def get_params():
# Get default parameters and adjust with user's input
params = c19_parameters.Parameters(
database=c19_parameters.Database(
local_path="/home/dynomante/projects/covid-19-kaggle/local_exec/articles_database_v14_02052020_test.sqlite"),
embedding=c19_parameters.Embedding(
local_path="/home/dynomante/projects/covid-19-kaggle/w2v_parquet_file_new_version.parquet")
)
try:
params.query.cosine_similarity_threshold = float(request.form["sim_threshold"])
except KeyError:
pass
try:
params.query.minimum_sentences_kept = int(request.form["n_sentence"])
except KeyError:
pass
try:
params.query.number_of_clusters = int(request.form["number_cluster"])
except KeyError:
pass
try:
params.query.min_feature_per_cluster = int(request.form["feature_per_cluster"])
except KeyError:
pass
return params
def main(query):
# Get parameters
params = parameters.Parameters(database=parameters.Database(
local_path="local_exec/articles_database_v8_07042020.sqlite",
kaggle_data_path="local_exec/kaggle_data"))
# Load pre-trained word vectors
embedding_model = embedding.Embedding(
parquet_embedding_path=params.embedding.local_path,
embeddings_dimension=params.embedding.dimensions,
sentence_embedding_method=params.embedding.word_aggregation_method,
weight_vectors=params.embedding.weight_with_tfidf)
# Get sentence data (including vector) from sentence table
sentences = query_matching.get_sentences_data(
db_path=params.database.local_path)
# Find the K closest sentence to the query
closest_sentences = query_matching.get_k_closest_sentences(
db_path=params.database.local_path,
query=query,
sentences=sentences,
embedding_model=embedding_model,
k=params.query.top_k_sentences)
def main():
# Get parameters
params = parameters.Parameters(first_launch=True)
# Load all articles (title, abstract and body) into the 'article' table.
database_utilities.create_db_and_load_articles(
db_path=params.database.local_path,
kaggle_data_path=params.database.kaggle_data_path,
first_launch=params.first_launch,
load_body=params.preprocessing.load_text_body)
# Load pre-trained word vectors
embedding_model = embedding.Embedding(
parquet_embedding_path=params.embedding.local_path,
embeddings_dimension=params.embedding.dimensions,
sentence_embedding_method=params.embedding.word_aggregation_method,
weight_vectors=params.embedding.weight_with_tfidf)
# Pre-process and vectorise all sentences
text_preprocessing.pre_process_and_vectorize_texts(
embedding_model=embedding_model,
db_path=params.database.local_path,
first_launch=params.first_launch,
stem_words=params.preprocessing.stem_words,
remove_num=params.preprocessing.remove_numeric)
def main():
params = parameters.Parameters(database=parameters.Database(
local_path="articles_database_v8_07042020.sqlite",
kaggle_data_path="kaggle_data"))
# Load all articles (title, abstract and body) into the 'article' table.
database_utilities.create_db_and_load_articles(
db_path=params.database.local_path,
kaggle_data_path=params.database.kaggle_data_path,
first_launch=params.first_launch,
only_newest=params.database.only_newest,
only_covid=params.database.only_covid,
enable_data_cleaner=params.database.enable_data_cleaner)
# Pre-process all sentences (no embedding)
text_preprocessing.pre_process_and_vectorize_texts(
embedding_model=None,
db_path=params.database.local_path,
first_launch=params.first_launch,
stem_words=params.preprocessing.stem_words,
remove_num=params.preprocessing.remove_numeric,
batch_size=params.preprocessing.batch_size,
max_body_sentences=params.preprocessing.max_body_sentences)
# Param have been set up with: https://www.aclweb.org/anthology/W16-2922.pdf
w2v_params = {
"sg": 1,
"hs": 1,
"sample": 1e-5,
"negative": 10,
"min_count": 20,
"size": 100,
"window": 7,
"seed": 42,
"workers": os.cpu_count(),
"iter": 10
}
# Train and save W2V and TFIDF as a parquet file DF.parquet
word2vec = word2vec_utilities.W2V(params.database.local_path,
tfidf_path="TFIDF.pkl",
w2v_path="W2V.bin",
w2v_params=w2v_params,
parquet_output_path="DF.parquet")
word2vec.train()
def main():
params = parameters.Parameters(
first_launch=True,
database=parameters.Database(
local_path=
"/home/dynomante/projects/covid-19-kaggle/local_exec/articles_database_v13_01052020.sqlite",
kaggle_data_path=
"/home/dynomante/projects/covid-19-kaggle/local_exec/kaggle_data",
only_newest=False,
only_covid=False),
preprocessing=parameters.PreProcessing(max_body_sentences=0,
stem_words=False),
# embedding=parameters.Embedding(
# local_path="resources/global_df_w2v_tfidf.parquet")
)
# Load all articles (title, abstract and body) into the 'article' table.
database_utilities.create_db_and_load_articles(
db_path=params.database.local_path,
kaggle_data_path=params.database.kaggle_data_path,
first_launch=params.first_launch,
only_newest=params.database.only_newest,
only_covid=params.database.only_covid,
enable_data_cleaner=params.database.enable_data_cleaner)
# Load pre-trained word vectors
# embedding_model = embedding.Embedding(
# parquet_embedding_path=params.embedding.local_path,
# embeddings_dimension=params.embedding.dimension,
# sentence_embedding_method=params.embedding.word_aggregation_method,
# weight_vectors=params.embedding.weight_with_tfidf)
embedding_model = None
# Pre-process and vectorise all sentences
text_preprocessing.pre_process_and_vectorize_texts(
embedding_model=embedding_model,
db_path=params.database.local_path,
first_launch=params.first_launch,
stem_words=params.preprocessing.stem_words,
remove_num=params.preprocessing.remove_numeric,
batch_size=params.preprocessing.batch_size,
max_body_sentences=params.preprocessing.max_body_sentences)
weight_vectors=params.embedding.weight_with_tfidf)
# Get sentence data (including vector) from sentence table
all_db_sentences = query_matching.get_sentences_data(
db_path=params.database.local_path)
return embedding_model, all_db_sentences
if __name__ == "__main__":
params = parameters.Parameters(
database=parameters.Database(
local_path=
"/home/dynomante/projects/covid-19-kaggle/local_exec/articles_database_v14_02052020_test.sqlite",
kaggle_data_path=
"/home/dynomante/projects/covid-19-kaggle/local_exec/kaggle_data"),
embedding=parameters.Embedding(
local_path=
"/home/dynomante/projects/covid-19-kaggle/w2v_parquet_file_new_version.parquet"
))
embedding_model, all_db_sentences = prepare_data(params)
query = "What do we know about Chloroquine to treat covid-19 induced by coronavirus?"
closest_sentences_df = query_matching.get_k_closest_sentences(
query=query,
all_sentences=all_db_sentences,
embedding_model=embedding_model,
minimal_number_of_sentences=params.query.minimum_sentences_kept,
similarity_threshold=params.query.cosine_similarity_threshold)
This script is an example on how to loop on multi queries to generate a MD report.
"""
import json
from copy import deepcopy
from time import time
from c19 import (clusterise_sentences, display_output, embedding, parameters,
query_matching)
queries_path = "resources/queries.json"
with open(queries_path) as json_file:
queries_data = json.load(json_file)
params = parameters.Parameters(
database=parameters.Database(
local_path="local_exec/articles_database_v12_16042020.sqlite",
kaggle_data_path="local_exec/kaggle_data"),
embedding=parameters.Embedding(
local_path="resources/global_df_w2v_tfidf.parquet"))
# Load pre-trained word vectors
embedding_model = embedding.Embedding(
parquet_embedding_path=params.embedding.local_path,
embeddings_dimension=params.embedding.dimension,
sentence_embedding_method=params.embedding.word_aggregation_method,
weight_vectors=params.embedding.weight_with_tfidf)
# Load sentences from SQLite
all_db_sentences_original = query_matching.get_sentences_data(
db_path=params.database.local_path)
# Loop over re-formulated queries
