Adversarial Inpainting of Medical Image Modalities

Numerous factors could lead to partial deteriorations of medical images. For example, metallic implants will lead to localized perturbations in MRI scans. This will affect further post-processing tasks such as attenuation correction in PET/MRI or radiation therapy planning. In this work, we propose the inpainting of medical images via Generative Adversarial Networks (GANs). The proposed framework incorporates two patch-based discriminator networks with additional style and perceptual losses for the inpainting of missing information in realistically detailed and contextually consistent manner. The proposed framework outperformed other natural image inpainting techniques both qualitatively and quantitatively on two different medical modalities.Comment: To be submitted to ICASSP 201

Retrospective correction of Rigid and Non-Rigid MR motion artifacts using GANs

Motion artifacts are a primary source of magnetic resonance (MR) image quality deterioration with strong repercussions on diagnostic performance. Currently, MR motion correction is carried out either prospectively, with the help of motion tracking systems, or retrospectively by mainly utilizing computationally expensive iterative algorithms. In this paper, we utilize a new adversarial framework, titled MedGAN, for the joint retrospective correction of rigid and non-rigid motion artifacts in different body regions and without the need for a reference image. MedGAN utilizes a unique combination of non-adversarial losses and a new generator architecture to capture the textures and fine-detailed structures of the desired artifact-free MR images. Quantitative and qualitative comparisons with other adversarial techniques have illustrated the proposed model performance.Comment: 5 pages, 2 figures, under review for the IEEE International Symposium for Biomedical Image

AeGAN: Time-Frequency Speech Denoising via Generative Adversarial Networks

Automatic speech recognition (ASR) systems are of vital importance nowadays in commonplace tasks such as speech-to-text processing and language translation. This created the need for an ASR system that can operate in realistic crowded environments. Thus, speech enhancement is a valuable building block in ASR systems and other applications such as hearing aids, smartphones and teleconferencing systems. In this paper, a generative adversarial network (GAN) based framework is investigated for the task of speech enhancement, more specifically speech denoising of audio tracks. A new architecture based on CasNet generator and an additional feature-based loss are incorporated to get realistically denoised speech phonetics. Finally, the proposed framework is shown to outperform other learning and traditional model-based speech enhancement approaches.Comment: 5 pages, 4 figures and 2 Tables. Accepted in EUSIPCO 202

MedGAN: Medical Image Translation using GANs

Image-to-image translation is considered a new frontier in the field of medical image analysis, with numerous potential applications. However, a large portion of recent approaches offers individualized solutions based on specialized task-specific architectures or require refinement through non-end-to-end training. In this paper, we propose a new framework, named MedGAN, for medical image-to-image translation which operates on the image level in an end-to-end manner. MedGAN builds upon recent advances in the field of generative adversarial networks (GANs) by merging the adversarial framework with a new combination of non-adversarial losses. We utilize a discriminator network as a trainable feature extractor which penalizes the discrepancy between the translated medical images and the desired modalities. Moreover, style-transfer losses are utilized to match the textures and fine-structures of the desired target images to the translated images. Additionally, we present a new generator architecture, titled CasNet, which enhances the sharpness of the translated medical outputs through progressive refinement via encoder-decoder pairs. Without any application-specific modifications, we apply MedGAN on three different tasks: PET-CT translation, correction of MR motion artefacts and PET image denoising. Perceptual analysis by radiologists and quantitative evaluations illustrate that the MedGAN outperforms other existing translation approaches.Comment: 16 pages, 8 figure

Person Identification and Body Mass Index: A Deep Learning-Based Study on Micro-Dopplers

Obtaining a smart surveillance requires a sensing system that can capture accurate and detailed information for the human walking style. The radar micro-Doppler ($\boldsymbol{\mu}$-D) analysis is proved to be a reliable metric for studying human locomotions. Thus, $\boldsymbol{\mu}$-D signatures can be used to identify humans based on their walking styles. Additionally, the signatures contain information about the radar cross section (RCS) of the moving subject. This paper investigates the effect of human body characteristics on human identification based on their $\boldsymbol{\mu}$-D signatures. In our proposed experimental setup, a treadmill is used to collect $\boldsymbol{\mu}$-D signatures of 22 subjects with different genders and body characteristics. Convolutional autoencoders (CAE) are then used to extract the latent space representation from the $\boldsymbol{\mu}$-D signatures. It is then interpreted in two dimensions using t-distributed stochastic neighbor embedding (t-SNE). Our study shows that the body mass index (BMI) has a correlation with the $\boldsymbol{\mu}$-D signature of the walking subject. A 50-layer deep residual network is then trained to identify the walking subject based on the $\boldsymbol{\mu}$-D signature. We achieve an accuracy of 98% on the test set with high signal-to-noise-ratio (SNR) and 84% in case of different SNR levels.Comment: Accepted in IEEE Radarconf1

ipA-MedGAN: Inpainting of Arbitrary Regions in Medical Imaging

Local deformations in medical modalities are common phenomena due to a multitude of factors such as metallic implants or limited field of views in magnetic resonance imaging (MRI). Completion of the missing or distorted regions is of special interest for automatic image analysis frameworks to enhance post-processing tasks such as segmentation or classification. In this work, we propose a new generative framework for medical image inpainting, titled ipA-MedGAN. It bypasses the limitations of previous frameworks by enabling inpainting of arbitrary shaped regions without a prior localization of the regions of interest. Thorough qualitative and quantitative comparisons with other inpainting and translational approaches have illustrated the superior performance of the proposed framework for the task of brain MR inpainting.Comment: Submitted to IEEE ICIP 202

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Wavelet-based Unsupervised Label-to-Image Translation

Semantic Image Synthesis (SIS) is a subclass of image-to-image translation where a semantic layout is used to generate a photorealistic image. State-of-the-art conditional Generative Adversarial Networks (GANs) need a huge amount of paired data to accomplish this task while generic unpaired image-to-image translation frameworks underperform in comparison, because they color-code semantic layouts and learn correspondences in appearance instead of semantic content. Starting from the assumption that a high quality generated image should be segmented back to its semantic layout, we propose a new Unsupervised paradigm for SIS (USIS) that makes use of a self-supervised segmentation loss and whole image wavelet based discrimination. Furthermore, in order to match the high-frequency distribution of real images, a novel generator architecture in the wavelet domain is proposed. We test our methodology on 3 challenging datasets and demonstrate its ability to bridge the performance gap between paired and unpaired models.Comment: arXiv admin note: substantial text overlap with arXiv:2109.1471