Mike Heithaus' field crew sets out a longline that has about 40 small hooks baited with mullett. They let the line soak for an hour before they check for sharks, Shark River

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514. This image is made available for non-commercial or educational use only.

Inventory of SINOPS project data sets

During the SINOPS project, an optimal state of the art simulation of the marine silicon cycle is attempted employing a biogeochemical ocean general circulation model (BOGCM) through three particular time steps relevant for global (paleo-) climate. In order to tune the model optimally, results of the simulations are compared to a comprehensive data set of 'real' observations. SINOPS' scientific data management ensures that data structure becomes homogeneous throughout the project. Practical work routine comprises systematic progress from data acquisition, through preparation, processing, quality check and archiving, up to the presentation of data to the scientific community. Meta-information and analytical data are mapped by an n-dimensional catalogue in order to itemize the analytical value and to serve as an unambiguous identifier. In practice, data management is carried out by means of the online-accessible information system PANGAEA, which offers a tool set comprising a data warehouse, Graphical Information System (GIS), 2-D plot, cross-section plot, etc. and whose multidimensional data model promotes scientific data mining. Besides scientific and technical aspects, this alliance between scientific project team and data management crew serves to integrate the participants and allows them to gain mutual respect and appreciation.

An Empirical Evaluation of Preconditioning Data for Accelerating Convex Hull Computations

The convex hull describes the extent or shape of a set of data and is used ubiquitously in computational geometry. Common algorithms to construct the convex hull on a finite set of n points (x,y) range from O(nlogn) time to O(n) time. However, it is often the case that a heuristic procedure is applied to reduce the original set of n points to a set of s < n points which contains the hull and so accelerates the final hull finding procedure. We present an algorithm to precondition data before building a 2D convex hull with integer coordinates, with three distinct advantages. First, for all practical purposes, it is linear; second, no explicit sorting of data is required and third, the reduced set of s points is constructed such that it forms an ordered set that can be directly pipelined into an O(n) time convex hull algorithm. Under these criteria a fast (or O(n)) pre-conditioner in principle creates a fast convex hull (approximately O(n)) for an arbitrary set of points. The paper empirically evaluates and quantifies the acceleration generated by the method against the most common convex hull algorithms. An extra acceleration of at least four times when compared to previous existing preconditioning methods is found from experiments on a dataset.

An Empirical Evaluation of Preconditioning Data for Accelerating Convex Hull Computations

The convex hull describes the extent or shape of a set of data and is used ubiquitously in computational geometry. Common algorithms to construct the convex hull on a finite set of n points (x,y) range from O(nlogn) time to O(n) time. However, it is often the case that a heuristic procedure is applied to reduce the original set of n points to a set of s < n points which contains the hull and so accelerates the final hull finding procedure. We present an algorithm to precondition data before building a 2D convex hull with integer coordinates, with three distinct advantages. First, for all practical purposes, it is linear; second, no explicit sorting of data is required and third, the reduced set of s points is constructed such that it forms an ordered set that can be directly pipelined into an O(n) time convex hull algorithm. Under these criteria a fast (or O(n)) pre-conditioner in principle creates a fast convex hull (approximately O(n)) for an arbitrary set of points. The paper empirically evaluates and quantifies the acceleration generated by the method against the most common convex hull algorithms. An extra acceleration of at least four times when compared to previous existing preconditioning methods is found from experiments on a dataset.

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.

Data-Adaptive Modeling using Convex Regression

Thesis (Ph.D.)--University of Washington, 2016-08

Convex Optimization Algorithms and Statistical Bounds for Learning Structured Models

Thesis (Ph.D.)--University of Washington, 2016-08

Project AWARE Sets New Records in 2015: 1,000 to Service, Friendships & Community

Project AWARE is the Iowa DNR's volunteer river cleanup.

Of sets of offsets: Cumulative impacts and strategies for compensatory restoration

Biodiversity offsets are increasingly advocated as a flexible approach to managing the ecological costs of economic development. Arguably, however, this remains an area where policy-making has run ahead of science. A growing number of studies identify limitations of offsets in achieving ecologically sustainable outcomes, pointing to ethical and implementation issues that may undermine their effectiveness. We develop a novel system dynamic modelling framework to analyze the no net loss objective of development and biodiversity offsets. The modelling framework considers a marine-based example, where resource abundance depends on a habitat that is affected by a sequence of development projects, and biodiversity offsets are understood as habitat restoration actions. The model is used to explore the implications of four alternative offset management strategies for a regulator, which differ in how net loss is measured, and whether and how the cumulative impacts of development are considered. Our results confirm that, when it comes to offsets as a conservation tool, the devil lies in the details. Approaches to determining the magnitude of offsets required, as well as their timing and allocation among multiple developers, can result in potentially complex and undesired sets of economic incentives, with direct impacts on the ability to meet the overall objective of ecologically sustainable development. The approach and insights are of direct interest to conservation policy design in a broad range of marine and coastal contexts.