Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Pediatric residents\u27 use of jargon during counseling about newborn genetic screening results

OBJECTIVE. The goal was to investigate pediatric residents’ usage of jargon during discussions about positive newborn screening test results. METHODS. An explicit-criteria abstraction procedure was used to identify jargon usage and explanations in transcripts of encounters between residents and standardized parents of a fictitious infant found to carry cystic fibrosis or sickle cell hemoglobinopathy. Residents were recruited from a series of educational workshops on how to inform parents about positive newborn screening test results. The time lag from jargon words to explanations was measured by using “statements,” each of which contained 1 subject and 1 predicate. RESULTS. Duplicate abstraction revealed reliability K of 0.92. The average number of unique jargon words per transcript was 20; the total jargon count was 72.3 words. There was an average of 7.5 jargon explanations per transcript, but the explained/ total jargon ratio was only 0.17. When jargon was explained, the average time lag from the first usage to the explanation was 8.2 statements. CONCLUSION. The large number of jargon words and the small number of explanations suggest that physicians’ counseling about newborn screening may be too complex for some parents

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Client-contractor bargaining on net present value in project scheduling with limited resources

The client-contractor bargaining problem addressed here is in the context of a multi-mode resource constrained project scheduling problem with discounted cash flows, which is formulated as a progress payments model. In this model, the contractor receives payments from the client at predetermined regular time intervals. The last payment is paid at the first predetermined payment point right after project completion. The second payment model considered in this paper is the one with payments at activity completions. The project is represented on an Activity-on-Node (AON) project network. Activity durations are assumed to be deterministic. The project duration is bounded from above by a deadline imposed by the client, which constitutes a hard constraint. The bargaining objective is to maximize the bargaining objective function comprised of the objectives of both the client and the contractor. The bargaining objective function is expected to reflect the two-party nature of the problem environment and seeks a compromise between the client and the contractor. The bargaining power concept is introduced into the problem by the bargaining power weights used in the bargaining objective function. Simulated annealing algorithm and genetic algorithm approaches are proposed as solution procedures. The proposed solution methods are tested with respect to solution quality and solution times. Sensitivity analyses are conducted among different parameters used in the model, namely the profit margin, the discount rate, and the bargaining power weights

Client-contractor bargaining on net present value in project scheduling with limited resources

The client-contractor bargaining problem addressed here is in the context of a multi-mode resource constrained project scheduling problem with discounted cash flows, which is formulated as a progress payments model. In this model, the contractor receives payments from the client at predetermined regular time intervals. The last payment is paid at the first predetermined payment point right after project completion. The second payment model considered in this paper is the one with payments at activity completions. The project is represented on an Activity-on-Node (AON) project network. Activity durations are assumed to be deterministic. The project duration is bounded from above by a deadline imposed by the client, which constitutes a hard constraint. The bargaining objective is to maximize the bargaining objective function comprised of the objectives of both the client and the contractor. The bargaining objective function is expected to reflect the two-party nature of the problem environment and seeks a compromise between the client and the contractor. The bargaining power concept is introduced into the problem by the bargaining power weights used in the bargaining objective function. Simulated annealing algorithm and genetic algorithm approaches are proposed as solution procedures. The proposed solution methods are tested with respect to solution quality and solution times. Sensitivity analyses are conducted among different parameters used in the model, namely the profit margin, the discount rate, and the bargaining power weights

A decision support system for fostering smart energy efficient districts

The role of ICT is becoming prominent in tackling some of the urban societal challenges such as energy wastage and increasing carbon emissions. In this context, the concept of DAREED aims to deliver an integrated decision support system (DSS) to drive energy efficiency and low carbon activities at both a building and district level. The main aim of this paper is to present the technical concept of the Best Practices recommendation component of the DAREED system. This component seeks to compare and identify existing best practices to recommend practical actions to various stakeholders (e.g. building managers, citizens) in order to improve energy performance considering the global needs of a building. This paper also discusses the context of the three field trial sites (based in UK, Spain and Italy) in which the DAREED platform along with the best practices tool is to be tested and validated.This work evolved in the context of the project DAREED (Decision support Advisor for innovative business models and useR engagement for smart Energy Efficient Districts), www.dareed.eu, a project cofunded by the EC within FP7, Grant agreement no: 609082

Capturing Scientific Knowledge on Medical Risk Factors

In this paper, we describe a model for representing scientific knowledge of risk factors in medicine in an explicit format which enables its use for automated reasoning. The resulting model supports linking the conclusions of up-to-date clinical research with data relating to individual patients. This model, which we have implemented as an ontology-based system using Linked Data, enables the capture of risk factor knowledge and serves as a translational research tool to apply that knowledge to assist with patient treatment, lifestyle, and education. Knowledge captured using this model can be disseminated for other intelligent systems to use for a variety of purposes, for example, to explore the state of the available medical knowledge

Ocean feature recognition using genetic algorithms with fuzzy fitness functions (GA/F3)

A model for genetic algorithms with semantic nets is derived for which the relationships between concepts is depicted as a semantic net. An organism represents the manner in which objects in a scene are attached to concepts in the net. Predicates between object pairs are continuous valued truth functions in the form of an inverse exponential function (e sub beta lxl). 1:n relationships are combined via the fuzzy OR (Max (...)). Finally, predicates between pairs of concepts are resolved by taking the average of the combined predicate values of the objects attached to the concept at the tail of the arc representing the predicate in the semantic net. The method is illustrated by applying it to the identification of oceanic features in the North Atlantic

Optimization as a design strategy. Considerations based on building simulation-assisted experiments about problem decomposition

In this article the most fundamental decomposition-based optimization method - block coordinate search, based on the sequential decomposition of problems in subproblems - and building performance simulation programs are used to reason about a building design process at micro-urban scale and strategies are defined to make the search more efficient. Cyclic overlapping block coordinate search is here considered in its double nature of optimization method and surrogate model (and metaphore) of a sequential design process. Heuristic indicators apt to support the design of search structures suited to that method are developed from building-simulation-assisted computational experiments, aimed to choose the form and position of a small building in a plot. Those indicators link the sharing of structure between subspaces ("commonality") to recursive recombination, measured as freshness of the search wake and novelty of the search moves. The aim of these indicators is to measure the relative effectiveness of decomposition-based design moves and create efficient block searches. Implications of a possible use of these indicators in genetic algorithms are also highlighted.Comment: 48 pages. 12 figures, 3 table

Combinatorial optimization and metaheuristics

Today, combinatorial optimization is one of the youngest and most active areas of discrete mathematics. It is a branch of optimization in applied mathematics and computer science, related to operational research, algorithm theory and computational complexity theory. It sits at the intersection of several fields, including artificial intelligence, mathematics and software engineering. Its increasing interest arises for the fact that a large number of scientific and industrial problems can be formulated as abstract combinatorial optimization problems, through graphs and/or (integer) linear programs. Some of these problems have polynomial-time (“efficient”) algorithms, while most of them are NP-hard, i.e. it is not proved that they can be solved in polynomial-time. Mainly, it means that it is not possible to guarantee that an exact solution to the problem can be found and one has to settle for an approximate solution with known performance guarantees. Indeed, the goal of approximate methods is to find “quickly” (reasonable run-times), with “high” probability, provable “good” solutions (low error from the real optimal solution). In the last 20 years, a new kind of algorithm commonly called metaheuristics have emerged in this class, which basically try to combine heuristics in high level frameworks aimed at efficiently and effectively exploring the search space. This report briefly outlines the components, concepts, advantages and disadvantages of different metaheuristic approaches from a conceptual point of view, in order to analyze their similarities and differences. The two very significant forces of intensification and diversification, that mainly determine the behavior of a metaheuristic, will be pointed out. The report concludes by exploring the importance of hybridization and integration methods