Update README.md
Browse files
README.md
CHANGED
|
@@ -1,3 +1,40 @@
|
|
| 1 |
-
---
|
| 2 |
-
license: cc-by-nc-4.0
|
| 3 |
-
---
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: cc-by-nc-4.0
|
| 3 |
+
---
|
| 4 |
+
# PathGen-CLIP
|
| 5 |
+
|
| 6 |
+
This is the official PathGen-CLIP trained based on **PathGen-1.6M: 1.6 Million Pathology Image-text Pairs Generation through Multi-agent Collaboration**
|
| 7 |
+
|
| 8 |
+
## Usage of Trained PathGen-CLIP series model
|
| 9 |
+
|
| 10 |
+
The trained PathGen-CLIP can be downloaded via this [**PathGen-CLIP**](https://pub-7a38cc906afa44a4a01533c288d0b1af.r2.dev/pathgenclip.pt) and the PathGen-CLIP-L via this [**PathGen-CLIP-L**](https://huggingface.co/jamessyx/PathGen-CLIP-L) (We also transform PathGen-CLIP-L to HF version [**PathGenCLIP-vit-large-patch14-hf**](https://huggingface.co/jamessyx/pathgenclip-vit-large-patch14-hf) to facilitate the integration into LLM).
|
| 11 |
+
|
| 12 |
+
```
|
| 13 |
+
pip install open_clip_torch
|
| 14 |
+
```
|
| 15 |
+
|
| 16 |
+
```python
|
| 17 |
+
import torch
|
| 18 |
+
from PIL import Image
|
| 19 |
+
import open_clip
|
| 20 |
+
|
| 21 |
+
model, _, preprocess = open_clip.create_model_and_transforms('ViT-B-16', pretrained='path/pathgen-clip.pt') // PathGen-CLIP
|
| 22 |
+
# model, _, preprocess = open_clip.create_model_and_transforms('ViT-B-16', pretrained='path/pathgen-clip-l.pt') // PathGen-CLIP-L
|
| 23 |
+
model.eval() # model in train mode by default, impacts some models with BatchNorm or stochastic depth active
|
| 24 |
+
tokenizer = open_clip.get_tokenizer('ViT-B-16')
|
| 25 |
+
|
| 26 |
+
image = preprocess(Image.open("example.png")).unsqueeze(0)
|
| 27 |
+
text = tokenizer(["An H&E image of tumor patch", "An H&E image of normal patch"])
|
| 28 |
+
|
| 29 |
+
with torch.no_grad(), torch.cuda.amp.autocast():
|
| 30 |
+
image_features = model.encode_image(image)
|
| 31 |
+
text_features = model.encode_text(text)
|
| 32 |
+
image_features /= image_features.norm(dim=-1, keepdim=True)
|
| 33 |
+
text_features /= text_features.norm(dim=-1, keepdim=True)
|
| 34 |
+
|
| 35 |
+
text_probs = (100.0 * image_features @ text_features.T).softmax(dim=-1)
|
| 36 |
+
|
| 37 |
+
print("Label probs:", text_probs)
|
| 38 |
+
```
|
| 39 |
+
|
| 40 |
+
|