README.md

---
license: apache-2.0
metrics:
- accuracy
pipeline_tag: image-feature-extraction
tags:
- 3D medical CLIP
- Image-text retrieval
---

M3D-CLIP is one of the works in the [M3D](https://github.com/BAAI-DCAI/M3D) series. 
It is a 3D medical CLIP model that aligns vision and language through contrastive loss on the [M3D-Cap](https://huggingface.co/datasets/GoodBaiBai88/M3D-Cap) dataset.
The vision encoder uses 3D ViT with 32\*256\*256 image size and 4\*16\*16 patch size.
The language encoder utilizes a pre-trained BERT as initialization.
The uses of M3D-CLIP:
1. 3D medical image and text retrieval task.
2. Aligned and powerful image and text features for downstream tasks.
3. Text-aligned visual encoders are excellent pre-trained models for visual and multi-modal tasks.


![comparison](M3D_CLIP_table.png)
![comparison](itr_result.png)

# Quickstart

```python
device = torch.device("cuda") # or cpu

tokenizer = AutoTokenizer.from_pretrained(
    "GoodBaiBai88/M3D-CLIP",
    model_max_length=512,
    padding_side="right",
    use_fast=False
)
model = AutoModel.from_pretrained(
    "GoodBaiBai88/M3D-CLIP",
    trust_remote_code=True
)
model = model.to(device=device)

# Prepare your 3D medical image:
# 1. The image shape needs to be processed as 1*32*256*256, considering resize and other methods.
# 2. The image needs to be normalized to 0-1, considering Min-Max Normalization.
# 3. The image format needs to be converted to .npy 
# 4. Although we did not train on 2D images, in theory, the 2D image can be interpolated to the shape of 1*32*256*256 for input.
    
image_path = ""
input_txt = ""

text_tensor = tokenizer(input_txt, max_length=512, truncation=True, padding="max_length", return_tensors="pt")
input_id = text_tensor["input_ids"].to(device=device)
attention_mask = text_tensor["attention_mask"].to(device=device)
image = np.load(image_path).to(device=device)

with torch.inference_mode():
    image_features = model.encode_image(image)[:, 0]
    text_features = model.encode_text(input_id, attention_mask)[:, 0]
```

# Citation

If you feel helpful from our work, please consider citing the following work:

```BibTeX
@misc{bai2024m3d,
      title={M3D: Advancing 3D Medical Image Analysis with Multi-Modal Large Language Models}, 
      author={Fan Bai and Yuxin Du and Tiejun Huang and Max Q. -H. Meng and Bo Zhao},
      year={2024},
      eprint={2404.00578},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}
```