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M-FLAG-MICCAI2023

M-FLAG: Medical Vision-Language Pre-training with Frozen Language Models and Latent Space Geometry Optimization, MICCAI 2023.

Installation

To clone this repository:

git clone https://github.com/cheliu-computation/M-FLAG-MICCAI2023.git

To install Python dependencies:

pip install -r requirements.txt

All experiments are implemented on A100 GPU.

Pre-train Dataset downloading

Datasets we used are as follows:

• MIMIC-CXR: We downloaded the MIMIC-CXR-JPG dataset as the radiographs. Paired medical reports can be downloaded in MIMIC-CXR.

Preprocessing

• First we follow MGCA preprocessing to extract a master csv includes all CXR scans associated with report. You can find in Preprocessing.
• Then, run 'ext_data.py' to extract all scans and save as a npy file. It will accelerate the pre-training stage.

Pre-training

We pre-trained MGCA on MIMIC-CXR using this command:

cd M-FLAG-MICCAI2023/pretrain
torchrun --nnodes=1 --nproc_per_node=2 main.py

Finetune on downstream tasks

We evlauate the performance of M-FLAG on three downstream tasks: classification, object detection and semantic segmentation.

For classification task, we follow CheXclusion, please follow their offical code to extract data and implement classification tasks.

For semantic segmentation and object detection, we follow MGCA offical configuration and code. The dataset can be found in MGCA repository.