Lauro Didier Lins

Nanocubes for Real-Time Exploration of Spatiotemporal Datasets

Consider real-time exploration of large multidimensional spatiotemporal datasets with billions of entries, each defined by a location, a time, and other attributes. Are certain attributes correlated spatially or temporally? Are there trends or outliers in the data? Answering these questions requires aggregation over arbitrary regions of the domain and attributes of the data. Many relational databases implement the well-known data cube aggregation operation, which in a sense precomputes every possible aggregate query over the database. Data cubes are sometimes assumed to take a prohibitively large amount of space, and to consequently require disk storage. In contrast, we show how to construct a data cube that fits in a modern laptops main memory, even for billions of entries; we call this data structure a nanocube. We present algorithms to compute and query a nanocube, and show how it can be used to generate well-known visual encodings such as heatmaps, histograms, and parallel coordinate plots. When compared to exact visualizations created by scanning an entire dataset, nanocube plots have bounded screen error across a variety of scales, thanks to a hierarchical structure in space and time. We demonstrate the effectiveness of our technique on a variety of real-world datasets, and present memory, timing, and network bandwidth measurements. We find that the timings for the queries in our examples are dominated by network and user-interaction latencies.

A comprehensive survey of cancer risks in extended families

Purpose:Cancer is familial; yet known cancer predisposition genes, as well as recognized environmental factors, explain only a small percentage of familial cancer clusters. This population-based description of cancer clustering describes patterns of cancer coaggregation suggestive of a genetic predisposition.Methods:Using a computerized genealogy of Utah families linked to a statewide cancer registry, we estimated the relative risks for 36 different cancer sites in first-, second-, and third-degree relatives of cancer cases, for each cancer site individually, and between cancer sites. We estimated the sex- and birth-year-specific rates for cancer using 1 million individuals in the resource. We applied these rates to groups of cases or relatives and compared the observed and expected numbers of cancers to estimate relative risks.Results:Many cancer sites show significantly elevated relative risks among distant relatives for cancer of the same site, strongly supporting a heritable contribution. Multiple combinations of cancer sites were observed among first-, second-, and third-degree relatives, suggesting the existence of heritable syndromes involving more than one cancer site.Conclusion:This complete description of coaggregation of cancer by site in a well-defined population provides a set of observations supporting heritable cancer predispositions and may support the existence of genetic factors for many different cancers.Genet Med 2012:14(1):107–114

VisMashup: Streamlining the Creation of Custom Visualization Applications

Visualization is essential for understanding the increasing volumes of digital data. However, the process required to create insightful visualizations is involved and time consuming. Although several visualization tools are available, including tools with sophisticated visual interfaces, they are out of reach for users who have little or no knowledge of visualization techniques and/or who do not have programming expertise. In this paper, we propose VisMashup, a new framework for streamlining the creation of customized visualization applications. Because these applications can be customized for very specific tasks, they can hide much of the complexity in a visualization specification and make it easier for users to explore visualizations by manipulating a small set of parameters. We describe the framework and how it supports the various tasks a designer needs to carry out to develop an application, from mining and exploring a set of visualization specifications (pipelines), to the creation of simplified views of the pipelines, and the automatic generation of the application and its interface. We also describe the implementation of the system and demonstrate its use in two real application scenarios.

An L-approach for packing (ℓ, w)-rectangles into rectangular and L-shaped pieces

This paper presents an approach using a recursive algorithm for packing (ℓ, w)-rectangles into larger rectangular and L-shaped pieces. Such a problem has actual applications for non-guillotine cutting and pallet/container loading. Our motivation for developing the L-approach is based on the fact that it can solve difficult pallet loading instances. Indeed, it is able to solve all testing problems (more than 20 000 representatives of infinite equivalence classes of the literature), including the 18 hard instances unresolved by other heuristics. We conjecture that the L-approach always finds optimum packings of (ℓ, w)-rectangles into rectangular pieces. Moreover, the approach may also be useful when dealing with cutting and packing problems involving L-shaped pieces.

BirdVis: Visualizing and Understanding Bird Populations

Birds are unrivaled windows into biotic processes at all levels and are proven indicators of ecological well-being. Understanding the determinants of species distributions and their dynamics is an important aspect of ecology and is critical for conservation and management. Through crowdsourcing, since 2002, the eBird project has been collecting bird observation records. These observations, together with local-scale environmental covariates such as climate, habitat, and vegetation phenology have been a valuable resource for a global community of educators, land managers, ornithologists, and conservation biologists. By associating environmental inputs with observed patterns of bird occurrence, predictive models have been developed that provide a statistical framework to harness available data for predicting species distributions and making inferences about species-habitat associations. Understanding these models, however, is challenging because they require scientists to quantify and compare multiscale spatialtemporal patterns. A large series of coordinated or sequential plots must be generated, individually programmed, and manually composed for analysis. This hampers the exploration and is a barrier to making the cross-species comparisons that are essential for coordinating conservation and extracting important ecological information. To address these limitations, as part of a collaboration among computer scientists, statisticians, biologists and ornithologists, we have developed BirdVis, an interactive visualization system that supports the analysis of spatio-temporal bird distribution models. BirdVis leverages visualization techniques and uses them in a novel way to better assist users in the exploration of interdependencies among model parameters. Furthermore, the system allows for comparative visualization through coordinated views, providing an intuitive interface to identify relevant correlations and patterns. We justify our design decisions and present case studies that show how BirdVis has helped scientists obtain new evidence for existing hypotheses, as well as formulate new hypotheses in their domain.

An n-tet graph approach for non-guillotine packings of n-dimensional boxes into an n-container

Abstract In this paper we propose a simple recursive uniform algorithm for the problem of packing n -dimensional boxes into an n -container. We are particularly concerned about the special case n =3 where the boxes can be packed in a given subset of their six possible positionings. Our method studies symmetries in the packings by the use of an ordered set of three directed graphs with the same edges (a 3- tet or triad ) and induced smaller structures of the same kind named minors . With the method, degeneracy and symmetry issues, which curtail the implicit enumeration to practically acceptable running times, become transparent. In order to illustrate the performance of the algorithm, computational results from solving randomly generated 3-D examples are presented and compared with the ones of a layers and knapsack approach. The present study has real world applications for the problems of pallet and container loading.

A First Study on Clustering Collections of Workflow Graphs

As workflow systems get more widely used, the number of workflows and the volume of provenance they generate has grown considerably. New tools and infrastructure are needed to allow users to interact with, reason about, and re-use this information. In this paper, we explore the use of clustering techniques to organize large collections of workflow and provenance graphs. We propose two different representations for these graphs and present an experimental evaluation, using a collection of 1,700 workflow graphs, where we study the trade-offs of these representations and the effectiveness of alternative clustering techniques.

Examining Statistics of Workflow Evolution Provenance: A First Study

Provenance (also referred to as audit trail, lineage, and pedigree) captures information about the steps used to generate a given data product. Such information provides documentation that is key to determining data quality and authorship, and necessary for preserving, reproducing, sharing and publishing the data. Workflow design, in particular for exploratory tasks (e.g., creating a visualization, mining a data set), requires an involved, trial-and-error process. To solve a problem, a user has to iteratively refine a workflow to experiment with different techniques and try different parameter values, as she formulates and test hypotheses. The maintenance of detailed provenance (or history) of this process has many benefits that go beyond documentation and result reproducibility. Notably, it supports several operations that facilitate exploration, including the ability to return to a previous workflow version in an intuitive way, to undo bad changes, to compare different workflows, and to be reminded of the actions that led to a particular result [2].

Enabling Advanced Visualization Tools in a Web-Based Simulation Monitoring System

Simulations that require massive amounts of computing power and generate tens of terabytes of data are now part of the daily lives of scientists. Analyzing and visualizing the results of these simulations as they are computed can lead not only to early insights but also to useful knowledge that can be provided as feedback to the simulation, avoiding unnecessary use of computing power. Our work is aimed at making advanced visualization tools available to scientists in a user-friendly, Web-based environment where they can be accessed anytime from anywhere. In the context of turbulent combustion for example, visualization is used to understand the coupling between turbulence and the turbulent mixing of scalars. Although isosurface generation is a useful technique in this scenario, computing and rendering isosurfaces one at a time is expensive and not particularly well-suited for such a Web-based framework. In this paper we propose the use of a summary structure, called contour tree, that captures the topological structure of a scalar field and guides the user in identifying useful isosurfaces. We have also designed an interface which has been integrated with a Web-based simulation monitoring system, that allows users to interact with and explore multiple isosurfaces.

A first study on strategies for generating workflow snippets

Workflows are increasingly being used to specify computational tasks, from simulations and data analysis to the creation of Web mashups. Recently, a number of public workflow repositories have become available, for example, myExperiment for scientific workflows, and Yahoo! Pipes. Workflow collections are also commonplace in many scientific projects. Having such collections opens up new opportunities for knowledge sharing and re-use. But for this to become a reality, mechanisms are needed that help users explore these collections and locate useful workflows. Although there has been work on querying workflows, not much attention has been given to presenting query results. In this paper, we take a first look at the requirements for workflow snippets and study alternative techniques for deriving concise, yet informative snippets.