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M3FM

★ 19 Open GitHub ↗

[npj Digital Medicine] A multimodal multidomain multilingual medical foundation model for zero shot clinical diagnosis

// repository documentation

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Demo code using the COV-CTR dataset for our M3FM. For other datasets, you need to send requests or download them from their official websites to access them.

## Environment
Clone the repo
```
git clone https://github.com/ai-in-health/M3FM
```
Install dependencies
```
conda create -n M3FM python==3.9
conda activate M3FM
# install a proper version of PyTorch
# see https://pytorch.org/get-started/previous-versions/
pip install pytorch>=1.10.1 torchvision>=0.11.2 torchaudio>=0.10.1 pytorch-cuda==11.8 -c pytorch -c nvidia

# install the rest dependencies
pip install -r requirements.txt
```
which should install in about 5 mins. We can run the code under `torch==2.2.1`. Other versions may work.

## Training
Here is an example of running command:
```
python M3FM.py
```

## Inference

Here is an example of running command:

Generate reports in English:
```
python inference.py --language English
```
Generate reports in Chinese
```
python inference.py --language Chinese
```
Generate reports in English and Chinese
```
python inference.py --language All
```

## Notes
1. To evaluate report generation, ensure that your system has installed JAVA. Here is an example:
   - Download from the official website (https://www.java.com/en/download/manual.jsp) to obtain, e.g., jdk-8u333-linux-x64.tar.gz
   - Unzip the file by running `tar -zxvf jdk-8u333-linux-x64.tar.gz`, and you will see the jre folder
   - Write the following lines to ~/.bashrc:
     - `echo "export JRE_HOME=path/to/jre" >> ~/.bashrc`
     - `echo "export PATH=${JRE_HOME}/bin:$PATH" >> ~/.bashrc`
   - Activate the settings by running `source ~/.bashrc`
   - See if the java has been installed: `java -version`
2. You should install packages `pycocoevalcap` and `pycocotools` (included in `requirement.txt`).
3. When calculating the `SPICE` metric, the code will try to automatically download two files `stanford-corenlp-3.6.0.jar` and `stanford-corenlp-3.6.0-models.jar`, and save them to ${pycocoevalcapPath}/spice/lib/. If you encounter a network issue, you can prepare these two files by yourself:
   - Download a zip file from https://nlp.stanford.edu/software/stanford-corenlp-full-2015-12-09.zip
   - Unzip it to get the above two files
   - Run `pip show pycocoevalcap` to see where the package has been installed
   - Move the two files to ${pycocoevalcapPath}/spice/lib/
4. To evaluate report generation, you should install the `stanfordcorenlp` package (included in `requirement.txt`), and download [stanford-corenlp-4.5.2](https://stanfordnlp.github.io/CoreNLP/history.html). The following is an example. Note that we set `corenlp_root = data/stanford-corenlp-4.5.2` in `configs/__init__.py`.
```
wget https://nlp.stanford.edu/software/stanford-corenlp-4.5.2.zip --no-check-certificate
wget https://nlp.stanford.edu/software/stanford-corenlp-4.5.2-models-german.jar --no-check-certificate
wget https://nlp.stanford.edu/software/stanford-corenlp-4.5.2-models-french.jar --no-check-certificate

unzip stanford-corenlp-4.5.2.zip -d data/
mv stanford-corenlp-4.5.2-models-german.jar data/stanford-corenlp-4.5.2/
mv stanford-corenlp-4.5.2-models-french.jar data/stanford-corenlp-4.5.2/
rm stanford-corenlp-4.5.2.zip
```

M3FM

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