mertsayar8 / radialog Goto Github PK

Authors: Chantal Pellegrini*, Ege Özsoy*, Benjamin Busam, Nassir Navab, Matthias Keicher

Conversational AI tools that can generate and discuss clinically correct radiology reports for a given medical image have the potential to transform radiology. Such a human-in-the-loop radiology assistant could facilitate a collaborative diagnostic process, thus saving time and improving the quality of reports. Towards this goal, we introduce RaDialog, the first thoroughly evaluated and publicly available large vision-language model for radiology report generation and interactive dialog. RaDialog effectively integrates visual image features and structured pathology findings with a large language model (LLM) while simultaneously adapting it to a specialized domain using parameter-efficient fine-tuning. To keep the conversational abilities of the underlying LLM, we propose a comprehensive, semi-automatically labeled, image-grounded instruct dataset for chest X-ray radiology tasks. By training with this dataset, our method achieves state-of-the-art clinical correctness in report generation and shows impressive abilities in interactive tasks such as correcting reports and answering questions, serving as a foundational step toward clinical dialog systems.

• clone this repository and move to the radialog directory with cd RaDialog
• Install the RaDialog environment with conda create --name radialog python=3.7
• Activate the environment with conda activate radialog
• Install the requirements with pip install -r requirements.txt
• Install hl-ml-multimodal with pip install hi-ml-multimodal==0.2.0
• Reinstall correct versions of torch and transformers with pip install torch==1.13.0 transformers==4.28.1
• Install java and set JAVA_HOME and PATH in local_config.py (we used jre1.8.0)

• Install the CheXbert environment with conda create --name chexbert python=3.7
• Activate the environment with conda activate chexbert
• Move to the chexbert directory with cd chexbert
• Install the requirements with pip install -r requirements.txt
• Set the absolute path to the chexbert env and folder in RaDialog/local_config.py

• Download the pretrained models from here
• place chexbert.pth in RaDialog/chexbert/src/checkpoint/
• unzip vicuna-7b-img-instruct.zip and vicuna-7b-img-report.zip and place folders into RaDialog/checkpoints/
• unzip chexpert_train and place folder into RaDialog/findings_classifier/checkpoints/
• unzip embs and place folder into RaDialog/pretraining/
• unzip checkpoint_4.pth and place it into outputs/stage1_pt_instruct_blip_origlr_img448/

• Download the MIMIC-CXR-JPG dataset from here
• The dataset should be saved in .../physionet.org/files/mimic-cxr-jpg
• Go to physionet.org/files/mimic-cxr-jpg/files/ and unzip mimic-cxr-2.0.0-split.csv.gz
• from here, dowload mimic-cxr-reports.zip
• unzip it and place the folder in the same directory as the MIMIC-CXR-JPG dataset (e.g. physionet.org/files/)
• in local_config.py set the path to the MIMIC-CXR dataset (e.g. .../physionet.org/files/)
• in model/lavis/defaults_report.yaml set the path to the MIMIC-CXR-JPG dataset (e.g. .../physionet.org/files/mimic-cxr-jpg/2.0.0 )

• go to the mimic-cxr folder in the code with cd mimic-cxr
• run python create_section_files.py to prepare the report data
• go back to the RaDialog directory with cd ..

• As MIMIC-CXR needs a certified PhysioNet account to be accessed, we can not publish our instruct dataset directly.
• We are working on publishing the instruct dataset on PhysioNet. In the meantime, you can create an instruct dataset yourself by following the steps below or just use our pre-trained model.
• The MIMIC-NLE data has to be generated first, as it also contains protected data. Follow the instructions here to generate the MIMIC-NLE data and set the path to the MIMIC-NLE data in local_config.py.
• For the correction task, you can write us, then we can share the used incorrect predictions with you.
• To generate data without Correction or Reasoning (MIMIC-NLE), please comment our line 335 or 336 in "create_data.py" accordingly.

Data for RaDialog-RG:

• run python -m data.create_data --mode "RG" to generate the report generation dataset in the required format (no instruct data)

Data for RaDialog-INS:

• run python -m data.create_data --mode "INS" to generate the instruct dataset

• run python demo.py --cfg-path pretraining/configs/blip2_pretrain_stage1_emb.yaml to start the demo
• connect to the demo with a browser at http://127.0.0.1:7860 and start chatting with RaDialog

• RaDialog-RG: run python test.py --prompt img_matching_examples_ig2_noexamples_IMG_findings --use_embs --num_workers 0 --lora_model checkpoints/vicuna-7b-img-report/checkpoint-11200
• RaDialog-INS: run python test.py --prompt img_matching_examples_ig2_noexamples_IMG_findings --use_embs --num_workers 0 --lora_model checkpoints/vicuna-7b-img-instruct/checkpoint-4800
• RaDialog-INS (correction): run python test.py --prompt img_matching_examples_ig2_noexamples_IMG_findings --use_embs --num_workers 0 --lora_model checkpoints/vicuna-7b-img-instruct/checkpoint-4800 --do_corr
• RaDialog-INS (findings QA): run python test.py --prompt img_matching_examples_ig2_noexamples_IMG_findings --use_embs --num_workers 0 --lora_model checkpoints/vicuna-7b-img-instruct/checkpoint-4800 --do_cp_all_qa (or --do_cp_bin_qa)

• run python -m findings_classifier.chexpert_train --train --run_name "train_chexbert"
• in chexpert_train.py set ckpt_path (line 152) to the path of the trained model you just trained
• then run python -m findings_classifier.chexpert_train --run_name "save_preds" to save the predictions of the trained model

• run python -m pretraining.train --cfg-path pretraining/configs/blip2_pretrain_stage1.yaml, we used the 4th epoch checkpoint
• run python -m pretraining.train --cfg-path pretraining/configs/blip2_pretrain_stage1_emb.yaml, to save the embeddings of the trained model

Train RaDialog-RG:

• run python finetune.py --use_embs True --base_model 'vicuna_v7' --output_dir 'checkpoints/lora-vicuna-7b-report' --wandb_run_name lora-vicuna-7b-report --prompt_template_name vicuna_v11 --data_path "data/data_files/mimic_cxr_reports_stratified.json" --cutoff_len 600 --num_epochs 10
• we used checkpoint-11200

Train RaDialog-INS:

• run python finetune.py --use_embs True --base_model 'vicuna_v7' --output_dir 'checkpoints/lora-vicuna-7b-instruct' --wandb_run_name lora-vicuna-7b-instruct --prompt_template_name vicuna_v11 --data_path "data/data_files/mimic_cxr_instruct_stratified.json" --cutoff_len 800 --num_epochs 10
• we used checkpoint-4800

To use a model from a checkpoint, you'll need to perform the following steps:

• make a copy of "pytorch_model.bin" and rename it to "adapter_model.bin"
• copy adapter_config.json to the checkpoint folder (it will be generated after the last epoch or you can copy it from the checkpoints we provide)