diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml new file mode 100644 index 00000000..2f29c2e2 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/mpm/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/resnet50_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml new file mode 100644 index 00000000..ba6195a9 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/mpm/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml new file mode 100644 index 00000000..2513d5b3 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/mpm/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/vgg16_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml new file mode 100644 index 00000000..4db31a7b --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/mpm/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml new file mode 100644 index 00000000..473915aa --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/span/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/resnet50_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml new file mode 100644 index 00000000..8b4fc22d --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/span/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml new file mode 100644 index 00000000..904d2a9a --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/span/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/vgg16_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml new file mode 100644 index 00000000..e4d00a26 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/span/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml new file mode 100644 index 00000000..8386fc40 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/top_k/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/resnet50_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml new file mode 100644 index 00000000..bd540de0 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/top_k/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml new file mode 100644 index 00000000..a02c4080 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/top_k/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/vgg16_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml new file mode 100644 index 00000000..f8c4e5f8 --- /dev/null +++ b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/eval_estimation/top_k/base + - /data/mmci/sl_group_1@data + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - _self_ diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml new file mode 100644 index 00000000..8ac87a27 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml @@ -0,0 +1,5 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/base + - /model/checkpoints/mmci_tl/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml new file mode 100644 index 00000000..e54c70e1 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml @@ -0,0 +1,5 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/base + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..de9a5f39 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..b6081695 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml new file mode 100644 index 00000000..3b571bda --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml @@ -0,0 +1,5 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/base + - /model/checkpoints/mmci_tl/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml new file mode 100644 index 00000000..c460f2c8 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml @@ -0,0 +1,5 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/base + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..850a4f58 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..9f1aede5 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml new file mode 100644 index 00000000..d388eac1 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml new file mode 100644 index 00000000..d9d95385 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..89996763 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} +pred_column: "pred_kernel_size=6" diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..b405fece --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} +pred_column: "pred_kernel_size=1" diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml new file mode 100644 index 00000000..dabfe82f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml new file mode 100644 index 00000000..fe5e2fa9 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..3959a107 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} +pred_column: "pred_kernel_size=7" diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..1c9e7e1f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} +pred_column: "pred_kernel_size=1" diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml new file mode 100644 index 00000000..d388eac1 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml new file mode 100644 index 00000000..d9d95385 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..4450314f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} +pred_column: "pred_kernel_size=5_k=4" diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..0519fb41 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} +pred_column: "pred_kernel_size=1_k=2" diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml new file mode 100644 index 00000000..dabfe82f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml new file mode 100644 index 00000000..fe5e2fa9 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..71f48a99 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} +pred_column: "pred_kernel_size=5_k=4" diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml new file mode 100644 index 00000000..472be9d3 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml @@ -0,0 +1,9 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224 + - /data/mmci/sl_group_1@data + - _self_ + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} +pred_column: "pred_kernel_size=1_k=4" diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml new file mode 100644 index 00000000..d388eac1 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base.yaml new file mode 100644 index 00000000..2885603d --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/base + +aggregation_method: "Max" +pred_column: "prediction" +t: ${model_data.slide_max_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..07285114 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml new file mode 100644 index 00000000..84c33573 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base + - /data/mmci/tl_test@data + +preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/base.yaml new file mode 100644 index 00000000..a98f533e --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/base + +aggregation_method: "Mean Pool Max" +pred_column: "pred_kernel_size=6" +t: ${model_data.slide_mpm_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..36f5c1cf --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/base.yaml new file mode 100644 index 00000000..f2fed72f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/base + +aggregation_method: "Span" +pred_column: "pred_k=5" +t: ${model_data.slide_span_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..d337beba --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/base.yaml new file mode 100644 index 00000000..ff629be5 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/base + +aggregation_method: "Top-k" +pred_column: "pred_kernel_size=5_k=4" +t: ${model_data.slide_top_k_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..b36ad3bc --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml new file mode 100644 index 00000000..d9d95385 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base.yaml new file mode 100644 index 00000000..47a4fe86 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/base + +aggregation_method: "Max" +pred_column: "prediction" +t: ${model_data.slide_max_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..050de748 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml new file mode 100644 index 00000000..13dbd0db --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base + - /data/mmci/tl_test@data + +preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/base.yaml new file mode 100644 index 00000000..06233b06 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/base + +aggregation_method: "Mean Pool Max" +pred_column: "pred_kernel_size=1" +t: ${model_data.slide_mpm_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..a2008124 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/base.yaml new file mode 100644 index 00000000..6c68075a --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/base + +aggregation_method: "Span" +pred_column: "pred_k=5" +t: ${model_data.slide_span_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..b923102d --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/base.yaml new file mode 100644 index 00000000..91329a79 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/base + +aggregation_method: "Top-k" +pred_column: "pred_kernel_size=1_k=2" +t: ${model_data.slide_top_k_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..37ce1b31 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml new file mode 100644 index 00000000..dabfe82f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base.yaml new file mode 100644 index 00000000..c999d254 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/base + +aggregation_method: "Max" +pred_column: "prediction" +t: ${model_data.slide_max_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..b7152834 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml new file mode 100644 index 00000000..827208a6 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base + - /data/mmci/tl_test@data + +preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/base.yaml new file mode 100644 index 00000000..dc21cebc --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/base + +aggregation_method: "Mean Pool Max" +pred_column: "pred_kernel_size=7" +t: ${model_data.slide_mpm_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..4dc48cbf --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/base.yaml new file mode 100644 index 00000000..828f5aa5 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/base + +aggregation_method: "Span" +pred_column: "pred_k=5" +t: ${model_data.slide_span_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..a7d6ab62 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/base.yaml new file mode 100644 index 00000000..bbfa7fe9 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/base + +aggregation_method: "Top-k" +pred_column: "pred_kernel_size=5_k=4" +t: ${model_data.slide_top_k_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..c0a75c58 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml new file mode 100644 index 00000000..fe5e2fa9 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml @@ -0,0 +1,4 @@ +# @package _global_ + +defaults: + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base.yaml new file mode 100644 index 00000000..fcc351ec --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/base + +aggregation_method: "Max" +pred_column: "prediction" +t: ${model_data.slide_max_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..68507789 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml new file mode 100644 index 00000000..ea6f6f28 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base + - /data/mmci/tl_test@data + +preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/base.yaml new file mode 100644 index 00000000..65bd3b4f --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/base + +aggregation_method: "Mean Pool Max" +pred_column: "pred_kernel_size=1" +t: ${model_data.slide_mpm_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..0ab876d8 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/base.yaml new file mode 100644 index 00000000..d52a4823 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/base + +aggregation_method: "Span" +pred_column: "pred_k=5" +t: ${model_data.slide_span_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..58b0e796 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/base.yaml new file mode 100644 index 00000000..16a0bd9a --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/base.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/base + +aggregation_method: "Top-k" +pred_column: "pred_kernel_size=1_k=4" +t: ${model_data.slide_top_k_threshold} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml new file mode 100644 index 00000000..4b22c9b2 --- /dev/null +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/base + - /data/mmci/sl_group_1@data + +preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/predict/images/base.yaml b/configs/experiment/predict/images/base.yaml index f9d913ea..6a355729 100644 --- a/configs/experiment/predict/images/base.yaml +++ b/configs/experiment/predict/images/base.yaml @@ -8,8 +8,3 @@ defaults: datamodule: batch_size: 64 num_workers: 8 - - predict: - uris: - - ${predict_data.tiles_filtered_uri_512} - diff --git a/configs/experiment/predict/images/resnet50/base.yaml b/configs/experiment/predict/images/resnet50/base.yaml index 72164123..e61a8d50 100644 --- a/configs/experiment/predict/images/resnet50/base.yaml +++ b/configs/experiment/predict/images/resnet50/base.yaml @@ -5,3 +5,8 @@ defaults: - /model/resnet50_model@model - /model/checkpoints/mmci_tl/resnet50@model_data - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_512} diff --git a/configs/experiment/predict/images/resnet50/base_224.yaml b/configs/experiment/predict/images/resnet50/base_224.yaml new file mode 100644 index 00000000..57d18cf7 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/base + - /model/resnet50_model@model + - /model/checkpoints/mmci_tl/resnet50_224@model_data + - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_224} diff --git a/configs/experiment/predict/images/resnet50/mpm_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/resnet50/mpm_estimation.yaml rename to configs/experiment/predict/images/resnet50/estimations/mpm_estimation.yaml diff --git a/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml new file mode 100644 index 00000000..7becb63b --- /dev/null +++ b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml @@ -0,0 +1,20 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/resnet50/base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.MeanPoolMaxAggregator + + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5, 6, 7] + +use_case: "Kernel Size Estimation (MPM Aggregator)" + diff --git a/configs/experiment/predict/images/resnet50/span_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/span_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/resnet50/span_estimation.yaml rename to configs/experiment/predict/images/resnet50/estimations/span_estimation.yaml diff --git a/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml new file mode 100644 index 00000000..8aa88a5e --- /dev/null +++ b/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/resnet50/base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + static: + extent_tile: 224 + stride_tile: 112 + cell_threshold: ${model_data.tile_threshold} + to_estimate: + k: [2, 3, 4, 5] + +use_case: "K Estimation (Span Aggregator)" diff --git a/configs/experiment/predict/images/resnet50/stain_mpm_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/resnet50/stain_mpm_estimation.yaml rename to configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation.yaml diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml new file mode 100644 index 00000000..c7a53eb4 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml @@ -0,0 +1,20 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/resnet50/stain_base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.MeanPoolMaxAggregator + + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5, 6, 7] + +use_case: "Kernel Size Estimation (MPM Aggregator)" + diff --git a/configs/experiment/predict/images/resnet50/stain_span_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/resnet50/stain_span_estimation.yaml rename to configs/experiment/predict/images/resnet50/estimations/stain_span_estimation.yaml diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml new file mode 100644 index 00000000..e532684a --- /dev/null +++ b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/resnet50/stain_base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + static: + extent_tile: 224 + stride_tile: 112 + cell_threshold: ${model_data.tile_threshold} + to_estimate: + k: [2, 3, 4, 5] + +use_case: "K Estimation (Span Aggregator)" diff --git a/configs/experiment/predict/images/resnet50/stain_top_k_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/resnet50/stain_top_k_estimation.yaml rename to configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation.yaml diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml new file mode 100644 index 00000000..f057b7f1 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/resnet50/stain_base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.TopKAggregator + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5] + k: [2, 3, 4] + +use_case: "Kernel Size & K Estimation (Top K Aggregator)" diff --git a/configs/experiment/predict/images/resnet50/top_k_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/resnet50/top_k_estimation.yaml rename to configs/experiment/predict/images/resnet50/estimations/top_k_estimation.yaml diff --git a/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml new file mode 100644 index 00000000..4c406a33 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/resnet50/base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.TopKAggregator + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5] + k: [2, 3, 4] + +use_case: "Kernel Size & K Estimation (Top K Aggregator)" diff --git a/configs/experiment/predict/images/resnet50/heatmaps/base_224.yaml b/configs/experiment/predict/images/resnet50/heatmaps/base_224.yaml new file mode 100644 index 00000000..dc08bd8c --- /dev/null +++ b/configs/experiment/predict/images/resnet50/heatmaps/base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/resnet50/base_224 + - /callbacks/heatmap@callbacks + - _self_ + +use_case: "Heatmaps" diff --git a/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml b/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml new file mode 100644 index 00000000..236de55a --- /dev/null +++ b/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/resnet50/heatmaps/base_224 + - /data/mmci/tl_val@predict_data + - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps/stain_base_224.yaml b/configs/experiment/predict/images/resnet50/heatmaps/stain_base_224.yaml new file mode 100644 index 00000000..02380023 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/heatmaps/stain_base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/resnet50/stain_base_224 + - /callbacks/heatmap@callbacks + - _self_ + +use_case: "Heatmaps" diff --git a/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml b/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml new file mode 100644 index 00000000..3f925e49 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/resnet50/heatmaps/stain_base_224 + - /data/mmci/tl_val@predict_data + - _self_ diff --git a/configs/experiment/predict/images/resnet50/stain_base.yaml b/configs/experiment/predict/images/resnet50/stain_base.yaml index ffbde6eb..c700662b 100644 --- a/configs/experiment/predict/images/resnet50/stain_base.yaml +++ b/configs/experiment/predict/images/resnet50/stain_base.yaml @@ -5,3 +5,8 @@ defaults: - /model/resnet50_model@model - /model/checkpoints/mmci_tl/resnet50_stain@model_data - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_512} diff --git a/configs/experiment/predict/images/resnet50/stain_base_224.yaml b/configs/experiment/predict/images/resnet50/stain_base_224.yaml new file mode 100644 index 00000000..214cb1b3 --- /dev/null +++ b/configs/experiment/predict/images/resnet50/stain_base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/base + - /model/resnet50_model@model + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_224} diff --git a/configs/experiment/predict/images/vgg16/base.yaml b/configs/experiment/predict/images/vgg16/base.yaml index 4165e069..7e2c7086 100644 --- a/configs/experiment/predict/images/vgg16/base.yaml +++ b/configs/experiment/predict/images/vgg16/base.yaml @@ -5,3 +5,8 @@ defaults: - /model/vgg16_model@model - /model/checkpoints/mmci_tl/vgg16@model_data - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_512} diff --git a/configs/experiment/predict/images/vgg16/base_224.yaml b/configs/experiment/predict/images/vgg16/base_224.yaml new file mode 100644 index 00000000..2262e324 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/base + - /model/vgg16_model@model + - /model/checkpoints/mmci_tl/vgg16_224@model_data + - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_224} diff --git a/configs/experiment/predict/images/vgg16/mpm_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/vgg16/mpm_estimation.yaml rename to configs/experiment/predict/images/vgg16/estimations/mpm_estimation.yaml diff --git a/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml new file mode 100644 index 00000000..3ec1b3e4 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml @@ -0,0 +1,20 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/vgg16/base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.MeanPoolMaxAggregator + + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5, 6, 7] + +use_case: "Kernel Size Estimation (MPM Aggregator)" + diff --git a/configs/experiment/predict/images/vgg16/span_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/span_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/vgg16/span_estimation.yaml rename to configs/experiment/predict/images/vgg16/estimations/span_estimation.yaml diff --git a/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml new file mode 100644 index 00000000..99a8ddf8 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/vgg16/base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + static: + extent_tile: 224 + stride_tile: 112 + cell_threshold: ${model_data.tile_threshold} + to_estimate: + k: [2, 3, 4, 5] + +use_case: "K Estimation (Span Aggregator)" diff --git a/configs/experiment/predict/images/vgg16/stain_mpm_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/vgg16/stain_mpm_estimation.yaml rename to configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation.yaml diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml new file mode 100644 index 00000000..f3e7d01d --- /dev/null +++ b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml @@ -0,0 +1,20 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/vgg16/stain_base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.MeanPoolMaxAggregator + + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5, 6, 7] + +use_case: "Kernel Size Estimation (MPM Aggregator)" + diff --git a/configs/experiment/predict/images/vgg16/stain_span_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/vgg16/stain_span_estimation.yaml rename to configs/experiment/predict/images/vgg16/estimations/stain_span_estimation.yaml diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml new file mode 100644 index 00000000..0c7db32d --- /dev/null +++ b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/vgg16/stain_base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + static: + extent_tile: 224 + stride_tile: 112 + cell_threshold: ${model_data.tile_threshold} + to_estimate: + k: [2, 3, 4, 5] + +use_case: "K Estimation (Span Aggregator)" diff --git a/configs/experiment/predict/images/vgg16/stain_top_k_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/vgg16/stain_top_k_estimation.yaml rename to configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation.yaml diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml new file mode 100644 index 00000000..eae21493 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/vgg16/stain_base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.TopKAggregator + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5] + k: [2, 3, 4] + +use_case: "Kernel Size & K Estimation (Top K Aggregator)" diff --git a/configs/experiment/predict/images/vgg16/top_k_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation.yaml similarity index 100% rename from configs/experiment/predict/images/vgg16/top_k_estimation.yaml rename to configs/experiment/predict/images/vgg16/estimations/top_k_estimation.yaml diff --git a/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml new file mode 100644 index 00000000..97217c4b --- /dev/null +++ b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml @@ -0,0 +1,19 @@ +# @package _global_ + +defaults: + - /callbacks/aggregator_estimation@callbacks + - /experiment/predict/images/vgg16/base_224 + - /data/mmci/sl_group_1@predict_data + - _self_ + +callbacks: + estimation_callback: + aggregator_cls_path: rationai.mlkit.metrics.TopKAggregator + static: + extent_tile: 224 + stride_tile: 112 + to_estimate: + kernel_size: [1, 2, 3, 4, 5] + k: [2, 3, 4] + +use_case: "Kernel Size & K Estimation (Top K Aggregator)" diff --git a/configs/experiment/predict/images/vgg16/heatmaps/base_224.yaml b/configs/experiment/predict/images/vgg16/heatmaps/base_224.yaml new file mode 100644 index 00000000..8fad03ef --- /dev/null +++ b/configs/experiment/predict/images/vgg16/heatmaps/base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/vgg16/base_224 + - /callbacks/heatmap@callbacks + - _self_ + +use_case: "Heatmaps" diff --git a/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml b/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml new file mode 100644 index 00000000..40109d33 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/vgg16/heatmaps/base_224 + - /data/mmci/tl_val@predict_data + - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps/stain_base_224.yaml b/configs/experiment/predict/images/vgg16/heatmaps/stain_base_224.yaml new file mode 100644 index 00000000..00680527 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/heatmaps/stain_base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/vgg16/stain_base_224 + - /callbacks/heatmap@callbacks + - _self_ + +use_case: "Heatmaps" diff --git a/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml b/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml new file mode 100644 index 00000000..07257527 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/vgg16/heatmaps/stain_base_224 + - /data/mmci/tl_val@predict_data + - _self_ diff --git a/configs/experiment/predict/images/vgg16/stain_base.yaml b/configs/experiment/predict/images/vgg16/stain_base.yaml index 308d2f1d..20782b52 100644 --- a/configs/experiment/predict/images/vgg16/stain_base.yaml +++ b/configs/experiment/predict/images/vgg16/stain_base.yaml @@ -5,3 +5,8 @@ defaults: - /model/vgg16_model@model - /model/checkpoints/mmci_tl/vgg16_stain@model_data - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_512} diff --git a/configs/experiment/predict/images/vgg16/stain_base_224.yaml b/configs/experiment/predict/images/vgg16/stain_base_224.yaml new file mode 100644 index 00000000..792aca11 --- /dev/null +++ b/configs/experiment/predict/images/vgg16/stain_base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/predict/images/base + - /model/vgg16_model@model + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - _self_ + +datamodule: + predict: + uris: + - ${predict_data.tiles_filtered_uri_224} diff --git a/configs/experiment/test/images/base.yaml b/configs/experiment/test/images/base.yaml index 803cda61..7f93f311 100644 --- a/configs/experiment/test/images/base.yaml +++ b/configs/experiment/test/images/base.yaml @@ -8,7 +8,3 @@ defaults: datamodule: batch_size: 64 num_workers: 8 - - test: - uris: - - ${test_data.tiles_filtered_uri_512} \ No newline at end of file diff --git a/configs/experiment/test/images/resnet50/base.yaml b/configs/experiment/test/images/resnet50/base.yaml index 070ed49f..76e4816d 100644 --- a/configs/experiment/test/images/resnet50/base.yaml +++ b/configs/experiment/test/images/resnet50/base.yaml @@ -5,3 +5,8 @@ defaults: - /model/resnet50_model@model - /model/checkpoints/mmci_tl/resnet50@model_data - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_512} diff --git a/configs/experiment/test/images/resnet50/base_224.yaml b/configs/experiment/test/images/resnet50/base_224.yaml new file mode 100644 index 00000000..f69ae438 --- /dev/null +++ b/configs/experiment/test/images/resnet50/base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/test/images/base + - /model/resnet50_model@model + - /model/checkpoints/mmci_tl/resnet50_224@model_data + - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_224} diff --git a/configs/experiment/test/images/resnet50/stain_base.yaml b/configs/experiment/test/images/resnet50/stain_base.yaml index 4e0be257..d8a52f6d 100644 --- a/configs/experiment/test/images/resnet50/stain_base.yaml +++ b/configs/experiment/test/images/resnet50/stain_base.yaml @@ -5,3 +5,8 @@ defaults: - /model/resnet50_model@model - /model/checkpoints/mmci_tl/resnet50_stain@model_data - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_512} diff --git a/configs/experiment/test/images/resnet50/stain_base_224.yaml b/configs/experiment/test/images/resnet50/stain_base_224.yaml new file mode 100644 index 00000000..04d57f7c --- /dev/null +++ b/configs/experiment/test/images/resnet50/stain_base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/test/images/base + - /model/resnet50_model@model + - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_224} diff --git a/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml b/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml new file mode 100644 index 00000000..5e8a0883 --- /dev/null +++ b/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml @@ -0,0 +1,14 @@ +# @package _global_ + +defaults: + - /callbacks/tile_threshold@callbacks + - /experiment/test/images/resnet50/stain_base_224 + - /data/mmci/tl_val@test_data + - _self_ + +datamodule: + test: + stratified_filter: true # tile threshold not estimated from negative tiles in positive slides + +tile_threshold: 0.8 # Pathologist's estimate +use_case: "Tile Threshold Estimation" diff --git a/configs/experiment/test/images/resnet50/test_suite/base_224.yaml b/configs/experiment/test/images/resnet50/test_suite/base_224.yaml new file mode 100644 index 00000000..41756bbe --- /dev/null +++ b/configs/experiment/test/images/resnet50/test_suite/base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /callbacks/combined_test_suite@callbacks + - /experiment/test/images/resnet50/base_224 + - _self_ + +use_case: "TL Test" diff --git a/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml b/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml new file mode 100644 index 00000000..fe006f05 --- /dev/null +++ b/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/test/images/resnet50/test_suite/base_224 + - /data/mmci/tl_test@test_data + - _self_ diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_base_224.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_base_224.yaml new file mode 100644 index 00000000..4c100cd6 --- /dev/null +++ b/configs/experiment/test/images/resnet50/test_suite/stain_base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /callbacks/combined_test_suite@callbacks + - /experiment/test/images/resnet50/stain_base_224 + - _self_ + +use_case: "TL Test" diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml new file mode 100644 index 00000000..92ebcecc --- /dev/null +++ b/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/test/images/resnet50/test_suite/stain_base_224 + - /data/mmci/tl_test@test_data + - _self_ diff --git a/configs/experiment/test/images/resnet50/tile_threshold_224.yaml b/configs/experiment/test/images/resnet50/tile_threshold_224.yaml new file mode 100644 index 00000000..65a1482e --- /dev/null +++ b/configs/experiment/test/images/resnet50/tile_threshold_224.yaml @@ -0,0 +1,14 @@ +# @package _global_ + +defaults: + - /callbacks/tile_threshold@callbacks + - /experiment/test/images/resnet50/base_224 + - /data/mmci/tl_val@test_data + - _self_ + +datamodule: + test: + stratified_filter: true # tile threshold not estimated from negative tiles in positive slides + +tile_threshold: 0.9 # Pathologist's estimate +use_case: "Tile Threshold Estimation" diff --git a/configs/experiment/test/images/vgg16/base.yaml b/configs/experiment/test/images/vgg16/base.yaml index 4f8d4beb..589951af 100644 --- a/configs/experiment/test/images/vgg16/base.yaml +++ b/configs/experiment/test/images/vgg16/base.yaml @@ -6,3 +6,7 @@ defaults: - /model/checkpoints/mmci_tl/vgg16@model_data - _self_ +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_512} diff --git a/configs/experiment/test/images/vgg16/base_224.yaml b/configs/experiment/test/images/vgg16/base_224.yaml new file mode 100644 index 00000000..0c243799 --- /dev/null +++ b/configs/experiment/test/images/vgg16/base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/test/images/base + - /model/vgg16_model@model + - /model/checkpoints/mmci_tl/vgg16_224@model_data + - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_224} diff --git a/configs/experiment/test/images/vgg16/stain_base.yaml b/configs/experiment/test/images/vgg16/stain_base.yaml index 6ab40e7e..5fa31c6b 100644 --- a/configs/experiment/test/images/vgg16/stain_base.yaml +++ b/configs/experiment/test/images/vgg16/stain_base.yaml @@ -5,3 +5,8 @@ defaults: - /model/vgg16_model@model - /model/checkpoints/mmci_tl/vgg16_stain@model_data - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_512} diff --git a/configs/experiment/test/images/vgg16/stain_base_224.yaml b/configs/experiment/test/images/vgg16/stain_base_224.yaml new file mode 100644 index 00000000..b0ccf0f1 --- /dev/null +++ b/configs/experiment/test/images/vgg16/stain_base_224.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /experiment/test/images/base + - /model/vgg16_model@model + - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - _self_ + +datamodule: + test: + uris: + - ${test_data.tiles_filtered_uri_224} diff --git a/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml b/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml new file mode 100644 index 00000000..60a3fba5 --- /dev/null +++ b/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml @@ -0,0 +1,14 @@ +# @package _global_ + +defaults: + - /callbacks/tile_threshold@callbacks + - /experiment/test/images/vgg16/stain_base_224 + - /data/mmci/tl_val@test_data + - _self_ + +datamodule: + test: + stratified_filter: true # tile threshold not estimated from negative tiles in positive slides + +tile_threshold: 0.8 # Pathologist's estimate +use_case: "Tile Threshold Estimation" diff --git a/configs/experiment/test/images/vgg16/test_suite/base_224.yaml b/configs/experiment/test/images/vgg16/test_suite/base_224.yaml new file mode 100644 index 00000000..ad5b6bc0 --- /dev/null +++ b/configs/experiment/test/images/vgg16/test_suite/base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /callbacks/combined_test_suite@callbacks + - /experiment/test/images/vgg16/base_224 + - _self_ + +use_case: "TL Test" diff --git a/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml b/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml new file mode 100644 index 00000000..48860f1c --- /dev/null +++ b/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/test/images/vgg16/test_suite/base_224 + - /data/mmci/tl_test@test_data + - _self_ diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_base_224.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_base_224.yaml new file mode 100644 index 00000000..2473fd0c --- /dev/null +++ b/configs/experiment/test/images/vgg16/test_suite/stain_base_224.yaml @@ -0,0 +1,8 @@ +# @package _global_ + +defaults: + - /callbacks/combined_test_suite@callbacks + - /experiment/test/images/vgg16/stain_base_224 + - _self_ + +use_case: "TL Test" diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml new file mode 100644 index 00000000..5b5c9ed7 --- /dev/null +++ b/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /experiment/test/images/vgg16/test_suite/stain_base_224 + - /data/mmci/tl_test@test_data + - _self_ diff --git a/configs/experiment/test/images/vgg16/tile_threshold_224.yaml b/configs/experiment/test/images/vgg16/tile_threshold_224.yaml new file mode 100644 index 00000000..45f714a9 --- /dev/null +++ b/configs/experiment/test/images/vgg16/tile_threshold_224.yaml @@ -0,0 +1,14 @@ +# @package _global_ + +defaults: + - /callbacks/tile_threshold@callbacks + - /experiment/test/images/vgg16/base_224 + - /data/mmci/tl_val@test_data + - _self_ + +datamodule: + test: + stratified_filter: true # tile threshold not estimated from negative tiles in positive slides + +tile_threshold: 0.9 # Pathologist's estimate +use_case: "Tile Threshold Estimation" diff --git a/configs/experiment/train/images/resnet50/base_224.yaml b/configs/experiment/train/images/resnet50/base_224.yaml new file mode 100644 index 00000000..f2eee477 --- /dev/null +++ b/configs/experiment/train/images/resnet50/base_224.yaml @@ -0,0 +1,17 @@ +# @package _global_ + +defaults: + - /experiment/train/images/base + - /datamodule/transforms/normalize_w_augments@transforms + - /model/resnet50_model@model + - _self_ + +model_name: "ResNet50 (224x224)" + +datamodule: + train: + uris: + - ${train_data.tiles_filtered_uri_224} + val: + uris: + - ${val_data.tiles_filtered_uri_224} diff --git a/configs/experiment/train/images/resnet50/base_stain_224.yaml b/configs/experiment/train/images/resnet50/base_stain_224.yaml new file mode 100644 index 00000000..d0a9ab98 --- /dev/null +++ b/configs/experiment/train/images/resnet50/base_stain_224.yaml @@ -0,0 +1,17 @@ +# @package _global_ + +defaults: + - /experiment/train/images/base + - /datamodule/transforms/normalize_w_stain_augments@transforms + - /model/resnet50_model@model + - _self_ + +model_name: "ResNet50 Stain (224x224)" + +datamodule: + train: + uris: + - ${train_data.tiles_filtered_uri_224} + val: + uris: + - ${val_data.tiles_filtered_uri_224} diff --git a/configs/experiment/train/images/resnet50/mmci_224.yaml b/configs/experiment/train/images/resnet50/mmci_224.yaml new file mode 100644 index 00000000..f5c06567 --- /dev/null +++ b/configs/experiment/train/images/resnet50/mmci_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/train/images/resnet50/base_224 + - /data/mmci/tl_train@train_data + - /data/mmci/tl_val@val_data + - _self_ diff --git a/configs/experiment/train/images/resnet50/mmci_stain_224.yaml b/configs/experiment/train/images/resnet50/mmci_stain_224.yaml new file mode 100644 index 00000000..14a400c0 --- /dev/null +++ b/configs/experiment/train/images/resnet50/mmci_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/train/images/resnet50/base_stain_224 + - /data/mmci/tl_train@train_data + - /data/mmci/tl_val@val_data + - _self_ diff --git a/configs/experiment/train/images/vgg16/base_224.yaml b/configs/experiment/train/images/vgg16/base_224.yaml new file mode 100644 index 00000000..28986510 --- /dev/null +++ b/configs/experiment/train/images/vgg16/base_224.yaml @@ -0,0 +1,17 @@ +# @package _global_ + +defaults: + - /experiment/train/images/base + - /datamodule/transforms/normalize_w_augments@transforms + - /model/vgg16_model@model + - _self_ + +model_name: "VGG-16 (224x224)" + +datamodule: + train: + uris: + - ${train_data.tiles_filtered_uri_224} + val: + uris: + - ${val_data.tiles_filtered_uri_224} diff --git a/configs/experiment/train/images/vgg16/base_stain_224.yaml b/configs/experiment/train/images/vgg16/base_stain_224.yaml new file mode 100644 index 00000000..994d5e18 --- /dev/null +++ b/configs/experiment/train/images/vgg16/base_stain_224.yaml @@ -0,0 +1,17 @@ +# @package _global_ + +defaults: + - /experiment/train/images/base + - /datamodule/transforms/normalize_w_stain_augments@transforms + - /model/vgg16_model@model + - _self_ + +model_name: "VGG-16 Stain (224x224)" + +datamodule: + train: + uris: + - ${train_data.tiles_filtered_uri_224} + val: + uris: + - ${val_data.tiles_filtered_uri_224} diff --git a/configs/experiment/train/images/vgg16/mmci_224.yaml b/configs/experiment/train/images/vgg16/mmci_224.yaml new file mode 100644 index 00000000..95128f7b --- /dev/null +++ b/configs/experiment/train/images/vgg16/mmci_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/train/images/vgg16/base_224 + - /data/mmci/tl_train@train_data + - /data/mmci/tl_val@val_data + - _self_ diff --git a/configs/experiment/train/images/vgg16/mmci_stain_224.yaml b/configs/experiment/train/images/vgg16/mmci_stain_224.yaml new file mode 100644 index 00000000..86c9ad80 --- /dev/null +++ b/configs/experiment/train/images/vgg16/mmci_stain_224.yaml @@ -0,0 +1,7 @@ +# @package _global_ + +defaults: + - /experiment/train/images/vgg16/base_stain_224 + - /data/mmci/tl_train@train_data + - /data/mmci/tl_val@val_data + - _self_ diff --git a/configs/model/checkpoints/mmci_tl/resnet50_224.yaml b/configs/model/checkpoints/mmci_tl/resnet50_224.yaml new file mode 100644 index 00000000..efa9c5b4 --- /dev/null +++ b/configs/model/checkpoints/mmci_tl/resnet50_224.yaml @@ -0,0 +1,23 @@ +defaults: + - base + - _self_ + +tile_threshold: 0.82 +slide_max_threshold: 0.9999972582 +slide_mpm_threshold: 0.9702595472 +slide_top_k_threshold: 0.9961571097 +slide_span_threshold: 0.5 # arbitrary - span predictions are binary + +checkpoint: "mlflow-artifacts:/65/d9bd39a0207c4b9484ad92574c50b503/artifacts/checkpoints/epoch=0-step=13889/checkpoint.ckpt" +public_checkpoint: "mlflow-artifacts:/38/abde571304794242be0c1630b7bd16ce/artifacts/resnet50_checkpoint.ckpt" + +model_name: "ResNet50 (224x224)" +slide_level_prediction_uris: + mean_pool_max: + mmci_sl_group_1: "mlflow-artifacts:/65/e87e9b41dfaf4a878069af2045f164ef/artifacts/tables/aggregated_predictions.json" + max: + mmci_sl_group_1: "mlflow-artifacts:/65/098f0fb5aad246389e39bfd2265247a4/artifacts/tables/aggregated_predictions.json" + top_k: + mmci_sl_group_1: "mlflow-artifacts:/65/f79c58db2f9f48148a61c9948bd04541/artifacts/tables/aggregated_predictions.json" + span: + mmci_sl_group_1: "mlflow-artifacts:/65/423dd217a0b94fbabaee1e1bdda156d8/artifacts/tables/aggregated_predictions.json" diff --git a/configs/model/checkpoints/mmci_tl/resnet50_stain_224.yaml b/configs/model/checkpoints/mmci_tl/resnet50_stain_224.yaml new file mode 100644 index 00000000..f59017ca --- /dev/null +++ b/configs/model/checkpoints/mmci_tl/resnet50_stain_224.yaml @@ -0,0 +1,23 @@ +defaults: + - base + - _self_ + +tile_threshold: 0.85 +slide_max_threshold: 0.9999930859 +slide_mpm_threshold: 0.9998937845 +slide_top_k_threshold: 0.9998824596 +slide_span_threshold: 0.5 # arbitrary - span predictions are binary + +checkpoint: "mlflow-artifacts:/65/80543b4ec2d14ca48384e6d52a7418fb/artifacts/checkpoints/epoch=0-step=55556/checkpoint.ckpt" +public_checkpoint: "mlflow-artifacts:/38/abde571304794242be0c1630b7bd16ce/artifacts/resnet50_stain_checkpoint.ckpt" + +model_name: "ResNet50 Stain (224x224)" +slide_level_prediction_uris: + mean_pool_max: + mmci_sl_group_1: "mlflow-artifacts:/65/a6e128babae44dab9d2785624e0107a0/artifacts/tables/aggregated_predictions.json" + max: + mmci_sl_group_1: "mlflow-artifacts:/65/eec60275b3c247a2b8fc486d1a46aa6f/artifacts/tables/aggregated_predictions.json" + top_k: + mmci_sl_group_1: "mlflow-artifacts:/65/d97f25bcecc24ad8bd223b3ae0af970f/artifacts/tables/aggregated_predictions.json" + span: + mmci_sl_group_1: "mlflow-artifacts:/65/254fc6852ea845c1b11d799e5d24d947/artifacts/tables/aggregated_predictions.json" diff --git a/configs/model/checkpoints/mmci_tl/vgg16_224.yaml b/configs/model/checkpoints/mmci_tl/vgg16_224.yaml new file mode 100644 index 00000000..993ba92f --- /dev/null +++ b/configs/model/checkpoints/mmci_tl/vgg16_224.yaml @@ -0,0 +1,23 @@ +defaults: + - base + - _self_ + +tile_threshold: 0.96 +slide_max_threshold: 0.999999999 +slide_mpm_threshold: 0.9995754957 +slide_top_k_threshold: 0.9999379516 +slide_span_threshold: 0.5 # arbitrary - span predictions are binary + +checkpoint: "mlflow-artifacts:/65/2b4986681bb24e1abd85a9108a7a49bb/artifacts/checkpoints/epoch=1-step=97226/checkpoint.ckpt" +public_checkpoint: "mlflow-artifacts:/38/abde571304794242be0c1630b7bd16ce/artifacts/vgg16_checkpoint.ckpt" + +model_name: "VGG-16 (224x224)" +slide_level_prediction_uris: + mean_pool_max: + mmci_sl_group_1: "mlflow-artifacts:/65/8ee0c7d3c61d46acad41262ce6a065ec/artifacts/tables/aggregated_predictions.json" + max: + mmci_sl_group_1: "mlflow-artifacts:/65/8b607e5204f548d28d11ac392fd4a835/artifacts/tables/aggregated_predictions.json" + top_k: + mmci_sl_group_1: "mlflow-artifacts:/65/17b3a4b3c9bc420ca4fff7c185063f36/artifacts/tables/aggregated_predictions.json" + span: + mmci_sl_group_1: "mlflow-artifacts:/65/ce1bdc240623403aa45cca7465d47b29/artifacts/tables/aggregated_predictions.json" diff --git a/configs/model/checkpoints/mmci_tl/vgg16_stain_224.yaml b/configs/model/checkpoints/mmci_tl/vgg16_stain_224.yaml new file mode 100644 index 00000000..912791ca --- /dev/null +++ b/configs/model/checkpoints/mmci_tl/vgg16_stain_224.yaml @@ -0,0 +1,24 @@ +defaults: + - base + - _self_ + +tile_threshold: 0.93 +slide_max_threshold: 0.999835372 +slide_mpm_threshold: 0.999294281 +slide_top_k_threshold: 0.9988395572 +slide_span_threshold: 0.5 # arbitrary - span predictions are binary + +checkpoint: "mlflow-artifacts:/65/98e0d43027664084aef1beebaeac7fff/artifacts/checkpoints/epoch=1-step=111115/checkpoint.ckpt" +public_checkpoint: "mlflow-artifacts:/38/abde571304794242be0c1630b7bd16ce/artifacts/vgg16_stain_checkpoint.ckpt" + + +model_name: "VGG-16 Stain (224x224)" +slide_level_prediction_uris: + mean_pool_max: + mmci_sl_group_1: "mlflow-artifacts:/65/b7a34bdffb2b4f729b5c8ce98d9921ce/artifacts/tables/aggregated_predictions.json" + max: + mmci_sl_group_1: "mlflow-artifacts:/65/a7495ce0ac2b4fb99d0cc55e912a970c/artifacts/tables/aggregated_predictions.json" + top_k: + mmci_sl_group_1: "mlflow-artifacts:/65/2bf6522353e34344aed0222c346f7230/artifacts/tables/aggregated_predictions.json" + span: + mmci_sl_group_1: "mlflow-artifacts:/65/a392285e4bde413bb8bf03e03d921d71/artifacts/tables/aggregated_predictions.json" diff --git a/notebooks/eval/non_inferiority.ipynb b/notebooks/eval/non_inferiority.ipynb index dd6c7a45..e2e25338 100644 --- a/notebooks/eval/non_inferiority.ipynb +++ b/notebooks/eval/non_inferiority.ipynb @@ -170,6 +170,78 @@ " \"pred_k=3\",\n", " ),\n", " },\n", + " \"resnet50_224\": {\n", + " \"max\": (\n", + " \"mlflow-artifacts:/65/098f0fb5aad246389e39bfd2265247a4/artifacts/tables/aggregated_predictions.json\",\n", + " \"prediction\",\n", + " ),\n", + " \"mpm\": (\n", + " \"mlflow-artifacts:/65/e87e9b41dfaf4a878069af2045f164ef/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=6\",\n", + " ),\n", + " \"topk\": (\n", + " \"mlflow-artifacts:/65/f79c58db2f9f48148a61c9948bd04541/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=5_k=4\",\n", + " ),\n", + " \"span\": (\n", + " \"mlflow-artifacts:/65/423dd217a0b94fbabaee1e1bdda156d8/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_k=5\",\n", + " ),\n", + " },\n", + " \"resnet50_stain_224\": {\n", + " \"max\": (\n", + " \"mlflow-artifacts:/65/eec60275b3c247a2b8fc486d1a46aa6f/artifacts/tables/aggregated_predictions.json\",\n", + " \"prediction\",\n", + " ),\n", + " \"mpm\": (\n", + " \"mlflow-artifacts:/65/a6e128babae44dab9d2785624e0107a0/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=1\",\n", + " ),\n", + " \"topk\": (\n", + " \"mlflow-artifacts:/65/d97f25bcecc24ad8bd223b3ae0af970f/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=1_k=2\",\n", + " ),\n", + " \"span\": (\n", + " \"mlflow-artifacts:/65/254fc6852ea845c1b11d799e5d24d947/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_k=5\",\n", + " ),\n", + " },\n", + " \"vgg16_224\": {\n", + " \"max\": (\n", + " \"mlflow-artifacts:/65/8b607e5204f548d28d11ac392fd4a835/artifacts/tables/aggregated_predictions.json\",\n", + " \"prediction\",\n", + " ),\n", + " \"mpm\": (\n", + " \"mlflow-artifacts:/65/8ee0c7d3c61d46acad41262ce6a065ec/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=7\",\n", + " ),\n", + " \"topk\": (\n", + " \"mlflow-artifacts:/65/17b3a4b3c9bc420ca4fff7c185063f36/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=5_k=4\",\n", + " ),\n", + " \"span\": (\n", + " \"mlflow-artifacts:/65/ce1bdc240623403aa45cca7465d47b29/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_k=5\",\n", + " ),\n", + " },\n", + " \"vgg16_stain_224\": {\n", + " \"max\": (\n", + " \"mlflow-artifacts:/65/a7495ce0ac2b4fb99d0cc55e912a970c/artifacts/tables/aggregated_predictions.json\",\n", + " \"prediction\",\n", + " ),\n", + " \"mpm\": (\n", + " \"mlflow-artifacts:/65/b7a34bdffb2b4f729b5c8ce98d9921ce/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=1\",\n", + " ),\n", + " \"topk\": (\n", + " \"mlflow-artifacts:/65/2bf6522353e34344aed0222c346f7230/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_kernel_size=1_k=4\",\n", + " ),\n", + " \"span\": (\n", + " \"mlflow-artifacts:/65/a392285e4bde413bb8bf03e03d921d71/artifacts/tables/aggregated_predictions.json\",\n", + " \"pred_k=5\",\n", + " ),\n", + " },\n", " \"gvit\": {\n", " \"max\": (\n", " \"mlflow-artifacts:/65/14059f41cc864b84b0c45a8967150b4a/artifacts/tables/aggregated_predictions.json\",\n", @@ -229,46 +301,62 @@ "name": "stderr", "output_type": "stream", "text": [ - "Downloading artifacts: 100%|██████████| 1/1 [00:00<00:00, 53.89it/s]\n", - "Downloading artifacts: 100%|██████████| 1/1 [00:00<00:00, 43.36it/s]\n", - "Downloading artifacts: 100%|██████████| 1/1 [00:00<00:00, 40.78it/s]\n", - "Downloading artifacts: 100%|██████████| 1/1 [00:00<00:00, 50.16it/s]\n", - "Downloading artifacts: 100%|██████████| 1/1 [00:00<00:00, 48.69it/s]\n", - 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return mlflow.artifacts.download_artifacts(uri)\n", "\n", "\n", - "assert len(DATA) == 10 # 10 models\n", + "assert len(DATA) == 14 # 14 models\n", "\n", "for model_name, methods in DATA.items():\n", " assert len(methods) == 4 # 4 aggr. methods\n", @@ -458,6 +546,10 @@ "resnet50_stain_df = evaluate_single_model(master_df, \"resnet50_stain\", margin)\n", "vgg16_df = evaluate_single_model(master_df, \"vgg16\", margin)\n", "vgg16_stain_df = evaluate_single_model(master_df, \"vgg16_stain\", margin)\n", + "resnet50_224_df = evaluate_single_model(master_df, \"resnet50_224\", margin)\n", + "resnet50_stain_224_df = evaluate_single_model(master_df, \"resnet50_stain_224\", margin)\n", + "vgg16_224_df = evaluate_single_model(master_df, \"vgg16_224\", margin)\n", + "vgg16_stain_224_df = evaluate_single_model(master_df, \"vgg16_stain_224\", margin)\n", "gvit_df = evaluate_single_model(master_df, \"gvit\", margin)\n", "gvit_stain_df = evaluate_single_model(master_df, \"gvit_stain\", margin)" ] @@ -827,7 +919,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 11, "id": "6ebe9ce8-e139-4092-b555-b838be8af66b", "metadata": {}, "outputs": [ @@ -908,7 +1000,7 @@ "2 span " ] }, - "execution_count": 9, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -919,7 +1011,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 12, "id": "ec92f096-2f05-495b-aac9-4b66bd26f2f1", "metadata": {}, "outputs": [ @@ -1000,7 +1092,7 @@ "2 resnet50_stain span " ] }, - "execution_count": 10, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } @@ -1011,7 +1103,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 13, "id": "10af5800-e5c7-49e4-8b64-ded5ad423a37", "metadata": {}, "outputs": [ @@ -1087,7 +1179,7 @@ "2 -0.040223 -0.061173 -0.021482 -0.024334 True vgg16 span" ] }, - "execution_count": 11, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -1098,7 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mean_deltaci_95_lowerci_95_upperupper_95non_inferiormodelmethod
00.0452470.0169510.0737680.069177Falseresnet50_224mpm
10.0441700.0169000.0717390.066910Falseresnet50_224topk
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mean_deltaci_95_lowerci_95_upperupper_95non_inferiormodelmethod
0-0.008204-0.0204030.0034670.001623Trueresnet50_stain_224mpm
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mean_deltaci_95_lowerci_95_upperupper_95non_inferiormodelmethod
00.1465710.1090780.1836450.177566Falsevgg16_224mpm
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mean_deltaci_95_lowerci_95_upperupper_95non_inferiormodelmethod
0-0.004084-0.0121540.0031790.002107Truevgg16_stain_224mpm
10.000383-0.0064480.0072170.006022Truevgg16_stain_224topk
2-0.173048-0.201552-0.143990-0.148353Truevgg16_stain_224span
\n", + "
" + ], + "text/plain": [ + " mean_delta ci_95_lower ci_95_upper upper_95 non_inferior \\\n", + "0 -0.004084 -0.012154 0.003179 0.002107 True \n", + "1 0.000383 -0.006448 0.007217 0.006022 True \n", + "2 -0.173048 -0.201552 -0.143990 -0.148353 True \n", + "\n", + " model method \n", + "0 vgg16_stain_224 mpm \n", + "1 vgg16_stain_224 topk \n", + "2 vgg16_stain_224 span " + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "vgg16_stain_224_df" + ] + }, + { + "cell_type": "code", + "execution_count": 15, "id": "5b6b384a-4d60-4c8a-b1e4-1dc1e281fe53", "metadata": {}, "outputs": [ @@ -1266,7 +1726,7 @@ "2 -0.403856 -0.428283 -0.377248 -0.382055 True gvit span" ] }, - "execution_count": 13, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -1277,7 +1737,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 16, "id": "e79890e4-99df-4049-a394-fb9f1b298949", "metadata": {}, "outputs": [ @@ -1358,7 +1818,7 @@ "2 span " ] }, - "execution_count": 14, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" }