Structured Sparsity: Discrete and Convex approaches

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure

Design and implementation of a generalized laboratory data model

<p>Abstract</p> <p>Background</p> <p>Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable.</p> <p>Results</p> <p>We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in <it>ad hoc </it>ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions.</p> <p>Conclusion</p> <p>The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.</p

The Urban Context: A Place to Eliminate Health Disparities and Build Organizational Capacity

This study seeks to examine the process of building the capacity to address health disparities in several urban African American neighborhoods. An inter-organizational network consisting of a research university, community members, community organizations, media partners, and foundations was formed to develop a community-based intervention designed to provide health promotion and disease prevention strategies for type 2 diabetes and hypertension. In-depth qualitative interviews (n = 18) with foundation executives and project directors, civic organization leadership, community leaders, county epidemiologist, and university partners were conducted. Our study contextualizes a process to build a public health partnership using cultural, community, organizational, and societal factors necessary to address health disparities. Results showed 5 important factors to build organizational capacity: leadership, institutional commitment, trust, credibility, and inter-organizational networks. These factors reflected other important organizational and community capacity indicators such as: community context, organizational policies, practices and structures, and the establishment of new commitments and partnerships important to comprehensively address urban health disparities. Understanding these factors to address African American health disparities will provide lessons learned for health educators, researchers, practitioners, foundations, and communities interested in building and sustaining capacity efforts through the design, implementation, and maintenance of a community-based health promotion interventionhttp://dx.doi.org/10.1080/10852352.2011.53016

Associations of Pregnancy Outcomes and PM2.5 in a National Canadian Study.

BackgroundNumerous studies have examined associations between air pollution and pregnancy outcomes, but most have been restricted to urban populations living near monitors.ObjectivesWe examined the association between pregnancy outcomes and fine particulate matter in a large national study including urban and rural areas.MethodsAnalyses were based on approximately 3 million singleton live births in Canada between 1999 and 2008. Exposures to PM2.5 (particles of median aerodynamic diameter ≤ 2.5 μm) were assigned by mapping the mother's postal code to a monthly surface based on a national land use regression model that incorporated observations from fixed-site monitoring stations and satellite-derived estimates of PM2.5. Generalized estimating equations were used to examine the association between PM2.5 and preterm birth (gestational age &lt; 37 weeks), term low birth weight (&lt; 2,500 g), small for gestational age (SGA; &lt; 10th percentile of birth weight for gestational age), and term birth weight, adjusting for individual covariates and neighborhood socioeconomic status (SES).ResultsIn fully adjusted models, a 10-μg/m(3) increase in PM2.5 over the entire pregnancy was associated with SGA (odds ratio = 1.04; 95% CI 1.01, 1.07) and reduced term birth weight (-20.5 g; 95% CI -24.7, -16.4). Associations varied across subgroups based on maternal place of birth and period (1999-2003 vs. 2004-2008).ConclusionsThis study, based on approximately 3 million births across Canada and employing PM2.5 estimates from a national spatiotemporal model, provides further evidence linking PM2.5 and pregnancy outcomes

Associations of pregnancy outcomes and PM2.5 in a national Canadian study

Background: Numerous studies have examined associations between air pollution and pregnancy outcomes, but most have been restricted to urban populations living near monitors. Objectives: We examined the association between pregnancy outcomes and fine particulate matter in a large national study including urban and rural areas. Methods: Analyses were based on approximately 3 million singleton live births in Canada between 1999 and 2008. Exposures to PM2.5 (particles of median aerodynamic diameter ≤ 2.5 μm) were assigned by mapping the mother’s postal code to a monthly surface based on a national land use regression model that incorporated observations from fixed-site monitoring stations and satellitederived estimates of PM2.5. Generalized estimating equations were used to examine the association between PM2.5 and preterm birth (gestational age < 37 weeks), term low birth weight (< 2,500 g), small for gestational age (SGA; < 10th percentile of birth weight for gestational age), and term birth weight, adjusting for individual covariates and neighborhood socioeconomic status (SES). Results: In fully adjusted models, a 10-μg/m3 increase in PM2.5 over the entire pregnancy was associated with SGA (odds ratio = 1.04; 95% CI 1.01, 1.07) and reduced term birth weight (-20.5 g; 95% CI -24.7, -16.4). Associations varied across subgroups based on maternal place of birth and period (1999-2003 vs. 2004-2008). Conclusions: This study, based on approximately 3 million births across Canada and employing PM2.5 estimates from a national spatiotemporal model, provides further evidence linking PM2.5 and pregnancy outcomes