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mention mean, std and feature dim explicitly in replicate instructions
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nkaenzig committed Oct 8, 2024
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Showing 1 changed file with 18 additions and 1 deletion.
19 changes: 18 additions & 1 deletion docs/user-guide/advanced/replicate_evaluations.md
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@ Evaluating the backbone with randomly initialized weights serves as a baseline t

```
MODEL_NAME="universal/vit_small_patch16_224_random" \
NORMALIZE_MEAN=[0.485,0.456,0.406] \
NORMALIZE_STD=[0.229,0.224,0.225] \
IN_FEATURES=384 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand All @@ -28,6 +31,9 @@ The next baseline model, uses a pretrained ViT-S16 backbone with ImageNet weight

```
MODEL_NAME="universal/vit_small_patch16_224_dino" \
NORMALIZE_MEAN=[0.485,0.456,0.406] \
NORMALIZE_STD=[0.229,0.224,0.225] \
IN_FEATURES=384 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand All @@ -40,6 +46,7 @@ on [GitHub](https://github.com/lunit-io/benchmark-ssl-pathology/releases/). To e
MODEL_NAME=pathology/lunit_vits16
NORMALIZE_MEAN=[0.70322989,0.53606487,0.66096631] \
NORMALIZE_STD=[0.21716536,0.26081574,0.20723464] \
IN_FEATURES=384 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand All @@ -49,6 +56,7 @@ eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
MODEL_NAME=pathology/lunit_vits8 \
NORMALIZE_MEAN=[0.70322989,0.53606487,0.66096631] \
NORMALIZE_STD=[0.21716536,0.26081574,0.20723464] \
IN_FEATURES=384 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand All @@ -59,6 +67,9 @@ eva predict_fit --config configs/vision/pathology/offline/<task>.yaml

```
MODEL_NAME=pathology/owkin_phikon \
NORMALIZE_MEAN=[0.485,0.456,0.406] \
NORMALIZE_STD=[0.229,0.224,0.225] \
IN_FEATURES=768 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand All @@ -69,8 +80,10 @@ be requested.

```
MODEL_NAME=pathology/mahmood_uni \
HF_TOKEN=<your-huggingace-token-for-downloading-the-model> \
NORMALIZE_MEAN=[0.485,0.456,0.406] \
NORMALIZE_STD=[0.229,0.224,0.225] \
IN_FEATURES=1024 \
HF_TOKEN=<your-huggingace-token-for-downloading-the-model> \
eva predict_fit --config configs/vision/phikon/offline/<task>.yaml
```

Expand All @@ -83,6 +96,7 @@ and available on [GitHub](https://github.com/kaiko-ai/towards_large_pathology_fm
MODEL_NAME=pathology/kaiko_vits16 \
NORMALIZE_MEAN=[0.5,0.5,0.5] \
NORMALIZE_STD=[0.5,0.5,0.5] \
IN_FEATURES=384 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand All @@ -95,6 +109,7 @@ and available on [GitHub](https://github.com/kaiko-ai/towards_large_pathology_fm
MODEL_NAME=pathology/kaiko_vits8 \
NORMALIZE_MEAN=[0.5,0.5,0.5] \
NORMALIZE_STD=[0.5,0.5,0.5] \
IN_FEATURES=384 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```

Expand Down Expand Up @@ -156,6 +171,8 @@ To evaluate the [Prov-Gigapath](https://github.com/prov-gigapath/prov-gigapath)

```
MODEL_NAME=pathology/prov_gigapath \
NORMALIZE_MEAN=[0.485,0.456,0.406] \
NORMALIZE_STD=[0.229,0.224,0.225] \
IN_FEATURES=1536 \
eva predict_fit --config configs/vision/pathology/offline/<task>.yaml
```
Expand Down

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