Prediction of tumour pathological subtype from genomic profile using sparse logistic regression with random effects

The purpose of this study is to highlight the application of sparse logistic regression models in dealing with prediction of tumour pathological subtypes based on lung cancer patients'' genomic information. We consider sparse logistic regression models to deal with the high dimensionality and correlation between genomic regions. In a hierarchical likelihood (HL) method, it is assumed that the random effects follow a normal distribution and its variance is assumed to follow a gamma distribution. This formulation considers ridge and lasso penalties as special cases. We extend the HL penalty to include a ridge penalty (called ‘HLnet’) in a similar principle of the elastic net penalty, which is constructed from lasso penalty. The results indicate that the HL penalty creates more sparse estimates than lasso penalty with comparable prediction performance, while HLnet and elastic net penalties have the best prediction performance in real data. We illustrate the methods in a lung cancer study.     

An elastic-net penalized expectile regression with applications

To perform variable selection in expectile regression, we introduce the elastic-net penalty into expectile regression and propose an elastic-net penalized expectile regression (ER-EN) model. We then adopt the semismooth Newton coordinate descent (SNCD) algorithm to solve the proposed ER-EN model in high-dimensional settings. The advantages of ER-EN model are illustrated via extensive Monte Carlo simulations. The numerical results show that the ER-EN model outperforms the elastic-net penalized least squares regression (LSR-EN), the elastic-net penalized Huber regression (HR-EN), the elastic-net penalized quantile regression (QR-EN) and conventional expectile regression (ER) in terms of variable selection and predictive ability, especially for asymmetric distributions. We also apply the ER-EN model to two real-world applications: relative location of CT slices on the axial axis and metabolism of tacrolimus (Tac) drug. Empirical results also demonstrate the superiority of the ER-EN model.     

Industrial Policy Capture in Taiwan and South Korea

Whatever the theoretical merits of an industrial policy, in practice state incentives in support of infant industry are difficult to withdraw once they have been granted. Infant maturation is thereby delayed, resulting in ‘policy capture’ which confers rents on the assisted firms at the expense of consumers and/or taxpayers. The process is well-documented in poorly managed economies pursuing autarkic industrial policies (Auty, 1994a). This article examines evidence of policy capture in well-managed economies pursuing competitive industrial policies. Examples are drawn from the heavy (and chemical) industry drives of South Korea (hereafter Korea) and Taiwan, but the research is first set in the context of the industrial policy debate.     

The Effects of Personality Type on Choices Made in Strategic Decision Situations*

Jung's personality-theory typology is used as a framework for exploring the effects of cognitive style on the type and radicalness of choices made in strategic decision situations. Extending the work of Haley and Stumpf [23], it is proposed that individuals with different personality-type preferences exhibit cognitive styles that are associated with specific biases in the pattern of choices they make. Through participation in an interactive behavioral simulation, 407 participants confronted over one hundred ill-structured decision situations and proposed whatever actions they perceived appropriate. The results support the hypothesized relationships that individuals with different personality-type preferences (i.e., sensing-thinking, intuition-thinking, sensing-feeling, and intuition-feeling) take patterns of actions that reflect specific biases (i.e., selective perception, positivity, social desirability, and reasoning-by-analogy, respectively). The implications of these findings for evaluating the likely effectiveness of strategic decisions and making senior-level staffing decisions are discussed.     

A Comment on Second-Order Polynomial Regression Models

In a recent article, Chatterjee and Greenwood [1] addressed the problem of multicollinearity in polynomial regression models. They noted that there is a high correlation between X and X²; therefore, a second-order polynomial model suffers the consequences of collinearity. Chatterjee and Greenwood [1] suggested a method they believe will overcome the problem. The contention of the present comment is that the suggested method accomplishes nothing and, indeed, has the potential to lead the unwary researcher to the wrong inference and misinterpretation of his results.     

Some Comments on the Validity of EOQ Formula under Inflationary Conditions

In an earlier issue of Decision Sciences, Jesse, Mitra, and Cox [1] examined the impact of inflationary conditions on the economic order quantity (EOQ) formula. Specifically, the authors analyzed the effect of inflation on order quantity decisions by means of a model that takes into account both inflationary trends and time discounting (over an infinite time horizon). In their analysis, the authors utilized two models: Current-dollars model and Constant-dollars model. These models were derived, of course, by setting up a total cost equation in the usual manner then finding the optimum order quantity that minimizes the total cost. Jesse, Mitra, and Cox [1] found that EOQ is approximately the same under both conditions; with or without inflation. However, we disagree with the conclusion drawn by [2] and show that EOQ will be different under inflationary conditions, provided that the inflationary conditions are properly accounted for in the formulation of the total cost model.     

Interactive Effects of Major Response Facilitators

Practitioners and researchers have long been interested in achieving the highest response rate within resource constraints on their mailed surveys. Achieving this high response rate typically has required the selection of the right mix of response-facilitating techniques. The selection decisions were generally made under the assumption that the response-facilitating techniques act independently of one another. The authors have examined the validity of this independence assumption by identifying the major response facilitators in use and then analyzing the results of 531 independent mail survey studies. The authors conclude that major facilitators do not function independently. In fact, it was found that significant joint action interactive effects on response rates do exist. Practitioners and researchers who are faced with the survey design decisions of choosing response facilitators can receive assistance by reviewing the results of this diverse collection of reported experiences.     

Is governing board behavior cyclical?

An empirically derived model of cyclical board behavior holds that following a nonrecurring founding period, a board typically progresses through a sequence of three distinct operating phases and then experiences a crisis that initiates the whole sequence over again. During each cycle, board members become progressively less interested in the agency's mission and programs and more interested in the board's bureaucratic procedures and the agency's reputation for success in the community. Although the sequence of phases is predictable, the timing of them is not. As a conceptual framework, the model integrates the results of a variety of valuable, but otherwise unrelated, studies of governing board behavior. The cyclical model can also be used as a diagnostic tool that can enable a board member, executive director, consultant, foundation officer, or public funder to analyze quickly a particular board's perspective and potential.     

Graphical representation of survival curves in the presence of time-dependent categorical covariates with application to liver transplantation

Graphical representation of survival curves is often used to illustrate associations between exposures and time-to-event outcomes. However, when exposures are time-dependent, calculation of survival probabilities is not straightforward. Our aim was to develop a method to estimate time-dependent survival probabilities and represent them graphically. Cox models with time-dependent indicators to represent state changes were fitted, and survival probabilities were plotted using pre-specified times of state changes. Time-varying hazard ratios for the state change were also explored. The method was applied to data from the Adult-to-Adult Living Donor Liver Transplantation Cohort Study (A2ALL). Survival curves showing a ‘split’ at a pre-specified time t allow for the qualitative comparison of survival probabilities between patients with similar baseline covariates who do and do not experience a state change at time t. Time since state change interactions can be visually represented to reflect changing hazard ratios over time. A2ALL study results showed differences in survival probabilities among those who did not receive a transplant, received a living donor transplant, and received a deceased donor transplant. These graphical representations of survival curves with time-dependent indicators improve upon previous methods and allow for clinically meaningful interpretation.     

Learning from a lot: Empirical Bayes for high‐dimensional model‐based prediction

Empirical Bayes is a versatile approach to “learn from a lot” in two ways: first, from a large number of variables and, second, from a potentially large amount of prior information, for example, stored in public repositories. We review applications of a variety of empirical Bayes methods to several well‐known model‐based prediction methods, including penalized regression, linear discriminant analysis, and Bayesian models with sparse or dense priors. We discuss “formal” empirical Bayes methods that maximize the marginal likelihood but also more informal approaches based on other data summaries. We contrast empirical Bayes to cross‐validation and full Bayes and discuss hybrid approaches. To study the relation between the quality of an empirical Bayes estimator and p, the number of variables, we consider a simple empirical Bayes estimator in a linear model setting. We argue that empirical Bayes is particularly useful when the prior contains multiple parameters, which model a priori information on variables termed “co‐data”. In particular, we present two novel examples that allow for co‐data: first, a Bayesian spike‐and‐slab setting that facilitates inclusion of multiple co‐data sources and types and, second, a hybrid empirical Bayes–full Bayes ridge regression approach for estimation of the posterior predictive interval.