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
searcher = pysearch.SimpleSearcher(COVIDEX_PATH)
query = 'asymptomatic transmission of COVID-19'
top_hits = searcher.search(query)
# Prints the first 5 hits
for i in range(0, 5):
print(f'{i+1:2} {top_hits[i].lucene_document.get("doi")} {top_hits[i].score:.5f} {top_hits[i].lucene_document.get("title")} ')
1 10.1101/2020.03.09.20033514 10.54510 The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak
2 10.1007/s11427-020-1661-4 10.45820 Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China
3 10.1101/2020.02.20.20025619 10.45820 Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China
4 10.18290 Advances on presymptomatic or asymptomatic carrier transmission of COVID-19
5 10.3760/cma.j.cn112338-20200228-00207 10.18290 [Advances on presymptomatic or asymptomatic carrier transmission of COVID-19]
from pyserini.search import pysearch
in_doc_title = top_hits[0].lucene_document.get("title")
in_doc_id = top_hits[0].lucene_document.get("id")
nnsearcher = pysearch.SimpleNearestNeighborSearcher(COVIDEX_RELATED_PATH)
nn_hits = nnsearcher.search(in_doc_id, 3)
k = 1
for k_hits in nn_hits:
print(f'top hits for centroid {k}')
for i in range(0, len(k_hits)):
if k_hits[i].id != in_doc_id:
sdoc = searcher.doc(k_hits[i].id)
title = sdoc.lucene_document().get('title')
print(f' {title[:75]} {k_hits[i].score:.5f}')
k += 1top hits for centroid 1
Optimal timing for social distancing during an epidemic 32.03171
Reducing the Impact of the Next Influenza Pandemic Using Household-Based Pu 31.84916
top hits for centroid 2
Asymptomatic Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infect 77.95080
On the Role of Asymptomatic Infection in Transmission Dynamics of Infectiou 76.57796
top hits for centroid 3
Detecting Differential Transmissibilities That Affect the Size of Self-Limi 75.30797
Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection 73.81608
import operator
reranked = []
for hits in nn_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)print('Related papers for:\n "' + in_doc_title + '"\n')
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)
