Update README.md

README.md

@@ -1,8 +1,151 @@
 ---
 tags:
-- image-classification
 - timm
+- feature-extraction
+- image-classification
 library_name: timm
-license: apache-2.0
+license: other
+license_name: kaiko-non-commercial
+license_link: https://github.com/kaiko-ai/towards_large_pathology_fms/blob/a62a0c54719d858371aefa0fcab6ec4b34c86c4c/LICENSE
+metrics:
+- accuracy
+model-index:
+- name: kaiko
+  results:
+  - task:
+      type: image-classification
+      name: Image Classification
+    dataset:
+      name: BACH
+      type: image-classification
+    metrics:
+    - type: accuracy
+      value: 0.810
+      name: Accuracy
+      verified: false
+  - task:
+      type: image-classification
+      name: Image Classification
+    dataset:
+      name: CRC-NCT-HE
+      type: image-classification
+    metrics:
+    - type: accuracy
+      value: 0.960
+      name: Accuracy
+      verified: false
+  - task:
+      type: image-classification
+      name: Image Classification
+    dataset:
+      name: MHIST
+      type: image-classification
+    metrics:
+    - type: accuracy
+      value: 0.826
+      name: Accuracy
+      verified: false
+  - task:
+      type: image-classification
+      name: Image Classification
+    dataset:
+      name: PCam
+      type: image-classification
+    metrics:
+    - type: accuracy
+      value: 0.898
+      name: Accuracy
+      verified: false
+  - task:
+      type: image-classification
+      name: Image Classification
+    dataset:
+      name: TP53
+      type: image-classification
+    metrics:
+    - type: accuracy
+      value: 0.651
+      name: Accuracy
+      verified: false
+  - task:
+      type: image-classification
+      name: Image Classification
+    dataset:
+      name: CoNSeP
+      type: image-classification
+    metrics:
+    - type: accuracy
+      value: 0.658
+      name: Accuracy
+      verified: false
 ---
+
 # Model card for vit_base_patch16_224.kaiko_ai_towards_large_pathology_fms
+
+![](https://github.com/kaiko-ai/towards_large_pathology_fms/blob/a62a0c54719d858371aefa0fcab6ec4b34c86c4c/docs/images/kaiko-logo.png?raw=true)
+
+## Model Details
+
+- **Model Type:** Feature backbone
+- **Model Stats:**
+  - Params: 86M (base)
+  - Image size: 224 x 224 x 3
+  - Patch size: 16 x 16 x 3
+- **Repository:** [github.com:kaiko-ai/towards_large_pathology_fms](https://github.com/kaiko-ai/towards_large_pathology_fms)
+- **Original Weights:** [github.com:kaiko-ai/towards_large_pathology_fms/0.0.1](https://github.com/kaiko-ai/towards_large_pathology_fms/releases/tag/0.0.1)
+- **Papers:**
+  - [Towards Large-Scale Training of Pathology Foundation Models](https://arxiv.org/abs/2404.15217)
+
+## Model Usage
+
+### Image Embeddings
+
+```python
+from torchvision.transforms import v2
+from PIL import Image
+import requests
+import torch
+import timm
+import io
+
+# get example histology image
+url = "https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcQc7_xZpGOfQT7sxKwf2w5lL4GAq6IX_CbTzP1NGeenzA&s"
+image = Image.open(io.BytesIO(requests.get(url).content))
+
+# load model from the hub
+model = timm.create_model(
+  model_name="hf-hub:1aurent/vit_base_patch16_224.kaiko_ai_towards_large_pathology_fms",
+  dynamic_img_size=True,
+  pretrained=True,
+).eval()
+
+# get image transform
+preprocessing = v2.Compose(
+  [
+    v2.ToImage(),
+    v2.Resize(size=224),
+    v2.CenterCrop(size=224),
+    v2.ToDtype(torch.float32, scale=True),
+    v2.Normalize(
+      mean=(0.5, 0.5, 0.5),
+      std=(0.5, 0.5, 0.5),
+    ),
+  ]
+)
+
+data = preprocessing(image).unsqueeze(0) # input is a (batch_size, num_channels, img_size, img_size) shaped tensor
+output = model(data)  # output is a (batch_size, num_features) shaped tensor
+```
+
+## Citation
+
+```bibtex
+@misc{ai2024largescale,
+  title         = {Towards Large-Scale Training of Pathology Foundation Models}, 
+  author        = {kaiko.ai and Nanne Aben and Edwin D. de Jong and Ioannis Gatopoulos and Nicolas Känzig and Mikhail Karasikov and Axel Lagré and Roman Moser and Joost van Doorn and Fei Tang},
+  year          = {2024},
+  eprint        = {2404.15217},
+  archivePrefix = {arXiv},
+  primaryClass  = {cs.CV}
+}
+```