Oufattole / meds-torch

MIT License
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Multimodal EHR Data Processing Enhancements #121

Closed Oufattole closed 2 weeks ago

Oufattole commented 2 weeks ago

This pull request implements multimodal data processing capabilities, combining electronic health records (EHR) with text data, while improving the overall data pipeline architecture.

Key Changes

  1. Test Data Generation

    • Created multimodal test datasets combining text and EHR data
    • Standardized test data generation using meds-transform runner and aces-cli
  2. Data Processing Pipeline

    • Added custom meds-transform stages for tensorizing multimodal data (specifically text and EHR data atm, but the implementation can easily be modified to include other modalities)
    • Implemented efficient storage of tokenized text in safetensor format
    • Integrated multimodal indexing system within nested ragged tensors
      • Each code receives a multimodal_idx
      • Index serves as key in multimodal safetensor for efficient data loading
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codecov-commenter commented 2 weeks ago

:warning: Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 89.60000% with 13 lines in your changes missing coverage. Please review.

Project coverage is 73.28%. Comparing base (de8082e) to head (4182363). Report is 93 commits behind head on dev.

Files with missing lines Patch % Lines
src/meds_torch/utils/custom_text_tensorization.py 77.77% 6 Missing :warning:
src/meds_torch/utils/custom_text_normalization.py 84.61% 4 Missing :warning:
src/meds_torch/utils/custom_text_tokenization.py 95.77% 3 Missing :warning:

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #121 +/- ## ========================================== + Coverage 64.80% 73.28% +8.47% ========================================== Files 10 51 +41 Lines 736 2777 +2041 ========================================== + Hits 477 2035 +1558 - Misses 259 742 +483 ```

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