medclip

MedCLIP: Fine-tuning a CLIP model on the ROCO medical dataset

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Summary

This repository contains the code for fine-tuning a CLIP model on the ROCO dataset, a dataset made of radiology images and a caption. This work is done as a part of the Flax/Jax community week organized by Hugging Face and Google.

Demo

You can try a Streamlit demo app that uses this model on 🤗 Spaces. You may have to signup for 🤗 Spaces private beta to access this app (screenshot shown below).

🤗 Hub Model card: https://huggingface.co/flax-community/medclip-roco

Dataset 🧩

Each image is accompanied by a textual caption. The caption length varies from a few characters (a single word) to 2,000 characters (multiple sentences). During preprocessing we remove all images that has a caption shorter than 10 characters. Training set: 57,780 images with their caption. Validation set: 7,200 Test set: 7,650

[ ] Give an example

Installation 💽

This repo depends on the master branch of Hugging Face - Transformers library. First you need to clone the transformers repository and then install it locally (preferably inside a virtual environment) with pip install -e ".[flax]".

The Model ⚙️

You can load the pretrained model from the Hugging Face Hub with

from medclip.modeling_hybrid_clip import FlaxHybridCLIP

model = FlaxHybridCLIP.from_pretrained("flax-community/medclip-roco")

Training

The model is trained using Flax/JAX on a cloud TPU-v3-8. You can fine-tune a CLIP model implemented in Flax by simply running sh run_medclip. This is the validation loss curve we observed when we trained the model using the run_medclip.sh script.

Limitations 🚨

The current model is capable of identifying if a given radiology image is a PET scan or an ultrasound scan. However it fails at identifying a brain scan from a lung scan. ❗️This model should not be used in a medical setting without further evaluations❗️.

Acknowledgements

Huge thanks to the Hugging Face 🤗 team and Google JAX/Flax team for organizing the community week and letting us use cloud compute for 2 weeks. We specially thank @patil-suraj & @patrickvonplaten for the continued support on Slack and the detailed feedback.

TODO

[ ] Evaluation on down-stream tasks

[ ] Zero-shot learning performance

[ ] Merge the demo app