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README_spelling.md

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README_spelling.md

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spelling --- The psynlp module for detecting and correcting spelling errors in clinical text.

The spelling submodule implements functionality for detecting spelling errors, generating and ranking replacement candidates, and using this as input to correct spelling errors. Correcting text is done using the SpellChecker class, while rankers are implemented in the Ranker class.

The general flow for correcting spelling consists of three steps:

  1. Find misspelled tokens -- find misspelled tokens based on OpenTaal word lists and a medical lexicon (found in psynlp/resources/lexicons/*.txt). Since these words combined do not (nearly) cover all terms used in clinical psychiatric text, we also add all tokens with a frequency >= frequency_threshold, as counted in all decursus and rapportage texts. Some additional logic is implemented, such as looking for compound words (behandelplanbespreking = behandelplan + bespreking) and checking whether there are numeric characters in a token.

  2. Suggest replacements -- based on the same lexicon used above, candidates are suggested based on similarity measured by edit distance (default <= 2). The EditDistTrie is used to suggest these candidates.

  3. Find the best replacement -- the best candidate out of all suggested replacements is determined by a ranker. Currently, two rankers are implemented: NoisyRanker, based on the noisy channel model (Lai, 2015), and EmbeddingRanker, based on word embeddings and misspelling context. Anecdotally, they work roughly equally well. By default the NoisyRanker is used.

Usage

from psyspell.spelling import SpellChecker
sp = SpellChecker(spacy_model="model_name")
sp.correct("patient is bekend met een depresieve stoornis")
>>> "patient is bekend met een depressieve stoornis"

API

SpellChecker::initialization

sc = SpellChecker(frequency_threshold=50,
	          use_ranker='noisy',
      	          many_texts=False,
	          verbose=False
Field Description
spacy_model The name of the spacy model that should be included in the global resource folder
frequency_threshold The threshold for tokens to be included in the lexicon.
use_ranker The ranker to be used. Full list is in the KNOWN_RANKERS variable, currently ['noisy', 'embedding']
many_texts Set to True when processing many texts (>10000-ish). Will take some extra time to initialize but processing will be faster.
verbose Verbosity

SpellChecker::functions

Function Description Returns
sc.add_vocab(vocabulary_list) Add more vocabulary to the lexicon of known words. --
sc.find_misspellings(text, context_window=10) Find misspellings in a text. [(misspelling, start_idx, end_idx, [context])]
sc.correct_misspellings(text) Suggest best for misspellings obtained in find_misspellings using the Ranker [(misspelling, start_idx, end_idx, best_correction)]
sc.correct(text) Correct and return text text

Ranker::initialization

r_noisy = NoisyRanker()
r_embed = EmbeddingRanker()

Ranker::functions

Function Description Returns
best_candidate(misspelled_word, candidates, context) Determine the best candidate replacement for a misspelling, potentially using its context. (best_candidate, score)
score_candidates(misspelled_word, candidates, context) Determine a score that ranks the candidate replacements [(candidate, score)]

Ranker::Interface

Use the following interface to define a custom ranker, and then in spellchecker.py add it to KNOWN_RANKERS and _init_ranker()

class CustomRanker(Ranker):
	def __init__(self):
		pass

	def score_candidates(self, misspelled_word, candidates, context):
		return [(candidate, score)]