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Register a new userMulti-Scale Input Strategies for Medulloblastoma Tumor Classification using Deep Transfer Learning
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Medulloblastoma (MB) is a primary central nervous system tumor and the most common malignant brain cancer among children. Neuropathologists perform microscopic inspection of histopathological tissue slides under a microscope to assess the severity of the tumor. This is a time-consuming task and often infused with observer variability. Recently, pre-trained convolutional neural networks (CNN) have shown promising results for MB subtype classification. Typically, high-resolution images are divided into smaller tiles for classification, while the size of the tiles has not been systematically evaluated. We study the impact of tile size and input strategy and classify the two major histopathological subtypes-Classic and Demoplastic/Nodular. To this end, we use recently proposed EfficientNets and evaluate tiles with increasing size combined with various downsampling scales. Our results demonstrate using large input tiles pixels followed by intermediate downsampling and patch cropping significantly improves MB classification performance. Our top-performing method achieves the AUC-ROC value of 90.90% compared to 84.53% using the previous approach with smaller input tiles.
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Medulloblastoma (MB) is the most common malignant brain tumor in childhood. The diagnosis is generally based on the microscopic evaluation of histopathological tissue slides. However, visual-only assessment of histopathological patterns is a tedious and time-consuming task and is also affected by observer variability. Hence, automated MB tumor classification could assist pathologists by promoting consistency and robust quantification. Recently, convolutional neural networks (CNNs) have been proposed for this task, while transfer learning has shown promising results. In this work, we propose an end-to-end MB tumor classification and explore transfer learning with various input sizes and matching network dimensions. We focus on differentiating between the histological subtypes classic and desmoplastic/nodular. For this purpose, we systematically evaluate recently proposed EfficientNets, which uniformly scale all dimensions of a CNN. Using a data set with 161 cases, we demonstrate that pre-trained EfficientNets with larger input resolutions lead to significant performance improvements compared to commonly used pre-trained CNN architectures. Also, we highlight the importance of transfer learning, when using such large architectures. Overall, our best performing method achieves an F1-Score of 80.1%.
Brain tumor is one of the leading causes of cancer-related death globally among children and adults. Precise classification of brain tumor grade (low-grade and high-grade glioma) at early stage plays a key role in successful prognosis and treatment planning. With recent advances in deep learning, Artificial Intelligence-enabled brain tumor grading systems can assist radiologists in the interpretation of medical images within seconds. The performance of deep learning techniques is, however, highly depended on the size of the annotated dataset. It is extremely challenging to label a large quantity of medical images given the complexity and volume of medical data. In this work, we propose a novel transfer learning based active learning framework to reduce the annotation cost while maintaining stability and robustness of the model performance for brain tumor classification. We employed a 2D slice-based approach to train and finetune our model on the Magnetic Resonance Imaging (MRI) training dataset of 203 patients and a validation dataset of 66 patients which was used as the baseline. With our proposed method, the model achieved Area Under Receiver Operating Characteristic (ROC) Curve (AUC) of 82.89% on a separate test dataset of 66 patients, which was 2.92% higher than the baseline AUC while saving at least 40% of labeling cost. In order to further examine the robustness of our method, we created a balanced dataset, which underwent the same procedure. The model achieved AUC of 82% compared with AUC of 78.48% for the baseline, which reassures the robustness and stability of our proposed transfer learning augmented with active learning framework while significantly reducing the size of training data.
Microscopic examination of tissues or histopathology is one of the diagnostic procedures for detecting colorectal cancer. The pathologist involved in such an examination usually identifies tissue type based on texture analysis, especially focusing on tumour-stroma ratio. In this work, we automate the task of tissue classification within colorectal cancer histology samples using deep transfer learning. We use discriminative fine-tuning with one-cycle-policy and apply structure-preserving colour normalization to boost our results. We also provide visual explanations of the deep neural networks decision on texture classification. With achieving state-of-the-art test accuracy of 96.2% we also embark on using deployment friendly architecture called SqueezeNet for memory-limited hardware.
Ovarian cancer is the most lethal cancer of the female reproductive organs. There are $5$ major histological subtypes of epithelial ovarian cancer, each with distinct morphological, genetic, and clinical features. Currently, these histotypes are determined by a pathologists microscopic examination of tumor whole-slide images (WSI). This process has been hampered by poor inter-observer agreement (Cohens kappa $0.54$-$0.67$). We utilized a textit{two}-stage deep transfer learning algorithm based on convolutional neural networks (CNN) and progressive resizing for automatic classification of epithelial ovarian carcinoma WSIs. The proposed algorithm achieved a mean accuracy of $87.54%$ and Cohens kappa of $0.8106$ in the slide-level classification of $305$ WSIs; performing better than a standard CNN and pathologists without gynecology-specific training.
Gliomas are among the most aggressive and deadly brain tumors. This paper details the proposed Deep Neural Network architecture for brain tumor segmentation from Magnetic Resonance Images. The architecture consists of a cascade of three Deep Layer Aggregation neural networks, where each stage elaborates the response using the feature maps and the probabilities of the previous stage, and the MRI channels as inputs. The neuroimaging data are part of the publicly available Brain Tumor Segmentation (BraTS) 2020 challenge dataset, where we evaluated our proposal in the BraTS 2020 Validation and Test sets. In the Test set, the experimental results achieved a Dice score of 0.8858, 0.8297 and 0.7900, with an Hausdorff Distance of 5.32 mm, 22.32 mm and 20.44 mm for the whole tumor, core tumor and enhanced tumor, respectively.
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