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Algorithm Submission Guide

Participants in the RARE25 Challenge will submit their algorithms as Grand Challenge (GC) inference containers. These are Docker-based containers that encapsulate your trained AI model (architecture and weights), along with all the required code to load a case (e.g., endoscopic image), run inference (e.g., neoplasia classification), and store the output for evaluation.

Inference containers are the core of the submission process on Grand Challenge and ensure reproducibility and secure evaluation on the closed validation set.

Baseline Algorithm and Template Repository 🧰

We provide a baseline submission repository with example code and instructions to get started. It contains a 2D CNN baseline algorithm trained on the public training data and includes:

  • Training scripts
  • Inference logic
  • Docker container setup

We recommend starting by submitting an unaltered version of the baseline container to familiarize yourself with the submission workflow.

Setting Up Your Environment 🔧

Ensure Docker 🐳 is installed and running on your machine. On Windows, we recommend using Windows Subsystem for Linux (WSL) with an Ubuntu distribution. For installation guidance, refer to Microsoft’s official WSL2 + Docker tutorial.

Building, Testing, and Exporting Your Algorithm Locally ⚙️

  1. Clone the baseline repository:

    git clone https://github.com/TUE-VCA/RARE25-baseline.git

    cd RARE25-baseline

  2. Test your inference container:

    ./do_test_run.sh

    This builds your container and tests it using dummy images from the ./test/ directory.

  3. Export the container:

    ./do_save.sh

    The result will be a .tar.gz file containing your Docker image, ready for upload.

Test Uploading Your Algorithm to Grand Challenge 🛰️

  1. Create a team (optional, but recommended) to collaborate with others.
  2. Navigate to Submit > Sanity Check on the RARE25 Grand Challenge page.
  3. Fill in the submission form and save.
  4. Go to your algorithm’s page, open the Containers tab, and click Upload a Container.
  5. Select your .tar.gz image and upload.
  6. After the upload, your container will be validated and become “Active” within 20–60 minutes.

Once active, test it on a sample image to ensure correctness.

📝 For more technical details, visit: GC Algorithms Documentation

Note: You may submit to the Sanity Check phase as many times as needed. Please thoroughly test your algorithms before submitting to the Open Development Phase to optimize your submissions. The Sanity Check also provides access to logs for debugging purposes.

Customizing the Baseline for Your Own Model 🛠️

To adapt the baseline:

  • Edit the logic in ./inference.py to integrate your model.
  • Add any dependencies to requirements.txt.
  • Copy new files via the Dockerfile.
  • Rebuild, test, and export your updated container.

Note: Your container must be self-contained. Internet access is disabled during evaluation. Test locally with --network=none to verify.

Submitting to the Leaderboards 📊

Open Development Phase Submission

Once your container is functional and uploaded:

  • Visit the Open Development Phase page.
  • Select your algorithm and submit.
  • If successful, your score will appear on the leaderboard within 24 hours.

Please make sure your submission complies with all challenge rules. Invalid or non-compliant submissions will be removed. ✅

Closed Testing Phase Submission

If you qualify for the final evaluation:

  1. Ensure your final algorithm is bug-free by re-submitting it to the Sanity Check.

  2. Prepare a brief technical document (PDF) describing:

    • Model architecture
    • Training strategy
    • Team members and affiliations

    This document is mandatory and should be uploaded in the "Supplementary File" field during submission. Also see Challenge Rules.

  3. Submit your final model on the Closed Testing Phase submission page. Only one submission per team is allowed. If multiple versions are submitted, only the most recent will be evaluated.

  4. Send an email to rare-challenge@tue.nl with:

    • Your team name
    • Member names
    • A link to your algorithm on Grand Challenge

This helps us communicate with your team about final evaluation and results.

We look forward to your innovative solutions and contributions to the RARE25 Challenge. Good luck! 🍀

For any questions, please reach out on the RARE25 Forum.