SpikeX - SpaCy Pipes for Knowledge Extraction

SpikeX is a collection of pipes ready to be plugged in a spaCy pipeline. It aims to help in building knowledge extraction tools with almost-zero effort.

What's new in SpikeX 0.5.0

WikiGraph has never been so lightning fast:

🌕 Performance mooning, thanks to the adoption of a sparse adjacency matrix to handle pages graph, instead of using igraph
🚀 Memory optimization, with a consumption cut by ~40% and a compressed size cut by ~20%, introducing new bidirectional dictionaries to manage data
📖 New APIs for a faster and easier usage and interaction
🛠 Overall fixes, for a better graph and a better pages matching

Pipes

WikiPageX links Wikipedia pages to chunks in text
ClusterX picks noun chunks in a text and clusters them based on a revisiting of the Ball Mapper algorithm, Radial Ball Mapper
AbbrX detects abbreviations and acronyms, linking them to their long form. It is based on scispacy's one with improvements
LabelX takes labelings of pattern matching expressions and catches them in a text, solving overlappings, abbreviations and acronyms
PhraseX creates a Doc's underscore extension based on a custom attribute name and phrase patterns. Examples are NounPhraseX and VerbPhraseX, which extract noun phrases and verb phrases, respectively
SentX detects sentences in a text, based on Splitta with refinements

Tools

WikiGraph with pages as leaves linked to categories as nodes
Matcher that inherits its interface from the spaCy's one, but built using an engine made of RegEx which boosts its performance

Install SpikeX

Some requirements are inherited from spaCy:

spaCy version: 2.3+
Operating system: macOS / OS X · Linux · Windows (Cygwin, MinGW, Visual Studio)
Python version: Python 3.6+ (only 64 bit)
Package managers: pip

Some dependencies use Cython and it needs to be installed before SpikeX:

pip install cython

Remember that a virtual environment is always recommended, in order to avoid modifying system state.

pip

At this point, installing SpikeX via pip is a one line command:

pip install spikex

Usage

Prerequirements

SpikeX pipes work with spaCy, hence a model its needed to be installed. Follow official instructions here. The brand new spaCy 3.0 is supported!

WikiGraph

A WikiGraph is built starting from some key components of Wikipedia: pages, categories and relations between them.

Auto

Creating a WikiGraph can take time, depending on how large is its Wikipedia dump. For this reason, we provide wikigraphs ready to be used:

Date	WikiGraph	Lang	Size (compressed)	Size (memory)
2021-05-20	enwiki_core	EN	1.3GB	8GB
2021-05-20	simplewiki_core	EN	20MB	130MB
2021-05-20	itwiki_core	IT	208MB	1.2GB
More coming...

SpikeX provides a command to shortcut downloading and installing a WikiGraph (Linux or macOS, Windows not supported yet):

spikex download-wikigraph simplewiki_core

Manual

A WikiGraph can be created from command line, specifying which Wikipedia dump to take and where to save it:

spikex create-wikigraph \
  <YOUR-OUTPUT-PATH> \
  --wiki <WIKI-NAME, default: en> \
  --version <DUMP-VERSION, default: latest> \
  --dumps-path <DUMPS-BACKUP-PATH> \

Then it needs to be packed and installed:

spikex package-wikigraph \
  <WIKIGRAPH-RAW-PATH> \
  <YOUR-OUTPUT-PATH>

Follow the instructions at the end of the packing process and install the distribution package in your virtual environment. Now your are ready to use your WikiGraph as you wish:

from spikex.wikigraph import load as wg_load

wg = wg_load("enwiki_core")
page = "Natural_language_processing"
categories = wg.get_categories(page, distance=1)
for category in categories:
    print(category)

>>> Category:Speech_recognition
>>> Category:Artificial_intelligence
>>> Category:Natural_language_processing
>>> Category:Computational_linguistics

Matcher

The Matcher is identical to the spaCy's one, but faster when it comes to handle many patterns at once (order of thousands), so follow official usage instructions here.

A trivial example:

from spikex.matcher import Matcher
from spacy import load as spacy_load

nlp = spacy_load("en_core_web_sm")
matcher = Matcher(nlp.vocab)
matcher.add("TEST", [[{"LOWER": "nlp"}]])
doc = nlp("I love NLP")
for _, s, e in matcher(doc):
  print(doc[s: e])

>>> NLP

WikiPageX

The WikiPageX pipe uses a WikiGraph in order to find chunks in a text that match Wikipedia page titles.

from spacy import load as spacy_load
from spikex.wikigraph import load as wg_load
from spikex.pipes import WikiPageX

nlp = spacy_load("en_core_web_sm")
doc = nlp("An apple a day keeps the doctor away")
wg = wg_load("simplewiki_core")
wpx = WikiPageX(wg)
doc = wpx(doc)
for span in doc._.wiki_spans:
  print(span._.wiki_pages)

>>> ['An']
>>> ['Apple', 'Apple_(disambiguation)', 'Apple_(company)', 'Apple_(tree)']
>>> ['A', 'A_(musical_note)', 'A_(New_York_City_Subway_service)', 'A_(disambiguation)', 'A_(Cyrillic)')]
>>> ['Day']
>>> ['The_Doctor', 'The_Doctor_(Doctor_Who)', 'The_Doctor_(Star_Trek)', 'The_Doctor_(disambiguation)']
>>> ['The']
>>> ['Doctor_(Doctor_Who)', 'Doctor_(Star_Trek)', 'Doctor', 'Doctor_(title)', 'Doctor_(disambiguation)']

ClusterX

The ClusterX pipe takes noun chunks in a text and clusters them using a Radial Ball Mapper algorithm.

from spacy import load as spacy_load
from spikex.pipes import ClusterX

nlp = spacy_load("en_core_web_sm")
doc = nlp("Grab this juicy orange and watch a dog chasing a cat.")
clusterx = ClusterX(min_score=0.65)
doc = clusterx(doc)
for cluster in doc._.cluster_chunks:
  print(cluster)

>>> [this juicy orange]
>>> [a cat, a dog]

AbbrX

The AbbrX pipe finds abbreviations and acronyms in the text, linking short and long forms together:

from spacy import load as spacy_load
from spikex.pipes import AbbrX

nlp = spacy_load("en_core_web_sm")
doc = nlp("a little snippet with an abbreviation (abbr)")
abbrx = AbbrX(nlp.vocab)
doc = abbrx(doc)
for abbr in doc._.abbrs:
  print(abbr, "->", abbr._.long_form)

>>> abbr -> abbreviation

LabelX

The LabelX pipe matches and labels patterns in text, solving overlappings, abbreviations and acronyms.

from spacy import load as spacy_load
from spikex.pipes import LabelX

nlp = spacy_load("en_core_web_sm")
doc = nlp("looking for a computer system engineer")
patterns = [
  [{"LOWER": "computer"}, {"LOWER": "system"}],
  [{"LOWER": "system"}, {"LOWER": "engineer"}],
]
labelx = LabelX(nlp.vocab, [("TEST", patterns)], validate=True, only_longest=True)
doc = labelx(doc)
for labeling in doc._.labelings:
  print(labeling, f"[{labeling.label_}]")

>>> computer system engineer [TEST]

PhraseX

The PhraseX pipe creates a custom Doc's underscore extension which fulfills with matches from phrase patterns.

from spacy import load as spacy_load
from spikex.pipes import PhraseX

nlp = spacy_load("en_core_web_sm")
doc = nlp("I have Melrose and McIntosh apples, or Williams pears")
patterns = [
  [{"LOWER": "mcintosh"}],
  [{"LOWER": "melrose"}],
]
phrasex = PhraseX(nlp.vocab, "apples", patterns)
doc = phrasex(doc)
for apple in doc._.apples:
  print(apple)

>>> Melrose
>>> McIntosh

SentX

The SentX pipe splits sentences in a text. It modifies tokens' is_sent_start attribute, so it's mandatory to add it before parser pipe in the spaCy pipeline:

from spacy import load as spacy_load
from spikex.pipes import SentX
from spikex.defaults import spacy_version

if spacy_version >= 3:
  from spacy.language import Language

  @Language.factory("sentx")
  def create_sentx(nlp, name):
      return SentX()

nlp = spacy_load("en_core_web_sm")
sentx_pipe = SentX() if spacy_version < 3 else "sentx"
nlp.add_pipe(sentx_pipe, before="parser")
doc = nlp("A little sentence. Followed by another one.")
for sent in doc.sents:
  print(sent)

>>> A little sentence.
>>> Followed by another one.

That's all folks

Feel free to contribute and have fun!

erre-quadro/spikex