v1.2.3

check whether patient_id exists in the meds_reader database because s…

v1.2.2

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

v1.2.1

What's Changed

• created a helper function to convert the existing huggingface dataset to an iterable dataset by @ChaoPang in #64

Full Changelog: v1.2.0...v1.2.1

v1.2.0

What's Changed

• Fix the data and model relative paths by @ChaoPang in #58
• Added units to meds to cehrbert data transformation and added unit in normalizing numeric values by @ChaoPang in #60
• Fixed the relative paths in the finetuning runner by @ChaoPang in #61
• The zero division bug for calculating the unit probabilities for numeric concepts by @ChaoPang in #62
• used the existing subject_split in meds_reader to split the cohort automatically instead of doing it manually by @ChaoPang in #63

Full Changelog: v1.1.9...v1.2.0

v1.1.9

Implemented TruncatedOnlineStatistics to collect truncated stats in a…

v1.1.8

What's Changed

• Update test prediction columns by @ChaoPang in #56

Full Changelog: v1.1.7...v1.1.8

v1.1.7

What's Changed

• Implement a custom do_predict because the HF trainer predict has memory leakage for large test sets by @ChaoPang in #55

Full Changelog: v1.1.6...v1.1.7

v1.1.6: Remove eval compute metrics (#54)

What's Changed

• Stopped using the transformers (4.39.3) trainer compute_metrics to calculate custom metrics as large validation sets will crash by @ChaoPang in #54

Full Changelog: v1.1.4...v1.1.6

v1.1.4

What's Changed

• Deleted all spark related code and included the new cehrbert_data dependency by @ChaoPang in #52
• added python-build.yml by @ChaoPang in #53

Full Changelog: v1.1.2...v1.1.4

v1.1.2

What's Changed

• Create pylint.yml by @ChaoPang in #46
• Apply pre-commit code formatters by @ChaoPang in #47
• updated the image references in README to reference the ones on github by @ChaoPang in #48
• removed fastparquet from the dependency list by @ChaoPang in #49
• removed the abosolute model and tokenizer paths from pretraining and finetuning by @ChaoPang in #50
• Updated meds_reader to 0.1.9 by @ChaoPang in #51

Full Changelog: https://github.com/cumc-dbmi/cehrbert/commits/v1.1.2