Modern approaches for evaluating treatment effect heterogeneity from clinical trials and observational data

In this paper, we review recent advances in statistical methods for the evaluation of the heterogeneity of treatment effects (HTE), including subgroup identification and estimation of individualized treatment regimens, from randomized clinical trials and observational studies. We identify several types of approaches using the features introduced in Lipkovich et al (Stat Med 2017;36: 136-196) that distinguish the recommended principled methods from basic methods for HTE evaluation that typically rely on rules of thumb and general guidelines (the methods are often referred to as common practices). We discuss the advantages and disadvantages of various principled methods as well as common measures for evaluating their performance. We use simulated data and a case study based on a historical clinical trial to illustrate several new approaches to HTE evaluation.

Inference on tree-structured subgroups with subgroup size and subgroup effect relationship in clinical trials

When multiple candidate subgroups are considered in clinical trials, we often need to make statistical inference on the subgroups simultaneously. Classical multiple testing procedures might not lead to an interpretable and efficient inference on the subgroups as they often fail to take subgroup size and subgroup effect relationship into account. In this paper, built on the selective traversed accumulation rules (STAR), we propose a data-adaptive and interactive multiple testing procedure for subgroups which can take subgroup size and subgroup effect relationship into account under prespecified tree structure. The proposed method is easy-to-implement and can lead to a more interpretable and efficient inference on prespecified tree-structured subgroups. Possible accommodations to post hoc identified tree-structure subgroups are also discussed in the paper. We demonstrate the merit of our proposed method by re-analyzing the panitumumab trial with the proposed method.

PhyloMed: a phylogeny-based test of mediation effect in microbiome

Microbiome data from sequencing experiments contain the relative abundance of a large number of microbial taxa with their evolutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the microbiome mediator challenges the validity of standard mediation analyses. We propose a phylogeny-based mediation analysis method called PhyloMed to address this challenge. Unlike existing methods that directly identify individual mediating taxa, PhyloMed discovers mediation signals by analyzing subcompositions defined on the phylogenic tree. PhyloMed produces well-calibrated mediation test p-values and yields substantially higher discovery power than existing methods.

Model-based and model-free deep features fusion for high performed human gait recognition

In the last decade, the need for a non-contact biometric model for recognizing candidates has increased, especially after the pandemic of COVID-19 appeared and spread worldwide. This paper presents a novel deep convolutional neural network (CNN) model that guarantees quick, safe, and precise human authentication via their poses and walking style. The concatenated fusion between the proposed CNN and a fully connected model has been formulated, utilized, and tested. The proposed CNN extracts the human features from two main sources: (1) human silhouette images according to model-free and (2) human joints, limbs, and static joint distances according to a model-based via a novel, fully connected deep-layer structure. The most commonly used dataset, CASIA gait families, has been utilized and tested. Numerous performance metrics have been evaluated to measure the system quality, including accuracy, specificity, sensitivity, false negative rate, and training time. Experimental results reveal that the proposed model can enhance recognition performance in a superior manner compared with the latest state-of-the-art studies. Moreover, the suggested system introduces a robust real-time authentication with any covariate conditions, scoring 99.8% and 99.6% accuracy in identifying casia (B) and casia (A) datasets, respectively.

Optimal false discovery rate control for large scale multiple testing with auxiliary information

Large-scale multiple testing is a fundamental problem in high dimensional statistical inference. It is increasingly common that various types of auxiliary information, reflecting the structural relationship among the hypotheses, are available. Exploiting such auxiliary information can boost statistical power. To this end, we propose a framework based on a two-group mixture model with varying probabilities of being null for different hypotheses a priori, where a shape-constrained relationship is imposed between the auxiliary information and the prior probabilities of being null. An optimal rejection rule is designed to maximize the expected number of true positives when average false discovery rate is controlled. Focusing on the ordered structure, we develop a robust EM algorithm to estimate the prior probabilities of being null and the distribution of p-values under the alternative hypothesis simultaneously. We show that the proposed method has better power than state-of-the-art competitors while controlling the false discovery rate, both empirically and theoretically. Extensive simulations demonstrate the advantage of the proposed method. Datasets from genome-wide association studies are used to illustrate the new methodology.

Covariate adaptive familywise error rate control for genome-wide association studies

The familywise error rate has been widely used in genome-wide association studies. With the increasing availability of functional genomics data, it is possible to increase detection power by leveraging these genomic functional annotations. Previous efforts to accommodate covariates in multiple testing focused on false discovery rate control, while covariate-adaptive procedures controlling the familywise error rate remain underdeveloped. Here, we propose a novel covariate-adaptive procedure to control the familywise error rate that incorporates external covariates which are potentially informative of either the statistical power or the prior null probability. An efficient algorithm is developed to implement the proposed method. We prove its asymptotic validity and obtain the rate of convergence through a perturbation-type argument. Our numerical studies show that the new procedure is more powerful than competing methods and maintains robustness across different settings. We apply the proposed approach to the UK Biobank data and analyse 27 traits with 9 million single-nucleotide polymorphisms tested for associations. Seventy-five genomic annotations are used as covariates. Our approach detects more genome-wide significant loci than other methods in 21 out of the 27 traits.

Filtering the rejection set while preserving false discovery rate control

Scientific hypotheses in a variety of applications have domain-specific structures, such as the tree structure of the International Classification of Diseases (ICD), the directed acyclic graph structure of the Gene Ontology (GO), or the spatial structure in genome-wide association studies. In the context of multiple testing, the resulting relationships among hypotheses can create redundancies among rejections that hinder interpretability. This leads to the practice of filtering rejection sets obtained from multiple testing procedures, which may in turn invalidate their inferential guarantees. We propose Focused BH, a simple, flexible, and principled methodology to adjust for the application of any pre-specified filter. We prove that Focused BH controls the false discovery rate under various conditions, including when the filter satisfies an intuitive monotonicity property and the p-values are positively dependent. We demonstrate in simulations that Focused BH performs well across a variety of settings, and illustrate this method's practical utility via analyses of real datasets based on ICD and GO.