---
license: apache-2.0
inference: false
tags:
- medical
- radiology report generation
- medical chatbot
datasets:
- mimic-cxr
library_name: transformers
---
RaDialog
📝 Paper • 🖥️ Github • 🗂️Dataset
• 🌐️Project Page
## Get Started
Clone repository:
```python
git clone https://huggingface.co/Chantal/RaDialog-interactive-radiology-report-generation
```
Install requirements:
```python
conda create -n llava_hf python=3.10
conda activate llava_hf
conda install pytorch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 pytorch-cuda=11.7 -c pytorch -c nvidia
pip install -r requirements.txt
```
Run RaDialog inference:
```python
from pathlib import Path
import io
import requests
import torch
from PIL import Image
import numpy as np
from huggingface_hub import snapshot_download
from LLAVA_Biovil.llava.mm_utils import tokenizer_image_token, get_model_name_from_path, KeywordsStoppingCriteria, remap_to_uint8
from LLAVA_Biovil.llava.model.builder import load_pretrained_model
from LLAVA_Biovil.llava.conversation import SeparatorStyle, conv_vicuna_v1
from LLAVA_Biovil.llava.constants import IMAGE_TOKEN_INDEX
from utils import create_chest_xray_transform_for_inference, init_chexpert_predictor
def load_model_from_huggingface(repo_id):
# Download model files
model_path = snapshot_download(repo_id=repo_id, revision="main", force_download=True)
model_path = Path(model_path)
tokenizer, model, image_processor, context_len = load_pretrained_model(model_path, model_base='liuhaotian/llava-v1.5-7b',
model_name="llava-v1.5-7b-task-lora_radialog_instruct_llava_biovil_unfrozen_2e-5_5epochs_v5_checkpoint-21000", load_8bit=False, load_4bit=False)
return tokenizer, model, image_processor, context_len
if __name__ == '__main__':
sample_img_path = "https://openi.nlm.nih.gov/imgs/512/294/3502/CXR3502_IM-1707-1001.png?keywords=Surgical%20Instruments,Cardiomegaly,Pulmonary%20Congestion,Diaphragm"
response = requests.get(sample_img_path)
image = Image.open(io.BytesIO(response.content))
image = remap_to_uint8(np.array(image))
image = Image.fromarray(image).convert("L")
tokenizer, model, image_processor, context_len = load_model_from_huggingface(repo_id="Chantal/RaDialog-interactive-radiology-report-generation")
cp_model, cp_class_names, cp_transforms = init_chexpert_predictor()
model.config.tokenizer_padding_side = "left"
cp_image = cp_transforms(image)
logits = cp_model(cp_image[None].half().cuda())
preds_probs = torch.sigmoid(logits)
preds = preds_probs > 0.5
pred = preds[0].cpu().numpy()
findings = cp_class_names[pred].tolist()
findings = ', '.join(findings).lower().strip()
conv = conv_vicuna_v1.copy()
REPORT_GEN_PROMPT = f". Predicted Findings: {findings}. You are to act as a radiologist and write the finding section of a chest x-ray radiology report for this X-ray image and the given predicted findings. Write in the style of a radiologist, write one fluent text without enumeration, be concise and don't provide explanations or reasons."
print("USER: ", REPORT_GEN_PROMPT)
conv.append_message("USER", REPORT_GEN_PROMPT)
conv.append_message("ASSISTANT", None)
text_input = conv.get_prompt()
# get the image
vis_transforms_biovil = create_chest_xray_transform_for_inference(512, center_crop_size=448)
image_tensor = vis_transforms_biovil(image).unsqueeze(0)
image_tensor = image_tensor.to(model.device, dtype=torch.bfloat16)
input_ids = tokenizer_image_token(text_input, tokenizer, IMAGE_TOKEN_INDEX, return_tensors='pt').unsqueeze(0).to(model.device)
stop_str = conv.sep if conv.sep_style != SeparatorStyle.TWO else conv.sep2
stopping_criteria = KeywordsStoppingCriteria([stop_str], tokenizer, input_ids)
# generate a report
with torch.inference_mode():
output_ids = model.generate(
input_ids,
images=image_tensor,
do_sample=False,
use_cache=True,
max_new_tokens=300,
stopping_criteria=[stopping_criteria],
pad_token_id=tokenizer.pad_token_id
)
pred = tokenizer.decode(output_ids[0, input_ids.shape[1]:]).strip().replace("", "")
print("ASSISTANT: ", pred)
# add prediction to conversation
conv.messages.pop()
conv.append_message("ASSISTANT", pred)
stop_str = conv.sep if conv.sep_style != SeparatorStyle.TWO else conv.sep2
stopping_criteria = KeywordsStoppingCriteria([stop_str], tokenizer, input_ids)
# generate a report
with torch.inference_mode():
output_ids = model.generate(
input_ids,
images=image_tensor,
do_sample=False,
use_cache=True,
max_new_tokens=300,
stopping_criteria=[stopping_criteria],
pad_token_id=tokenizer.pad_token_id
)
pred = tokenizer.decode(output_ids[0, input_ids.shape[1]:]).strip().replace("", "")
print("ASSISTANT: ", pred)
# add prediction to conversation
conv.messages.pop()
conv.append_message("ASSISTANT", pred)
conv.append_message("USER", "Translate this report to easy language for a patient to understand.")
conv.append_message("ASSISTANT", None)
text_input = conv.get_prompt()
print("USER: ", "Translate this report to easy language for a patient to understand.")
# generate easy language report
input_ids = tokenizer_image_token(text_input, tokenizer, IMAGE_TOKEN_INDEX, return_tensors='pt').unsqueeze(0).to(model.device)
with torch.inference_mode():
output_ids = model.generate(
input_ids,
images=image_tensor,
do_sample=False,
use_cache=True,
max_new_tokens=300,
stopping_criteria=[stopping_criteria],
pad_token_id=tokenizer.pad_token_id
)
pred = tokenizer.decode(output_ids[0, input_ids.shape[1]:]).strip().replace("", "")
print("ASSISTANT: ", pred)
```
## ✏️ Citation
```
@article{pellegrini2023radialog,
title={RaDialog: A Large Vision-Language Model for Radiology Report Generation and Conversational Assistance},
author={Pellegrini, Chantal and {\"O}zsoy, Ege and Busam, Benjamin and Navab, Nassir and Keicher, Matthias},
journal={arXiv preprint arXiv:2311.18681},
year={2023}
}
```