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cfg_Misc_Seg_3d.json
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{
"model_nature" : "Segmentation",
"model_name" : "Vessel_seg_UNET",
"is_3d": true,
"isDepthFirst": true,
"batch_dim_present": false,
"default" : true,
"dataset" : "IXI_MRA",
"test_run" : "final_test",
"resize" : 120,
"centre_crop" : 120,
"mean_vec" : [0.485, 0.456, 0.406],
"std_vec" : [0.229, 0.224, 0.225],
"patch_overlap": 12,
"_comment": "If you dont want to use patcher mention patch_size as -1",
"patch_size": 64,
"log_level" : "INFO",
"output_path" : "/project/ardas/TorchEsegeta_latest/results/",
"amp_enbled" : true,
"share_gpu_threads": 2,
"timeout_enabled": false,
"_comment": "set time in seconds",
"timeout_time": 3600,
"methods" : [
{ "method_name" : "captum_Saliency",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Saliency heat map",
"device_id" : "cuda:6",
"share_gpu": true,
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"abs": false, "nt_type": "smoothgrad", "n_samples" : 10, "affine_size": 4}
},
{ "method_name" : "captum_Feature_Ablation",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": true,
"title" : "Feature ablation",
"device_id" : "cuda:0",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"perturbations_per_eval": 2,"nt_type": "smoothgrad", "n_samples" : 2, "affine_size": 4}
},
{ "method_name" : "captum_Integrated_Gradients",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Integrated gradient heat map",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"nt_type": "smoothgrad", "n_samples" : 2, "affine_size": 4}
},
{ "method_name" : "captum_occlusion",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": true,
"title" : "Occlusion sensitivity heat map",
"device_id" : "cuda:0",
"patch_required": false,
"use": false,
"uncertainity": true,
"keywords": {"sliding_window_shapes": "1,11,11,11" ,"strides": 3, "nt_type": "smoothgrad", "n_samples" : 2, "affine_size": 4 }
},
{ "method_name" : "captum_guided_backprop",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Guided back propagation heat map",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"nt_type": "smoothgrad", "n_samples" : 10, "affine_size": 4}
},
{ "method_name" : "captum_deep_lift",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Deep Lift heat map",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"nt_type": "smoothgrad", "n_samples" : 2, "affine_size": 4}
},
{ "method_name" : "captum_deconvolution",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "blended_heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Deconvolution heat map",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"nt_type": "smoothgrad", "n_samples" : 5,"affine_size": 4}
},
{ "method_name" : "captum_guided_grad_cam",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Guided grad cam heat map",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5","nt_type": "smoothgrad", "n_samples" : 5, "affine_size": 4}
},
{ "method_name" : "captum_layer_activaltion",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Layer activation maps layer4",
"device_id" : "cuda:6",
"_comment": "Patcher won't work for this method as the input and the layer activation size is differerent",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5", "neuron_start": 0, "neuron_end" : 5, "affine_size": 4}
},
{ "method_name" : "cnn_vis_guided_backprop",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Guided backpropagation (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"firstLayer": "Conv1.conv[0]","affine_size": 4}
},
{ "method_name" : "cnn_vis_integrated_grad",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Integrated Gradient (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"n_samples": 2, "firstLayer": "Conv1.conv[0]","affine_size": 4
}
},
{ "method_name" : "cnn_vis_guided_grad_cam",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Guided Grad cam for Conv5 (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5.conv[0]", "firstLayer": "Conv1.conv[0]","affine_size": 4}
},
{ "method_name" : "cnn_vis_score_cam",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Score cam for Conv5 (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5.conv[0]", "affine_size": 4}
},
{ "method_name" : "captum_layer_conductance",
"_comment" : "If object has no attribute '_non_persistent_buffers_set' issue occurs, run with single device",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Layer conductance for Conv5",
"device_id" : "cuda:5",
"_comment" : "This method doesn't ork with patcher as the conv output size is different",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv2","device_ids": [5,6], "affine_size": 4}
},
{ "method_name" : "cnn_vis_vanilla_backprop",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Vanilla backpropagation (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"firstLayer":"Conv1.conv[0]","affine_size": 4}
},
{ "method_name" : "cnn_vis_grad_cam",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Grad cam for Conv 5 (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5.conv[0]", "affine_size": 4 }
},
{ "method_name" : "cnn_vis_grad_times_image",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Grad Times Image (CNN Visualization)",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"firstLayer":"Conv1.conv[0]","affine_size": 4}
},
{ "method_name" : "captum_layer_grad_shap",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Layer gradient shap for Conv1",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv1","attribute_to_layer_input": true , "affine_size": 4}
},
{ "method_name" : "torchray_excitation_backprop",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "Excitation Backpropagation for Conv5",
"device_id" : "cuda:6",
"_comment" : "this methods won't work with patcher",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv2", "affine_size": 4}
},
{ "method_name" : "torchray_contrast_excitation_backprop",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "Contrastive excitation backpropagation for layer 4",
"device_id" : "cuda:6",
"_comment" : "this methods won't work with patcher",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5", "contrast_layer": "Conv1", "classifier_layer": "Conv", "affine_size": 4}
},
{ "method_name" : "captum_gradient_shap",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Gradient Shap",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"n_samples" : 5, "stdiv": 1.0, "affine_size": 4 }
},
{ "method_name" : "captum_internal_influence",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": true,
"title" : "Internal influence for layer 4",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv2", "device_ids": [6,5,4,3],"affine_size": 4}
},
{ "method_name" : "captum_input_x_gradient",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": true,
"title" : "Input X gradient",
"device_id" : "cuda:6",
"share_gpu": true,
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"affine_size": 4}
},
{ "method_name" : "captum_deep_lift_shap",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "positive",
"show_colorbar": true,
"title" : "Deep lift shap",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"affine_size": 4}
},
{ "method_name" : "lucent_render_vis",
"_comment": ["For lucent library methods, multi-label layers should be joined by '_' instad on '.' ",
"Like to access CONV block inside Block1 mention, Block1_conv, also run it on cuda 0"],
"library" : "lucent",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "",
"device_id" : "cuda:0",
"_comment" : "This method doesn't work with patcher",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"_comment": "Keep the shape small, other wise requires lot of gpu",
"keywords": {"layer": "Conv3_conv:0","affine_size": 4, "shape": [64, 64, 64]}
},
{ "method_name" : "captum_LayerGradientXActivation",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": false,
"title" : "Layer Gradient XActivation",
"device_id" : "cuda:6",
"_comment" : "Patcher won't work as the attribution output is of different size",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv1.conv[0]", "affine_size": 4}
},
{ "method_name" : "captum_LayerDeepLift",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": false,
"title" : "Layer Deep Lift",
"device_id" : "cuda:6",
"_comment": "Patcher won't work as the attribution output is of different size",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv5.conv[0]","attribute_to_layer_input": true, "affine_size": 4}
},
{ "method_name" : "captum_LayerGradCam",
"library" : "captum",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": true,
"title" : "Layer Grad Cam",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer": "Conv1", "affine_size": 4}
},
{ "method_name" : "torchray_Deconv",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "Deconvnet",
"device_id" : "cuda:6",
"_comment": "Patcher won't work due to underline library implementation",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"affine_size": 4}
},
{ "method_name" : "torchray_Gradcam",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "Gradcam for Conv2",
"device_id" : "cuda:6",
"_comment": "Patcher won't work due to underline library implementation",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer" : "Conv2.conv[0]", "affine_size": 4}
},
{ "method_name" : "torchray_Gradient",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "Torchray Gradient",
"device_id" : "cuda:6",
"_comment": "Patcher won't work due to underline library implementation",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"affine_size": 4}
},
{ "method_name" : "torchray_Guidedbackprop",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "guided Back Propagation",
"device_id" : "cuda:6",
"_comment": "Patcher won't work due to underline library implementation",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"affine_size": 4}
},
{ "method_name" : "torchray_Linearapprox",
"library" : "torchray",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": true,
"title" : "Linear Approx for Conv 2",
"device_id" : "cuda:6",
"_comment": "Patcher won't work due to underline library implementation",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer" : "Conv2","affine_size": 4}
},
{ "method_name" : "cnn_vis_layer_activation_guided_backprop",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Layer Activation with Guided backpropagation",
"device_id" : "cuda:6",
"patch_required": true,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer" : "Conv", "filter_pos" : 0, "firstLayer":"Conv1.conv[0]", "affine_size": 4}
},
{ "method_name" : "cnn_vis_layer_visualization",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Layer visualization (CNN Vis)",
"device_id" : "cuda:4",
"_comment": "Patcher won't work as the layer output is of different size",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer" : "Conv5.conv[0]", "filter_pos" : 5, "affine_size": 4}
},
{ "method_name" : "cnn_vis_DeepDream",
"library" : "CNN Visualization",
"inpt_transform_req" : false,
"visualize_method" : "",
"sign": "",
"show_colorbar": false,
"title" : "Deep Dream (CNN Vis)",
"device_id" : "cuda:6",
"_comment": "Patcher won't work as the layer output is of different size",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"layer" : "Conv5.conv", "filter_pos" : 5, "init_color_low" : 180, "init_color_high" : 200, "shape": [1,1,32, 128, 128], "affine_size": 4}
},
{ "method_name" : "captum_ShapleyValueSampling",
"library" : "captum",
"_comment": "Not really for image data.Takes forever to run on image data",
"inpt_transform_req" : false,
"visualize_method" : "heat_map",
"sign": "all",
"show_colorbar": true,
"title" : "Shapley Value Sampling",
"device_id" : "cuda:0",
"patch_required": false,
"use": false,
"uncertainity_metrics": false,
"uncertainity_cascading": 0,
"keywords": {"n_samples" : 10}
}
],
"explain_methods" : [
{ "method_name" : "lime_segmentation",
"library" : "lime",
"inpt_transform_req" : false,
"device_id" : "cuda:6",
"use": false,
"keywords": {"top_labels": 5, "num_samples": 5, "num_features" : 5, "depth": 32}
}
]
}