Clustering transformed compositional data using K-means,with applications in gene expression and bicycle sharing system data

Although there is no shortage of clustering algorithms proposed in the literature, the question of the most relevant strategy for clustering compositional data (i.e. data whose rows belong to the simplex) remains largely unexplored in cases where the observed value is equal or close to zero for one or more samples. This work is motivated by the analysis of two applications, both focused on the categorization of compositional profiles: (1) identifying groups of co-expressed genes from high-throughput RNA sequencing data, in which a given gene may be completely silent in one or more experimental conditions; and (2) finding patterns in the usage of stations over the course of one week in the Velib' bicycle sharing system in Paris, France. For both of these applications, we make use of appropriately chosen data transformations, including the Centered Log Ratio and a novel extension called the Log Centered Log Ratio, in conjunction with the K-means algorithm. We use a non-asymptotic penalized criterion, whose penalty is calibrated with the slope heuristics, to select the number of clusters. Finally, we illustrate the performance of this clustering strategy, which is implemented in the Bioconductor package coseq, on both the gene expression and bicycle sharing system data.     

A Shiny Update to an Old Experiment Game

ABSTRACT

Games can be a powerful tool for learning about statistical methodology. Effective game design involves a fine balance between caricature and realism, to simultaneously illustrate salient concepts in a controlled setting and serve as a testament to real-world applicability. Striking that balance is particularly challenging in response surface and design domains, where real-world scenarios often play out over long time scales, during which theories are revised, model and inferential techniques are improved, and knowledge is updated. Here, I present a game, borrowing liberally from one first played over 40 years ago, which attempts to achieve that balance while reinforcing a cascade of topics in modern nonparametric response surfaces, sequential design, and optimization. The game embeds a blackbox simulation within a shiny app whose interface is designed to simulate a realistic information–availability setting, while offering a stimulating, competitive environment wherein students can try out new methodology, and ultimately appreciate its power and limitations. Interface, rules, timing with course material, and evaluation are described, along with a “case study” involving a cohort of students at Virginia Tech. Supplementary materials for this article are available online.     

A Note on Estimation of a Distribution Function in a Nonparametric Set-up Using Stein’s Shrinkage Estimation Technique

Based on Stein’s famous shrinkage estimation of a multivariate normal distribution, we propose a new type of estimators of the distribution function of a random variable in a nonparametric setup. The proposed estimators are then compared with the empirical distribution function, which is the best equivariant estimator under a well-known loss function. Our extensive simulation study shows that our proposed estimators can perform better for moderate to large sample sizes.     

复杂环境下地震灾害应急救灾协同机制:一个实证分析

灾害应急管理是国家治理体系与治理能力建设,维护经济社会发展长治久安,以及实现"中国梦"、"两个一百年"奋斗目标的重要基石,也是中国特色社会主义制度更加巩固和优越性充分展现的战略部署。根据治理理论与协同学理论,通过对汶川、玉树等高原地震应急救灾的问卷调查和案例资料,探讨了政府主导社会基于支持保障体系的应急救灾协同机制实现路径,阐述了破坏性地震应急救灾何以协同、为何协同以与如何协同的内在逻辑及其现实要求,提出了加强灾害应急管理及科学引导社会参与救灾等优化对策。     

从社会回应模式看青少年离家出走现象

青少年离家出走问题已经成为全球性的社会现象,以西方研究社会问题的社会历史视角为基础提出的两个核心观点为"社会现象成为社会问题经历了发展的过程"和"社会各种人群或组织在社会问题的发展过程中给与了回应",从中可提炼出新的社会问题的研究模式,即社会回应模式。并通过应用中国"青少年离家出走"现象的发展过程来探讨这一社会回应模式在中国的适用性十分必要。研究发现,20世纪80年代至21世纪初期间(1980-2003年),青少年离家出走这一社会现象在中国经历了六大阶段的发展过程,并且在整个过程中,社会各人群对这一社会现象都有回应,但相应的社会回应和社会回应的研究仍存在不足。因此,对理论的进一步验证需要填充更多实证的数据,未来研究要进一步关注社会现象新一轮的发展历程和社会回应。     

Joint modified block replacement and production/inventory control policy for a failure-prone manufacturing cell

This paper considers a joint preventive maintenance (PM) and production/inventory control policy of an unreliable single machine, mono-product manufacturing cell with stochastic non-negligible corrective and preventive delays. The production/inventory control policy, which is based on the hedging point policy (HPP), consists in building and maintaining a safety stock of finished products in order to respond to demand and to avoid shortages during maintenance actions. Without considering the impact of preventive and corrective actions on the overall performance of the production system, most authors working in the reliability and maintainability domains confirm that the age-based preventive maintenance policy (ARP) outperforms the classical block-replacement policy (BRP). In order to reduce wastage incurred by the classical BRP, we consider a modified block replacement policy (MBRP), which consists in canceling a preventive maintenance action if the time elapsed since the last maintenance action exceeds a specified time threshold. The main objective of this paper is to determine the joint optimal policy that minimizes the overall cost, which is composed of corrective and preventive maintenance costs as well as inventory holding and backlog costs. A simulation model mimicking the dynamic and stochastic behavior of the manufacturing cell, based on more realistic considerations of the real behavior of industrial manufacturing cells, is proposed. Based on simulation results, the joint optimal MBRP/HPP parameters are obtained through a numerical approach that combines design of experiment, analysis of variance and response surface methodologies. The joint optimal MBRP/HPP policy is compared to classical joint ARP/HPP and BRP/HPP optimal policies, and the results show that the proposed MBRP/HPP outperforms the latter. Sensitivity analyses are also carried out in order to confirm the superiority of the proposed MBRP/HPP, and it is observed that for practitioners, the proposed joint MBRP/HPP offers not only cost savings, but is also easy to manage, as compared to the ARP/HPP policy.     

Polynomial regression analysis and response surface methodology in leadership research

Congruence has served as an important research framework for many leadership research topics. Perhaps the most frequently used methodological/statistical approach for testing the congruence framework is polynomial regression analysis (PRA) with response surface methodology (RSM). As this approach was introduced to organizational sciences more than two decades ago, we can now identify the main issues with the use of this approach in leadership research. To systematically investigate these issues, we first review how PRA and RSM have been used in various leadership studies. We then review the levels-of-analysis and rater model assumptions prevalent in PRA in terms of multilevel techniques, choice of centering options, and issues of endogeneity. Finally, to better understand the inconsistencies and variabilities that exist in leadership research, we review the use of two main RSM features and summarize additional statistical techniques for assessment in this realm. Overall, we aim to promote the rigorousness of this methodology within the study of congruence in leadership research by enhancing its capability in theory testing and building.     

我国能源强度变化的影响因素分析及其实证研究

以1990-2008年能源强度统计数据为样本,利用脉冲响应函数与方差分解模型,对能源强度变化影响因素的动态作用特征及其影响效果进行了研究。实证结果表明：能源强度自身与第二产业比重对能源强度影响程度较大,能源价格变动与技术进步也对能源强度有一定影响,影响因素共同通过内在联结关系与相互作用机制,能够对提高能源效率起到积极作用。     

有序响应变量的贝叶斯模型选择及其在COPD疾病防治中的应用

慢性阻塞性肺病(COPD)是一种发病率、死亡率都非常高的疾病，且COPD的诊断和严重程度分级依赖于肺功能的检查，但是由于肺功能检查仪器价格昂贵，使得这项检查在很多经济欠发达地区尤其是农村基层医院并没有普及。本文基于有序响应变量模型致力于研究一种便于基层和社区使用的可以初步判别COPD病情的模型，以期提高我国基层和社区的COPD 防治水平。利用贝叶斯变量选择方法和数据增强的潜变量策略得到了易于实施的Gibbs后验抽样算法。数值模拟分析进一步说明了本文提出的有序响应变量贝叶斯模型选择方法的有效性，实例分析得到了易于判别COPD严重程度的稀疏模型。     

The Risk of Photochemical Reactions

In January 1987, an incident occurred at a petrochemical complex in Salavat, Russia. The incident resulted in the poisioning of 17 people by the products of photochemical smog. This paper describes the incident and discusses the possibility of chemical reactions that pose toxic hazardous situations for chemical plant personnel. Pollutants present in the atmosphere as a result of continuous releases can result in the formation of toxic substances and the poisioning of people, even when permissible levels of concentrations are not exceeded for the initial pollutants. In addition, this paper addresses the need to consider the possibility of secondary chemical reactions in the environment while planning chemical plant activity.