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Commits on Mar 10, 2025

• clean up the cached files after saving the datasets to the disk (#92)

  ChaoPang

  authoredMar 10, 2025
  771e5b3

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• only generate patients who have visits in _meds_to_cehrbert_generator (#91)

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  ChaoPang

  authoredMar 10, 2025
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Commits on Feb 24, 2025

• Cehrbert streaming for meds (#90)

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  ChaoPang

  authoredFeb 24, 2025
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Commits on Feb 18, 2025

• lossened up the huggingface dependencies (#89)

  ChaoPang

  authoredFeb 18, 2025
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Commits on Feb 12, 2025

• changed to the partial match to the meds_birth code instead of the exact match (#88)

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  ChaoPang

  authoredFeb 12, 2025
  3c4a053

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Commits on Feb 3, 2025

• New cehrbert data backward compatible (#86)

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  ChaoPang

  authoredFeb 3, 2025
  8ed2cae

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• New cehrbert data backward compatible (#85)

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  ChaoPang

  authoredFeb 3, 2025
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Commits on Jan 29, 2025

• upgraded cehrbert_data to 0.0.5 (#84)

  ChaoPang

  authoredJan 29, 2025
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Commits on Jan 15, 2025

• added patient_splits_folder to evaluation (#83)

  ChaoPang

  authoredJan 15, 2025
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Commits on Dec 9, 2024

• fixed a bug in reading the predicted_boolean_probability for computing auc (#82)

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  ChaoPang

  authoredDec 9, 2024
  5bcbd61

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• updated the prediction output schema to be compatible with the meds-evaluation (#81)

  ChaoPang

  authoredDec 9, 2024
  07292d0

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Commits on Dec 6, 2024

• Fixed transformers==4.40.0 and tokenizers==0.19.9 in pyproject.toml (#80)

  ChaoPang

  authoredDec 6, 2024
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Commits on Dec 5, 2024

• upgraded tokenizer (#79)

  ChaoPang

  authoredDec 5, 2024
  e338f17

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• added a check on birth_datetime in the meds to cehrbert data conversion (#78)

  ChaoPang

  authoredDec 5, 2024
  3f9b1c1

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• upgraded transformers (#77)

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  ChaoPang

  authoredDec 5, 2024
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Commits on Nov 29, 2024

• Missing output names (#76)

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  ChaoPang

  authoredNov 29, 2024
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Commits on Nov 15, 2024

• fixed the streaming bug (#75)

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  ChaoPang

  authoredNov 15, 2024
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Commits on Nov 13, 2024

• Fixed Fine-tune example code (#74)

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  joshuasami

  authoredNov 13, 2024
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Commits on Nov 1, 2024

• changed the field from is_data_in_med to is_data_in_meds in DataTrainingArguments; added a parse_dynamic_arguments to extend the argument parser more flexibly (#72)

  ChaoPang

  authoredNov 1, 2024
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Commits on Oct 30, 2024

• Meds conversion time token fix (#71)

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  ChaoPang

  authoredOct 30, 2024
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Commits on Oct 27, 2024

• fixed the MEDS ED visit type (#70)

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  ChaoPang

  authoredOct 27, 2024
  e39f1bc

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• Fix omop meds order (#68)

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  ChaoPang

  authoredOct 27, 2024
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Commits on Oct 25, 2024

• fixed potential issues in finetuning (#67)

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  ChaoPang

  authoredOct 25, 2024
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• check whether patient_id exists in the meds_reader database because subject_splits can contain more patients than the dataset (#66)

  ChaoPang

  authoredOct 25, 2024
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Commits on Oct 14, 2024

• upgraded cehrbert_data from v0.0.3 to v0.0.4 (#65)

  ChaoPang

  authoredOct 14, 2024
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Commits on Oct 11, 2024

• Convert OMOP MEDS data to CEHR-BERT data by linking events by visit_id (#59)

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  ChaoPang

  authoredOct 11, 2024
  1540a78

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Commits on Oct 10, 2024

• created a helper function to convert the existing huggingface dataset to an iterable dataset (#64)

  ChaoPang

  authoredOct 10, 2024
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• used the existing subject_split to split the cohort automatically instead of doing it manually (#63)

  ChaoPang

  authoredOct 10, 2024
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Commits on Oct 9, 2024

• handled the cases where the unit count is zero, this could happen when there is only unit and in addition there is only one value associated with that unit (#62)

  ChaoPang

  authoredOct 9, 2024
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• Fixed the relative paths in the finetuning runner (#61)

  ChaoPang

  authoredOct 9, 2024
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• Added units to meds to cehrbert data transformation and added unit in normalizing numeric values (#60)

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  ChaoPang

  authoredOct 9, 2024
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• Fix the data and model relative paths (#58)

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  ChaoPang

  authoredOct 9, 2024
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Commits on Sep 13, 2024

• Implemented TruncatedOnlineStatistics to collect truncated stats in a distributed way (#57)

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  ChaoPang

  authoredSep 13, 2024
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Commits on Sep 11, 2024

• Update test prediction columns (#56)

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  ChaoPang

  authoredSep 11, 2024
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Commits on Sep 10, 2024

• Implement a custom do_predict because the HF trainer predict has memory leakage for large test sets (#55)

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  ChaoPang

  authoredSep 10, 2024
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