COVIDEX_RELATED_PATH='/home/tteofili/dev/anserini/lucene-index-covid-biobert-centroids'
COVIDEX_PATH='/home/tteofili/dev/anserini/lucene-index-covid-2020-04-03'
import json
import os
import numpy
os.environ["JAVA_HOME"] = "/usr/lib/jvm/java-11-openjdk"
from pyserini.index import pyutils
index_utils = pyutils.IndexReaderUtils(COVIDEX_PATH)
from pyserini.search import pysearch
import operator
searcher = pysearch.SimpleSearcher(COVIDEX_PATH)
query = 'asymptomatic transmission of COVID-19'
thits = searcher.search(query)
in_doc_title = thits[0].lucene_document.get("title")
in_doc_id = thits[0].lucene_document.get("id")
print('Related papers for:\n "' + in_doc_title + '"\n')
nnsearcher = pysearch.SimpleNearestNeighborSearcher(COVIDEX_RELATED_PATH)
k_hits = nnsearcher.search(in_doc_id, 3)
reranked = []
for hits in k_hits:
for i in range(0, len(hits)):
term = hits[i].id
if term != in_doc_id:
sdoc = searcher.doc(term)
title = sdoc.lucene_document().get('title')
reranked.append([title, hits[i].score])
reranked.sort(key=operator.itemgetter(1), reverse=True)
for i in range(len(reranked)):
print(f'{i+1:2} {reranked[i][0][:75]}... ({reranked[i][1]:.5f})')Related papers for:
"The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak"
1 Asymptomatic Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infect... (77.95080)
2 On the Role of Asymptomatic Infection in Transmission Dynamics of Infectiou... (76.57796)
3 Detecting Differential Transmissibilities That Affect the Size of Self-Limi... (75.30797)
4 Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection... (73.81608)
5 Optimal timing for social distancing during an epidemic... (32.03171)
6 Reducing the Impact of the Next Influenza Pandemic Using Household-Based Pu... (31.84916)
