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)
2021-04-01	enwiki_core	EN	1.1GB	5.9GB
2021-04-01	simplewiki_core	EN	19MB	120MB
2021-04-01	itwiki_core	IT	189MB	1.1GB
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!