Biometrics最新文献

High-throughput screening, in which large numbers of compounds are traditionally studied one-at-a-time in multiwell plates against specific targets, is widely used across many areas of the biological sciences, including drug discovery. To improve the effectiveness of these screens, we propose a new class of supersaturated designs that guide the construction of pools of compounds in each well. Because the size of the pools is typically limited by the particular application, the new designs accommodate this constraint and are part of a larger procedure that we call Constrained Row Screening or CRowS. We develop an efficient computational procedure to construct the CRowS designs, provide some initial lower bounds on the average squared off-diagonal values of their main-effects information matrix, and study the impact of the constraint on design quality. We also show via simulation that CRowS is statistically superior to the traditional one-compound-one-well approach as well as an existing pooling method, and demonstrate the use of the new methodology on a Verona Integron-encoded Metallo-$beta$-lactamase-2 assay.

In many genomic studies, gene co-expression graphs are influenced by subject-level covariates like single nucleotide polymorphisms. Traditional Gaussian graphical models ignore these covariates and estimate only population-level networks, potentially masking important heterogeneity. Covariate-dependent Gaussian graphical regressions address this limitation by regressing the precision matrix on covariates, thereby modeling how graph structures vary with high-dimensional subject-specific covariates. To fit the model, we adopt a multi-task learning approach that achieves lower error rates than node-wise regressions. Yet, the important problem of statistical inference in this setting remains largely unexplored. We propose a class of debiased estimators based on multi-task learners, which can be computed quickly and separately. In a key step, we introduce a novel projection technique for estimating the inverse covariance matrix, reducing optimization costs to scale with the sample size n. Our debiased estimators achieve fast convergence and asymptotic normality, enabling valid inference. Simulations demonstrate the utility of the method, and an application to a brain cancer gene-expression dataset reveals meaningful biological relationships.

Advances in wearable technologies and health interventions delivered by smartphones have greatly increased the accessibility of mobile health (mHealth) interventions. Micro-randomized trials (MRTs) are designed to assess the effectiveness of the mHealth intervention and introduce a novel class of causal estimands called "causal excursion effects." These estimands enable the evaluation of how intervention effects change over time and are influenced by individual characteristics or context. Existing methods for analyzing causal excursion effects assume known randomization probabilities, complete observations, and a linear nuisance function with prespecified features of the high-dimensional observed history. However, in complex mobile systems, these assumptions often fall short: randomization probabilities can be uncertain, observations may be incomplete, and the granularity of mHealth data makes linear modeling difficult. To address this issue, we propose a flexible and doubly robust inferential procedure, called "DR-WCLS," for estimating causal excursion effects from a meta-learner perspective. We present the bidirectional asymptotic properties of the proposed estimators and compare them with existing methods both theoretically and through extensive simulations. The results show a consistent and more efficient estimate, even with missing observations or uncertain treatment randomization probabilities. Finally, the practical utility of the proposed methods is demonstrated by analyzing data from a multi-institution cohort of first-year medical residents in the United States.

Multi-state models are widely used to study complex interrelated life events. In resource-limited settings, nested case-control (NCC) sampling may be employed to extract subsamples from a cohort for an event of interest, followed by a conditional likelihood analysis. However, conditioning restricts the reuse of NCC data for studying additional events. An alternative approach constructs pseudolikelihoods using inverse probability weighting (IPW) for inference with NCC data. Existing IPW-based pseudolikelihood methods focus primarily on estimating relative risks for multiple outcomes or secondary endpoints. In this work, we extend these methods to predict transition probabilities under general multi-state models and evaluate their efficiency. As the standard IPW methods for the prediction of transition probabilities may suffer from inefficiency, we propose two novel approaches for more efficient prediction and derive explicit variance estimates for these methods. The first approach calibrates the design weights using cohort-level information, while the second jointly models transitions originating from the same state. A simulation study demonstrates that either approach substantially improves efficiency and that their combined application yields further gains. We illustrate these methods with real data from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial.

The mean survival is the key ingredient of the decision process in several applications, notably in health economic evaluations. It is defined as the area under the complete survival curve, thus necessitating extrapolation of the observed data. This may be achieved in a more stable manner by borrowing long term evidence from registry and demographic data. In this article, we employ a Bayesian mortality model and transfer its projections in order to construct the baseline population that acts as an anchor of the survival model. We then propose extrapolation methods based on flexible parametric poly-hazard models which can naturally accommodate diverse shapes, including non-proportional hazards and crossing survival curves, while typically maintaining a natural interpretation as a data generating mechanism. We estimate the mean survival and related estimands in 3 cases, namely breast cancer, advanced melanoma, and cardiac arrhythmia. Specifically, we evaluate the survival disadvantage of triple-negative breast cancer cases, the efficacy of combining immunotherapy with mRNA cancer therapeutics for melanoma treatment and the suitability of implantable cardioverter defibrilators for cardiac arrhythmia. The last is conducted in a competing risks context illustrating how working on the cause-specific hazard alone minimizes potential instability. The results suggest that the proposed approach offers a flexible, interpretable, and robust approach when survival extrapolation is required.

The heterogeneous treatment effect plays a crucial role in precision medicine. There is evidence that real-world data, even subject to biases, can be employed as supplementary evidence for randomized clinical trials to improve the statistical efficiency of the heterogeneous treatment effect estimation. In this paper, for survival data with right censoring, we consider estimating the heterogeneous treatment effect, defined as the difference of the treatment-specific conditional restricted mean survival times given covariates, by synthesizing evidence from randomized clinical trials and the real-world data with possible biases. We define an omnibus bias function to characterize the effect of biases caused by unmeasured confounders, censoring, and outcome heterogeneity, and further, identify it by combining the trial and real-world data. We propose a penalized sieve method to estimate the heterogeneous treatment effect and the bias function. We further study the theoretical properties of the proposed integrative estimators based on the theory of reproducing kernel Hilbert space and empirical process. The proposed methodology outperforms the approach solely based on the trial data through simulation studies and an integrative analysis of the data from a randomized trial and a real-world registry on early-stage non-small-cell lung cancer.

Ordinary differential equations (ODEs) are widely considered for modeling the dynamics of complex systems across various scientific areas. To identify the structure of high-dimensional sparse ODEs from noisy time-course data, most existing methods adopt a frequentist perspective, while uncertainty quantification in parameter estimation remains challenging. Under an additive ODE model assumption, we present a Bayesian hierarchical collocation method to provide better quantification of uncertainty. Our framework unifies the likelihood, integrated ODE constraints and a group-wise sparse penalty, allowing for simultaneous system identification and trajectory estimation. We demonstrate the favorable performance of the proposed method through simulation studies, where the recovered system trajectories and estimated additive components are compared with other recent methods. A real data example of gene regulatory networks is provided to illustrate the methodology.

Online health communities (OHCs) provide a platform for patients and those related to share and communicate, making complex medical information more digestible and actionable. Health communication within OHCs can be impacted by other information sources. This study examines cross-platform health communication by mining Breastcancer.org (the largest online breast cancer community) and Twitter (now X). Early analyses of OHCs, Twitter, and other online platforms often adopt simple measures like word frequency, and more recent research has shifted towards word co-occurrence network analysis. Relatively, cross-platform communication analysis is limited, and the adopted techniques have drawbacks. We propose a new cross-platform communication model that collectively analyzes word co-occurrence networks and word frequency vectors. Here, the former describe the structural contents of health communication, and the latter describe the volumes. This model offers a nuanced perspective, accommodates temporal variations, and is examined for its theoretical and numerical properties. Collected from January 2010 to December 2020, the analyzed data contains over 1 395 000 tweets and 517 000 posts. Our analysis suggests that the Twitter's topics on breast cancer significantly impact the contents and volumes in the OHC. Distinct time phases are observed, with notable peaks during 2012-2013 and 2015-2018. This study can provide a venue for better understanding health communication and new insights into two highly important online platforms.

Hidden Markov models (HMMs) are widely used to characterize latent state transition patterns in substance use. However, traditional HMM frameworks are incompetent when dealing with the complexities introduced by high-dimensional risk factors and varying time intervals, particularly in determining the number of hidden states and selecting variables for state transition parameters. To tackle the analytical challenges in the Population Assessment of Tobacco and Health (PATH) Study, a nationally representative longitudinal cohort study on tobacco use, we propose a continuous-time HMM framework with a regularization algorithm to identify multi-dimensional risk factors underlying complex poly-tobacco use transitions. We develop an elastic-net regularization on the transition covariates to identify informative covariates and improve model estimation accuracy. The inclusion of key covariates enables accurate determination of the number of hidden states. We incorporate survey weights and information on strata and clustering throughout the modeling framework. We demonstrate the validity of our approach in determining state numbers, identifying informative covariates, and estimating model parameters through a series of simulations. Application of the proposed approach to PATH data analysis revealed several demographic, behavioral, and psychosocial factors that contribute to the differential risks of transition between tobacco-use states among youth and young adults. The model's capacity in identifying high-dimensional risk factors for underlying hidden variables substantiates its potential for enhancing public health research and informing interventions.