Critical Values for the One-Sided Two-Sample Kolmogorov-Smirnov Statistic

3-D Quantum-Inspired Self-Supervised Tensor Network for Volumetric Segmentation of Medical Images

This article introduces a novel shallow 3-D self-supervised tensor neural network in quantum formalism for volumetric segmentation of medical images with merits of obviating training and supervision. The proposed network is referred to as the 3-D quantum-inspired self-supervised tensor neural network (3-D-QNet). The underlying architecture of 3-D-QNet is composed of a trinity of volumetric layers, viz., input, intermediate, and output layers interconnected using an S -connected third-order neighborhood-based topology for voxelwise processing of 3-D medical image data, suitable for semantic segmentation. Each of the volumetric layers contains quantum neurons designated by qubits or quantum bits. The incorporation of tensor decomposition in quantum formalism leads to faster convergence of network operations to preclude the inherent slow convergence problems faced by the classical supervised and self-supervised networks. The segmented volumes are obtained once the network converges. The suggested 3-D-QNet is tailored and tested on the BRATS 2019 Brain MR image dataset and the Liver Tumor Segmentation Challenge (LiTS17) dataset extensively in our experiments. The 3-D-QNet has achieved promising dice similarity (DS) as compared with the time-intensive supervised convolutional neural network (CNN)-based models, such as 3-D-UNet, voxelwise residual network (VoxResNet), Dense-Res-Inception Net (DRINet), and 3-D-ESPNet, thereby showing a potential advantage of our self-supervised shallow network on facilitating semantic segmentation.

Qutrit-Inspired Fully Self-Supervised Shallow Quantum Learning Network for Brain Tumor Segmentation

Classical self-supervised networks suffer from convergence problems and reduced segmentation accuracy due to forceful termination. Qubits or bilevel quantum bits often describe quantum neural network models. In this article, a novel self-supervised shallow learning network model exploiting the sophisticated three-level qutrit-inspired quantum information system, referred to as quantum fully self-supervised neural network (QFS-Net), is presented for automated segmentation of brain magnetic resonance (MR) images. The QFS-Net model comprises a trinity of a layered structure of qutrits interconnected through parametric Hadamard gates using an eight-connected second-order neighborhood-based topology. The nonlinear transformation of the qutrit states allows the underlying quantum neural network model to encode the quantum states, thereby enabling a faster self-organized counterpropagation of these states between the layers without supervision. The suggested QFS-Net model is tailored and extensively validated on the Cancer Imaging Archive (TCIA) dataset collected from the Nature repository. The experimental results are also compared with state-of-the-art supervised (U-Net and URes-Net architectures) and the self-supervised QIS-Net model and its classical counterpart. Results shed promising segmented outcomes in detecting tumors in terms of dice similarity and accuracy with minimum human intervention and computational resources. The proposed QFS-Net is also investigated on natural gray-scale images from the Berkeley segmentation dataset and yields promising outcomes in segmentation, thereby demonstrating the robustness of the QFS-Net model.

A tutorial comparing different covariate balancing methods with an application evaluating the causal effects of substance use treatment programs for adolescents

Randomized controlled trials are the gold standard for measuring causal effects. However, they are often not always feasible, and causal treatment effects must be estimated from observational data. Observational studies do not allow robust conclusions about causal relationships unless statistical techniques account for the imbalance of pretreatment confounders across groups and key assumptions hold. Propensity score and balance weighting (PSBW) are useful techniques that aim to reduce the observed imbalances between treatment groups by weighting the groups to look alike on the observed confounders. Notably, there are many methods available to estimate PSBW. However, it is unclear a priori which will achieve the best trade-off between covariate balance and effective sample size for a given application. Moreover, it is critical to assess the validity of key assumptions required for robust estimation of the needed treatment effects, including the overlap and no unmeasured confounding assumptions. We present a step-by-step guide to the use of PSBW for estimation of causal treatment effects that includes steps on how to evaluate overlap before the analysis, obtain estimates of PSBW using multiple methods and select the optimal one, check for covariate balance on multiple metrics, and assess sensitivity of findings (both the estimated treatment effect and statistical significance) to unobserved confounding. We illustrate the key steps using a case study examining the relative effectiveness of substance use treatment programs and provide a user-friendly Shiny application that can implement the proposed steps for any application with binary treatments.

Robust RNA-seq data analysis using an integrated method of ROC curve and Kolmogorov-Smirnov test

It is a common approach to dichotomize a continuous biomarker in clinical setting for the convenience of application. Analytically, results from using a dichotomized biomarker are often more reliable and resistant to outliers, bi-modal and other unknown distributions. There are two commonly used methods for selecting the best cut-off value for dichotomization of a continuous biomarker, using either maximally selected chi-square statistic or a ROC curve, specifically the Youden Index. In this paper, we explained that in many situations, it is inappropriate to use the former. By using the Maximum Absolute Youden Index (MAYI), we demonstrated that the integration of a MAYI and the Kolmogorov-Smirnov test is not only a robust non-parametric method, but also provides more meaningful p value for selecting the cut-off value than using a Mann-Whitney test. In addition, our method can be applied directly in clinical settings.

Automatic segmentation of white matter hyperintensities from brain magnetic resonance images in the era of deep learning and big data - A systematic review

BACKGROUND

White matter hyperintensities (WMH), of presumed vascular origin, are visible and quantifiable neuroradiological markers of brain parenchymal change. These changes may range from damage secondary to inflammation and other neurological conditions, through to healthy ageing. Fully automatic WMH quantification methods are promising, but still, traditional semi-automatic methods seem to be preferred in clinical research. We systematically reviewed the literature for fully automatic methods developed in the last five years, to assess what are considered state-of-the-art techniques, as well as trends in the analysis of WMH of presumed vascular origin.

METHOD

We registered the systematic review protocol with the International Prospective Register of Systematic Reviews (PROSPERO), registration number - CRD42019132200. We conducted the search for fully automatic methods developed from 2015 to July 2020 on Medline, Science direct, IEE Explore, and Web of Science. We assessed risk of bias and applicability of the studies using QUADAS 2.

RESULTS

The search yielded 2327 papers after removing 104 duplicates. After screening titles, abstracts and full text, 37 were selected for detailed analysis. Of these, 16 proposed a supervised segmentation method, 10 proposed an unsupervised segmentation method, and 11 proposed a deep learning segmentation method. Average DSC values ranged from 0.538 to 0.91, being the highest value obtained from an unsupervised segmentation method. Only four studies validated their method in longitudinal samples, and eight performed an additional validation using clinical parameters. Only 8/37 studies made available their methods in public repositories.

CONCLUSIONS

We found no evidence that favours deep learning methods over the more established k-NN, linear regression and unsupervised methods in this task. Data and code availability, bias in study design and ground truth generation influence the wider validation and applicability of these methods in clinical research.

Description and first application of a new technique to measure the gravitational mass of antihydrogen

Physicists have long wondered whether the gravitational interactions between matter and antimatter might be different from those between matter and itself. Although there are many indirect indications that no such differences exist and that the weak equivalence principle holds, there have been no direct, free-fall style, experimental tests of gravity on antimatter. Here we describe a novel direct test methodology; we search for a propensity for antihydrogen atoms to fall downward when released from the ALPHA antihydrogen trap. In the absence of systematic errors, we can reject ratios of the gravitational to inertial mass of antihydrogen >75 at a statistical significance level of 5%; worst-case systematic errors increase the minimum rejection ratio to 110. A similar search places somewhat tighter bounds on a negative gravitational mass, that is, on antigravity. This methodology, coupled with ongoing experimental improvements, should allow us to bound the ratio within the more interesting near equivalence regime.