Update README.md
Browse files
README.md
CHANGED
|
@@ -1,3 +1,87 @@
|
|
| 1 |
-
---
|
| 2 |
-
license: mit
|
| 3 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: mit
|
| 3 |
+
library_name: pytorch
|
| 4 |
+
tags:
|
| 5 |
+
- Medical Vsion-Language Pre-Training
|
| 6 |
+
- BenchX
|
| 7 |
+
---
|
| 8 |
+
|
| 9 |
+
# M-FLAG Checkpoint Model Card
|
| 10 |
+
|
| 11 |
+
A retrained M-FLAG model for benchmarking medical vision-language pre-training methods within the BenchX framework.
|
| 12 |
+
|
| 13 |
+
## Model Details
|
| 14 |
+
- **Model Type**: M-FLAG
|
| 15 |
+
- **Architecture**: ResNet-50 image encoder and CXR-BERT text encoder
|
| 16 |
+
- **Original Papers**: [M-FLAG: Medical Vision-Language Pre-training with Frozen Language Models and Latent Space Geometry Optimization](https://arxiv.org/abs/2307.08347)
|
| 17 |
+
- **Benchmark Paper**: [BenchX: A Unified Benchmark Framework for Medical Vision-Language Pretraining on Chest X-Rays](https://arxiv.org/abs/2410.21969)
|
| 18 |
+
- **Benchmark Framework**: https://github.com/yangzhou12/BenchX
|
| 19 |
+
|
| 20 |
+
## Intended Use
|
| 21 |
+
- **Primary Use Cases**:
|
| 22 |
+
- Benchmarking performance for Medical Image Classification
|
| 23 |
+
- Benchmarking performance for Medical Image Segmentation
|
| 24 |
+
- Benchmarking performance for Medical Report Generation
|
| 25 |
+
|
| 26 |
+
## Pre-Training Data
|
| 27 |
+
- **Dataset**:
|
| 28 |
+
- Data source(s): MIMIC-CXR
|
| 29 |
+
- Types of medical images: Frontal chest X-rays
|
| 30 |
+
- Text data type: Associated radiology reports
|
| 31 |
+
|
| 32 |
+
## Prerequisites
|
| 33 |
+
|
| 34 |
+
Please follow the [instruction](https://github.com/yangzhou12/BenchX/blob/release/README.md#installation) to install BenchX.
|
| 35 |
+
|
| 36 |
+
## Training & Evaluation
|
| 37 |
+
|
| 38 |
+
### 1. Classification
|
| 39 |
+
|
| 40 |
+
To fine-tune M-FLAG for classification, run this command:
|
| 41 |
+
|
| 42 |
+
```
|
| 43 |
+
python bin/train.py config/classification/<dataset_name>/M-FLAG.yml
|
| 44 |
+
```
|
| 45 |
+
|
| 46 |
+
### 2. Segmentation
|
| 47 |
+
To fine-tune M-FLAG for segmentation, run this command:
|
| 48 |
+
|
| 49 |
+
```
|
| 50 |
+
python mmsegmentation/tools/train.py config/benchmark/<dataset_name>/M-FLAG.yml
|
| 51 |
+
```
|
| 52 |
+
|
| 53 |
+
### 3. Report Generation
|
| 54 |
+
To fine-tune M-FLAG for report generation, run this command:
|
| 55 |
+
```
|
| 56 |
+
python bin/train.py config/report_generation/<dataset_name>/M-FLAG.yml
|
| 57 |
+
```
|
| 58 |
+
|
| 59 |
+
### 4. Evaluation
|
| 60 |
+
To evaluate fine-tuned M-FLAG models, run:
|
| 61 |
+
|
| 62 |
+
```
|
| 63 |
+
# For classification and report generation
|
| 64 |
+
python bin/test.py config/<task_name>/<dataset_name>/M-FLAG.yml validator.splits=[test] ckpt_dir=<path_to_checkpoint>
|
| 65 |
+
|
| 66 |
+
# For segmentation
|
| 67 |
+
python mmsegmentation/tools/my_test.py mmsegmentation/config/<dataset_name>/M-FLAG.yml <path_to_checkpoint>
|
| 68 |
+
```
|
| 69 |
+
|
| 70 |
+
## Citations
|
| 71 |
+
```bibtex
|
| 72 |
+
@inproceedings{huang2021M-FLAG,
|
| 73 |
+
title={M-FLAG: Medical Vision-Language Pre-training with Frozen Language Models and Latent Space Geometry Optimization},
|
| 74 |
+
author={Liu, Che and Cheng, Sibo and Chen, Chen and Qiao, Mengyun and Zhang, Weitong and Shah, Anand and Bai, Wenjia and Arcucci, Rossella},
|
| 75 |
+
booktitle={Proceedings of MICCAI},
|
| 76 |
+
pages={637--647},
|
| 77 |
+
year={2023},
|
| 78 |
+
}
|
| 79 |
+
```
|
| 80 |
+
```bibtex
|
| 81 |
+
@inproceedings{zhou2024benchx,
|
| 82 |
+
title={BenchX: A Unified Benchmark Framework for Medical Vision-Language Pretraining on Chest X-Rays},
|
| 83 |
+
author={Yang Zhou, Tan Li Hui Faith, Yanyu Xu, Sicong Leng, Xinxing Xu, Yong Liu, Rick Siow Mong Goh},
|
| 84 |
+
booktitle={Proceedings of NeurIPS},
|
| 85 |
+
year={2024}
|
| 86 |
+
}
|
| 87 |
+
```
|