arXiv subjects

Ukash Nakarmi

Publications and source records attributed to Ukash Nakarmi.

8 recordsLinked to original sources

arXiv2024

Adaptive Extensions of Unbiased Risk Estimators for Unsupervised Magnetic Resonance Image Denoising

The application of Deep Neural Networks (DNNs) to image denoising has notably challenged traditional denoising methods, particularly within complex noise scenarios prevalent in medical imaging. Despite the effectiveness of traditional and some DNN-based methods, their reliance on high-quality, noiseless ground truth images limits their practical utility. In response to this, our work introduces and benchmarks innovative unsupervised learning strategies, notably Stein's Unbiased Risk Estimator (SURE), its extension (eSURE), and our novel implementation, the Extended Poisson Unbiased Risk Estimator (ePURE), within medical imaging frameworks. This paper presents a comprehensive evaluation of these methods on MRI data afflicted with Gaussian and Poisson noise types, a scenario typical in medical imaging but challenging for most denoising algorithms. Our main contribution lies in the effective adaptation and implementation of the SURE, eSURE, and particularly the ePURE frameworks for medical images, showcasing their robustness and efficacy in environments where traditional noiseless ground truth cannot be obtained.

eess.IV↗

arXiv2024

Rapid Sensing of Heat Stress using Machine Learning of Micrographs of Red Blood Cells Dispersed in Liquid Crystals

An imbalance between bodily heat production and heat dissipation leads to heat stress in organisms. In addition to diminished animal well-being, heat stress is detrimental to the poultry industry as poultry entails fast growth and high yield, resulting in greater metabolic activity and higher body heat production. When stressed, cells overexpress heat shock proteins (such as HSP70, a well-established intracellular stress indicator) and may undergo changes in their mechanical properties. Liquid crystals (LCs, fluids with orientational order) have been recently employed to rapidly characterize changes in mechanical properties of cells enabling a means of optically reporting the presence of disease in organisms. In this work, we explore the difference in the expression of HSP70 to a change in the LC response pattern via the use of convolutional neural networks (CNNs). The machine-learning (ML) models were trained on hundreds of such LC-response micrographs of chicken red blood cells with and without heat stress. Trained models exhibited remarkable accuracy of up to 99% on detecting the presence of heat stress in unseen microscope samples. We also show that crosslinking the chicken and human RBCs using glutaraldehyde in order to simulate a diseased cell was an efficient strategy for planning, building, training, and evaluating ML models. Overall, our efforts build towards the rapid detection of disease in organisms, which is accompanied by a distinct change in the mechanical properties of cells. We aim to eventuate CNN-enabled LC-sensors can rapidly report the presence of disease in scenarios where human judgment could be prohibitively difficult or slow.

physics.bio-ph↗

arXiv2024

Towards an Algebraic Framework For Approximating Functions Using Neural Network Polynomials

We make the case for neural network objects and extend an already existing neural network calculus explained in detail in Chapter 2 on \cite{bigbook}. Our aim will be to show that, yes, indeed, it makes sense to talk about neural network polynomials, neural network exponentials, sine, and cosines in the sense that they do indeed approximate their real number counterparts subject to limitations on certain of their parameters, $q$, and $\varepsilon$. While doing this, we show that the parameter and depth growth are only polynomial on their desired accuracy (defined as a 1-norm difference over $\mathbb{R}$), thereby showing that this approach to approximating, where a neural network in some sense has the structural properties of the function it is approximating is not entire intractable.

cs.LG↗

arXiv2021

Self-Learned Kernel Low Rank Approach TO Accelerated High Resolution 3D Diffusion MRI

Diffusion Magnetic Resonance Imaging (dMRI) is a promising method to analyze the subtle changes in the tissue structure. However, the lengthy acquisition time is a major limitation in the clinical application of dMRI. Different image acquisition techniques such as parallel imaging, compressed sensing, has shortened the prolonged acquisition time but creating high-resolution 3D dMRI slices still requires a significant amount of time. In this study, we have shown that high-resolution 3D dMRI can be reconstructed from the highly undersampled k-space and q-space data using a Kernel LowRank method. Our proposed method has outperformed the conventional CS methods in terms of both image quality and diffusion maps constructed from the diffusion-weighted images

eess.IV↗

arXiv2020

Spectral Decomposition in Deep Networks for Segmentation of Dynamic Medical Images

Dynamic contrast-enhanced magnetic resonance imaging (DCE- MRI) is a widely used multi-phase technique routinely used in clinical practice. DCE and similar datasets of dynamic medical data tend to contain redundant information on the spatial and temporal components that may not be relevant for detection of the object of interest and result in unnecessarily complex computer models with long training times that may also under-perform at test time due to the abundance of noisy heterogeneous data. This work attempts to increase the training efficacy and performance of deep networks by determining redundant information in the spatial and spectral components and show that the performance of segmentation accuracy can be maintained and potentially improved. Reported experiments include the evaluation of training/testing efficacy on a heterogeneous dataset composed of abdominal images of pediatric DCE patients, showing that drastic data reduction (higher than 80%) can preserve the dynamic information and performance of the segmentation model, while effectively suppressing noise and unwanted portion of the images.

physics.med-ph↗

arXiv2020

Kernel Bi-Linear Modeling for Reconstructing Data on Manifolds: The Dynamic-MRI Case

This paper establishes a kernel-based framework for reconstructing data on manifolds, tailored to fit the dynamic-(d)MRI-data recovery problem. The proposed methodology exploits simple tangent-space geometries of manifolds in reproducing kernel Hilbert spaces and follows classical kernel-approximation arguments to form the data-recovery task as a bi-linear inverse problem. Departing from mainstream approaches, the proposed methodology uses no training data, employs no graph Laplacian matrix to penalize the optimization task, uses no costly (kernel) pre-imaging step to map feature points back to the input space, and utilizes complex-valued kernel functions to account for k-space data. The framework is validated on synthetically generated dMRI data, where comparisons against state-of-the-art schemes highlight the rich potential of the proposed approach in data-recovery problems.

cs.LG↗

arXiv2019

Diagnostic Image Quality Assessment and Classification in Medical Imaging: Opportunities and Challenges

Magnetic Resonance Imaging (MRI) suffers from several artifacts, the most common of which are motion artifacts. These artifacts often yield images that are of non-diagnostic quality. To detect such artifacts, images are prospectively evaluated by experts for their diagnostic quality, which necessitates patient-revisits and rescans whenever non-diagnostic quality scans are encountered. This motivates the need to develop an automated framework capable of accessing medical image quality and detecting diagnostic and non-diagnostic images. In this paper, we explore several convolutional neural network-based frameworks for medical image quality assessment and investigate several challenges therein.

eess.IV↗

arXiv2019

Bi-Linear Modeling of Data Manifolds for Dynamic-MRI Recovery

This paper puts forth a novel bi-linear modeling framework for data recovery via manifold-learning and sparse-approximation arguments and considers its application to dynamic magnetic-resonance imaging (dMRI). Each temporal-domain MR image is viewed as a point that lies onto or close to a smooth manifold, and landmark points are identified to describe the point cloud concisely. To facilitate computations, a dimensionality reduction module generates low-dimensional/compressed renditions of the landmark points. Recovery of the high-fidelity MRI data is realized by solving a non-convex minimization task for the linear decompression operator and those affine combinations of landmark points which locally approximate the latent manifold geometry. An algorithm with guaranteed convergence to stationary solutions of the non-convex minimization task is also provided. The aforementioned framework exploits the underlying spatio-temporal patterns and geometry of the acquired data without any prior training on external data or information. Extensive numerical results on simulated as well as real cardiac-cine and perfusion MRI data illustrate noteworthy improvements of the advocated machine-learning framework over state-of-the-art reconstruction techniques.

eess.IV↗