kshingle 0.10.0
Split strings into (character-based) k-shingles
License: Apache License 2.0
Requires Python: >=3.6

|PyPI version| |DOI| |PyPi downloads|

kshingle
========

Utility functions to split a string into character-level k-shingles,
shingle sets, sequences of k-shingles.

The package ``kshingle`` can be deployed for the following use cases:

-  `Character-level Shingling for MinHash/LSH <#usage-for-minhashing>`__
   : The result is a set of unique shingles for each document.
-  `Transform text into Input Sequences for
   NNs <#usage-for-input-sequences>`__ : The result is input sequence
   with k features.

Install package
---------------

.. code:: sh

   pip install "kshingle>=0.10.0,<1"

Usage for MinHashing
--------------------

Please note that the package ``kshingle`` only addresses character-level
shingles, and **not** combining word tokens (n-grams, w-shingling).

Generate Shingle Sets
~~~~~~~~~~~~~~~~~~~~~

For algorithms like MinHash
(e.g. `datasketch <https://github.com/ekzhu/datasketch>`__ package) a
document (i.e. a string) must be split into a set of unique shingles.

.. code:: py

   import kshingle as ks
   shingles = ks.shingleset_k("abc", k=3)
   # {'a', 'ab', 'abc', 'b', 'bc', 'c'}

.. code:: py

   import kshingle as ks
   shingles = ks.shingleset_range("abc", 2, 3)
   # {'ab', 'abc', 'bc', 'c'}

.. code:: py

   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.

.. code:: py

   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
~~~~~~~~~~~~~~~~

.. code:: py

   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)

Utility functions
~~~~~~~~~~~~~~~~~

.. code:: py

   import kshingle as ks
   metric = ks.jaccard_strings("Bericht", "berichten", k=5)
   # 0.5128205128205128

References
~~~~~~~~~~

-  A. Z. Broder, “On the resemblance and containment of documents,” in
   Proceedings. Compression and Complexity of SEQUENCES 1997 (Cat.
   No.97TB100171), Salerno, Italy, 1998, pp. 21–29, doi:
   `10.1109/SEQUEN.1997.666900 <https://doi.org/10.1109/SEQUEN.1997.666900>`__
-  Ch. 3 in: J. Leskovec, A. Rajaraman, and J. D. Ullman, Mining of
   Massive Datasets, 2nd ed. Cambridge: Cambridge University Press,
   2014. URL: http://infolab.stanford.edu/~ullman/mmds/book.pdf
-  “MinHash,” Wikipedia. Apr. 17, 2021, Accessed: May 01, 2021.
   Available:
   https://en.wikipedia.org/w/index.php?title=MinHash&oldid=1018264865.

Usage for Input Sequences
-------------------------

Convert a string to a sequences of shingles
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Using the ``k`` parameter

.. code:: py

   import kshingle as ks
   shingles = ks.shingleseqs_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``

.. code:: py

   import kshingle as ks
   shingles = ks.shingleseqs_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

.. code:: py

   import kshingle as ks
   shingles = ks.shingleseqs_list("aBc DeF", klist=[2, 5])
   # [['aB', 'Bc', 'c ', ' D', 'De', 'eF'],
   #  ['aBc D', 'Bc De', 'c DeF']]

Padding
~~~~~~~

The functions ``shingleseqs_k``, ``shingleseqs_range``, and
``shingleseqs_list`` can pad the sequence with a ``placeholder``
element. The ``padding`` modes are

-  ``center`` : Pad on both sides (The ``evenpad='pre' | 'post``
   parameter is only available for ``padding='center'``, and applied on
   sequences with even ``n``-shingles)
-  ``pre`` : Pad at the beginning of the sequence
-  ``post`` : Pad at the end of sequence

.. code:: py

   import kshingle as ks
   shingles = ks.shingleseqs_list("1234567", k=5, padding='center', evenpad='pre', placeholder='x')
   [[f"{s:^5}" for s in seq] for seq in shingles]

::

   [['  1  ', '  2  ', '  3  ', '  4  ', '  5  ', '  6  ', '  7  '],
    ['  x  ', ' 12  ', ' 23  ', ' 34  ', ' 45  ', ' 56  ', ' 67  '],
    ['  x  ', ' 123 ', ' 234 ', ' 345 ', ' 456 ', ' 567 ', '  x  '],
    ['  x  ', '  x  ', '1234 ', '2345 ', '3456 ', '4567 ', '  x  '],
    ['  x  ', '  x  ', '12345', '23456', '34567', '  x  ', '  x  ']]

Identify Vocabulary of unique shingles
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: py

   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.shingleseqs_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
~~~~~~~~~~~~~~~~~~~~~~

.. code:: py

   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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: py

   import kshingle as ks
   data = ['abc d abc de abc def', 'abc defg abc def gh abc def ghi']
   shingled = [ks.shingleseqs_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.encode_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.

.. code:: py

   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.shingleseqs_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.encode_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.shingleseqs_list(s, klist=klist) for s in data]
   encoded = encode_with_vocab(shingled, VOCAB, unkid)
   # ...

Collectively Exhaustive Wildcard Shingling (CEWS)
-------------------------------------------------

CEWS is a selection algorithm for k-shingles with wildcards to build a
vocabulary list.

Extract and count shingles
~~~~~~~~~~~~~~~~~~~~~~~~~~

First, build a database ``db`` with shingles as keys and the occurence
within a corpus as values.

.. code:: py

   from collections import Counter
   import kshingle as ks
   import itertools

   # load the corpora
   docs = ["...", "..."]

   # loop over all documents
   db = Counter()
   for doc in docs:
       # extract all shingles of different k-length (no wildcards!)
       shingles = ks.shingleseqs_k(doc, k=5)  # bump it up to 8
       # count all unique shingles, and add the result
       db += Counter(itertools.chain(*shingles))

   db = dict(db)
   len(db)

Extra: Augment text by adding typological errors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In order to increase the generalizibility of a trained ML model, we can
use text augmentation to produce possible edge case of errornous text.
High quality corpora try to avoid such errors, and corpora based
laymen’s text might not include each possible edge case.

.. code:: py

   import augtxt.keyboard_layouts as kbl
   from augtxt.augmenters import wordaug
   import numpy as np
   from collections import Counter

   # Augmentation settings: Probability of typological errors
   settings = [
       {'p': 0.50, 'fn': 'typo.drop_n_next_twice', 'args': {'loc': ['m', 'e'], 'keep_case': [True, False]} },
       {'p': 0.50, 'fn': 'typo.swap_consecutive', 'args': {'loc': ['m', 'e'], 'keep_case': [True, False]} },
       {'p': 0.25, 'fn': 'typo.pressed_twice', 'args': {'loc': 'u', 'keep_case': [True, False]} },
       {'p': 0.25, 'fn': 'typo.drop_char', 'args': {'loc': ['m', 'e'], 'keep_case': [True, False]} },
       {'p': 0.25, 'fn': 'typo.pressed_shiftalt', 'args': {'loc': ['b', 'm'], 'keymap': kbl.macbook_us, 'trans': kbl.keyboard_transprob}},
   ]
   # Number of augmentation rounds (i.e. the total count will be 10-1000x larger)
   n_augm_rounds = 10
   # maximum percentage of augmentions
   pct_augmented = 0.1 
   pct_augmented *= (1.0 + np.prod([cfg['p'] for cfg in settings]))
   # Count factor for original shingle
   n_factor_original = int((n_augm_rounds / pct_augmented) * (1 - pct_augmented))
   # reproducibility
   np.random.seed(seed=42)

   # loop over shingle frequency database (`db`)
   db2 = Counter()
   for original in db.keys():
       augmented = [wordaug(original, settings) for _ in range(n_augm_rounds)]
       # count all unique augmented shingles, and add the result
       db2 += Counter(augmented)
       # count the original shingle
       db2[original] += n_factor_original

   db2 = dict(db2)
   len(db2)

Select the shingles (CEWS), create pattern list, and encode data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: py

   # use `db` or `db2` (see above)
   import kshingle as ks
   memo = ks.cews(db2, max_wildcards=1, min_samples_leaf=10, threshold=0.9)

   # ensure that certain shingles are in the memoization cache
   #memo = {k: db[k] for k in ["i.e.", "e.g."]}
   #memo = ks.cews(db2, memo=memo, max_wildcards=1, min_samples_leaf=10, threshold=0.9)

   # `min_samples_leaf` as pecentage
   #memo = ks.cews(db2, max_wildcards=1, min_samples_leaf=0.0005, threshold=0.9)

   # try to stop early when reaching a target vocab size
   #memo = ks.cews(db2, max_wildcards=1, vocab_size=500, min_samples_leaf='auto', threshold=0.9)

   # test rare edge cases first
   #memo = ks.cews(db2, max_wildcards=1, priority='rare', min_samples_leaf=1, threshold=0.9)

   # Build a pattern list
   PATTERNS = ks.shingles_to_patterns(memo, wildcard='\uFFFF')
   unkid = sum([len(pats) for pats in PATTERNS.values()])

Finally, we can start to encode data

.. code:: py

   # Encode data
   encoded, shingled = ks.encode_multi_match_text(
       text, k=5, PATTERNS=PATTERNS, num_matches=3, unkid=unkid)

   # is slower
   # encoded, shingled = ks.encode_multi_match_corpus(
   #     [text], k=5, PATTERNS=PATTERNS, num_matches=3, unkid=unkid)

Appendix
--------

Installation
~~~~~~~~~~~~

The ``kshingle`` `git repo <http://github.com/ulf1/kshingle>`__ is
available as `PyPi package <https://pypi.org/project/kshingle>`__

::

   pip install kshingle
   pip install git+ssh://git@github.com/ulf1/kshingle.git

Commands
~~~~~~~~

Install a virtual environment

::

   python3 -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``

Publish

.. code:: sh

   pandoc README.md --from markdown --to rst -s -o README.rst
   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 <https://github.com/ulf1/kshingle/issues/new>`__
for support.

Contributing
~~~~~~~~~~~~

Please contribute using `Github
Flow <https://guides.github.com/introduction/flow/>`__. Create a branch,
add commits, and `open a pull
request <https://github.com/ulf1/kshingle/compare/>`__.

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