count = 0, 0
map_sum, map_doc_count = 0, 0
fold_count = 0
for fold in range(folds):
# try:
# Prepare the training and query data
train_data, query_data, docSubset = data.folded_link_prediction_split(MinLinkCountEval, fold, folds)
train_data = prepareForTraining(train_data) # make symmetric, if necessary, after split, so we
# can compare symmetric with non-symmetric models
print ("\n\nFold %d\n" % fold + ("-" * 80))
# Train the model
if model_uses_lda(sample_model):
model = mdl.newModelFromExisting(sample_model, withLdaModel=ldaModel)
train_tops = mdl.newQueryState(train_data, model, withLdaTopics=ldaTopics)
else:
model = mdl.newModelFromExisting(sample_model)
train_tops = mdl.newQueryState(train_data, model)
model, train_tops, (train_itrs, train_vbs, train_likes) = \
mdl.train(train_data, model, train_tops, train_plan)
print ("Training perplexity is %.2f " % perplexity_from_like(mdl.log_likelihood(train_data, model, train_tops), train_data.word_count))
# Infer the expected link probabilities
min_link_probs = mdl.min_link_probs(model, train_tops, train_tops, query_data.links, docSubset)
predicted_link_probs = mdl.link_probs(model, train_tops, train_tops, min_link_probs, docSubset)
expected_links = query_data.links[docSubset, :]
# Evaluation 1/3: Precision and Recall at M
precs, recs, doc_counts = mean_prec_rec_at (expected_links, predicted_link_probs, at=ms, groups=[(0,3), (3,5), (5,10), (10,1000)])
print ("Fold %2d: Mean-Precisions at \n" % fold, end="")
printTable("Precision", precs, doc_counts, ms)
printTable("Recall", recs, doc_counts, ms)
combi_precs, _ = combine_map(combi_precs, combi_dcounts, precs, doc_counts)
combi_recs, combi_dcounts = combine_map(combi_recs, combi_dcounts, recs, doc_counts)
# Evaluation 2/3: Mean Reciprocal-Rank
mrr = mean_reciprocal_rank(expected_links, predicted_link_probs)
print ("Mean reciprocal-rank : %f" % mrr)
mrr_sum += mrr * expected_links.shape[0]
mrr_doc_count += expected_links.shape[0]
# Evaluation 3/3: Mean Average-Precision
map = mean_average_prec (expected_links, predicted_link_probs)
print ("Mean Average Precision : %f" % map)
map_sum += map * expected_links.shape[0]
map_doc_count += expected_links.shape[0]
# Save the files if necessary and move onto the next fold if required
model_files = save_if_necessary(model_files, model_dir, model, data, fold, train_itrs, train_vbs, train_likes, train_tops, train_tops, mdl)
fold_count += 1
if fold_count == target_folds:
break
# except Exception as e:
# print("Fold " + str(fold) + " failed: " + str(e))
print ("-" * 80 + "\n\n Final Results\n\n")
printTable("Precision", combi_precs, combi_dcounts, ms)
printTable("Recall", combi_recs, combi_dcounts, ms)
print("Mean reciprocal-rank: %f" % (mrr_sum / mrr_doc_count))
print("Mean average-precision: %f" % (map_sum / map_doc_count))
return model_files
def link_split_prec_rec (data, mdl, sample_model, train_plan, folds, target_folds=None, model_dir=None, ldaModel=None, ldaTopics=None):
'''
Train on all the words and half the links. Predict the remaining links.
Evaluate using precision at m using as values of m 50, 100, 250, and 500,
and additionally recall at m
Cross validation may be used, but note we're always evaluating on training
data.
:param data: the DataSet object with the data
:param mdl: the module with the train etc. functin
:param sample_model: a preconfigured model which is cloned at the start of each
cross-validation run
:param train_plan: the training plan (number of iterations etc.)
:param folds: the number of folds to cross validation
:param target_folds: the number of folds to complete before finishing. Set
to folds by default
:param model_dir: if not none, and folds > 1, the models are stored in this
directory.
:param ldaModel: for those models that utilise and LDA component, a pre-trained
LDA model can be supplied.
:param ldaTopics: the topics of all documents in the corpus as given by the ldaModel
:return: the list of model files stored
'''
ms = [10, 20, 30, 40, 50, 75, 100, 150, 250, 500]
model_files = []
assert folds > 1, "Need at least two folds for this to make any sense whatsoever"
def prepareForTraining(data):
if mdl.is_undirected_link_predictor():
result = data.copy()
result.convert_to_undirected_graph()
result.convert_to_binary_link_matrix()
return result
else:
return data
if ldaModel is not None:
(_, _, _, _, ldaModel, ldaTopics, _) = ldaModel
if target_folds is None:
target_folds = folds
combi_precs, combi_recs, combi_dcounts = None, None, None
mrr_sum, mrr_doc_count = 0, 0
map_sum, map_doc_count = 0, 0
for fold in range(target_folds):
model = mdl.newModelFromExisting(sample_model, withLdaModel=ldaModel) \
if sample_model.name == LRO_MODEL_NAME \
else mdl.newModelFromExisting(sample_model)
train_data, query_data = data.link_prediction_split(symmetric=False)
train_data = prepareForTraining(train_data) # make symmetric, if necessary, after split, so we
# can compare symmetric with non-symmetric models
train_tops = mdl.newQueryState(train_data, model)
model, train_tops, (train_itrs, train_vbs, train_likes) = \
mdl.train(train_data, model, train_tops, train_plan)
print ("Training perplexity is %.2f " % perplexity_from_like(mdl.log_likelihood(train_data, model, train_tops), train_data.word_count))
min_link_probs = mdl.min_link_probs(model, train_tops, query_data.links)
predicted_link_probs = mdl.link_probs(model, train_tops, min_link_probs)
expected_links = query_data.links
precs, recs, doc_counts = mean_prec_rec_at (expected_links, predicted_link_probs, at=ms, groups=[(0,3), (3,5), (5,10), (10,1000)])
print ("Fold %2d: Mean-Precisions at \n" % fold, end="")
printTable("Precision", precs, doc_counts, ms)
printTable("Recall", recs, doc_counts, ms)
mrr = mean_reciprocal_rank(expected_links, predicted_link_probs)
print ("Mean reciprocal-rank : %f" % mrr)
mrr_sum += mrr * expected_links.shape[0]
mrr_doc_count += expected_links.shape[0]
map = mean_average_prec (expected_links, predicted_link_probs)
print ("Mean Average Precision : %f" % map)
map_sum += map * expected_links.shape[0]
map_doc_count += expected_links.shape[0]
combi_precs, _ = combine_map(combi_precs, combi_dcounts, precs, doc_counts)
combi_recs, combi_dcounts = combine_map(combi_recs, combi_dcounts, recs, doc_counts)
model_files = save_if_necessary(model_files, model_dir, model, data, fold, train_itrs, train_vbs, train_likes, train_tops, train_tops, mdl)
print ("-" * 80 + "\n\n Final Results\n\n")
printTable("Precision", combi_precs, combi_dcounts, ms)
printTable("Recall", combi_recs, combi_dcounts, ms)
print("Mean reciprocal-rank: %f" % (mrr_sum / mrr_doc_count))
return model_files
def cross_val_and_eval_perplexity(data, mdl, sample_model, train_plan, query_plan, num_folds, fold_run_count=-1, model_dir= None):
'''
Uses cross-validation go get the average perplexity. If folds == 1 a special path is
triggered where perplexity is evaluated on the training data, and the results are
not saved to disk, even if model_dir is not none
:param data: the DataSet object with the data
:param mdl: the module with the train etc. functin
:param sample_model: a preconfigured model which is cloned at the start of each
cross-validation run
:param train_plan: the training plan (number of iterations etc.)
:param query_plan: the query play (number of iterations etc.)
:param num_folds: the number of folds to cross validation
:param fold_run_count: for debugging stop early after processing the number
of the folds
:param model_dir: if not none, the models are stored in this directory.
:return: the list of model files stored
'''
model_files = []
if fold_run_count < 1:
fold_run_count = num_folds
if num_folds == 1:
model = mdl.newModelFromExisting(sample_model)
query = mdl.newQueryState(data, model)
model, train_tops, (train_itrs, train_vbs, train_likes) = mdl.train(data, model, query, train_plan)
likely = mdl.log_likelihood(data, model, train_tops)
perp = perplexity_from_like(likely, data.word_count)
print("Train-set Likelihood: %12f" % (likely))
print("Train-set Perplexity: %12f" % (perp))
model_files = save_if_necessary(model_files, model_dir, model, data, 0, train_itrs, train_vbs, train_likes, train_tops, train_tops, mdl)
return model_files
query_like_sum = 0 # to calculate the overall likelihood and
query_wcount_sum = 0 # perplexity for the whole dataset
train_like_sum = 0
train_wcount_sum = 0
folds_finished = 0 # count of folds that finished successfully
fold = 0
while fold < num_folds and folds_finished < fold_run_count:
try:
train_data, query_data = data.cross_valid_split(fold, num_folds)
# Train the model
print ("Duplicating model template... ", end="")
model = mdl.newModelFromExisting(sample_model)
print ("Done.\nCreating query state...")
train_tops = mdl.newQueryState(train_data, model)
print ("Starting training")
model, train_tops, (train_itrs, train_vbs, train_likes) \
= mdl.train(train_data, model, train_tops, train_plan)
train_like = mdl.log_likelihood (train_data, model, train_tops)
train_word_count = train_data.word_count
train_perp = perplexity_from_like(train_like, train_word_count)
print ("DEBUG Train perplexity is " + str(train_perp))
# Query the model - if there are no features we need to split the text
print ("Starting query.")
query_estim, query_eval = query_data.doc_completion_split()
query_tops = mdl.newQueryState(query_estim, model)
model, query_tops = mdl.query(query_estim, model, query_tops, query_plan)
query_like = mdl.log_likelihood(query_eval, model, query_tops)
query_word_count = query_eval.word_count
query_perp = perplexity_from_like(query_like, query_word_count)
# Keep a record of the cumulative likelihood and query-set word-count
train_like_sum += train_like
train_wcount_sum += train_word_count
query_like_sum += query_like
query_wcount_sum += query_word_count
folds_finished += 1
# Write out the output
print("Fold %d: Train-set Perplexity: %12.3f \t Query-set Perplexity: %12.3f" % (fold, train_perp, query_perp))
print("")
# Save the model
model_files = save_if_necessary(model_files, model_dir, model, data, fold, train_itrs, train_vbs, train_likes, train_tops, query_tops, mdl)
# except Exception as e:
# traceback.print_exc()
# print("Abandoning fold %d due to the error : %s" % (fold, str(e)))
finally:
fold += 1
print ("Total (%d): Train-set Likelihood: %12.3f \t Train-set Perplexity: %12.3f" % (folds_finished, train_like_sum, perplexity_from_like(train_like_sum, train_wcount_sum)))
print ("Total (%d): Query-set Likelihood: %12.3f \t Query-set Perplexity: %12.3f" % (folds_finished, query_like_sum, perplexity_from_like(query_like_sum, query_wcount_sum)))
return model_files