A model-based multithreshold method for subgroup identification

A general framework for subgroup detection via one-step value difference estimation

Recent statistical methodology for precision medicine has focused on either identification of subgroups with enhanced treatment effects or estimating optimal treatment decision rules so that treatment is allocated in a way that maximizes, on average, predefined patient outcomes. Less attention has been given to subgroup testing, which involves evaluation of whether at least a subgroup of the population benefits from an investigative treatment, compared to some control or standard of care. In this work, we propose a general framework for testing for the existence of a subgroup with enhanced treatment effects based on the difference of the estimated value functions under an estimated optimal treatment regime and a fixed regime that assigns everyone to the same treatment. Our proposed test does not require specification of the parametric form of the subgroup and allows heterogeneous treatment effects within the subgroup. The test applies to cases when the outcome of interest is either a time-to-event or a (uncensored) scalar, and is valid at the exceptional law. To demonstrate the empirical performance of the proposed test, we study the type I error and power of the test statistics in simulations and also apply our test to data from a Phase III trial in patients with hematological malignancies.

Change-plane analysis for subgroup detection with a continuous treatment

Detecting and characterizing subgroups with differential effects of a binary treatment has been widely studied and led to improvements in patient outcomes and population risk management. Under the setting of a continuous treatment, however, such investigations remain scarce. We propose a semiparametric change-plane model and consequently a doubly robust test statistic for assessing the existence of two subgroups with differential treatment effects under a continuous treatment. The proposed testing procedure is valid when either the baseline function for the covariate effects or the generalized propensity score function for the continuous treatment is correctly specified. The asymptotic distributions of the test statistic under the null and local alternative hypotheses are established. When the null hypothesis of no subgroup is rejected, the change-plane parameters that define the subgroups can be estimated. This paper provides a unified framework of the change-plane method to handle various types of outcomes, including the exponential family of distributions and time-to-event outcomes. Additional extensions with nonparametric estimation approaches are also provided. We evaluate the performance of our proposed methods through extensive simulation studies under various scenarios. An application to the Health Effects of Arsenic Longitudinal Study with a continuous environmental exposure of arsenic is presented.

Latent group detection in functional partially linear regression models

In this paper, we propose a functional partially linear regression model with latent group structures to accommodate the heterogeneous relationship between a scalar response and functional covariates. The proposed model is motivated by a salinity tolerance study of barley families, whose main objective is to detect salinity tolerant barley plants. Our model is flexible, allowing for heterogeneous functional coefficients while being efficient by pooling information within a group for estimation. We develop an algorithm in the spirit of the K-means clustering to identify latent groups of the subjects under study. We establish the consistency of the proposed estimator, derive the convergence rate and the asymptotic distribution, and develop inference procedures. We show by simulation studies that the proposed method has higher accuracy for recovering latent groups and for estimating the functional coefficients than existing methods. The analysis of the barley data shows that the proposed method can help identify groups of barley families with different salinity tolerant abilities.

Change plane model averaging for subgroup identification

Central to personalized medicine and tailored therapies is discovering the subpopulations that account for treatment effect heterogeneity and are likely to benefit more from given interventions. In this article, we introduce a change plane model averaging method to identify subgroups characterized by linear combinations of predictive variables and multiple cut-offs. We first fit a sequence of statistical models, each incorporating the thresholding effect of one particular covariate. The estimation of submodels is accomplished through an iterative integration of a change point detection method and numerical optimization algorithms. A frequentist model averaging approach is then employed to linearly combine the submodels with optimal weights. Our approach can deal with high-dimensional settings involving enormous potential grouping variables by adopting the sparsity-inducing penalties. Simulation studies are conducted to investigate the prediction and subgrouping performance of the proposed method, with a comparison to various competing subgroup detection methods. Our method is applied to a dataset from a warfarin pharmacogenetics study, producing some new findings.

A reference-free R-learner for treatment recommendation

Assigning optimal treatments to individual patients based on their characteristics is the ultimate goal of precision medicine. Deriving evidence-based recommendations from observational data while considering the causal treatment effects and patient heterogeneity is a challenging task, especially in situations of multiple treatment options. Herein, we propose a reference-free R-learner based on a simplex algorithm for treatment recommendation. We showed through extensive simulation that the proposed method produced accurate recommendations that corresponded to optimal treatment outcomes, regardless of the reference group. We used the method to analyze data from the Systolic Blood Pressure Intervention Trial (SPRINT) and achieved recommendations consistent with the current clinical guidelines.

Association of Concussion History and Prolonged Recovery in Youth

OBJECTIVE

To determine the number of prior concussions associated with increased incidence of persistent postconcussive symptoms (PPCS) in a cohort of acutely concussed pediatric patients.

DESIGN

Prospective observational cohort study.

SETTING

Three university-affiliated concussion clinics.

PARTICIPANTS

Two hundred seventy participants (14.9 ± 1.9 years, 62% male, 54% with prior concussion) were assessed within 14 days of concussion and followed to clinical recovery. Participants with a second head injury before clinical recovery were excluded.

MEASURES AND MAIN OUTCOME

Concussion history, current injury characteristics, recovery time, and risk for prolonged recovery from current concussion.

RESULTS

There was no statistically significant change in PPCS risk for participants with 0, 1 or 2 prior concussions; however, participants with 3 or more prior concussions had a significantly greater risk of PPCS. Twelve participants sustained a subsequent concussion after clinical recovery from their first injury and were treated as a separate cohort. Our secondary analysis found that these participants took longer to recover and had a greater incidence of PPCS during recovery from their latest concussion.

CONCLUSION

Pediatric patients with a history of 3 or more concussions are at greater risk of PPCS than those with fewer than 3 prior concussions.

Multi-threshold proportional hazards model and subgroup identification

We propose a novel two-stage procedure for change point detection and parameter estimation in a multi-threshold proportional hazards model. In the first stage, we estimate the number of thresholds by formulating the threshold detection problem as a variable selection problem and applying the penalized partial likelihood approach. In the second stage, the change point locations are refined by a grid search and the standard inference for segment regression can then follow. The proposed model and estimation procedure could lend support to subgroup identification and personalized treatment recommendation in medical research. We establish the consistency of the threshold estimators and regression coefficient estimators under technical conditions. The finite sample performance of the method is demonstrated via simulation studies and two cancer data examples.

Personalized treatment selection using observational data

Estimating the optimal treatment regime based on individual patient characteristics has been a topic of discussion in many forums. Advanced computational power has added momentum to this discussion over the last two decades and practitioners have been advocating the use of new methods in determining the best treatment. Treatments that are geared toward the 'best' outcome for a patient based on his/her genetic markers and characteristics are of high importance. In this article, we develop an approach to predict the optimal personalized treatment based on observational data. We have used inverse probability of treatment weighted machine learning methods to obtain score functions to predict the optimal treatment. Extensive simulation studies showed that our proposed method has desirable performance in selecting the optimal treatment. We provided a case study to examine the Statin use on cognitive function to illustrate the use of our proposed method.

Assessing effect heterogeneity of a randomized treatment using conditional inference trees

Treatment effect heterogeneity occurs when individual characteristics influence the effect of a treatment. We propose a novel approach that combines prognostic score matching and conditional inference trees to characterize effect heterogeneity of a randomized binary treatment. One key feature that distinguishes our method from alternative approaches is that it controls the Type I error rate, that is, the probability of identifying effect heterogeneity if none exists and retains the underlying subgroups. This feature makes our technique particularly appealing in the context of clinical trials, where there may be significant costs associated with erroneously declaring that effects differ across population subgroups. Treatment effect heterogeneity trees are able to identify heterogeneous subgroups, characterize the relevant subgroups and estimate the associated treatment effects. We demonstrate the efficacy of the proposed method using a comprehensive simulation study and illustrate our method using a nutrition trial dataset to evaluate effect heterogeneity within a patient population.

Three Versions of the Perceived Stress Scale: Psychometric Evaluation in a Nationally Representative Sample of Chinese Adults during the COVID-19 Pandemic

(1) Background: The COVID-19 outbreak has created pressure in people’s daily lives, further threatening public health. Thus, it is important to assess people’s perception of stress during COVID-19 for both research and practical purposes. The Perceived Stress Scale (PSS) is one of the most widely used instruments to measure perceived stress; however, previous validation studies focused on specific populations, possibly limiting the generalization of results. (2) Methods: This study tested the psychometric properties of three versions of the Chinese Perceived Stress Scale (CPSS-14, CPSS-10, and CPSS-4) in the Chinese general population during the COVID-19 pandemic. A commercial online survey was employed to construct a nationally representative sample of 1133 adults in Mainland China (548 males and 585 females) during a one-week period. (3) Results: The two-factor (positivity and negativity) solution for the three versions of the CPSS showed a good fit with the data. The CPSS-14 and CPSS-10 had very good reliability and the CPSS-4 showed acceptable reliability, supporting the concurrent validity of the CPSS. (4) Conclusions: All three versions of the CPSS appear to be appropriate for use in research with samples of adults in the Chinese general population under the COVID-19 crisis. The CPSS-10 and CPSS-14 both have strong psychometric properties, but the CPSS-10 would have more utility because it is shorter than the CPSS-14. However, the CPSS-4 is an acceptable alternative when administration time is limited.

Principal component regression-based contrast-enhanced ultrasound evaluation system for the management of BI-RADS US 4A breast masses: objective assistance for radiologists

A portion of detected breast masses might be overrated by using the Breast Imaging-Reporting and Data System ultrasonography (BI-RADS US) lexicon. A principal component regression-based contrast-enhanced ultrasound (PCR-CEUS) evaluation system was built to quantitatively illustrate whether CEUS could help radiologists to differentiate 4A masses. The PCR-CEUS evaluation system, based on principal component analysis (PCA) and logistic regression, was verified by random assignment into training and test sets and shown to reduce the data dimension and avoid collinearity in CEUS variables. This prospective study consecutively collected 238 patients with 238 4A masses confirmed pathologically. All enrolled patients accepted CEUS examination. The diagnostic performance of senior and junior radiologists, PCR-CEUS and combined methods was compared. The PCR-CEUS system had consistent diagnostic performance in both the training and test sets, with an area under the curve (AUC) of 0.831 (0.765-0.897), 0.798 (0.7034-0.892) and 0.854 (0.765-0.943) (all P > 0.05). The AUC of the combined diagnostic model (PCR-CEUS + Senior radiologists) was higher than that of senior radiologists, and the combined model had higher sensitivity (0.875 (0.781-0.969) vs. 0.729 (0.603-0.855)) without compromising specificity. Furthermore, the AUC and specificity of the combined model (PCR-CEUS + Junior radiologists) (0.852 (0.787-0.916)) was higher than that of junior radiologists (0.665 (0.592-0.737) (P < 0.00001)). PCR-CEUS demonstrated good ability in differentiating malignant BI-RADS-US 4A masses and was helpful for both senior and junior radiologists.

Multithreshold change plane model: Estimation theory and applications in subgroup identification

We propose a multithreshold change plane regression model which naturally partitions the observed subjects into subgroups with different covariate effects. The underlying grouping variable is a linear function of observed covariates and thus multiple thresholds produce change planes in the covariate space. We contribute a novel two-stage estimation approach to determine the number of subgroups, the location of thresholds, and all other regression parameters. In the first stage we adopt a group selection principle to consistently identify the number of subgroups, while in the second stage change point locations and model parameter estimates are refined by a penalized induced smoothing technique. Our procedure allows sparse solutions for relatively moderate- or high-dimensional covariates. We further establish the asymptotic properties of our proposed estimators under appropriate technical conditions. We evaluate the performance of the proposed methods by simulation studies and provide illustrations using two medical data examples. Our proposal for subgroup identification may lead to an immediate application in personalized medicine.