High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics

We describe studies in molecular profiling and biological pathway analysis that use sparse latent factor and regression models for microarray gene expression data. We discuss breast cancer applications and key aspects of the modeling and computational methodology. Our case studies aim to investigate and characterize heterogeneity of structure related to specific oncogenic pathways, as well as links between aggregate patterns in gene expression profiles and clinical biomarkers. Based on the metaphor of statistically derived "factors" as representing biological "subpathway" structure, we explore the decomposition of fitted sparse factor models into pathway subcomponents and investigate how these components overlay multiple aspects of known biological activity. Our methodology is based on sparsity modeling of multivariate regression, ANOVA, and latent factor models, as well as a class of models that combines all components. Hierarchical sparsity priors address questions of dimension reduction and multiple comparisons, as well as scalability of the methodology. The models include practically relevant non-Gaussian/nonparametric components for latent structure, underlying often quite complex non-Gaussianity in multivariate expression patterns. Model search and fitting are addressed through stochastic simulation and evolutionary stochastic search methods that are exemplified in the oncogenic pathway studies. Supplementary supporting material provides more details of the applications, as well as examples of the use of freely available software tools for implementing the methodology.     

Testing Set-Point Theory in a Swiss National Sample: Reaction and Adaptation to Major Life Events

Set-point theory posits that individuals react to the experience of major life events, but quickly adapt back to pre-event baseline levels of subjective well-being in the years following the event. A large, nationally representative panel study of Swiss households was used to examine set-point theory by investigating the extent of adaptation following the experience of marriage, childbirth, widowhood, unemployment, and disability. Our results demonstrate that major life events are associated with marked changes in life satisfaction and, for some events (e.g., marriage, disability), these changes are relatively long lasting even when accounting for normative, age related changes.     

Online control by attributes in the presence of classification errors with variable inspection interval

ABSTRACT

The procedure for online control by attribute consists of inspecting a single item at every m items produced (m ≥ 2). On each inspection, it is determined whether the fraction of the produced conforming items decreased. If the inspected item is classified as non conforming, the productive process is adjusted so that the conforming fraction returns to its original status. A generalization observed in the literature is to consider inspection errors and vary the inspection interval. This study presents an extension of this model by considering that the inspected item can be rated independently r (r ≥ 1) times. The process is adjusted every time the number of conforming classifications is less than a, 1 ≤ a ≤ r. This method uses the properties of an ergodic Markov chain to obtain the expression for the average cost of this control system. The genetic algorithm methodology is used to search for the optimal parameters that minimize the expected cost. The procedure is illustrated by a numerical example.     

Some Dimensions of Adult Status

Quand la femme changea radicalement tout à coup de statut en revenant aux Etudes a plein temps entre les âges de trente et de cinquante ans, cette innovation rendit explieites un certain nombre de postulats au sujet des rôles de l'adulte dans notre société quant à la définition du rôle, la compétence qu'il requiert, le pragmatisme de notre vie sociale et la variété des tâches que l'adulte y détient. Elle mit à jour aussi le caractére des relations interpersonnelles implicite dans le statut de l'adulte.
Le dilemme des étudiants adultes c'est que, si le contenu de leurs rôles est défini, leurs expectatives au sujet de rapports réciproques n'étaient pas satisfaites.     

Sexual‐Minority and Heterosexual Youths' Peer Relationships: Experiences,Expectations, and Implications for Well‐Being

The current study compared the peer relationships and well‐being of 60 sexual‐minority (i.e., nonheterosexual) and 65 heterosexual youths between the ages of 15 and 23. Sexual‐minority youths had comparable self‐esteem, mastery, and perceived stress as did heterosexuals, but greater negative affect. Younger sexual‐minority male adolescents had smaller overall peer networks than did young male heterosexuals, whereas older male and female sexual minorities had larger numbers of extremely close friends within their networks than did heterosexuals. Younger sexual‐minority adolescents had lost or drifted away from more friends than did heterosexuals. Regardless of age, sexual‐minority youths reported disproportionately high worries about losing friends, low feelings of control in their romantic relationships, and fears of never finding the type of romantic relationship they wanted. Sexual‐minority youths that were “out” to more heterosexual peers had larger peer networks but more friendship loss and friendship worries. Youths' relationship experiences and concerns mediated sexual identity differences in negative affect.     

Comprehensive definitions of breakdown points for independent and dependent observations

Summary. We provide a new definition of breakdown in finite samples, with an extension to asymptotic breakdown. Previous definitions centre on defining a critical region for either the parameter or the objective function. If for a particular outlier configuration the critical region is entered, breakdown is said to occur. In contrast with the traditional approach, we leave the definition of the critical region implicit. Our proposal encompasses previous definitions of breakdown in linear and non-linear regression settings. In some cases, it leads to a different and more intuitive notion of breakdown than other procedures that are available. An important advantage of our new definition is that it also applies to models for dependent observations where current definitions of breakdown typically fail. We illustrate our suggestion by using examples from linear and non-linear regression, and time series.     

Connectivity and Resilience: A Multidimensional Analysis of Infrastructure Impacts in the Southwestern Amazon

Infrastructure is a worldwide policy priority for national development via regional integration into the global economy. However, economic, ecological and social research draws contrasting conclusions about the consequences of infrastructure. We present a synthetic approach to the study of infrastructure, focusing on a multidimensional treatment of indicators of connectivity and resilience. As our study case, we adopt a tri-national frontier in the southwestern Amazon being integrated by a highway, and use survey data for rural leaders to evaluate the relationship of community connectivity to market towns and social-ecological resilience. The findings show varying relationships among different dimensions of connectivity and resilience, which bear implications regarding indicator approaches to the study of infrastructure impacts.     

Estimating the Reliability of Single-Item Life Satisfaction Measures: Results from Four National Panel Studies

Life satisfaction is often assessed using single-item measures. However, estimating the reliability of these measures can be difficult because internal consistency coefficients cannot be calculated. Existing approaches use longitudinal data to isolate occasion-specific variance from variance that is either completely stable or variance that changes systematically over time. In these approaches, reliable occasion-specific variance is typically treated as measurement error, which would negatively bias reliability estimates. In the current studies, panel data and multivariate latent state-trait models are used to isolate reliable occasion-specific variance from random error and to estimate reliability for scores from single-item life satisfaction measures. Across four nationally representative panel studies with a combined sample size of over 68,000, reliability estimates increased by an average of 16% when the multivariate model was used instead of the more standard univariate longitudinal model.     

Robustness of the student t based M-estimator

This paper considers the maximum likelihood type (M) estimator based on Student's t distribution for the location/scale model. The Student t M-estimator is generally thought to be robust to outliers. This paper shows that this is only true if the degrees of freedom parameter is kept fixed. By contrast, if the degrees of freedom parameter is also estimated from the data, the influence functions for the scale and degrees of freedom parameter become unbounded. Moreover, the influence function of the location parameter remains bounded, but its change-of-variance function is unboi~nded. The intuitioil behind these results is explained in the paper. The rates at which both the influence functions and the change-of-variance function diverge to infinity, are very slow. Tliis implies that outliers have to be extremely large in order to become detrimental to the performance of the Student t based M-estimator with estimated degrees of freedom. The theoretical results are illustrated in a a simulation experiment using several related competing estimators and several distributions for the error process.