Muhammad Asad

Muhammad Asad, Reuben Dorent, Tom Vercauteren

The FastGeodis package provides an efficient implementation for computing Geodesic and Euclidean distance transforms (or a mixture of both), targeting efficient utilisation of CPU and GPU hardware. In particular, it implements the paralellisable raster scan method from Criminisi et al. (2009), where elements in a row (2D) or plane (3D) can be computed with parallel threads. This package is able to handle 2D as well as 3D data, where it achieves up to a 20x speedup on a CPU and up to a 74x speedup on a GPU as compared to an existing open-source library (Wang, 2020) that uses a non-parallelisable single-thread CPU implementation. The performance speedups reported here were evaluated using 3D volume data on an Nvidia GeForce Titan X (12 GB) with a 6-Core Intel Xeon E5-1650 CPU. Further in-depth comparison of performance improvements are discussed in the FastGeodis documentation: https://fastgeodis.readthedocs.io

Navodini Wijethilake, Aaron Kujawa, Reuben Dorent et al.

Vestibular Schwannoma (VS) typically grows from the inner ear to the brain. It can be separated into two regions, intrameatal and extrameatal respectively corresponding to being inside or outside the inner ear canal. The growth of the extrameatal regions is a key factor that determines the disease management followed by the clinicians. In this work, a VS segmentation approach with subdivision into intra-/extra-meatal parts is presented. We annotated a dataset consisting of 227 T2 MRI instances, acquired longitudinally on 137 patients, excluding post-operative instances. We propose a staged approach, with the first stage performing the whole tumour segmentation and the second stage performing the intra-/extra-meatal segmentation using the T2 MRI along with the mask obtained from the first stage. To improve on the accuracy of the predicted meatal boundary, we introduce a task-specific loss which we call Boundary Distance Loss. The performance is evaluated in contrast to the direct intrameatal extrameatal segmentation task performance, i.e. the Baseline. Our proposed method, with the two-stage approach and the Boundary Distance Loss, achieved a Dice score of 0.8279+-0.2050 and 0.7744+-0.1352 for extrameatal and intrameatal regions respectively, significantly improving over the Baseline, which gave Dice score of 0.7939+-0.2325 and 0.7475+-0.1346 for the extrameatal and intrameatal regions respectively.

Muhammad Asad, Lucas Fidon, Tom Vercauteren

Automatic segmentation of lung lesions associated with COVID-19 in CT images requires large amount of annotated volumes. Annotations mandate expert knowledge and are time-intensive to obtain through fully manual segmentation methods. Additionally, lung lesions have large inter-patient variations, with some pathologies having similar visual appearance as healthy lung tissues. This poses a challenge when applying existing semi-automatic interactive segmentation techniques for data labelling. To address these challenges, we propose an efficient convolutional neural networks (CNNs) that can be learned online while the annotator provides scribble-based interaction. To accelerate learning from only the samples labelled through user-interactions, a patch-based approach is used for training the network. Moreover, we use weighted cross-entropy loss to address the class imbalance that may result from user-interactions. During online inference, the learned network is applied to the whole input volume using a fully convolutional approach. We compare our proposed method with state-of-the-art using synthetic scribbles and show that it outperforms existing methods on the task of annotating lung lesions associated with COVID-19, achieving 16% higher Dice score while reducing execution time by 3$\times$ and requiring 9000 lesser scribbles-based labelled voxels. Due to the online learning aspect, our approach adapts quickly to user input, resulting in high quality segmentation labels. Source code for ECONet is available at: https://github.com/masadcv/ECONet-MONAILabel.

Muhammad Asad, Ahmed Moustafa, Takayuki Ito

In the past few decades, machine learning has revolutionized data processing for large scale applications. Simultaneously, increasing privacy threats in trending applications led to the redesign of classical data training models. In particular, classical machine learning involves centralized data training, where the data is gathered, and the entire training process executes at the central server. Despite significant convergence, this training involves several privacy threats on participants' data when shared with the central cloud server. To this end, federated learning has achieved significant importance over distributed data training. In particular, the federated learning allows participants to collaboratively train the local models on local data without revealing their sensitive information to the central cloud server. In this paper, we perform a convergence comparison between classical machine learning and federated learning on two publicly available datasets, namely, logistic-regression-MNIST dataset and image-classification-CIFAR-10 dataset. The simulation results demonstrate that federated learning achieves higher convergence within limited communication rounds while maintaining participants' anonymity. We hope that this research will show the benefits and help federated learning to be implemented widely.

Muhammad Asad, Rilwan Basaru, S M Masudur Rahman Al Arif et al.

In recent years, Convolutional Neural Networks (CNNs) have enabled significant advancements to the state-of-the-art in computer vision. For classification tasks, CNNs have widely employed probabilistic output and have shown the significance of providing additional confidence for predictions. However, such probabilistic methodologies are not widely applicable for addressing regression problems using CNNs, as regression involves learning unconstrained continuous and, in many cases, multi-variate target variables. We propose a PRObabilistic Parametric rEgression Loss (PROPEL) that facilitates CNNs to learn parameters of probability distributions for addressing probabilistic regression problems. PROPEL is fully differentiable and, hence, can be easily incorporated for end-to-end training of existing CNN regression architectures using existing optimization algorithms. The proposed method is flexible as it enables learning complex unconstrained probabilities while being generalizable to higher dimensional multi-variate regression problems. We utilize a PROPEL-based CNN to address the problem of learning hand and head orientation from uncalibrated color images. Our experimental validation and comparison with existing CNN regression loss functions show that PROPEL improves the accuracy of a CNN by enabling probabilistic regression, while significantly reducing required model parameters by $10 \times$, resulting in improved generalization as compared to the existing state-of-the-art.