def main(args):
cur_dir = os.getcwd()
adjacency_folder = os.path.join(cur_dir, args.adj_folder)
training_genes_file = os.path.join(cur_dir, args.train_genes_file)
training_labels_file = os.path.join(cur_dir, args.train_labels_file)
all_genes_file = os.path.join(cur_dir, args.all_genes_file)
list_D = args.list_D
list_C = args.list_C
list_d = args.list_d
list_r = args.list_r
training_genes = util.load_list_from_file(training_genes_file)
training_labels = [int(l) for l in util.load_list_from_file(training_labels_file)]
all_genes = util.load_list_from_file(all_genes_file)
# Creating list of graphs
print("Unifying graphs...")
if args.use_vec:
graphs = gu.create_graphs(adjacency_folder_path=adjacency_folder, list_attr_path=args.node_vecs_file)
else:
graphs = gu.create_graphs(adjacency_folder_path=adjacency_folder)
# Computing kernel matrices
print("Computing graph kernels...")
kernel_matrices = []
for D in list_D:
for C in list_C:
g_union = gu.union_graphs(graphs=graphs, deg_threshold=D, cli_threshold=C)
for d in list_d:
for r in list_r:
vec = graph.CDNK_Vectorizer(d=d, r=r, L=len(graphs), n_nodes=len(graphs[0].nodes()),
discrete=not args.use_vec)
kernel_matrices.append(vec.cdnk(g=g_union))
print("Evaluating model...")
if args.use_lou:
val = Validation(kernels=kernel_matrices, all_genes=all_genes, training_genes=training_genes,
training_labels=training_labels)
print('============')
print('Performances')
auc = val.validate_leave_one_out()
print(auc)
else:
val = Validation(kernels=kernel_matrices, all_genes=all_genes, training_genes=training_genes, training_labels=training_labels, n_folds=5)
print('============')
print('Performances')
aucs = val.validate_kfolds()
for auc in aucs:
print(auc)
print('-----------')
print(np.mean(aucs))
def __init__(self, gfile, tagdict):
self.dict = defaultdict(list)
self.mapping = {}
self.tagdict = tagdict
self.feedback = defaultdict(list)
self.processed = {}
c = 1
n = 0
t = 0
goldlist = util.load_list_from_file(gfile)
self.feedback[c] = []
for g in goldlist:
if g == '\n' or g == '':
c += 1
t = 0
self.feedback[c] = []
else:
wrd, tag = g.split("\t")
self.feedback[c].append(None)
self.dict[c].append({'w':wrd,'t':tag,'a':[]})
self.mapping[n] = {}
self.mapping[n]['sid'] = c
self.mapping[n]['tid'] = t
n += 1
t += 1
def __init__(self):
self.sorted_conns_list = self.get_sorted_conns_list()
self.cpos_dict = self.get_CPOS_dict()
self.prev_C_dict = self.get_prev_C_dict()
self.prevPOS_dict = self.get_prevPOS_dict()
self.prevPOS_CPOS_dict = self.get_prevPOS_CPOS_dict()
self.C_next_dict = self.get_C_next_dict()
self.nextPOS_dict = self.get_nextPOS_dict()
self.CPOS_nextPOS_dict = self.get_CPOS_nextPOS()
self.CParent_to_root_path_dict = self.get_CParent_to_root_path_dict()
self.compressed_CParent_to_root_path_dict = self.get_compressed_CParent_to_root_path_dict(
)
self.self_category_dict = self.get_self_category_dict()
self.parent_category_dict = self.get_parent_category_dict()
self.left_sibling_category_dict = self.get_left_sibling_category_dict()
self.right_sibling_category_dict = self.get_right_sibling_category_dict(
)
self.conn_self_category_dict = self.get_conn_self_category_dict()
self.conn_parent_category_dict = self.get_conn_parent_category_dict()
self.conn_left_sibling_category_dict = self.get_conn_left_sibling_category_dict(
)
self.conn_right_sibling_category_dict = self.get_conn_right_sibling_category_dict(
)
self.self_parent_dict = self.get_self_parent_dict()
self.self_right_dict = self.get_self_right_dict()
self.self_left_dict = self.get_self_left_dict()
self.parent_left_dict = self.get_parent_left_dict()
self.parent_right_dict = self.get_parent_right_dict()
self.left_right_dict = self.get_left_right_dict()
self.conn_category = self.get_conn_category_dict()
''' mine '''
self.dict_conn_lower_case = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_LOWER_CASE)
self.dict_conn = util.load_dict_from_file(config.CONNECTIVE_DICT_CONN)
self.dict_prevPOS_C = util.load_dict_from_file(
config.CONNECTIVE_DICT_PREVPOS_C)
self.dict_self_category_to_root_path = util.load_dict_from_file(
config.CONNECTIVE_DICT_SELF_CATEGORY_TO_ROOT_PATH)
self.dict_CParent_to_root_path_node_names = util.load_dict_from_file(
config.CONNECTIVE_DICT_CPARENT_TO_ROOT_PATH_NODE_NAMES)
self.dict_conn_connCtx = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_CONNCTX)
self.dict_conn_rightSiblingCtx = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_RIGHTSIBLINGCTX)
self.dict_conn_leftSiblingCtx = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_LEFTSIBLINGCTX)
self.dict_conn_left_right_SiblingCtx = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_LEFT_RIGHT_SIBLINGCTX)
self.dict_conn_parent_category_Ctx = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_PARENT_CATEGORY_CTX)
self.dict_rightSibling_production_rules = util.load_dict_from_file(
config.CONNECTIVE_DICT_CONN_RIGHTSIBLING_PRODUCTION_RULES)
self.word2vec_conns_list = util.load_list_from_file(
config.WORD2VEC_CONNS_PATH)
def getLowestCompetence(comp_file_path):
list = util.load_list_from_file(comp_file_path)
lowest = 1
index = -1
for i, val in enumerate(list[0].split("\t")):
if (max(float(val), lowest) == lowest):
lowest = float(val)
index = i
return index
def main(args):
adjacency_folder = args.adj_folder
training_genes_file = args.train_genes_file
training_labels_file = args.train_labels_file
all_genes_file = args.all_genes_file
list_D = args.list_D
list_C = args.list_C
list_d = args.list_d
list_r = args.list_r
training_genes = util.load_list_from_file(training_genes_file)
training_labels = [
int(l) for l in util.load_list_from_file(training_labels_file)
]
all_genes = util.load_list_from_file(all_genes_file)
# Creating list of graphs
graphs = gu.create_graphs(adjacency_folder_path=adjacency_folder)
# Computing kernel matrices
kernel_matrices = []
for D in list_D:
for C in list_C:
g_union = gu.union_graphs(graphs=graphs,
deg_threshold=D,
cli_threshold=C)
for d in list_d:
for r in list_r:
vec = graph.CDNK_Vectorizer(d=d,
r=r,
L=len(graphs),
n_nodes=len(graphs[0].nodes()))
kernel_matrices.append(vec.cdnk(g=g_union))
val = Validation(kernels=kernel_matrices,
all_genes=all_genes,
training_genes=training_genes,
training_labels=training_labels)
auc = val.validation()
print(auc)
def readGold(gold, sentences):
goldlist = []
sentdict = {}
# read gold file
gold = util.load_list_from_file(gold)
for line in gold:
if line != '\n' and line != '':
word, tag = line.split('\t')
# new, unknown tag? add to dictionary
if tag not in sentences.tagdict:
newTag = len(sentences.tagdict) + 1
sentences.tagdict[tag] = newTag
util.write_dict_keys_to_file(sentences.tagdict,
'./dict/tags.txt')
goldlist.append(sentences.tagdict[tag])
return goldlist
def get_sorted_conns_list(self):
# print "loading sorted_conns_list ..."
return util.load_list_from_file(config.SORTED_ExpConn_PATH)
from sklearn.metrics import accuracy_score
from sklearn import cross_validation
import random
from sklearn import svm
import util
seed = 7
np.random.seed(seed)
#label_path = "/media/dinh/DATA/Test/graph_labels/CPDB"
label_path = "/home/dinh/fast-disk/Weisfeiler_GK/scikit-learn-graph/scripts/graph_labels/CPDB"
#kernel_folder_path = "/media/dinh/DATA/Test/kernels/cpdb_reduce/"
kernel_folder_path = "/home/dinh/fast-disk/Weisfeiler_GK/scikit-learn-graph/scripts/kernels/cpdb/"
#save_file = "/media/dinh/DATA/Test/results/cpdb_nested_3"
save_file = "/home/dinh/fast-disk/Weisfeiler_GK/scikit-learn-graph/scripts/results_cv/cpdb"
pre_labels = [int(label) for label in util.load_list_from_file(label_path)]
"""Loading kernels"""
pre_list_kernels = []
kernel_names = util.list_files_in_folder(kernel_folder_path)
for kernel_name in kernel_names:
pre_list_kernels.append(
np.fromfile(kernel_folder_path + kernel_name).reshape(
len(pre_labels), len(pre_labels)))
svm_paras = [1e-0, 1e+1, 1e+2, 1e+3, 1e+4]
n_folds = 10
"""Model selection"""
def model_selection(list_kernels=None,
svm_paras=None,
def evaluate(adjacency_path=None,
node_label_folder=None,
all_gene_path=None,
train_gene_folder=None,
train_label_folder=None,
n_iters=None,
n_hops=None,
n_clusters=None,
svm_paras=None,
save_folder=None):
all_genes = util.load_list_from_file(all_gene_path)
number_svm_parameters = len(svm_paras)
dict_gene_idx = {}
for idx, gene in enumerate(all_genes):
dict_gene_idx[gene] = idx
graph = util.create_graph(adjacency_path=adjacency_path)
for n_cluster in n_clusters:
util.node_labeling(g=graph,
label_path=node_label_folder + str(n_cluster))
for n_iter in n_iters:
WLvect = WLVectorizer(r=n_iter)
iters_features = WLvect.transform([graph])
M = iters_features[0][0]
for iter_id in range(1, n_iter + 1):
M = M + iters_features[iter_id][0]
print 'Done WL compuation'
sys.stdout.flush()
for n_hop in n_hops:
print 'Begining DWL compuation'
sys.stdout.flush()
G = util.deepwl(graph=graph, feature_matrix=M, n_hop=n_hop)
print "Size of G", G.shape
print 'Done DWL compuation'
sys.stdout.flush()
for disease_idx in range(12):
list_training_genes = util.load_list_from_file(
train_gene_folder + str(disease_idx))
list_training_labels = util.load_list_from_file(
train_label_folder + str(disease_idx))
list_training_labels = [
int(e) for e in list_training_labels
]
list_qscores = [[] for i in range(number_svm_parameters)]
for gene_idx, gene in enumerate(list_training_genes):
list_training_genes_del = list_training_genes[:]
del list_training_genes_del[gene_idx]
training_genes_idx = [
dict_gene_idx[g] for g in list_training_genes_del
]
list_training_labels_del = list_training_labels[:]
del list_training_labels_del[gene_idx]
unknown_genes_idx = [dict_gene_idx[gene]]
for idx in range(len(all_genes)):
if (idx not in training_genes_idx) and (
idx != dict_gene_idx[gene]):
unknown_genes_idx.append(idx)
Mtr = util.extract_submatrix(training_genes_idx,
training_genes_idx, G)
M_unknown = util.extract_submatrix(
unknown_genes_idx, training_genes_idx, G)
for idx_svm, svm_para in enumerate(svm_paras):
clf = svm.SVC(C=svm_para, kernel='precomputed')
clf.fit(Mtr, list_training_labels_del)
scores = clf.decision_function(M_unknown)
len_scores = len(scores)
qscore = float(
sum([int(scores[0] > val)
for val in scores])) / len_scores
list_qscores[idx_svm].append(qscore)
# computing auc
save_lines = []
for qscores_idx, qscores in enumerate(list_qscores):
fpr, tpr, thresholds = metrics.roc_curve(
list_training_labels, qscores, pos_label=1)
auc = metrics.auc(fpr, tpr)
line = str(n_cluster) + "_" + str(n_iter) + "_" + str(
n_hop) + "_" + str(qscores_idx) + ":\t" + str(
auc) + "\n"
save_lines.append(line)
f = open(save_folder + str(disease_idx), 'w')
f.writelines(save_lines)
f.close()
# Loading dictionnaries from files
with open('../common/data/annotated/hashtags.json', 'r') as file:
dict_hashtags = json.load(file)
with open('../common/data/annotated/words_lemmatized.json', 'r', encoding="utf-8") as file:
dict_words = json.load(file)
# "Like it"
# dict_words = util.load_word_classification_ilikeit('../common/data/external/06032019-POLARITY-JEUXDEMOTS-FR.csv')
with open('../common/data/annotated/emojis.json', 'r') as file:
dict_emojis = json.load(file)
heavy_negatives_list = util.load_list_from_file('../common/data/annotated/heavy_negatives_filtered.txt')
mildly_heavy_negatives_list = util.load_list_from_file('../common/data/annotated/midly_heavy_negatives_filtered.txt')
dict_date = {}
dict_correspondances = {
"positif": 1,
"negatif": -1,
"neutre": 0
}
# data = util.get_all_tweets()
data = util.get_all_unique_tweets()
tweets_polarity = {}
cpt_neg_words = 0
def run_iteration(options, sentences, table, c):
#####
# create new annotator from best predictions and get N tags for the predictions with
# the highest entropy and update the new annotator (feedback from oracle)
# either replace a random annotator in every round
bad_guy = random.choice(range(len(table)))
# or replace the one with the lowest competence (don't! doesn't work well...)
if options.lowest:
bad_guy = getLowestCompetence('./competence')
replaceLowestCompetenceByMACEpred(bad_guy, table, predlist, c)
# print "Replace annotator ", bad_guy
# select table entry with highest entropy
# returns a list with row indices for the rows
# in the table that have the highest entropy (from file "entropy" created by MACE)
N = 1
indices = sentences.entropy(N)
#### don't use: indices = sentences.entropyMajority(predlist, N)
#indi = sentences.get_entropy_for_row(N)
print "ENTROPY: ", indices
#print "MAJORITY: ", indi
print
for ind in indices:
print "Option: ", options.simulation
if options.simulation:
print "run simulation........................."
# either from the gold standard (AL simulation)
tag = sentences.getOracleTag(ind)
else:
print "ask oracle............................."
# or from the oracle (real AL)
tag = sentences.getAnnotation(ind, c)
util.print_log("TAG: " + tag.upper() + "\n")
# now use oracle tags as feedback, combined with the predlist features from MACE
# create control file and rerun EM
if options.feedback:
sentences.write_feedback_to_file(options.feedback, bad_guy)
sentences.update_predictions(bad_guy)
sentences.backupFiles(c)
# read updated predictions from file (with feedback from oracle/AL simulation)
#table = util.readPredictions(options.path)
# convert tags to numerical representation
#table = convert2num(table, tagdict)
# run MACE
if options.entropies:
if options.feedback:
command = "java -jar ./MACE.jar --controls feedback --entropies preds.csv"
else:
command = "java -jar ./MACE.jar --entropies preds.csv"
else:
if options.feedback:
command = "java -jar ./MACE.jar --controls feedback preds.csv"
else:
command = "java -jar ./MACE.jar preds.csv"
if options.restarts:
newarg = "MACE.jar --restarts " + options.restarts
command = command.replace("MACE.jar", newarg)
if options.vanilla:
newarg = "MACE.jar --em "
command = command.replace("MACE.jar", newarg)
os.system(command)
# read MACE predictions
predlist = util.load_list_from_file('prediction')
# if we have a gold file, evaluate best predictions against gold
if options.goldstandard != False:
evalTagger(options.goldstandard, sentences)
evalPredictions(options.goldstandard, predlist, sentences)
def run_cmd_interface():
# parse command line options
optparser = OptionParser()
optparser.add_option("-p",
"--predfile",
dest="path",
default="../data/output",
help="path to dir with predictions",
metavar="DIR")
optparser.add_option("-g",
"--gold",
dest="goldstandard",
default=False,
help="read gold standard annotations (optional)")
optparser.add_option(
"-f",
"--feedback",
dest="feedback",
default=False,
help="read feedback from oracle annotations (optional)")
optparser.add_option(
"-e",
"--entropies",
dest="entropies",
default=False,
help="print entropies for each instance to file (MACE)")
optparser.add_option(
"-m",
"--majority",
dest="majority",
default=False,
help="instead of posterior entropies, use majority vote")
optparser.add_option("-r",
"--restarts",
dest="restarts",
default=False,
help="number of random model initialisations")
optparser.add_option("-s",
"--simulation",
dest="simulation",
default=False,
help="run program as AL simulation")
optparser.add_option("-v",
"--vanilla",
dest="vanilla",
default=False,
help="run program with vanilla EM")
optparser.add_option("-l",
"--lowest",
dest="lowest",
default=False,
help="replace annotator with the lowest competence")
(options, args) = optparser.parse_args()
tagdict = util.load_dict_from_file('./dict/tags.txt')
mapping = util.load_mapping_from_file('./dict/mapping.txt')
# read gold standard (or, if no gold annotations exist, list with word tokens)
sentences = Sentences(options.goldstandard, tagdict)
# read predictions from file
table = util.readPredictions(options.path)
# add predictions
sentences.addPredictions(table)
# convert tags to numerical representation
table = convert2num(table, sentences)
# print table content to csv file
sentences.printCSV()
# and update table with existing predictions from experiment (preds.csv)
# run MACE
if options.entropies:
command = "java -jar ./MACE.jar --entropies preds.csv"
else:
command = "java -jar ./MACE.jar preds.csv"
if options.restarts:
newarg = "MACE.jar --restarts " + options.restarts
command = command.replace("MACE.jar", newarg)
if options.vanilla:
newarg = "MACE.jar --em "
command = command.replace("MACE.jar", newarg)
os.system(command)
# read MACE predictions
predlist = util.load_list_from_file('prediction')
# if we have a gold file, evaluate best predictions against gold
if options.goldstandard != False:
evalTagger(options.goldstandard, sentences)
evalPredictions(options.goldstandard, predlist, sentences)
# FIXME: the max range should also be a parameter (right now the number of iterations is hard-coded)
# also, it should be able to end/continue with the annotation at every point in time...
for c in range(0, 500):
run_iteration(options, sentences, table, c)