Biometrics最新文献

Despite the importance of age-specific fertility for ecology and evolution, the methods for modeling and inference have proven considerably limited. However, other disciplines have long focused on exploring and developing a vast number of models. Here, I provide an overview of the different models proposed since the 1940s by formal demographers, statisticians, and social scientists, most of which are unknown to the ecological and evolutionary communities. I describe how these fall into 2 main categories, namely polynomials and those based on probability density functions. I discuss their merits in terms of their overall behavior and how well they represent the different stages of fertility. Despite many alternative models, inference on age-specific fertility has usually been limited to simple least squares. Although this might be sufficient for human data, I hope to demonstrate that inference requires more sophisticated approaches for ecological and evolutionary datasets. To illustrate how inference and model choice can be achieved on different types of typical ecological and evolutionary data, I present the new R package Bayesian Fertility Trajectory Analysis, which I apply to published aggregated data for lions and baboons. I then conduct a simulation study to test its performance on individual-level data. I show that appropriate inference and model selection can be achieved even when a small number of parents are followed.

A new family of precision Bayesian dose optimization designs, PGen I-II, based on early efficacy, early toxicity, and long-term time to treatment failure is proposed. A PGen I-II design refines a Gen I-II design by accounting for patient heterogeneity characterized by subgroups that may be defined by prognostic levels, disease subtypes, or biomarker categories. The design makes subgroup-specific decisions, which may be to drop an unacceptably toxic or inefficacious dose, randomize patients among acceptable doses, or identify a best dose in terms of treatment success defined in terms of time to failure over long-term follow-up. A piecewise exponential distribution for failure time is assumed, including subgroup-specific effects of dose, response, and toxicity. Latent variables are used to adaptively cluster subgroups found to have similar dose-outcome distributions, with the model simplified to borrow strength between subgroups in the same cluster. Guidelines and user-friendly computer software for implementing the design are provided. A simulation study is reported that shows the PGen I-II design is superior to similarly structured designs that either assume patient homogeneity or conduct separate trials within subgroups.

The predictive value of a covariate is often of interest in studies with a survival endpoint. A common situation is that there are some well established predictors and a potential valuable new marker. The challenge is how to judge the potentially added predictive value of this new marker. We propose to use the positive predictive value (PPV) curve based on a nonparametric scoring rule. The estimand of interest is viewed as a single transformation of the underlying data generating probability measure, which allows us to develop a robust nonparametric estimator of the PPV by first calculating the corresponding efficient influence function. We provide asymptotic results and illustrate the approach with numerical studies and with 2 cancer data studies.

There exists a substantial body of literature that discusses regression analysis of interval-censored failure time data and also many methods have been proposed for handling the presence of a cured subgroup. However, only limited research exists on the problems incorporating change points, with or without a cured subgroup, which can occur in various contexts such as clinical trials where disease risks may shift dramatically when certain biological indicators exceed specific thresholds. To fill this gap, we consider a class of partly linear transformation models within the mixture cure model framework and propose a sieve maximum likelihood estimation approach using Bernstein polynomials and piecewise linear functions for inference. Additionally, we provide a data-driven adaptive procedure to identify the number and locations of change points and establish the asymptotic properties of the proposed method. Extensive simulation studies demonstrate the effectiveness and practical utility of the proposed methods, which are applied to the real data from a breast cancer study that motivated this work.

The spatial transcriptomics (ST) clustering plays a crucial role in elucidating the tissue spatial heterogeneity. An accurate ST clustering result can greatly benefit downstream biological analyses. As various ST clustering approaches are proposed in recent years, comparing their clustering accuracy becomes important in benchmarking studies. However, the widely used metric, adjusted Rand index (ARI), totally ignores the spatial information in ST data, which prevents ARI from fully evaluating spatial ST clustering methods. We propose a spatially aware Rand index (spRI) as well as spatially aware adjusted Rand index (spARI) that incorporate the spatial distance information. Specifically, when comparing two partitions, spRI provides a disagreement object pair with a weight relying on the distance of the two objects, whereas Rand index assigns a zero weight to it. This spatially aware feature of spRI adaptively differentiates disagreement object pairs based on their distinct distances, providing a useful evaluation metric that favors spatial coherence of clustering. The spARI is obtained by adjusting spRI for random chances such that its expectation takes zero under an appropriate null model. Statistical properties of spRI and spARI are discussed. The applications to simulation study and two ST datasets demonstrate the improved utilities of spARI compared to ARI in evaluating ST clustering methods.

A covariance-on-covariance regression model is introduced in this manuscript. It is assumed that there exists (at least) a pair of linear projections on outcome covariance matrices and predictor covariance matrices such that a log-linear model links the variances in the projection spaces, as well as additional covariates of interest. An ordinary least square type of estimator is proposed to simultaneously identify the projections and estimate model coefficients. Under regularity conditions, the proposed estimator is asymptotically consistent. The superior performance of the proposed approach over existing methods is demonstrated via simulation studies. Applying to data collected in the Human Connectome Project Aging study, the proposed approach identifies 3 pairs of brain networks, where functional connectivity within the resting-state network predicts functional connectivity within the corresponding task-state network. The 3 networks correspond to a global signal network, a task-related network, and a task-unrelated network. The findings are consistent with existing knowledge about brain function.

Individualized treatment rules tailor treatments to patients based on clinical, demographic, and other characteristics. Estimation of individualized treatment rules requires the identification of individuals who benefit most from the particular treatments and thus the detection of variability in treatment effects. To develop an effective individualized treatment rule, data from multisite studies may be required due to the low power provided by smaller datasets for detecting the often small treatment-covariate interactions. However, sharing of individual-level data is sometimes constrained. Furthermore, sparsity may arise in 2 senses: different data sites may recruit from different populations, making it infeasible to estimate identical models or all parameters of interest at all sites, and the number of non-zero parameters in the model for the treatment rule may be small. To address these issues, we adopt a 2-stage Bayesian meta-analysis approach to estimate individualized treatment rules which optimize expected patient outcomes using multisite data without disclosing individual-level data beyond the sites. Simulation results demonstrate that our approach can provide consistent estimates of the parameters which fully characterize the optimal individualized treatment rule. We estimate the optimal Warfarin dose strategy using data from the International Warfarin Pharmacogenetics Consortium, where data sparsity and small treatment-covariate interaction effects pose additional statistical challenges.

Quantifying associations between short-term exposure to ambient air pollution and health outcomes is an important public health priority. Many studies have investigated the association considering delayed effects within the past few days. Adaptive cumulative exposure distributed lag non-linear models (ACE-DLNMs) quantify associations between health outcomes and cumulative exposure that is specified in a data-adaptive way. While the ACE-DLNM framework is highly interpretable, it is limited to continuous outcomes and does not scale well to large datasets. Motivated by a large analysis of daily pollution and respiratory hospitalization counts in Canada between 2001 and 2018, we propose a generalized ACE-DLNM incorporating penalized splines, improving upon existing ACE-DLNM methods to accommodate general response types. We then develop a computationally efficient estimation strategy based on profile likelihood and Laplace approximate marginal likelihood with Newton-type methods. We demonstrate the performance and practical advantages of the proposed method through simulations. In application to the motivating analysis, the proposed method yields more stable inferences compared to generalized additive models with fixed exposures, while retaining interpretability.

Copy number alterations (CNA) are important drivers and markers of clonal structures within tumors. Understanding these structures at single-cell resolution is crucial to advancing cancer treatments. The objective is to cluster single cells into clones and identify CNA events in each clone. Early attempts often sacrifice the intrinsic link between cell clustering and clonal CNA detection for simplicity and rely heavily on human input for critical parameters such as the number of clones. Here, we develop a Bayesian model to utilize single-cell RNA sequencing (scRNA-seq) data for automatic analysis of intra-tumoral clonal structure concerning CNAs, without reliance on prior knowledge. The model clusters cells into sub-tumoral clones, identifies the number of clones, and simultaneously infers the clonal CNA profiles. It synergistically incorporates input from gene expression and germline single-nucleotide polymorphisms. A Gibbs sampling algorithm has been implemented and is available as an R package Chloris. We demonstrate that our new method compares strongly against existing software tools in terms of both cell clustering and CNA profile identification accuracy. Application to human metastatic melanoma and anaplastic thyroid tumor data demonstrates accurate clustering of tumor and non-tumor cells and reveals clonal CNA profiles that highlight functional gene expression differences between clones from the same tumor.