Split strings into (character-based) k-shingles
Project description
Utility functions to split a string into (character-based) k-shingles, shingle sets, sequences of k-shingles.
Install package
pip install kshingle>=0.4.1
Usage for MinHashing
Generate Shingle Sets
For algorithms like MinHash (e.g. datasketch package) a document (i.e. a string) must be split into a set of unique shingles.
import kshingle as ks
shingles = ks.shingleset_k("abc", k=3)
# {'a', 'ab', 'abc', 'b', 'bc', 'c'}
import kshingle as ks
shingles = ks.shingleset_range("abc", 2, 3)
# {'ab', 'abc', 'bc', 'c'}
import kshingle as ks
shingles = ks.shingleset_list("abc", [1, 3])
# {'a', 'abc', 'b', 'c'}
Wildcard Shingle Sets
Typos can lead to rare shingles, that don’t match with the correct spelling. The longer the shingled text, the less important the effect of typos. However, short text strings will produce less shingles, i.e. the variance of the similarity due to typos is much higher for short text strings than for large text documents. In order to smooth this effect, we can generate variants of a specfic shingle by replacing characters with a wildcard characters (e.g. special unicode characters such as U+FFFF).
Example: With k=5 the document "aBc DeF" would result in 25 unique shingles without assumned typos. For each of these shingles, we enumerate all variants of up to 2 typos. This leads to a total of 152 unique shingles with no typo, 1 typo, and 2 typos.
import kshingle as ks
shingles = ks.shingleset_k("aBc DeF", k=5) # -> 25 shingles
shingles = shingles.union(
ks.wildcard_shinglesets(shingles, n_max_wildcards=2)) # -> 152 shingles
datasketch usage
import datasketch
import kshingle as ks
# Enable wildcard variants and check the results
with_wildcard = False
s1 = ks.shingleset_k("Die Zeitung wird zugestellt.", k=5)
s2 = ks.shingleset_k("Der Bericht wird zugestellt", k=5)
if with_wildcard:
s1 = s1.union(ks.wildcard_shinglesets(s1, 2))
s2 = s1.union(ks.wildcard_shinglesets(s2, 2))
m1 = datasketch.MinHash(num_perm=128)
for s in s1:
m1.update(s.encode('utf8'))
m2 = datasketch.MinHash(num_perm=128)
for s in s2:
m2.update(s.encode('utf8'))
m1.jaccard(m2)
Usage for Input Sequences
Convert a string to a sequences of shingles
Using the k parameter
import kshingle as ks
shingles = ks.shingling_k("aBc DeF", k=3)
# [['a', 'B', 'c', ' ', 'D', 'e', 'F'],
# ['aB', 'Bc', 'c ', ' D', 'De', 'eF'],
# ['aBc', 'Bc ', 'c D', ' De', 'DeF']]
Using a range for k
import kshingle as ks
shingles = ks.shingling_range("aBc DeF", n_min=2, n_max=3)
# [['aB', 'Bc', 'c ', ' D', 'De', 'eF'],
# ['aBc', 'Bc ', 'c D', ' De', 'DeF']]
Using a specific list of k values
import kshingle as ks
shingles = ks.shingling_list("aBc DeF", klist=[2, 5])
# [['aB', 'Bc', 'c ', ' D', 'De', 'eF'],
# ['aBc D', 'Bc De', 'c DeF']]
Identify Vocabulary of unique shingles
import kshingle as ks
data = [
'Ceratosaurus („Horn-Echse“) ist eine Gattung theropoder Dinosaurier aus dem Oberjura von Nordamerika und Europa.',
'Charakteristisch für diesen zweibeinigen Fleischfresser waren drei markante Hörner auf dem Schädel sowie eine Reihe kleiner Osteoderme (Hautknochenplatten), die über Hals, Rücken und Schwanz verlief.',
'Er ist der namensgebende Vertreter der Ceratosauria, einer Gruppe basaler (ursprünglicher) Theropoden.'
]
shingled = [ks.shingling_k(s, k=6) for s in data]
VOCAB = ks.identify_vocab(
shingled, sortmode='log-x-length', n_min_count=2, n_max_vocab=20)
print(VOCAB)
Upsert a word to VOCAB
import kshingle as ks
VOCAB = ['a', 'b']
# insert because "[UNK]" doesn't exist
VOCAB, idx = ks.upsert_word_to_vocab(VOCAB, "[UNK]")
print(idx, VOCAB)
# 2 ['a', 'b', '[UNK]']
# don't insert because "[UNK]" already exists
VOCAB, idx = ks.upsert_word_to_vocab(VOCAB, "[UNK]")
print(idx, VOCAB)
# 2 ['a', 'b', '[UNK]']
Encode sequences of shingles
import kshingle as ks
data = ['abc d abc de abc def', 'abc defg abc def gh abc def ghi']
shingled = [ks.shingling_k(s, k=5) for s in data]
VOCAB = ks.identify_vocab(shingled, n_max_vocab=10)
VOCAB, unkid = ks.upsert_word_to_vocab(VOCAB, "[UNK]")
# Encode all sequences
encoded = ks.encoded_with_vocab(shingled, VOCAB, unkid)
Find k
For bigger k values, the generate longer shingles that occur less frequent. And less frequent shingles might be excluded in ks.identify_vocab. As a result at some upper k value the generated sequences only contains [UNK] encoded elements. The function ks.shrink_k_backwards identifies k values that generate sequences that contain at least one encoded shingle across all examples.
import kshingle as ks
data = ['abc d abc de abc def', 'abc defg abc def gh abc def ghi']
# Step 1: Build a VOCAB
shingled = [ks.shingling_k(s, k=9) for s in data]
VOCAB = ks.identify_vocab(shingled, n_max_vocab=10)
VOCAB, unkid = ks.upsert_word_to_vocab(VOCAB, "[UNK]")
encoded = ks.encoded_with_vocab(shingled, VOCAB, unkid)
# Identify k's that are actually used
klist = ks.shrink_k_backwards(encoded, unkid)
# Step 2: Shingle sequences again
shingled = [ks.shingling_list(s, klist=klist) for s in data]
encoded = encoded_with_vocab(shingled, VOCAB, unkid)
# ...
Padding
Padding should be done with Keras pad_sequences
from tensorflow.keras.preprocessing.sequence import pad_sequences
import torch
import kshingle as ks
# Add [PAD] token
VOCAB, padidx = ks.upsert_word_to_vocab(VOCAB, "[PAD]")
# Pad each example with Keras
cfg = {'maxlen': 150, 'dtype': 'int32', 'padding': 'pre', 'truncating': 'pre', 'value': padidx}
padded = [pad_sequences(ex, **cfg).transpose() for ex in encoded]
# Convert to Pytorch
padded = torch.LongTensor(padded)
Appendix
Installation
The kshingle git repo is available as PyPi package
pip install kshingle
pip install git+ssh://git@github.com/ulf1/kshingle.git
Commands
Install a virtual environment
python3.6 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt --no-cache-dir
pip install -r requirements-dev.txt --no-cache-dir
(If your git repo is stored in a folder with whitespaces, then don’t use the subfolder .venv. Use an absolute path without whitespaces.)
Python commands
Check syntax: flake8 --ignore=F401 --exclude=$(grep -v '^#' .gitignore | xargs | sed -e 's/ /,/g')
Run Unit Tests: pytest
Upload to PyPi with twine: python setup.py sdist && twine upload -r pypi dist/*
Clean up
find . -type f -name "*.pyc" | xargs rm
find . -type d -name "__pycache__" | xargs rm -r
rm -r .pytest_cache
rm -r .venv
Support
Please open an issue for support.
Contributing
Please contribute using Github Flow. Create a branch, add commits, and open a pull request.
Project details
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