Trends and concerns in digital cartography

CISRG discussion paper ;

A Comprehensive Survey of Isocontouring Methods: Applications, Limitations and Perspectives

This paper provides a comprehensive overview of approaches to the determination of isocontours and isosurfaces from given data sets. Different algorithms are reported in the literature for this purpose, which originate from various application areas, such as computer graphics or medical imaging procedures. In all these applications, the challenge is to extract surfaces with a specific isovalue from a given characteristic, so called isosurfaces. These different application areas have given rise to solution approaches that all solve the problem of isocontouring in their own way. Based on the literature, the following four dominant methods can be identified: the marching cubes algorithms, the tessellation-based algorithms, the surface nets algorithms and the ray tracing algorithms. With regard to their application, it can be seen that the methods are mainly used in the fields of medical imaging, computer graphics and the visualization of simulation results. In our work, we provide a broad and compact overview of the common methods that are currently used in terms of isocontouring with respect to certain criteria and their individual limitations. In this context, we discuss the individual methods and identify possible future research directions in the field of isocontouring

Brain Tumor Segmentation with Deep Neural Networks

In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we've found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test dataset reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster

Schema Migration from Relational Databases to NoSQL Databases with Graph Transformation and Selective Denormalization

We witnessed a dramatic increase in the volume, variety and velocity of data leading to the era of big data. The structure of data has become highly flexible leading to the development of many storage systems that are different from the traditional structured relational databases where data is stored in “tables,” with columns representing the lowest granularity of data. Although relational databases are still predominant in the industry, there has been a major drift towards alternative database systems that support unstructured data with better scalability leading to the popularity of “Not Only SQL.” Migration from relational databases to NoSQL databases has become a significant area of interest when it involves enormous volumes of data with a large number of concurrent users. Many migration methodologies have been proposed each focusing a specific NoSQL family. This paper proposes a heuristics based graph transformation method to migrate a relational database to MongoDB called Graph Transformation with Selective Denormalization and compares the migration with a table level denormalization method. Although this paper focuses on MongoDB, the heuristics algorithm is generalized enough to be applied to other NoSQL families. Experimental evaluation with TPC-H shows that Graph Transformation with Selective Denormalization migration method has lower query execution times with lesser hardware footprint like lower space requirement, disk I/O, CPU utilization compared to that of table level denormalization

FDive: Learning Relevance Models using Pattern-based Similarity Measures

The detection of interesting patterns in large high-dimensional datasets is difficult because of their dimensionality and pattern complexity. Therefore, analysts require automated support for the extraction of relevant patterns. In this paper, we present FDive, a visual active learning system that helps to create visually explorable relevance models, assisted by learning a pattern-based similarity. We use a small set of user-provided labels to rank similarity measures, consisting of feature descriptor and distance function combinations, by their ability to distinguish relevant from irrelevant data. Based on the best-ranked similarity measure, the system calculates an interactive Self-Organizing Map-based relevance model, which classifies data according to the cluster affiliation. It also automatically prompts further relevance feedback to improve its accuracy. Uncertain areas, especially near the decision boundaries, are highlighted and can be refined by the user. We evaluate our approach by comparison to state-of-the-art feature selection techniques and demonstrate the usefulness of our approach by a case study classifying electron microscopy images of brain cells. The results show that FDive enhances both the quality and understanding of relevance models and can thus lead to new insights for brain research.Comment: 12 pages, 7 figures, 2 tables, LaTeX; corrected typo; added DO

Re-assessing the diversity of negative strand RNA viruses in insects.

The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding-complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Big data reduction framework for value creation in sustainable enterprises

Value creation is a major sustainability factor for enterprises, in addition to profit maximization and revenue generation. Modern enterprises collect big data from various inbound and outbound data sources. The inbound data sources handle data generated from the results of business operations, such as manufacturing, supply chain management, marketing, and human resource management, among others. Outbound data sources handle customer-generated data which are acquired directly or indirectly from customers, market analysis, surveys, product reviews, and transactional histories. However, cloud service utilization costs increase because of big data analytics and value creation activities for enterprises and customers. This article presents a novel concept of big data reduction at the customer end in which early data reduction operations are performed to achieve multiple objectives, such as a) lowering the service utilization cost, b) enhancing the trust between customers and enterprises, c) preserving privacy of customers, d) enabling secure data sharing, and e) delegating data sharing control to customers. We also propose a framework for early data reduction at customer end and present a business model for end-to-end data reduction in enterprise applications. The article further presents a business model canvas and maps the future application areas with its nine components. Finally, the article discusses the technology adoption challenges for value creation through big data reduction in enterprise applications

Geographic Information Systems: The Developer\u27s Perspective

Geographic information systems, which manage data describing the surface of the earth, are becoming increasingly popular. This research details the current state of the art of geographic data processing in terms of the needs of the geographic information system developer. The research focuses chiefly on the geographic data model--the basic building block of the geographic information system. The two most popular models, tessellation and vector, are studied in detail, as well as a number of hybrid data models. In addition, geographic database management is discussed in terms of geographic data access and query processing. Finally, a pragmatic discussion of geographic information system design is presented covering such topics as distributed database considerations and artificial intelligence considerations