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Commits on Jul 26, 2024

• Merge pull request #148 from galileosteinberg/ner-benchmark

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• Added readme output.

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  b915c1c

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• Removed debugging print statements and unused imports

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• Update annotation test for new stopwords

  bgyori

  committed
  c05e872

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• Reorganize imports

  bgyori

  committed
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• Adjust test for updated stopwords

  bgyori

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• Sort NERN stoplist alphabetically

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• Change more indentation

  bgyori

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• Fix indentation

  bgyori

  committed
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• NER script derives BioIDBenchmarker class

  galileosteinberg

  committed
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• Fixed formatting issues

  galileosteinberg

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Commits on Jul 25, 2024

• Extended stopwords; moved stop words file to resources and logic into ner module

  galileosteinberg

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• Annotate not accepting spans <= 1, added progress bars

  galileosteinberg

  committed
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• Changes to app.py

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  committed
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• Modified to work with annotation objects

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• Committing changes to app.py with NER class.

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• Commit with changes to gilda evaluation logic. Returns metrics for both top matches and all matches.

  galileosteinberg

  committed
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• Make annotation return a list of scored matches

  

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• dded implementation of a stoplist for NER, set membership for for matching reference annotations, counter for most common false positives in bioid_ner_benchmark.py. Implemented a condition in the N…

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• Initial implementation of NER benchmark.

  galileosteinberg

  committed
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• Merge pull request #147 from gyorilab/use-coords

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Commits on Jul 24, 2024

• Update docstring

  kkaris

  committed
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• Fix typo

  kkaris

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• Use specific variables for start and end coordinates for clarity

  kkaris

  committed
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• Assume splitter function returns coordinates instead of sentences

  kkaris

  committed
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• Merge pull request #146 from gyorilab/ner_improve

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• Fix the role of raw vs processed words

  bgyori

  committed
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• Implement sentence offset tracking with spaces

  bgyori

  committed
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• Add tests for NER punctuation

  bgyori

  committed
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• Use raw word offset in choosing spaces

  bgyori

  committed
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• Handle punctuation during annotation

  bgyori

  committed
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• Use absolute imports

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Commits on Jul 23, 2024

• Merge pull request #145 from galileosteinberg/tab-navigation

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  bgyori

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• Remove ordered argument

  bgyori

  committed
  ab3f9e0

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• Update examples for annotation

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