def query(query, subSet, useFeatures, usePageRank, useTFIDF, useClustering, useRecommend, topN=100):
results = {}
if not useFeatures and not usePageRank and not useTFIDF and not useClustering and not useRecommend:
return None
query = normalizeString(query, datasets.STOPWORDS, lemmatization).split()
print "Querying with: %r" % query
if useFeatures:
results['IF'] = features.queryFeatures(query, subSet)
prevMethod = 'IF'
if usePageRank:
results['PR'] = pagerank.queryPageRank(query, subSet)
if useTFIDF:
results['TI'] = TFIDF.queryTFIDF(query, subSet)
if useClustering:
results['CL'] = clustering.queryClustering(query, subSet)
prevMethod = 'CL'
if useRecommend:
results['RE'] = recommend.queryRecommend(query, subSet)
prevMethod = 'RE'
endresults = collections.defaultdict(float)
# Loop through all pmid's after having ID set sliced like subSet prescribes
for pmid in [pmid for pmid in datasets.IDS if str(pmid).startswith(subSet)]:
i = 0
if useFeatures and results['IF'].has_key(pmid):
i += 1
endresults[pmid] += results['IF'][pmid] * 1.0 # Weighted modifier, if required
if usePageRank and results['PR'].has_key(pmid):
i += 1
endresults[pmid] += results['PR'][pmid] * 1.0 # Weighted modifier, if required
if useTFIDF and results['TI'].has_key(pmid):
i += 1
endresults[pmid] += results['TI'][pmid] * 1.0 # Weighted modifier, if required
if useClustering and results['CL'].has_key(pmid):
i += 1
endresults[pmid] += results['CL'][pmid] * 1.0 # Weighted modifier, if required
if useRecommend and results['RE'].has_key(pmid):
i += 1
endresults[pmid] += results['RE'][pmid] * 1.0 # Weighted modifier, if required
if i > 0:
endresults[pmid] /= i # Divide by the amount of succesful techniques ran on this pmid
normalizeScore(endresults)
# Return the topN results, sorted descending by score
return sorted(endresults.items(), key=operator.itemgetter(1), reverse=True)[:topN]
def queryPageRank(query, subSet, independentRun=False, topN=None):
"""Generic function to set up the datasets, and create normalized scoring (0 to 1) for a specific module technique.
Also used when independent running of the module technique (no preprocessing of query) is wanted.
Keyword arguments:
query -- (list/str) the processed query word list (pass a string if independentRun = True)
subSet -- (str) supply a subset (based on globalsubset please) to the function, this is also used in retrieving/saving datasets.
independentRun -- (bool) if a independentRun is desired this allows a string query (default False)
topN -- (int) return the highest N results
Returns -- sorted list: [pmid: score] of topN results (highest first).
"""
citations = sliceDict(datasets.CITATIONS, subSet)
# Debug
# citations = {1:[2,3,4,5],2:[],3:[],4:[], 5:[]}
citedby = dataloader.loadProcessed("citedby", "citations", subSet)
if citedby is None:
citedby = collections.defaultdict(list)
print "PageRank is generating the inverse subset of citations"
for ref, papersCitingRef in citations.iteritems():
for pmid in papersCitingRef:
citedby[pmid].append(ref)
dataloader.saveProcessed(citedby, "citedby", "citations", subSet, saveBZ2=True)
if independentRun:
query = searches.prepareQuery(query)
print "Querying PageRank with: %r" % query
results = dataloader.loadProcessed("resultsPageRank", "citations-citedby", subSet)
if results is None:
results = pageRank(citations, citedby)
dataloader.saveProcessed(results, "resultsPageRank", "citations-citedby", subSet, saveBZ2=True)
normalizeScore(results)
if independentRun:
results = sorted(results.items(), key=operator.itemgetter(1), reverse=True)[:topN]
return results
def queryTFIDF(query, subSet, independentRun=False, topN=None):
"""Generic function to set up the datasets, and create normalized scoring (0 to 1) for a specific module technique.
Also used when independent running of the module technique (no preprocessing of query) is wanted.
Keyword arguments:
query -- (list/str) the processed query word list (pass a string if independentRun = True)
subSet -- (str) supply a subset (based on globalsubset please) to the function, this is also used in retrieving/saving datasets.
independentRun -- (bool) if a independentRun is desired this allows a string query (default False)
topN -- (int) return the highest N results
Returns -- sorted list: [pmid: score] of topN results (highest first).
"""
abstracts = {}
titles = {}
merged = {}
titles = dataloader.loadProcessed("normalized", "titles", subSet)
if titles is None:
print "TFIDF is generating the processed subset of SUMMARIES"
titles = {pmid: paper_info.title for pmid, paper_info in datasets.SUMMARIES.iteritems()}
titles = sliceDict(titles, subSet)
titles = normalizeDocuments(titles, datasets.STOPWORDS, lemmatization)
dataloader.saveProcessed(titles, "normalized", "titles", subSet, saveBZ2=True)
abstracts = dataloader.loadProcessed("normalized", "abstracts", subSet)
if abstracts is None:
print "TFIDF is generating the processed subset of ABSTRACTS"
abstracts = sliceDict(datasets.ABSTRACTS, subSet)
abstracts = normalizeDocuments(abstracts, datasets.STOPWORDS, lemmatization)
dataloader.saveProcessed(abstracts, "normalized", "abstracts", subSet, saveBZ2=True)
if independentRun:
query = searches.prepareQuery(query)
print "Querying TFIDF with: %r" % query
merged = dataloader.loadProcessed("mergedTFIDF", "titles-abstracts", subSet)
if merged is None:
merged = {}
for pmid, doc in titles.iteritems():
merged[pmid] = doc + abstracts[pmid]
# Finally run tfidf
merged = TFIDF(merged)
dataloader.saveProcessed(merged, "mergedTFIDF", "titles-abstracts", subSet, saveBZ2=True)
results = {}
for pmid, tfidfscores in merged.iteritems():
score = 0.0
for term, termscore in tfidfscores.iteritems():
for qword in query:
if qword in term:
score += termscore
results[pmid] = score
normalizeScore(results)
if independentRun:
results = sorted(results.items(), key=operator.itemgetter(1), reverse=True)[:topN]
return results
def queryTFIDF(query, subSet, independentRun=False, topN=None):
"""Generic function to set up the datasets, and create normalized scoring (0 to 1) for a specific module technique.
Also used when independent running of the module technique (no preprocessing of query) is wanted.
Keyword arguments:
query -- (list/str) the processed query word list (pass a string if independentRun = True)
subSet -- (str) supply a subset (based on globalsubset please) to the function, this is also used in retrieving/saving datasets.
independentRun -- (bool) if a independentRun is desired this allows a string query (default False)
topN -- (int) return the highest N results
Returns -- sorted list: [pmid: score] of topN results (highest first).
"""
abstracts = {}
titles = {}
merged = {}
titles = dataloader.loadProcessed("normalized", "titles", subSet)
if titles is None:
print "TFIDF is generating the processed subset of SUMMARIES"
titles = {
pmid: paper_info.title
for pmid, paper_info in datasets.SUMMARIES.iteritems()
}
titles = sliceDict(titles, subSet)
titles = normalizeDocuments(titles, datasets.STOPWORDS, lemmatization)
dataloader.saveProcessed(titles,
"normalized",
"titles",
subSet,
saveBZ2=True)
abstracts = dataloader.loadProcessed("normalized", "abstracts", subSet)
if abstracts is None:
print "TFIDF is generating the processed subset of ABSTRACTS"
abstracts = sliceDict(datasets.ABSTRACTS, subSet)
abstracts = normalizeDocuments(abstracts, datasets.STOPWORDS,
lemmatization)
dataloader.saveProcessed(abstracts,
"normalized",
"abstracts",
subSet,
saveBZ2=True)
if independentRun:
query = searches.prepareQuery(query)
print "Querying TFIDF with: %r" % query
merged = dataloader.loadProcessed("mergedTFIDF", "titles-abstracts",
subSet)
if merged is None:
merged = {}
for pmid, doc in titles.iteritems():
merged[pmid] = doc + abstracts[pmid]
# Finally run tfidf
merged = TFIDF(merged)
dataloader.saveProcessed(merged,
"mergedTFIDF",
"titles-abstracts",
subSet,
saveBZ2=True)
results = {}
for pmid, tfidfscores in merged.iteritems():
score = 0.0
for term, termscore in tfidfscores.iteritems():
for qword in query:
if qword in term:
score += termscore
results[pmid] = score
normalizeScore(results)
if independentRun:
results = sorted(results.items(),
key=operator.itemgetter(1),
reverse=True)[:topN]
return results