Dynamic Maps: Representations of Change in Geospatial Modeling and Visualization

By coining the descriptive phrase ―user-centric geographic cosmology, Goodchild (1998), challenges the geographically oriented to address GIS in the broadest imaginable context: as interlocutor between persons and geo-phenomena. This investigation responds both in a general way, and more specifically, to the representations of change in GIS modeling and visualization leading to dynamic mapping. The investigation, consisting of a report and a series of experiments, explores and demonstrates prototype workarounds that enhance GIS capabilities by drawing upon ideas, techniques, and components from agent-based modeling and visualization software, and suggests shifts at the conceptual, methodological, and technical levels. The workarounds and demonstrations presented here are four-dimensional visualizations, representing changes and behaviors of different types of entities such as living creatures, mobile assets, features, structures, and surfaces, using GIS, agent-based modeling and animation techniques. In a typical case, a creature begins as a point feature in GIS, becomes a mobile and interactive object in agent-based modeling, and is fleshed out to three dimensions in an animated representation. In contrast, a land surface remains much the same in all three stages. The experiments address change in location, orientation, shape, visual attributes, viewpoint, scale, and speed in applications representing predator-prey, search and destroy, sense and locate and urban sprawl. During the experiments, particular attention is paid to factors of modeling and visualization involved in engaging human sensing and cognitive abilities

Web Archive Services Framework for Tighter Integration Between the Past and Present Web

Web archives have contained the cultural history of the web for many years, but they still have a limited capability for access. Most of the web archiving research has focused on crawling and preservation activities, with little focus on the delivery methods. The current access methods are tightly coupled with web archive infrastructure, hard to replicate or integrate with other web archives, and do not cover all the users\u27 needs. In this dissertation, we focus on the access methods for archived web data to enable users, third-party developers, researchers, and others to gain knowledge from the web archives. We build ArcSys, a new service framework that extracts, preserves, and exposes APIs for the web archive corpus. The dissertation introduces a novel categorization technique to divide the archived corpus into four levels. For each level, we will propose suitable services and APIs that enable both users and third-party developers to build new interfaces. The first level is the content level that extracts the content from the archived web data. We develop ArcContent to expose the web archive content processed through various filters. The second level is the metadata level; we extract the metadata from the archived web data and make it available to users. We implement two services, ArcLink for temporal web graph and ArcThumb for optimizing the thumbnail creation in the web archives. The third level is the URI level that focuses on using the URI HTTP redirection status to enhance the user query. Finally, the highest level in the web archiving service framework pyramid is the archive level. In this level, we define the web archive by the characteristics of its corpus and building Web Archive Profiles. The profiles are used by the Memento Aggregator for query optimization

Natural Language Processing: Integration of Automatic and Manual Analysis

There is a current trend to combine natural language analysis with research questions from the humanities. This requires an integration of automatic analysis with manual analysis, e.g. to develop a theory behind the analysis, to test the theory against a corpus, to generate training data for automatic analysis based on machine learning algorithms, and to evaluate the quality of the results from automatic analysis. Manual analysis is traditionally the domain of linguists, philosophers, and researchers from other humanities disciplines, who are often not expert programmers. Automatic analysis, on the other hand, is traditionally done by expert programmers, such as computer scientists and more recently computational linguists. It is important to bring these communities, their tools, and data closer together, to produce analysis of a higher quality with less effort. However, promising cooperations involving manual and automatic analysis, e.g. for the purpose of analyzing a large corpus, are hindered by many problems: - No comprehensive set of interoperable automatic analysis components is available. - Assembling automatic analysis components into workflows is too complex. - Automatic analysis tools, exploration tools, and annotation editors are not interoperable. - Workflows are not portable between computers. - Workflows are not easily deployable to a compute cluster. - There are no adequate tools for the selective annotation of large corpora. - In automatic analysis, annotation type systems are predefined, but manual annotation requires customizability. - Implementing new interoperable automatic analysis components is too complex. - Workflows and components are not sufficiently debuggable and refactorable. - Workflows that change dynamically via parametrization are not readily supported. - The user has no control over workflows that rely on expert skills from a different domain, undocumented knowledge, or third-party infrastructures, e.g. web services. In cooperation with researchers from the humanities, we develop innovative technical solutions and designs to facilitate the use of automatic analysis and to promote the integration of manual and automatic analysis. To address these issues, we set foundations in four areas: - Usability is improved by reducing the complexity of the APIs for building workflows and creating custom components, improving the handling of resources required by such components, and setting up auto-configuration mechanisms. - Reproducibility is improved through a concept for self-contained, portable analysis components and workflows combined with a declarative modeling approach for dynamic parametrized workflows, that facilitates avoiding unnecessary auxiliary manual steps in automatic workflows. - Flexibility is achieved by providing an extensive collection of interoperable automatic analysis components. We also compare annotation type systems used by different automatic analysis components to locate design patterns that allow for customization when used in manual analysis tasks. - Interactivity is achieved through a novel "annotation-by-query" process combining corpus search with annotation in a multi-user scenario. The process is supported by a web-based tool. We demonstrate the adequacy of our concepts through examples which represent whole classes of research problems. Additionally, we integrated all our concepts into existing open-source projects, or we implemented and published them within new open-source projects

The Pharmacoepigenomics Informatics Pipeline and H-GREEN Hi-C Compiler: Discovering Pharmacogenomic Variants and Pathways with the Epigenome and Spatial Genome

Over the last decade, biomedical science has been transformed by the epigenome and spatial genome, but the discipline of pharmacogenomics, the study of the genetic underpinnings of pharmacological phenotypes like drug response and adverse events, has not. Scientists have begun to use omics atlases of increasing depth, and inferences relating to the bidirectional causal relationship between the spatial epigenome and gene expression, as a foundational underpinning for genetics research. The epigenome and spatial genome are increasingly used to discover causative regulatory variants in the significance regions of genome-wide association studies, for the discovery of the biological mechanisms underlying these phenotypes and the design of genetic tests to predict them. Such variants often have more predictive power than coding variants, but in the area of pharmacogenomics, such advances have been radically underapplied. The majority of pharmacogenomics tests are designed manually on the basis of mechanistic work with coding variants in candidate genes, and where genome wide approaches are used, they are typically not interpreted with the epigenome. This work describes a series of analyses of pharmacogenomics association studies with the tools and datasets of the epigenome and spatial genome, undertaken with the intent of discovering causative regulatory variants to enable new genetic tests. It describes the potent regulatory variants discovered thereby to have a putative causative and predictive role in a number of medically important phenotypes, including analgesia and the treatment of depression, bipolar disorder, and traumatic brain injury with opiates, anxiolytics, antidepressants, lithium, and valproate, and in particular the tendency for such variants to cluster into spatially interacting, conceptually unified pathways which offer mechanistic insight into these phenotypes. It describes the Pharmacoepigenomics Informatics Pipeline (PIP), an integrative multiple omics variant discovery pipeline designed to make this kind of analysis easier and cheaper to perform, more reproducible, and amenable to the addition of advanced features. It described the successes of the PIP in rediscovering manually discovered gene networks for lithium response, as well as discovering a previously unknown genetic basis for warfarin response in anticoagulation therapy. It describes the H-GREEN Hi-C compiler, which was designed to analyze spatial genome data and discover the distant target genes of such regulatory variants, and its success in discovering spatial contacts not detectable by preceding methods and using them to build spatial contact networks that unite disparate TADs with phenotypic relationships. It describes a potential featureset of a future pipeline, using the latest epigenome research and the lessons of the previous pipeline. It describes my thinking about how to use the output of a multiple omics variant pipeline to design genetic tests that also incorporate clinical data. And it concludes by describing a long term vision for a comprehensive pharmacophenomic atlas, to be constructed by applying a variant pipeline and machine learning test design system, such as is described, to thousands of phenotypes in parallel. Scientists struggled to assay genotypes for the better part of a century, and in the last twenty years, succeeded. The struggle to predict phenotypes on the basis of the genotypes we assay remains ongoing. The use of multiple omics variant pipelines and machine learning models with omics atlases, genetic association, and medical records data will be an increasingly significant part of that struggle for the foreseeable future.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/145835/1/ariallyn_1.pd

24th International Conference on Information Modelling and Knowledge Bases

In the last three decades information modelling and knowledge bases have become essentially important subjects not only in academic communities related to information systems and computer science but also in the business area where information technology is applied. The series of European – Japanese Conference on Information Modelling and Knowledge Bases (EJC) originally started as a co-operation initiative between Japan and Finland in 1982. The practical operations were then organised by professor Ohsuga in Japan and professors Hannu Kangassalo and Hannu Jaakkola in Finland (Nordic countries). Geographical scope has expanded to cover Europe and also other countries. Workshop characteristic - discussion, enough time for presentations and limited number of participants (50) / papers (30) - is typical for the conference. Suggested topics include, but are not limited to: 1. Conceptual modelling: Modelling and specification languages; Domain-specific conceptual modelling; Concepts, concept theories and ontologies; Conceptual modelling of large and heterogeneous systems; Conceptual modelling of spatial, temporal and biological data; Methods for developing, validating and communicating conceptual models. 2. Knowledge and information modelling and discovery: Knowledge discovery, knowledge representation and knowledge management; Advanced data mining and analysis methods; Conceptions of knowledge and information; Modelling information requirements; Intelligent information systems; Information recognition and information modelling. 3. Linguistic modelling: Models of HCI; Information delivery to users; Intelligent informal querying; Linguistic foundation of information and knowledge; Fuzzy linguistic models; Philosophical and linguistic foundations of conceptual models. 4. Cross-cultural communication and social computing: Cross-cultural support systems; Integration, evolution and migration of systems; Collaborative societies; Multicultural web-based software systems; Intercultural collaboration and support systems; Social computing, behavioral modeling and prediction. 5. Environmental modelling and engineering: Environmental information systems (architecture); Spatial, temporal and observational information systems; Large-scale environmental systems; Collaborative knowledge base systems; Agent concepts and conceptualisation; Hazard prediction, prevention and steering systems. 6. Multimedia data modelling and systems: Modelling multimedia information and knowledge; Contentbased multimedia data management; Content-based multimedia retrieval; Privacy and context enhancing technologies; Semantics and pragmatics of multimedia data; Metadata for multimedia information systems. Overall we received 56 submissions. After careful evaluation, 16 papers have been selected as long paper, 17 papers as short papers, 5 papers as position papers, and 3 papers for presentation of perspective challenges. We thank all colleagues for their support of this issue of the EJC conference, especially the program committee, the organising committee, and the programme coordination team. The long and the short papers presented in the conference are revised after the conference and published in the Series of “Frontiers in Artificial Intelligence” by IOS Press (Amsterdam). The books “Information Modelling and Knowledge Bases” are edited by the Editing Committee of the conference. We believe that the conference will be productive and fruitful in the advance of research and application of information modelling and knowledge bases. Bernhard Thalheim Hannu Jaakkola Yasushi Kiyok

Financial Crimes in Web3-empowered Metaverse: Taxonomy, Countermeasures, and Opportunities

At present, the concept of metaverse has sparked widespread attention from the public to major industries. With the rapid development of blockchain and Web3 technologies, the decentralized metaverse ecology has attracted a large influx of users and capital. Due to the lack of industry standards and regulatory rules, the Web3-empowered metaverse ecosystem has witnessed a variety of financial crimes, such as scams, code exploit, wash trading, money laundering, and illegal services and shops. To this end, it is especially urgent and critical to summarize and classify the financial security threats on the Web3-empowered metaverse in order to maintain the long-term healthy development of its ecology. In this paper, we first outline the background, foundation, and applications of the Web3 metaverse. Then, we provide a comprehensive overview and taxonomy of the security risks and financial crimes that have emerged since the development of the decentralized metaverse. For each financial crime, we focus on three issues: a) existing definitions, b) relevant cases and analysis, and c) existing academic research on this type of crime. Next, from the perspective of academic research and government policy, we summarize the current anti-crime measurements and technologies in the metaverse. Finally, we discuss the opportunities and challenges in behavioral mining and the potential regulation of financial activities in the metaverse. The overview of this paper is expected to help readers better understand the potential security threats in this emerging ecology, and to provide insights and references for financial crime fighting.Comment: 24pages, 6 figures, 140 references, submitted to the Open Journal of the Computer Societ

Generation and Applications of Knowledge Graphs in Systems and Networks Biology

The acceleration in the generation of data in the biomedical domain has necessitated the use of computational approaches to assist in its interpretation. However, these approaches rely on the availability of high quality, structured, formalized biomedical knowledge. This thesis has the two goals to improve methods for curation and semantic data integration to generate high granularity biological knowledge graphs and to develop novel methods for using prior biological knowledge to propose new biological hypotheses. The first two publications describe an ecosystem for handling biological knowledge graphs encoded in the Biological Expression Language throughout the stages of curation, visualization, and analysis. Further, the second two publications describe the reproducible acquisition and integration of high-granularity knowledge with low contextual specificity from structured biological data sources on a massive scale and support the semi-automated curation of new content at high speed and precision. After building the ecosystem and acquiring content, the last three publications in this thesis demonstrate three different applications of biological knowledge graphs in modeling and simulation. The first demonstrates the use of agent-based modeling for simulation of neurodegenerative disease biomarker trajectories using biological knowledge graphs as priors. The second applies network representation learning to prioritize nodes in biological knowledge graphs based on corresponding experimental measurements to identify novel targets. Finally, the third uses biological knowledge graphs and develops algorithmics to deconvolute the mechanism of action of drugs, that could also serve to identify drug repositioning candidates. Ultimately, the this thesis lays the groundwork for production-level applications of drug repositioning algorithms and other knowledge-driven approaches to analyzing biomedical experiments

Trusted Provenance with Blockchain - A Blockchain-based Provenance Tracking System for Virtual Aircraft Component Manufacturing

The importance of provenance in the digital age has led to significant interest in utilizing blockchain technology for tamper-proof storage of provenance data. This thesis proposes a blockchain-based provenance tracking system for the certification of aircraft components. The aim is to design and implement a system that can ensure the trustworthy, tamper-resistant storage of provenance documents originating from an aircraft manufacturing process. To achieve this, the thesis presents a systematic literature review, which provides a comprehensive overview of existing works in the field of provenance and blockchain technology. After obtaining strategies to utilize blockchain for the storage of provenance data on the blockchain, a system was designed to meet the requirements of stakeholders in the aviation industry. The thesis utilized a systematic approach to gather requirements by conducting interviews with stakeholders. The system was implemented using a combination of smart contracts and a graphical user interface to provide tamper-resistant, traceable storage of relevant data on a transparent blockchain. An evaluation based on the requirements identified during the requirement engineering process found that the proposed system meets all identified requirements. Overall, this thesis offers insight into a potential application of blockchain technology in the aviation industry and provides a valuable resource for researchers and industry professionals seeking to leverage blockchain technology for provenance tracking and certification purpose