Formal Representation of the SS-DB Benchmark and Experimental Evaluation in EXTASCID

Evaluating the performance of scientific data processing systems is a difficult task considering the plethora of application-specific solutions available in this landscape and the lack of a generally-accepted benchmark. The dual structure of scientific data coupled with the complex nature of processing complicate the evaluation procedure further. SS-DB is the first attempt to define a general benchmark for complex scientific processing over raw and derived data. It fails to draw sufficient attention though because of the ambiguous plain language specification and the extraordinary SciDB results. In this paper, we remedy the shortcomings of the original SS-DB specification by providing a formal representation in terms of ArrayQL algebra operators and ArrayQL/SciQL constructs. These are the first formal representations of the SS-DB benchmark. Starting from the formal representation, we give a reference implementation and present benchmark results in EXTASCID, a novel system for scientific data processing. EXTASCID is complete in providing native support both for array and relational data and extensible in executing any user code inside the system by the means of a configurable metaoperator. These features result in an order of magnitude improvement over SciDB at data loading, extracting derived data, and operations over derived data.Comment: 32 pages, 3 figure

Evaluating the Impact of Data Placement to Spark and SciDB with an Earth Science Use Case

We investigate the impact of data placement for two Big Data technologies, Spark and SciDB, with a use case from Earth Science where data arrays are multidimensional. Simultaneously, this investigation provides an opportunity to evaluate the performance of the technologies involved. Two datastores, HDFS and Cassandra, are used with Spark for our comparison. It is found that Spark with Cassandra performs better than with HDFS, but SciDB performs better yet than Spark with either datastore. The investigation also underscores the value of having data aligned for the most common analysis scenarios in advance on a shared nothing architecture. Otherwise, repartitioning needs to be carried out on the fly, degrading overall performance

PROcess Based Diagnostics PROBE

Many of the aspects of the climate system that are of the greatest interest (e.g., the sensitivity of the system to external forcings) are emergent properties that arise via the complex interplay between disparate processes. This is also true for climate models most diagnostics are not a function of an isolated portion of source code, but rather are affected by multiple components and procedures. Thus any model-observation mismatch is hard to attribute to any specific piece of code or imperfection in a specific model assumption. An alternative approach is to identify diagnostics that are more closely tied to specific processes -- implying that if a mismatch is found, it should be much easier to identify and address specific algorithmic choices that will improve the simulation. However, this approach requires looking at model output and observational data in a more sophisticated way than the more traditional production of monthly or annual mean quantities. The data must instead be filtered in time and space for examples of the specific process being targeted.We are developing a data analysis environment called PROcess-Based Explorer (PROBE) that seeks to enable efficient and systematic computation of process-based diagnostics on very large sets of data. In this environment, investigators can define arbitrarily complex filters and then seamlessly perform computations in parallel on the filtered output from their model. The same analysis can be performed on additional related data sets (e.g., reanalyses) thereby enabling routine comparisons between model and observational data. PROBE also incorporates workflow technology to automatically update computed diagnostics for subsequent executions of a model. In this presentation, we will discuss the design and current status of PROBE as well as share results from some preliminary use cases

Raster Time Series: Learning and Processing

As the amount of remote sensing data is increasing at a high rate, due to great improvements in sensor technology, efficient processing capabilities are of utmost importance. Remote sensing data from satellites is crucial in many scientific domains, like biodiversity and climate research. Because weather and climate are of particular interest for almost all living organisms on earth, the efficient classification of clouds is one of the most important problems. Geostationary satellites such as Meteosat Second Generation (MSG) offer the only possibility to generate long-term cloud data sets with high spatial and temporal resolution. This work, therefore, addresses research problems on efficient and parallel processing of MSG data to enable new applications and insights. First, we address the lack of a suitable processing chain to generate a long-term Fog and Low Stratus (FLS) time series. We present an efficient MSG data processing chain that processes multiple tasks simultaneously, and raster data in parallel using the Open Computing Language (OpenCL). The processing chain delivers a uniform FLS classification that combines day and night approaches in a single method. As a result, it is possible to calculate a year of FLS rasters quite easy. The second topic presents the application of Convolutional Neural Networks (CNN) for cloud classification. Conventional approaches to cloud detection often only classify single pixels and ignore the fact that clouds are highly dynamic and spatially continuous entities. Therefore, we propose a new method based on deep learning. Using a CNN image segmentation architecture, the presented Cloud Segmentation CNN (CS-CNN) classifies all pixels of a scene simultaneously. We show that CS-CNN is capable of processing multispectral satellite data to identify continuous phenomena such as highly dynamic clouds. The proposed approach provides excellent results on MSG satellite data in terms of quality, robustness, and runtime, in comparison to Random Forest (RF), another widely used machine learning method. Finally, we present the processing of raster time series with a system for Visualization, Transformation, and Analysis (VAT) of spatio-temporal data. It enables data-driven research with explorative workflows and uses time as an integral dimension. The combination of various raster and vector data time series enables new applications and insights. We present an application that combines weather information and aircraft trajectories to identify patterns in bad weather situations

Data Infrastructure for Medical Research

While we are witnessing rapid growth in data across the sciences and in many applications, this growth is particularly remarkable in the medical domain, be it because of higher resolution instruments and diagnostic tools (e.g. MRI), new sources of structured data like activity trackers, the wide-spread use of electronic health records and many others. The sheer volume of the data is not, however, the only challenge to be faced when using medical data for research. Other crucial challenges include data heterogeneity, data quality, data privacy and so on. In this article, we review solutions addressing these challenges by discussing the current state of the art in the areas of data integration, data cleaning, data privacy, scalable data access and processing in the context of medical data. The techniques and tools we present will give practitioners — computer scientists and medical researchers alike — a starting point to understand the challenges and solutions and ultimately to analyse medical data and gain better and quicker insights

Adaptive Asynchronous Control and Consistency in Distributed Data Exploration Systems

Advances in machine learning and streaming systems provide a backbone to transform vast arrays of raw data into valuable information. Leveraging distributed execution, analysis engines can process this information effectively within an iterative data exploration workflow to solve problems at unprecedented rates. However, with increased input dimensionality, a desire to simultaneously share and isolate information, as well as overlapping and dependent tasks, this process is becoming increasingly difficult to maintain. User interaction derails exploratory progress due to manual oversight on lower level tasks such as tuning parameters, adjusting filters, and monitoring queries. We identify human-in-the-loop management of data generation and distributed analysis as an inhibiting problem precluding efficient online, iterative data exploration which causes delays in knowledge discovery and decision making. The flexible and scalable systems implementing the exploration workflow require semi-autonomous methods integrated as architectural support to reduce human involvement. We, thus, argue that an abstraction layer providing adaptive asynchronous control and consistency management over a series of individual tasks coordinated to achieve a global objective can significantly improve data exploration effectiveness and efficiency. This thesis introduces methodologies which autonomously coordinate distributed execution at a lower level in order to synchronize multiple efforts as part of a common goal. We demonstrate the impact on data exploration through serverless simulation ensemble management and multi-model machine learning by showing improved performance and reduced resource utilization enabling a more productive semi-autonomous exploration workflow. We focus on the specific genres of molecular dynamics and personalized healthcare, however, the contributions are applicable to a wide variety of domains

Earth Observation Open Science and Innovation

geospatial analytics; social observatory; big earth data; open data; citizen science; open innovation; earth system science; crowdsourced geospatial data; citizen science; science in society; data scienc

Maximizing Insight from Modern Economic Analysis

The last decade has seen a growing trend of economists exploring how to extract different economic insight from "big data" sources such as the Web. As economists move towards this model of analysis, their traditional workflow starts to become infeasible. The amount of noisy data from which to draw insights presents data management challenges for economists and limits their ability to discover meaningful information. This leads to economists needing to invest a great deal of energy in training to be data scientists (a catch-all role that has grown to describe the usage of statistics, data mining, and data management in the big data age), with little time being spent on applying their domain knowledge to the problem at hand. We envision an ideal workflow that generates accurate and reliable results, where results are generated in near-interactive time, and systems handle the "heavy lifting" required for working with big data. This dissertation presents several systems and methodologies that bring economists closer to this ideal workflow, helping them address many of the challenges faced in transitioning to working with big data sources like the Web. To help users generate accurate and reliable results, we present approaches to identifying relevant predictors in nowcasting applications, as well as methods for identifying potentially invalid nowcasting models and their inputs. We show how a streamlined workflow, combined with pruning and shared computation, can help handle the heavy lifting of big data analysis, allowing users to generate results in near-interactive time. We also present a novel user model and architecture for helping users avoid undesirable bias when doing data preparation: users interactively define constraints for transformation code and the data that the code produces, and an explain-and-repair system satisfies these constraints as best it can, also providing an explanation for any problems along the way. These systems combined represent a unified effort to streamline the transition for economists to this new big data workflow.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/144007/1/dol_1.pd

Pre-processing, classification and semantic querying of large-scale Earth observation spaceborne/airborne/terrestrial image databases: Process and product innovations.

By definition of Wikipedia, “big data is the term adopted for a collection of data sets so large and complex that it becomes difficult to process using on-hand database management tools or traditional data processing applications. The big data challenges typically include capture, curation, storage, search, sharing, transfer, analysis and visualization”. Proposed by the intergovernmental Group on Earth Observations (GEO), the visionary goal of the Global Earth Observation System of Systems (GEOSS) implementation plan for years 2005-2015 is systematic transformation of multisource Earth Observation (EO) “big data” into timely, comprehensive and operational EO value-adding products and services, submitted to the GEO Quality Assurance Framework for Earth Observation (QA4EO) calibration/validation (Cal/Val) requirements. To date the GEOSS mission cannot be considered fulfilled by the remote sensing (RS) community. This is tantamount to saying that past and existing EO image understanding systems (EO-IUSs) have been outpaced by the rate of collection of EO sensory big data, whose quality and quantity are ever-increasing. This true-fact is supported by several observations. For example, no European Space Agency (ESA) EO Level 2 product has ever been systematically generated at the ground segment. By definition, an ESA EO Level 2 product comprises a single-date multi-spectral (MS) image radiometrically calibrated into surface reflectance (SURF) values corrected for geometric, atmospheric, adjacency and topographic effects, stacked with its data-derived scene classification map (SCM), whose thematic legend is general-purpose, user- and application-independent and includes quality layers, such as cloud and cloud-shadow. Since no GEOSS exists to date, present EO content-based image retrieval (CBIR) systems lack EO image understanding capabilities. Hence, no semantic CBIR (SCBIR) system exists to date either, where semantic querying is synonym of semantics-enabled knowledge/information discovery in multi-source big image databases. In set theory, if set A is a strict superset of (or strictly includes) set B, then A B. This doctoral project moved from the working hypothesis that SCBIR computer vision (CV), where vision is synonym of scene-from-image reconstruction and understanding EO image understanding (EO-IU) in operating mode, synonym of GEOSS ESA EO Level 2 product human vision. Meaning that necessary not sufficient pre-condition for SCBIR is CV in operating mode, this working hypothesis has two corollaries. First, human visual perception, encompassing well-known visual illusions such as Mach bands illusion, acts as lower bound of CV within the multi-disciplinary domain of cognitive science, i.e., CV is conditioned to include a computational model of human vision. Second, a necessary not sufficient pre-condition for a yet-unfulfilled GEOSS development is systematic generation at the ground segment of ESA EO Level 2 product. Starting from this working hypothesis the overarching goal of this doctoral project was to contribute in research and technical development (R&D) toward filling an analytic and pragmatic information gap from EO big sensory data to EO value-adding information products and services. This R&D objective was conceived to be twofold. First, to develop an original EO-IUS in operating mode, synonym of GEOSS, capable of systematic ESA EO Level 2 product generation from multi-source EO imagery. EO imaging sources vary in terms of: (i) platform, either spaceborne, airborne or terrestrial, (ii) imaging sensor, either: (a) optical, encompassing radiometrically calibrated or uncalibrated images, panchromatic or color images, either true- or false color red-green-blue (RGB), multi-spectral (MS), super-spectral (SS) or hyper-spectral (HS) images, featuring spatial resolution from low (> 1km) to very high (< 1m), or (b) synthetic aperture radar (SAR), specifically, bi-temporal RGB SAR imagery. The second R&D objective was to design and develop a prototypical implementation of an integrated closed-loop EO-IU for semantic querying (EO-IU4SQ) system as a GEOSS proof-of-concept in support of SCBIR. The proposed closed-loop EO-IU4SQ system prototype consists of two subsystems for incremental learning. A primary (dominant, necessary not sufficient) hybrid (combined deductive/top-down/physical model-based and inductive/bottom-up/statistical model-based) feedback EO-IU subsystem in operating mode requires no human-machine interaction to automatically transform in linear time a single-date MS image into an ESA EO Level 2 product as initial condition. A secondary (dependent) hybrid feedback EO Semantic Querying (EO-SQ) subsystem is provided with a graphic user interface (GUI) to streamline human-machine interaction in support of spatiotemporal EO big data analytics and SCBIR operations. EO information products generated as output by the closed-loop EO-IU4SQ system monotonically increase their value-added with closed-loop iterations