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Abstract The advancements in high-throughput technologies provide exciting opportunities to obtain multi-omics data from the same individuals in a biomedical study, and joint analyses of data from multiple sources offer many benefits. However, the occurrence of missing values is an inevitable issue in multi-omics data because measurements such as mRNA gene expression levels often require invasive tissue sampling from patients. Common approaches for addressing missing measurements include analyses based on observations with complete data or multiple imputation methods. In this paper, we propose a novel integrative multi-omics analytical framework based onp-value weight adjustment in order to incorporate observations with incomplete data into the analysis. By splitting the data into a complete set with full information and an incomplete set with missing measurements, we introduce mechanisms to derive weights and weight-adjustedp-values from the two sets. Through simulation analyses, we demonstrate that the proposed framework achieves considerable statistical power gains compared to a complete case analysis or multiple imputation approaches. We illustrate the implementation of our proposed framework in a study of preterm infant birth weights by a joint analysis of DNA methylation, mRNA, and the phenotypic outcome. Supplementary materials accompanying this paper appear online. 

Positronium lifetime imaging (PLI) is a newly demonstrated technique possible with time-of-flight (TOF) positron emission tomography (PET), capable of producing an image reflecting the lifetime of the positron, more precisely ortho-positronium (o-Ps), before annihilation, in addition to the traditional uptake image of the PET tracer. Due to the limited time resolution of TOF-PET systems and the added complexities in physics and statistics, lifetime image reconstruction presents a challenge. Recently, we described a maximum-likelihood approach for PLI by considering only o-Ps. In real-world scenarios, other populations of positrons that exhibit different lifetimes also exist. This paper introduces a novel two-component model aimed at enhancing the accuracy of o-Ps lifetime images. Through simulation studies, we compare this new model with the existing single-component model and demonstrate its superior performance in accurately capturing complex lifetime distributions. 

Spatiotemporal data analysis with massive zeros is widely used in many areas such as epidemiology and public health. We use a Bayesian framework to fit zero-inflated negative binomial models and employ a set of latent variables from Pólya-Gamma distributions to derive an efficient Gibbs sampler. The proposed model accommodates varying spatial and temporal random effects through Gaussian process priors, which have both the simplicity and flexibility in modeling nonlinear relationships through a covariance function. To conquer the computation bottleneck that GPs may suffer when the sample size is large, we adopt the nearest-neighbor GP approach that approximates the covariance matrix using local experts. For the simulation study, we adopt multiple settings with varying sizes of spatial locations to evaluate the performance of the proposed model such as spatial and temporal random effects estimation and compare the result to other methods. We also apply the proposed model to the COVID-19 death counts in the state of Florida, USA from 3/25/2020 through 7/29/2020 to examine relationships between social vulnerability and COVID-19 deaths. 

We introduce a novel sufficient dimension-reduction (SDR) method which is robust against outliers using α-distance covariance (dCov)in dimension-reduction problems. Under very mild conditions on the predictors, the central subspace is effectively estimated and model-free without estimating link function based on the projection on the Stiefel manifold. We establish the convergence property of the pro-posed estimation under some regularity conditions. We compare the performance of our method with existing SDR methods by simulation and real data analysis and show that our algorithm improves the computational efficiency and effectiveness. 

While matrix-covariate regression models have been studied in many existing works, classical statistical and computational methods for the analysis of the regression coefficient estimation are highly affected by high dimensional matrix-valued covariates. To address these issues, this paper proposes a framework of matrix-covariate regression models based on a low-rank constraint and an additional regularization term for structured signals, with considerations of models of both continuous and binary responses. We propose an efficient Riemannian-steepest-descent algorithm for regression coefficient estimation. We prove that the consistency of the proposed estimator is in the order of O(sqrt{r(q+m)+p}/sqrt{n}), where r is the rank, p x m is the dimension of the coefficient matrix and p is the dimension of the coefficient vector. When the rank r is small, this rate improves over O(sqrt{qm+p}/sqrt{n}), the consistency of the existing work (Li et al. in Electron J Stat 15:1909-1950, 2021) that does not apply a rank constraint. In addition, we prove that all accumulation points of the iterates have similar estimation errors asymptotically and substantially attaining the minimax rate. We validate the proposed method through a simulated dataset on two-dimensional shape images and two real datasets of brain signals and microscopic leucorrhea images. 

The positronium lifetime imaging (PLI) reconstruction is a technique used in time-of-flight (TOF) positron emission tomography (PET) imaging that involves measuring the lifespan of positronium, which is a metastable electron-positron pair that arises when a PET molecule releases a positron, prior to its annihilation. We have previously developed a maximum likelihood (ML) algorithm for PLI reconstruction and demonstrated that it can generate quantitatively accurate lifetime images for a 570 ps (pico-seconds) TOF PET system. In this study, we conducted further investigations into the statistical properties of the algorithm, including the variability of the reconstruction results, the sensitivity of the algorithm to the number of acquired PLI events and its robustness to hyperparameter choices. Our findings indicate that the proposed ML method produces sufficiently stable lifetime images to enable reliable distinction of regions of interest. Moreover, the number of PLI events required to produce quantitatively accurate lifetime images is computationally plausible. These results demonstrate the potential of our ML algorithm for advancing the capabilities of TOF PET imaging. 

Positronium Lifetime Image (PLI) reconstruction is a technique used in time-of-flight (TOF) Positron emission tomography (PET) imaging that involves measuring the lifespan of positronium, which is a metastable electron-positron pair that arises when a PET molecule releases a positron, prior to its annihilation. In our previous work, we demonstrated that our proposed maximum likelihood (ML) algorithm for PLI reconstruction can generate quantitatively accurate lifetime images for a 570 ps TOF PET system. In this study, we conducted further investigations into the statistical properties of the algorithm, including the variability of the reconstruction results, the sensitivity of the algorithm to the number of acquired PLI events and its robustness to hyperparameter choices. Our findings indicate that the proposed ML method produces sufficiently stable lifetime images to enable reliable distinction of regions of interest and the number of PLI events required to produce quantitatively accurate lifetime images is computationally plausible. These results demonstrate the potential of our ML algorithm for advancing the capabilities of TOF PET imaging. 

The North American deer mice (Peromyscus maniculatus) have been used as an environmental change indicator in North America. Since precipitation and temperature changes affect plant productivity and deer mouse habitats, they are substantial factors of deer mouse population radical variations. Therefore, modeling their association is important for monitoring dynamic changes of the deer mouse amounts per trap and relationships among weather variables such as precipitation, maximum and minimum temperatures. We acquired the National Ecological Observatory Network (NEON) data of deer mouse monthly amounts in traps for 2013 through 2022 in the contiguous United States from long-term study sites maintained for monitoring spatial differences and temporal changes in populations. We categorize the contiguous United States into six regions associated with climates. The proposed method identifies important factors of temperature and precipitation seasonal patterns with the month and year temporal effect interacting with the proposed climate-related regions.