BioExp 0.0.2

Deep Learning model analysis toolbox

BioExp

Explaining Deep Learning Models which perform various image processing tasks in the medical domain.

Citations

If you use BioExp, please cite our work:

@article{natekar2019demystifying,
  title={Demystifying Brain Tumour Segmentation Networks: Interpretability and Uncertainty Analysis},
  author={Natekar, Parth and Kori, Avinash and Krishnamurthi, Ganapathy},
  journal={arXiv preprint arXiv:1909.01498},
  year={2019}
}

Defined Pipeline

Features

BioExp supports the following interpretability methods:

• Model Dissection Analysis
• Model Ablation Analysis
• Model Uncertainty Analysis
  • Epistemic Uncertainty using Bayesian Dropout
  • Aleatoric Uncertainty using Test Time Augmentation
• GradCAM
• Activation Maximization

Installation

Running of the explainability pipeline requires a GPU and several deep learning modules.

Requirements

• 'pandas'
• 'numpy'
• 'scipy==1.6.0'
• 'matplotlib'
• 'pillow'
• 'simpleITK'
• 'opencv-python'
• 'tensorflow-gpu==1.14'
• 'keras'
• 'keras-vis'
• 'lucid'

The following command will install only the dependencies listed above.

pip install "BioExp[gpu]"

or 

pip install "BioExp[cpu]"

Ablation

Usage

from BioExp.spatial import Ablation

A = spatial.Ablation(model = model, 
				weights_pth = weights_path, 
				metric      = dice_label_coef, 
				layer_name  = layer_name, 
				test_image  = test_image, 
				gt 	    = gt, 
				classes     = infoclasses, 
				nclasses    = 4)

df = A.ablate_filter(step = 1)

Dissection

Usage

from BioExp.spatial import Dissector

layer_name = 'conv2d_3'
infoclasses = {}
for i in range(1): infoclasses['class_'+str(i)] = (i,)
infoclasses['whole'] = (1,2,3)

dissector = Dissector(model=model,
                        layer_name = layer_name)

threshold_maps = dissector.get_threshold_maps(dataset_path = data_root_path,
                                                save_path  = savepath,
                                                percentile = 85)
dissector.apply_threshold(image, threshold_maps, 
                        nfeatures =9, 
                        save_path = savepath, 
                        ROI       = ROI)

dissector.quantify_gt_features(image, gt, 
                        threshold_maps, 
                        nclasses   = infoclass, 
                        nfeatures  = 9, 
                        save_path  = savepath,
                        save_fmaps = False, 
                        ROI        = ROI)

Results

GradCAM

Usage

from BioExp.spatial import cam

dice = flow.cam(model, img, gt, 
				nclasses = nclasses, 
				save_path = save_path, 
				layer_idx = -1, 
				threshol = 0.5,
				modifier = 'guided')

Results

Activation Maximization

Usage

from BioExp.concept.feature import Feature_Visualizer

class Load_Model(Model):

  model_path = '../../saved_models/model_flair_scaled/model.pb'
  image_shape = [None, 1, 240, 240]
  image_value_range = (0, 10)
  input_name = 'input_1'

E = Feature_Visualizer(Load_Model, savepath = '../results/', regularizer_params={'L1':1e-3, 'rotate':8})
a = E.run(layer = 'conv2d_17', class_ = 'None', channel = 95, transforms=True)

##Activation Results

Uncertainty

Usage

from BioExp.uncertainty import uncertainty

D = uncertainty(test_image)
            
# for aleatoric
mean, var = D.aleatoric(model, iterations = 50)

# for epistemic
mean, var = D.epistemic(model, iterations = 50)
 
# for combined
mean, var = D.combined(model, iterations = 50)

Results

Radiomics

Usage

from BioExp.helpers import radfeatures
feat_extractor = radfeatures.ExtractRadiomicFeatures(image, mask, save_path = pth)
df = feat_extractor.all_features()

Contact

• Avinash Kori ([e-mail])
• Parth Natekar ([e-mail])