RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, we propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. We introduce RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, our tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC.

In this paper, we design and evaluate a practical AMC system that can be readily deployed to provide robust performance in various real-time commercial scenarios. Thus, our main goal is to develop a robust AMC algorithm with low computational complexity for easy implementation and practical deployment. To this end, we utilize recently revitalized machine learning based approaches used for various classification purposes. In our proposed AMC architecture, we first propose various statistics that serve as features of the AMC signals; next, we design an artificial neural network (ANN) based classifier that performs AMC over a wide range of SNRs. We employ Nesterov accelerated adaptive moment (NADAM) estimation technique to improve the classification performance of our ANN. Further, to establish the practical feasibility of our proposed architecture, we implement it on a SDR testbed. The proposed ANN-based classifier is shown to outperforms the hybrid hierarchical AMC (HH-AMC) system and is flexible enough to easily expand the dictionary of modulation formats for other applications.

In this paper, we show that SVRG and SARAH can be modified to be fundamentally faster than all of the other standard algorithms that minimize the sum of $n$ smooth functions, such as SAGA, SAG, SDCA, and SDCA without duality. Most finite sum algorithms follow what we call the ``span assumption'': Their updates are in the span of a sequence of component gradients chosen in a random IID fashion. In the big data regime, where the condition number $\kappa=O(n)$, the span assumption prevents algorithms from converging to an approximate solution of accuracy $\epsilon$ in less than $n\ln(1/\epsilon)$ iterations. SVRG and SARAH do not follow the span assumption since they are updated with a hybrid of full-gradient and component-gradient information. We show that because of this, they can be up to $\Omega(1+(\ln(n/\kappa))_+)$ times faster. In particular, to obtain an accuracy $\epsilon = 1/n^\alpha$ for $\kappa=n^\beta$ and $\alpha,\beta\in(0,1)$, modified SVRG requires $O(n)$ iterations, whereas algorithms that follow the span assumption require $O(n\ln(n))$ iterations. Moreover, we present lower bound results that show this speedup is optimal, and provide analysis to help explain why this speedup exists. With the understanding that the span assumption is a point of weakness of finite sum algorithms, future work may purposefully exploit this to yield faster algorithms in the big data regime.

We present a method for automated, depth-resolved extraction of the attenuation coefficient from Optical Coherence Tomography (OCT) data. In contrast to previous automated, depth-resolved methods, the Depth-Resolved Confocal (DRC) technique derives an invertible mapping between the measured OCT intensity data and the attenuation coefficient while considering the confocal function and sensitivity fall-off, which are critical to ensure accurate measurements of the attenuation coefficient in practical settings (e.g., clinical endoscopy). We also show that further improvement of the estimated attenuation coefficient is possible by formulating image denoising as a convex optimization problem that we term Intensity Weighted Horizontal Total Variation (iwhTV). The performance and accuracy of DRC alone and DRC+iwhTV are validated with simulated data, optical phantoms, and ex-vivo porcine tissue. Our results suggest that implementation of DRC+iwhTV represents a novel way to improve OCT contrast for better tissue characterization through quantitative imaging.

We present primal-dual decomposition algorithms for convex optimization problems with cost functions $f(x)+g(Ax)$, where $f$ and $g$ have inexpensive proximal operators and $A$ can be decomposed as a sum of two structured matrices. The methods are based on the Douglas--Rachford splitting algorithm applied to various splittings of the primal-dual optimality conditions. We discuss applications to image deblurring problems with nonquadratic data fidelity terms, different types of convex regularization, and simple convex constraints. In these applications, the primal-dual splitting approach allows us to handle general boundary conditions for the blurring operator. Numerical results indicate that the primal-dual splitting methods compare favorably with the alternating direction method of multipliers, the Douglas--Rachford algorithm applied to a reformulated primal problem, and the Chambolle--Pock primal-dual algorithm.