05441 Abstracts Collection -- Managing and Mining Genome Information: Frontiers in Bioinformatics

From 30.10.05 to 04.11.05, the Dagstuhl Seminar 05441 ``Managing and Mining Genome Information: Frontiers in Bioinformatics\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Classification management and use in a networked environment : the case of the Universal Decimal Classification

In the Internet information space, advanced information retrieval (IR) methods and automatic text processing are used in conjunction with traditional knowledge organization systems (KOS). New information technology provides a platform for better KOS publishing, exploitation and sharing both for human and machine use. Networked KOS services are now being planned and developed as powerful tools for resource discovery. They will enable automatic contextualisation, interpretation and query matching to different indexing languages. The Semantic Web promises to be an environment in which the quality of semantic relationships in bibliographic classification systems can be fully exploited. Their use in the networked environment is, however, limited by the fact that they are not prepared or made available for advanced machine processing. The UDC was chosen for this research because of its widespread use and its long-term presence in online information retrieval systems. It was also the first system to be used for the automatic classification of Internet resources, and the first to be made available as a classification tool on the Web. The objective of this research is to establish the advantages of using UDC for information retrieval in a networked environment, to highlight the problems of automation and classification exchange, and to offer possible solutions. The first research question was is there enough evidence of the use of classification on the Internet to justify further development with this particular environment in mind? The second question is what are the automation requirements for the full exploitation of UDC and its exchange? The third question is which areas are in need of improvement and what specific recommendations can be made for implementing the UDC in a networked environment? A summary of changes required in the management and development of the UDC to facilitate its full adaptation for future use is drawn from this analysis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Master of Arts

thesisWhile the majority of linguistic theories concerned with semantic interpretation assume some form of compositionalityâ€"the notion that the meaning of a complex expression comes from the meanings of its constituent parts and their structural arrangementâ€" several linguistic phenomena exist which seem to challenge (strict) compositionality on both theoretical and empirical grounds. One such phenomena, termed complement coercion, has gained considerable attention in psycholinguistic research in recent years, as these constructions appear not only to involve a semantic type-mismatch, but also interpretive properties which are not overtly expressed. Given recent arguments that the so-called “coercion verbs” may not constitute a homogeneous set with respect to the processing of coercion constructions, the present thesis conducts an experimental investigation into the empirical validity of this claim, reporting evidence that appears to challenge it. The findings that both aspectual and psychological verbs display evidence of complement coercion are discussed in terms of their implications for competing hypotheses

Algorithms for Geometric Optimization and Enrichment in Industrialized Building Construction

The burgeoning use of industrialized building construction, coupled with advances in digital technologies, is unlocking new opportunities to improve the status quo of construction projects being over-budget, delayed and having undesirable quality. Yet there are still several objective barriers that need to be overcome in order to fully realize the full potential of these innovations. Analysis of literature and examples from industry reveal the following notable barriers: (1) geometric optimization methods need to be developed for the stricter dimensional requirements in industrialized construction, (2) methods are needed to preserve model semantics during the process of generating an updated as-built model, (3) semantic enrichment methods are required for the end-of-life stage of industrialized buildings, and (4) there is a need to develop pragmatic approaches for algorithms to ensure they achieve required computational efficiency. The common thread across these examples is the need for developing algorithms to optimize and enrich geometric models. To date, a comprehensive approach paired with pragmatic solutions remains elusive. This research fills this gap by presenting a new approach for algorithm development along with pragmatic implementations for the industrialized building construction sector. Computational algorithms are effective for driving the design, analysis, and optimization of geometric models. As such, this thesis develops new computational algorithms for design, fabrication and assembly, onsite construction, and end-of-life stages of industrialized buildings. A common theme throughout this work is the development and comparison of varied algorithmic approaches (i.e., exact vs. approximate solutions) to see which is optimal for a given process. This is implemented in the following ways. First, a probabilistic method is used to simulate the accumulation of dimensional tolerances in order to optimize geometric models during design. Second, a series of exact and approximate algorithms are used to optimize the topology of 2D panelized assemblies to minimize material use during fabrication and assembly. Third, a new approach to automatically update geometric models is developed whereby initial model semantics are preserved during the process of generating an as-built model. Finally, a series of algorithms are developed to semantically enrich geometric models to enable industrialized buildings to be disassembled and reused. The developments made in this research form a rational and pragmatic approach to addressing the existing challenges faced in industrialized building construction. Such developments are shown not only to be effective in improving the status quo in the industry (i.e., improving cost, reducing project duration, and improving quality), but also for facilitating continuous innovation in construction. By way of assessing the potential impact of this work, the proposed algorithms can reduce rework risk during fabrication and assembly (65% rework reduction in the case study for the new tolerance simulation algorithm), reduce waste during manufacturing (11% waste reduction in the case study for the new panel unfolding and nesting algorithms), improve accuracy and automation of as-built model generation (model error reduction from 50.4 mm to 5.7 mm in the case study for the new parametric BIM updating algorithms), reduce lifecycle cost for adapting industrialized buildings (15% reduction in capital costs in the computational building configurator) and reducing lifecycle impacts for reusing structural systems from industrialized buildings (between 54% to 95% reduction in average lifecycle impacts for the approach illustrated in Appendix B). From a computational standpoint, the novelty of the algorithms developed in this research can be described as follows. Complex geometric processes can be codified solely on the innate properties of geometry – that is, by parameterizing geometry and using methods such as combinatorial optimization, topology can be optimized and semantics can be automatically enriched for building assemblies. Employing the use of functional discretization (whereby continuous variable domains are converted into discrete variable domains) is shown to be highly effective for complex geometric optimization approaches. Finally, the algorithms encapsulate and balance the benefits posed by both parametric and non-parametric schemas, resulting in the ability to achieve both high representational accuracy and semantically rich information (which has previously not been achieved or demonstrated). In summary, this thesis makes several key improvements to industrialized building construction. One of the key findings is that rather than pre-emptively determining the best suited algorithm for a given process or problem, it is often more pragmatic to derive both an exact and approximate solution and then decide which is optimal to use for a given process. Generally, most tasks related to optimizing or enriching geometric models is best solved using approximate methods. To this end, this research presents a series of key techniques that can be followed to improve the temporal performance of algorithms. The new approach for developing computational algorithms and the pragmatic demonstrations for geometric optimization and enrichment are expected to bring the industry forward and solve many of the current barriers it faces

Social and Semantic Contexts in Tourist Mobile Applications

The ongoing growth of the World Wide Web along with the increase possibility of access information through a variety of devices in mobility, has defi nitely changed the way users acquire, create, and personalize information, pushing innovative strategies for annotating and organizing it. In this scenario, Social Annotation Systems have quickly gained a huge popularity, introducing millions of metadata on di fferent Web resources following a bottom-up approach, generating free and democratic mechanisms of classi cation, namely folksonomies. Moving away from hierarchical classi cation schemas, folksonomies represent also a meaningful mean for identifying similarities among users, resources and tags. At any rate, they suff er from several limitations, such as the lack of specialized tools devoted to manage, modify, customize and visualize them as well as the lack of an explicit semantic, making di fficult for users to bene fit from them eff ectively. Despite appealing promises of Semantic Web technologies, which were intended to explicitly formalize the knowledge within a particular domain in a top-down manner, in order to perform intelligent integration and reasoning on it, they are still far from reach their objectives, due to di fficulties in knowledge acquisition and annotation bottleneck. The main contribution of this dissertation consists in modeling a novel conceptual framework that exploits both social and semantic contextual dimensions, focusing on the domain of tourism and cultural heritage. The primary aim of our assessment is to evaluate the overall user satisfaction and the perceived quality in use thanks to two concrete case studies. Firstly, we concentrate our attention on contextual information and navigation, and on authoring tool; secondly, we provide a semantic mapping of tags of the system folksonomy, contrasted and compared to the expert users' classi cation, allowing a bridge between social and semantic knowledge according to its constantly mutual growth. The performed user evaluations analyses results are promising, reporting a high level of agreement on the perceived quality in use of both the applications and of the speci c analyzed features, demonstrating that a social-semantic contextual model improves the general users' satisfactio

The classification of gene products in the molecular biology domain: Realism, objectivity, and the limitations of the Gene Ontology

Background: Controlled vocabularies in the molecular biology domain exist to facilitate data integration across database resources. One such tool is the Gene Ontology (GO), a classification designed to act as a universal index for gene products from any species. The Gene Ontology is used extensively in annotating gene products and analysing gene expression data, yet very little research exists from a library and information science perspective exploring the design principles, philosophy and social role of ontologies in biology. Aim: To explore how molecular biologists, in creating the Gene Ontology, devised guidelines and rules for determining which scientific concepts are included in the ontology, and the criteria for how these concepts are represented. Methods: A domain analysis approach was used to devise a mixed methodology to study the design of the Gene Ontology. Concept analysis of a GO term and a critical discourse analysis of GO developer mailing list texts were used to test whether ontological realism is a tenable basis for constructing objective ontologies. A comparison of the current GO vocabulary construction guidelines and a study of the reasons why GO terms are removed from the ontology further explored the justifications for the design of the Gene Ontology. Finally, a content analysis of published GO papers examined how authors use and cite GO data and terminology. Results: Gene Ontology terms can be presented according to different epistemologies for concepts, indicating that ontological realism is not the only way objective ontologies can be designed. Social roles and the exercise of power were found to play an important role in determining ontology content, and poor synonym control, a lack of clear warrant for deciding terminology and arbitrary decisions to delete and invent new terms undermine the objectivity and universal applicability of the Gene Ontology. Authors exhibited poor compliance with GO data citation policies, and in re-wording and misquoting GO terminology, risk exacerbating the semantic problems this controlled vocabulary was designed to solve. Conclusions: The failure of the Gene Ontology to define what is meant by a molecular function, the exercise of power by GO developers in clearing contentious concepts from the ontology, and the strict adherence to ontological realism, which marginalises social and subjective ways of classifying scientific concepts, limits the utility of the ontology as a tool to unify the molecular biology domain. These limitations to the Gene Ontology design could be overcome with the development of lighter, pluralistic, user-controlled ‘open ontologies’ for gene products that can work alongside more traditional, ‘top-down’ developed vocabularies

Maximum Governance: Managerial Populism and Violent Infrastructures in the New India

Alongside rampant state violence, the systematic disenfranchisement of minorities and a draconian approach to dissent, since 2014 India has been the site of a relentless project of managerial competence. Projects like the Aadhaar biometric identity programme, the government’s embrace of performance indices, and the construction of a massive new capital in central Delhi – the case studies at the heart of this thesis – promise a new, transforming nation, characterised by Narendra Modi’s slogan “maximum governance, minimum government”. Dramatizing efficiency and transparency against the perceived inefficiency and corruption of the old India, such projects’ aesthetics allow a violent Hindu majoritarian government to claim global respectability and leadership and underwrite an aspirational managerial populism. At the same time, the apparatus of maximum governance – which encompasses not just PR and advertising but also novel forms of measurement and identification, laws, regulations, organizational processes and built environments – is bringing about radical shifts in Indian state and society. Empowering new kinds of agents and institutions, these infrastructures are at the core of a vast project of neoliberal redistribution, leading to exclusion and impoverishment, while cementing Hindu majoritarian power. Most worryingly, the ever-shifting ambiguity of maximum governance elides contradiction and short circuits failure, presenting a predicament for democracy and dissent

Discovering Conserved cis-Regulatory Elements That Regulate Expression in Caenorhabditis elegans

The aim of this dissertation is two-fold:: 1) To catalog all cis-regulatory elements within the intergenic and intronic regions surrounding every gene in C.elegans: i.e. the regulome) and: 2) to determine which cis-regulatory elements are associated with expression under specific conditions. We initially use PhyloNet to predict conserved motifs with instances in about half of the protein-coding genes. This initial first step was valuable as it recovered some known elements and cis-regulatory modules. Yet the results had a lot of redundant motifs and sites, and the approach was not efficiently scalable to the entire regulome of C. elegans or other higher-order eukaryotes. Magma: Multiple Aligner of Genomic Multiple Alignments) overcomes these shortcomings by using efficient clustering and memory management algorithms. Additionally, it implements a fast greedy set-cover solution to significantly reduce redundant motifs. These differences make Magma ~70 times faster than PhyloNet and Magma-based predictions occur near ~99% of all C. elegans protein-coding genes. Furthermore, we show tractable scaling for higher-order eukaryotes with larger regulomes. Finally, we demonstrate that a Magma-predicted motif, which represents the binding specificity for HLH-30, plays a critical role in the host-defense to pathogenic infections. This novel finding shows that hlh-30(-) animals are more susceptible to S. aureus and P. aeruginosa than their wild type counterparts