BioMoQA-Triage

BioMoQA-Triage is a pipeline for BioMoQA literature triage, combining FastAPI, Celery, MongoDB, and Redis with an ensemble of fine-tuned RoBERTa models.

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Repository Structure

BioMoQA-api/
├── api/                      # API service (FastAPI + Celery workers)
├── model/                    # Model checkpoints (downloaded via script)
├── download_checkpoints.sh   # Script to download model checkpoints
└── README.md                 # (this file)

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Documentation

• API Service Documentation Details on endpoints, job handling, Docker setup, and worker configuration.

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Setup

Download Model Checkpoints

Before running the API, you need to download the fine-tuned PubMedBERT model checkpoints:

./download_checkpoints.sh

This script will:

• Download model checkpoints from the S3 bucket
• Store them in model/checkpoints/

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Quickstart

To launch the API stack with Docker:

cd api
docker compose up --build

The API will be available at http://localhost:8501.

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License

MIT License