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kilonzi
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May 1, 2025
Co-authored-by: John Kitonyo <johnkilonzi@outlook.com>
Co-authored-by: John Kitonyo <johnkilonzi@outlook.com>
Co-authored-by: John Kitonyo <johnkilonzi@outlook.com>
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This pull request introduces a deployment pipeline for the PCLR model, including schema definitions, Docker containerization, and preprocessing/postprocessing scripts. The changes focus on defining input/output formats, creating a Dockerized environment for processing, and implementing scripts for preparing and finalizing data.
Deployment Pipeline Setup:
Model Schema Definition:
Added a JSON schema in
pclr_model_schema.jsonto specify the model's input (ecg_tensor) and output (embed) formats, including their shapes and data types.Dockerfile for Processing:
Created a
Dockerfileto set up a lightweight Python 3.9-based environment for running the preprocessing (prepare.py) and postprocessing (finalize.py) scripts. It installs dependencies fromrequirements.txtand sets the entry point to Python.Data Processing Scripts:
Preprocessing Script (
prepare.py):Added a script to process raw ECG files into HDF5 tensor format. It reads input CSVs, extracts ECG data from files, interpolates and normalizes the data, and saves it in a structured HDF5 format.
Postprocessing Script (
finalize.py):Added a script to merge model predictions with input metadata. It reads a CSV of metadata and a JSON of predictions, validates dimensions, and outputs a combined CSV with embeddings appended.
Dependencies:
Added a
requirements.txtfile listing the necessary Python libraries (pandas,numpy,h5py,smart-open[gcs]) for preprocessing and postprocessing.