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At least 19 records

Standard Lexicons, Coding Systems and Ontologies for Interoperability and Semantic Computation in Imaging

Standard clinical terms, codes, and ontologies promote clarity and interoperability. Within radiology, there is a variety of relevant content resources, tools and technologies. These provide the basis for fundamental imaging workflows such as reporting and billing, and also facilitate a range of applications in quality improvement and research. This article reviews the key characteristics of lexicons, coding systems, and ontologies. A number of standards are described, including International Classification of Diseases-10-Clinical Modification (ICD-10-CM), Current Procedural Terminology (CPT), Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), Logical Observation Identifiers Names and Codes (LOINC), and RadLex. Tools for accessing this material are reviewed, such as the National Center for Biomedical Ontology BioPortal system. Web services are discussed as a mechanism for semantic application development. Several example systems, workflows, and research applications using semantic technology are also surveyed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Computing quality scores and uncertainty for approximate pattern matching in geospatial semantic graphs

Geospatial semantic graphs provide a robust foundation for representing and analyzing remote sensor data. In particular, they support a variety of pattern search operations that capture the spatial and temporal relationships among the objects and events in the data. However, in the presence of large data corpora, even a carefully constructed search query may return a large number of unintended matches. This work considers the problem of calculating a quality score for each match to the query, given that the underlying data are uncertain. As a result, we present a preliminary evaluation of three methods for determining both match quality scores and associated uncertainty bounds, illustrated in the context of an example based on overhead imagery data.

97 MATHEMATICS AND COMPUTING↗

High-performance Computing Applied to Semantic Databases

To-date, the application of high-performance computing resources to Semantic Web data has largely focused on commodity hardware and distributed memory platforms. In this paper we make the case that more specialized hardware can offer superior scaling and close to an order of magnitude improvement in performance. In particular we examine the Cray XMT. Its key characteristics, a large, global shared-memory, and processors with a memory-latency tolerant design, offer an environment conducive to programming for the Semantic Web and have engendered results that far surpass current state of the art. We examine three fundamental pieces requisite for a fully functioning semantic database: dictionary encoding, RDFS inference, and query processing. We show scaling up to 512 processors (the largest configuration we had available), and the ability to process 20 billion triples completely in-memory.

99 GENERAL AND MISCELLANEOUS↗

High-performance computing applied to semantic databases.

To-date, the application of high-performance computing resources to Semantic Web data has largely focused on commodity hardware and distributed memory platforms. In this paper we make the case that more specialized hardware can offer superior scaling and close to an order of magnitude improvement in performance. In particular we examine the Cray XMT. Its key characteristics, a large, global shared-memory, and processors with a memory-latency tolerant design, offer an environment conducive to programming for the Semantic Web and have engendered results that far surpass current state of the art. We examine three fundamental pieces requisite for a fully functioning semantic database: dictionary encoding, RDFS inference, and query processing. We show scaling up to 512 processors (the largest configuration we had available), and the ability to process 20 billion triples completely in-memory.

99 GENERAL AND MISCELLANEOUS↗

Semantic Annotation of Computational Components

This paper describes a methodology to specify machine-processable semantic descriptions of computational components to enable them to be shared and reused. A particular focus of this scheme is to enable automatic compositon of such components into simple work-flows.

Vanderbilt, Peter↗

Trend Analysis in Biomedical Texts via Vector Space Model Synonym Extraction

Accurate synonym extraction is a highly desired tool in computational semantics and natural language processing (NLP). Intrinsic to many current language models is the Vector Space Model (VSM) whereby linguistic properties are modeled by real vectors of small length compared to the document size. Here, several vector models are discussed. Utilizing the open source Word2Vec tool, temporal trends in biomedical abstracts from MEDLINE have been analyzed via a unique transformation matrix method. Additionally, accuracy of the word vector method and clustering of temporal trends are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗

Methods and apparatus for multi-resolution replication of files in a parallel computing system using semantic information

Techniques are provided for storing files in a parallel computing system using different resolutions. A method is provided for storing at least one file generated by a distributed application in a parallel computing system. The file comprises one or more of a complete file and a sub-file. The method comprises the steps of obtaining semantic information related to the file; generating a plurality of replicas of the file with different resolutions based on the semantic information; and storing the file and the plurality of replicas of the file in one or more storage nodes of the parallel computing system. The different resolutions comprise, for example, a variable number of bits and/or a different sub-set of data elements from the file. A plurality of the sub-files can be merged to reproduce the file.

97 MATHEMATICS AND COMPUTING↗

Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giant Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SLEEC: Semantics-Rich Libraries for Effective Exascale Computation. Final Technical Report

SLEEC (Semantics-rich Libraries for Effective Exascale Computation) was a project funded by the Department of Energy X-Stack Program, award number DE-SC0008629. The initial project period was September 2012–August 2015. The project was renewed for an additional year, expiring August 2016. Finally, the project received a no-cost extension, leading to a final expiry date of August 2017. Modern applications, especially those intended to run at exascale, are not written from scratch. Instead, they are built by stitching together various carefully-written, hand-tuned libraries. Correctly composing these libraries is difficult, but traditional compilers are unable to effectively analyze and transform across abstraction layers. Domain specific compilers integrate semantic knowledge into compilers, allowing them to transform applications that use particular domain-specific languages, or domain libraries. But they do not help when new domains are developed, or applications span multiple domains. SLEEC aims to fix these problems. To do so, we are building generic compiler and runtime infrastructures that are semantics-aware but not domain-specific. By performing optimizations related to the semantics of a domain library, the same infrastructure can be made generic and apply across multiple domains.

97 MATHEMATICS AND COMPUTING↗

Orbital Debris Ontology, Terminology, and Knowledge Modeling

The looming threat orbital debris poses to assets in orbit demands solutions. As the orbital population grows, so does this hazard, but so does the sea of data. The problem is also an opportunity for interdisciplinary innovation and cooperation. This paper focuses on the data and information management aspect of developing solutions for a sustainable and safe orbital space environment. The corresponding author’s in-progress work to develop an orbital debris domain ontology is summarized in order to discuss knowledge modeling for this domain. Methodological approaches of this effort can also contribute to standards efforts and address terminological and policy questions. Leveraging the growing volumes of orbital debris and space situational awareness (SSA) data will create a more complete picture of the orbital space environment. Part of the solution will be: consistent and correct data interpretation, sharing orbital debris and SSA data in one form or another, terminology development & harmonization, and knowledge or domain modeling. To facilitate this, [Rovetto, 2015/16] discussed ontology development for the orbital debris domain. This paper lists concepts from that paper, and subsequently developed concepts [2-9]. Ontology engineering is an interdisciplinary field related to knowledge representation and reasoning in artificial intelligence, semantic technologies and the so-called semantic web. An ontology is effectively a computable and semantically rich terminology that presents a knowledge or domain model for a topic area. Expressions of knowledge or assertions are stored using formally defined term. This knowledge base is reasoned over to yield answers to queries, among other things. Ontologies have been developed in knowledge-based projects across various disciplines, and used for such things as search engines, chatbots, enterprise knowledge graphs, etc. Ontologies support: interoperability, automated reasoning, data sharing and integration, data search and retrieval, and communicating the meaning of data. The Orbital Debris Ontology (ODO), and related ontologies [Rovetto & Kelso 2016] [Rovetto 2016, 2017], were proposed to help achieve this. ODO, for instance, is intended as a domain ontology that can be used across federated databases, offering an explicitly specified set of concepts describing the orbital debris domain. Its meaning-rich taxonomy will provide a sharable semantics for orbital debris data to, in part, consistently communicate the meaning of data to both humans and machines, and tag data elements in space object catalogs to help afford inference tasks, decision support, knowledge discovery, and information integration. ODO and the SSA ontology (SSAO) is part of the overall Orbital Space Domain Ontology concept, which is conceived as a broader domain reference ontology. It aims to provide a knowledge representation structure of the orbital space environment, a common semantic model, and develop a sharable terminology. Collectively this will provide common meaning for datasets, a high-level taxonomy or classification for orbital space objects, and thus means to characterize space objects. Ongoing efforts have included using visualizations, R, JSON-LD, and contemporary semantic technologies. Potential applications and interdisciplinary partnerships include web-based platforms, web apps, visualizations, and academia projects. Community input and participation may yield a more widely understood domain model as well as facilitate terminological standards. For example, the proposed conceptual, terminological and ontological analysis may contribute to such efforts as the Space Debris Mitigation Requirements in the International Standards Organization by developing more precise, consistent and coherent terms and definitions. Projects that seek to develop in-house ontologies can use ODO and related ontologies as domain reference ontologies. This paper was developed independent of author affiliations. Readers are encouraged to contact corresponding author(1) with general interest and potential opportunities to support or realize the described project.

Robert J. Rovetto↗

Behavior Computation for Smart Grid Software Analysis

Smart grid embedded software is subject to intrusion and compromise with potentially serious consequences. Current methods of cybersecurity analysis are increasingly challenged by the scope the problem. Oak Ridge National Laboratory (ORNL) is pioneering the new technology of software behavior computation to help address these risks. Software behavior computation and its instantiation in Function eXtraction (FX) systems apply mathematical foundations of denotational semantics to compute the behavior of software in all circumstances of use. Research has shown how to make the effects of recursion-theoretic limitations on this process arbitrarily small. Behavior computation operates on the functional semantics of programs, and is not subject to the limitations of syntactic recognition or testing. ORNL is applying FX technology to help evaluate cyber security properties in smart grid systems, with initial focus on vulnerabilities in embedded software that controls smart meters.

denotational semantics↗

Linking consistency with object/thread semantics - An approach to robust computation

This paper presents an object/thread based paradigm that links data consistency with object/thread semantics. The paradigm can be used to achieve a wide range of consistency semantics from strict atomic transactions to standard process semantics. The paradigm supports three types of data consistency. Object programmers indicate the type of consistency desired on a per-operation basis and the system performs automatic concurrency control and recovery management to ensure that those consistency requirements are met. This allows programmers to customize consistency and recovery on a per-application basis without having to supply complicated, custom recovery management schemes. The paradigm allows robust and nonrobust computation to operate concurrently on the same data in a well defined manner. The operating system needs to support only one vehicle of computation - the thread.

Chen, Raymond C.↗

Computer processing through distance-based quality score method in geospatial-temporal semantic graphs

A computer-implemented method of improving processing of overhead image data by a processor using a distance-based quality score in a geospatial-temporal semantic graph. An allowable range for each attribute in the subgraph search template is defined. For each match in a comparison, attribute values of each match element are compared against the preferred range and the allowable range to compute a corresponding distance of each match attribute from the subgraph search template. A corresponding overall match quality score is determined for each match from the subgraph search template, wherein determining the corresponding overall match qualities is performed using a corresponding required quality score and a corresponding optional quality score. All corresponding overall match quality scores are sorted into an ordered list and then displayed.

97 MATHEMATICS AND COMPUTING↗

Automatic Estimation of Verified Floating-Point Round-Off Errors via Static Analysis

This paper introduces a static analysis technique for computing formally verified round-off error bounds of floating-point functional expressions. The technique is based on a denotational semantics that computes a symbolic estimation of floating-point round-o errors along with a proof certificate that ensures its correctness. The symbolic estimation can be evaluated on concrete inputs using rigorous enclosure methods to produce formally verified numerical error bounds. The proposed technique is implemented in the prototype research tool PRECiSA (Program Round-o Error Certifier via Static Analysis) and used in the verification of floating-point programs of interest to NASA.

Moscato, Mariano↗