How to feed CoreNLP some pre-labeled Named Entities?

Question

I want to use Standford CoreNLP to pull out Coreferences and start working on the Dependencies of pre-labeled text. I eventually hope to build graph nodes and edges between related Named Entities. I am working in python, but using nltk's java functions to call the "edu.stanford.nlp.pipeline.StanfordCoreNLP" jar directly (which is what nltk does behind the scenes anyway).

My pre-labeled text is in this format:

PRE-LABELED:  During his youth, [PERSON: Alexander III of Macedon] was tutored by [PERSON: Aristotle] until age 16.  Following the conquest of [LOCATION: Anatolia], [PERSON: Alexander] broke the power of [LOCATION: Persia] in a series of decisive battles, most notably the battles of [LOCATION: Issus] and [LOCATION: Gaugamela].  He subsequently overthrew [PERSON: Persian King Darius III] and conquered the [ORGANIZATION: Achaemenid Empire] in its entirety.

What I tried to do is tokenize my sentences myself, building a list of tuples in IOB format: [ ("During","O"), ("his","O"), ("youth","O"), ("Alexander","B-PERSON"), ("III","I-PERSON"), ...]

However, I can't figure out how to tell CoreNLP to take this tuple list as a starting point, building additional Named Entities that weren't initially labeled and finding coreferences on these new, higher-quality tokenized sentences. I obviously tried simply striping out my labels, and letting CoreNLP do this by itself, but CoreNLP is just not as good at finding the Named Entities as the human-tagged pre-labeled text.

I need an output as below. I understand that it will be difficult to use Dependencies to get Edges in this way, but I need to see how far I can get.

DESIRED OUTPUT:
[Person 1]:
Name: Alexander III of Macedon
Mentions:
* "Alexander III of Macedon"; Sent1 [4,5,6,7] # List of tokens
* "Alexander"; Sent2 [6]
* "He"; Sent3 [1]
Edges:
* "Person 2"; "tutored by"; "Aristotle"

[Person 2]:
Name: Aristotle
[....]

How can I feed CoreNLP some pre-identified Named Entities, and still get help with additional Named Entities, with Coreference, and with Basic Dependencies?

PS Note that this is not a duplicate of NLTK Named Entity Recognition with Custom Data . I'm not trying to train a new classifier with my pre-labeled NER, I'm only trying to add CoreNLP's to my own when running coreference (including mentions) and dependencies on a given sentence.

Answer 1

The answer is to make a Rules file with Additional TokensRegexNER Rules .

I used a regex to group out the labeled names. From this I built a rules tempfile which I passed to the corenlp jar with -ner.additional.regexner.mapping mytemprulesfile .

Alexander III of Macedon    PERSON      PERSON,LOCATION,ORGANIZATION,MISC
Aristotle                   PERSON      PERSON,LOCATION,ORGANIZATION,MISC
Anatolia                    LOCATION    PERSON,LOCATION,ORGANIZATION,MISC
Alexander                   PERSON      PERSON,LOCATION,ORGANIZATION,MISC
Persia                      LOCATION    PERSON,LOCATION,ORGANIZATION,MISC
Issus                       LOCATION    PERSON,LOCATION,ORGANIZATION,MISC
Gaugamela                   LOCATION    PERSON,LOCATION,ORGANIZATION,MISC
Persian King Darius III     PERSON      PERSON,LOCATION,ORGANIZATION,MISC
Achaemenid Empire           ORGANIZATION    PERSON,LOCATION,ORGANIZATION,MISC

I have aligned this list for readability, but these are tab-separated values.

An interesting finding is that some multi-word pre-labeled entities stay multi-word as originally labeled, whereas running corenlp without the rules files will sometimes split these tokens into separate entities.

I had wanted to specifically identify the named-entity tokens, figuring it would make coreferences easier, but I guess this will do for now. How often are entity names identical but unrelated within one document, anyway?

Example (execution takes ~70secs)

import os, re, tempfile, json, nltk, pprint
from subprocess import PIPE
from nltk.internals import (
    find_jar_iter,
    config_java,
    java,
    _java_options,
    find_jars_within_path,
)

def ExtractLabeledEntitiesByRegex( text, regex ):
    rgx = re.compile(regex)
    nelist = []
    for mobj in rgx.finditer( text ):
        ne = mobj.group('ner')
        try:
            tag = mobj.group('tag')
        except IndexError:
            tag = 'PERSON'
        mstr = text[mobj.start():mobj.end()]
        nelist.append( (ne,tag,mstr) )
    cleantext = rgx.sub("\g<ner>", text)
    return (nelist, cleantext)

def GenerateTokensNERRules( nelist ):
    rules = ""
    for ne in nelist:
        rules += ne[0]+'\t'+ne[1]+'\tPERSON,LOCATION,ORGANIZATION,MISC\n'
    return rules

def GetEntities( origtext ):
    nelist, cleantext = ExtractLabeledEntitiesByRegex( origtext, '(\[(?P<tag>[a-zA-Z]+)\:\s*)(?P<ner>(\s*\w)+)(\s*\])' )

    origfile = tempfile.NamedTemporaryFile(mode='r+b', delete=False)
    origfile.write( cleantext.encode('utf-8') )
    origfile.flush()
    origfile.seek(0)
    nerrulefile = tempfile.NamedTemporaryFile(mode='r+b', delete=False)
    nerrulefile.write( GenerateTokensNERRules(nelist).encode('utf-8') )
    nerrulefile.flush()
    nerrulefile.seek(0)

    java_options='-mx4g'
    config_java(options=java_options, verbose=True)
    stanford_jar = '../stanford-corenlp-full-2018-10-05/stanford-corenlp-3.9.2.jar'
    stanford_dir = os.path.split(stanford_jar)[0]
    _classpath = tuple(find_jars_within_path(stanford_dir))

    cmd = ['edu.stanford.nlp.pipeline.StanfordCoreNLP',
        '-annotators','tokenize,ssplit,pos,lemma,ner,parse,coref,coref.mention,depparse,natlog,openie,relation',
        '-ner.combinationMode','HIGH_RECALL',
        '-ner.additional.regexner.mapping',nerrulefile.name,
        '-coref.algorithm','neural',
        '-outputFormat','json',
        '-file',origfile.name
        ]

    # java( cmd, classpath=_classpath, stdout=PIPE, stderr=PIPE )
    stdout, stderr = java( cmd, classpath=_classpath, stdout=PIPE, stderr=PIPE )    # Couldn't get working- stdin=textfile
    PrintJavaOutput( stdout, stderr )

    origfilenametuple = os.path.split(origfile.name)
    jsonfilename = origfilenametuple[len(origfilenametuple)-1] + '.json'

    os.unlink( origfile.name )
    os.unlink( nerrulefile.name )
    origfile.close()
    nerrulefile.close()

    with open( jsonfilename ) as jsonfile:
        jsondata = json.load(jsonfile)

    currentid = 0
    entities = []
    for sent in jsondata['sentences']:
        for thisentity in sent['entitymentions']:
            tag = thisentity['ner']
            if tag == 'PERSON' or tag == 'LOCATION' or tag == 'ORGANIZATION':
                entity = {
                    'id':currentid,
                    'label':thisentity['text'],
                    'tag':tag
                }
                entities.append( entity )
                currentid += 1

    return entities

#### RUN ####
corpustext = "During his youth, [PERSON:Alexander III of Macedon] was tutored by [PERSON: Aristotle] until age 16.  Following the conquest of [LOCATION: Anatolia], [PERSON: Alexander] broke the power of [LOCATION: Persia] in a series of decisive battles, most notably the battles of [LOCATION: Issus] and [LOCATION: Gaugamela].  He subsequently overthrew [PERSON: Persian King Darius III] and conquered the [ORGANIZATION: Achaemenid Empire] in its entirety."

entities = GetEntities( corpustext )
for thisent in entities:
    pprint.pprint( thisent )

Output

{'id': 0, 'label': 'Alexander III of Macedon', 'tag': 'PERSON'}
{'id': 1, 'label': 'Aristotle', 'tag': 'PERSON'}
{'id': 2, 'label': 'his', 'tag': 'PERSON'}
{'id': 3, 'label': 'Anatolia', 'tag': 'LOCATION'}
{'id': 4, 'label': 'Alexander', 'tag': 'PERSON'}
{'id': 5, 'label': 'Persia', 'tag': 'LOCATION'}
{'id': 6, 'label': 'Issus', 'tag': 'LOCATION'}
{'id': 7, 'label': 'Gaugamela', 'tag': 'LOCATION'}
{'id': 8, 'label': 'Persian King Darius III', 'tag': 'PERSON'}
{'id': 9, 'label': 'Achaemenid Empire', 'tag': 'ORGANIZATION'}
{'id': 10, 'label': 'He', 'tag': 'PERSON'}