From 65dde013e3cebf2e05a41e3a98f41f06971d31b1 Mon Sep 17 00:00:00 2001 From: Nicolas Kaenzig Date: Tue, 8 Oct 2024 15:25:16 +0200 Subject: [PATCH] quoted mean & std value lists --- .../advanced/replicate_evaluations.md | 60 +++++++++---------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/docs/user-guide/advanced/replicate_evaluations.md b/docs/user-guide/advanced/replicate_evaluations.md index 342cedf5..a85ae19b 100644 --- a/docs/user-guide/advanced/replicate_evaluations.md +++ b/docs/user-guide/advanced/replicate_evaluations.md @@ -19,8 +19,8 @@ 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] \ +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/.yaml ``` @@ -31,8 +31,8 @@ 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] \ +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/.yaml ``` @@ -44,8 +44,8 @@ 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] \ +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/.yaml ``` @@ -54,8 +54,8 @@ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` MODEL_NAME=pathology/lunit_vits8 \ -NORMALIZE_MEAN=[0.70322989,0.53606487,0.66096631] \ -NORMALIZE_STD=[0.21716536,0.26081574,0.20723464] \ +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/.yaml ``` @@ -67,8 +67,8 @@ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` MODEL_NAME=pathology/owkin_phikon \ -NORMALIZE_MEAN=[0.485,0.456,0.406] \ -NORMALIZE_STD=[0.229,0.224,0.225] \ +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/.yaml ``` @@ -80,8 +80,8 @@ be requested. ``` MODEL_NAME=pathology/mahmood_uni \ -NORMALIZE_MEAN=[0.485,0.456,0.406] \ -NORMALIZE_STD=[0.229,0.224,0.225] \ +NORMALIZE_MEAN="[0.485,0.456,0.406]" \ +NORMALIZE_STD="[0.229,0.224,0.225]" \ IN_FEATURES=1024 \ HF_TOKEN= \ eva predict_fit --config configs/vision/phikon/offline/.yaml @@ -94,8 +94,8 @@ 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] \ +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/.yaml ``` @@ -107,8 +107,8 @@ 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] \ +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/.yaml ``` @@ -120,8 +120,8 @@ and available on [GitHub](https://github.com/kaiko-ai/towards_large_pathology_fm ``` MODEL_NAME=pathology/kaiko_vitb16 \ -NORMALIZE_MEAN=[0.5,0.5,0.5] \ -NORMALIZE_STD=[0.5,0.5,0.5] \ +NORMALIZE_MEAN="[0.5,0.5,0.5]" \ +NORMALIZE_STD="[0.5,0.5,0.5]" \ IN_FEATURES=768 \ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` @@ -133,8 +133,8 @@ and available on [GitHub](https://github.com/kaiko-ai/towards_large_pathology_fm ``` MODEL_NAME=pathology/kaiko_vitb16 \ -NORMALIZE_MEAN=[0.5,0.5,0.5] \ -NORMALIZE_STD=[0.5,0.5,0.5] \ +NORMALIZE_MEAN="[0.5,0.5,0.5]" \ +NORMALIZE_STD="[0.5,0.5,0.5]" \ IN_FEATURES=768 \ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` @@ -146,8 +146,8 @@ and available on [GitHub](https://github.com/kaiko-ai/towards_large_pathology_fm ``` MODEL_NAME=pathology/kaiko_vitl14 \ -NORMALIZE_MEAN=[0.5,0.5,0.5] \ -NORMALIZE_STD=[0.5,0.5,0.5] \ +NORMALIZE_MEAN="[0.5,0.5,0.5]" \ +NORMALIZE_STD="[0.5,0.5,0.5]" \ IN_FEATURES=1024 \ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` @@ -159,8 +159,8 @@ were released on [HuggingFace](https://huggingface.co/bioptimus/H-optimus-0). ``` MODEL_NAME=pathology/bioptimus_h_optimus_0 \ -NORMALIZE_MEAN=[0.707223,0.578729,0.703617] \ -NORMALIZE_STD=[0.211883,0.230117,0.177517] \ +NORMALIZE_MEAN="[0.707223,0.578729,0.703617]" \ +NORMALIZE_STD="[0.211883,0.230117,0.177517]" \ IN_FEATURES=1536 \ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` @@ -171,8 +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] \ +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/.yaml ``` @@ -185,8 +185,8 @@ a proprietary dataset of one million slides, available for download on ``` MODEL_NAME=pathology/histai_hibou_b \ -NORMALIZE_MEAN=[0.7068,0.5755,0.722] \ -NORMALIZE_STD=[0.195,0.2316,0.1816] \ +NORMALIZE_MEAN="[0.7068,0.5755,0.722]" \ +NORMALIZE_STD="[0.195,0.2316,0.1816]" \ IN_FEATURES=768 \ eva predict_fit --config configs/vision/pathology/offline/.yaml ``` @@ -198,8 +198,8 @@ a proprietary dataset of one million slides, available for download on ``` MODEL_NAME=pathology/histai_hibou_l \ -NORMALIZE_MEAN=[0.7068,0.5755,0.722] \ -NORMALIZE_STD=[0.195,0.2316,0.1816] \ +NORMALIZE_MEAN="[0.7068,0.5755,0.722]" \ +NORMALIZE_STD="[0.195,0.2316,0.1816]" \ IN_FEATURES=1024 \ eva predict_fit --config configs/vision/pathology/offline/.yaml ```