Domain-specific Properties Research Articles

Analysis of schema structures in the Linked Open Data graph based on unique subject URIs, pay-level domains, and vocabulary usage

The Linked Open Data (LOD) graph represents a web-scale distributed knowledge graph interlinking information about entities across various domains. A core concept is the lack of pre-defined schema which actually allows for flexibly modelling data from all kinds of domains. However, Linked Data does exhibit schema information in a twofold way: by explicitly attaching RDF types to the entities and implicitly by using domain-specific properties to describe the entities. In this paper, we present and apply different techniques for investigating the schematic information encoded in the LOD graph at different levels of granularity. We investigate different information theoretic properties of so-called Unique Subject URIs (USUs) and measure the correlation between the properties and types that can be observed for USUs on a large-scale semantic graph data set. Our analysis provides insights into the information encoded in the different schema characteristics. Two major findings are that implicit schema information is far more discriminative and that applications involving schema information based on either types or properties alone will only capture between 63.5 and 88.1 % of the schema information contained in the data. As the level of discrimination depends on how data providers model and publish their data, we have conducted in a second step an investigation based on pay-level domains (PLDs) as well as the semantic level of vocabularies. Overall, we observe that most data providers combine up to 10 vocabularies to model their data and that every fifth PLD uses a highly structured schema.

Propagation of constraints along model transformations using triple graph grammars and borrowed context

Fundamental properties of model transformations based on triple graph grammars (TGGs) have been studied extensively including syntactical correctness, completeness, termination and functional behavior. But up to now, it is an open problem how domain specific properties that are valid for a source model can be preserved along model transformations such that the transformed properties are valid for the derived target model. This question shows up in enterprise modeling. Here, modeling activities related to different domains are handled by different parties, and their models need to be consistent and integrated into one holistic enterprise model later on. So, support for decentralized modeling processes is needed. One technical aspect of the needed support in this case is the (bidirectional) propagation of constraints because that enables one party to understand and check the constraints of another party. Therefore, we analyze in the framework of TGGs how to propagate constraints from a source model to an integrated model and, afterwards, to a target model, such that, whenever the source model satisfies the source constraint, also the integrated and target model satisfy the corresponding integrated and target constraint. In our main new results we show under which conditions this is possible.

On Alethic Disjunctivism

Alethic pluralism is the view that truth requires different treatment in different domains of discourse. The basic idea is that different properties play important roles in the analysis of truth in different domains of discourse, such as discourse about the material world, moral discourse, and mathematical discourse, to take three examples. Alethic disjunctivism is a kind of alethic pluralism, and is the view that truth is to be identified with the disjunctive property that is formed using each of the domain-specific properties as disjuncts (i.e., in the view's simplest form, truth is the property of either having domain-specific property 1, or domain-specific property 2, and so on). This paper evaluates the prospects for alethic disjunctivism. In particular, it outlines the proper formulation of the view, and assesses some concerns that the disjunctive property lacks the pedigree necessary to be considered a truth property. I begin by briefly outlining the motivations for alethic pluralism, before noting four general constraints on formulations of the view. I then consider a ‘simple’ formulation of alethic disjunctivism, and recommend an amendment. I then demonstrate that the candidate truth property specified by this new formulation is able to meet the central constraints required for it to be considered a viable formulation of alethic pluralism. The final part of this demonstration involves making some distinctions between different kinds of disjunctive properties, and arguing that disjunctive properties are not necessarily highly abundant properties: some are more sparse than others.

A framework for testing first-order logic axioms in program verification

Program verification systems based on automated theorem provers rely on user-provided axioms in order to verify domain-specific properties of code. However, formulating axioms correctly (that is, formalizing properties of an intended mathematical interpretation) is non-trivial in practice, and avoiding or even detecting unsoundness can sometimes be difficult to achieve. Moreover, speculating soundness of axioms based on the output of the provers themselves is not easy since they do not typically give counterexamples. We adopt the idea of model-based testing to aid axiom authors in discovering errors in axiomatizations. To test the validity of axioms, users define a computational model of the axiomatized logic by giving interpretations to the function symbols and constants in a simple declarative programming language. We have developed an axiom testing framework that helps automate model definition and test generation using off-the-shelf tools for meta-programming, property-based random testing, and constraint solving. We have experimented with our tool to test the axioms used in Auto-Cert, a program verification system that has been applied to verify aerospace flight code using a first-order axiomatization of navigational concepts, and were able to find counterexamples for a number of axioms.

Propagation of Constraints along Model Transformations Based on Triple Graph Grammars

Model transformations based on triple graph grammars (TGGs) have been applied in several practical case studies and they convince by their intuitive and descriptive way of specifying bidirectional model transformations. Moreover, fundamental properties have been extensively studied including syntactical correctness, completeness, termination and functional behaviour. But up to now, it is an open problem how domain specific properties that are valid for a source model can be preserved along model transformations such that the transformed properties are valid for the derived target model. In this paper, we analyse in the framework of TGGs how to propagate constraints from a source model to an integrated and target model such that, whenever the source model satisfies the source constraint also the integrated and target model satisfy the corresponding integrated and target constraint. In our main new results we show under which conditions this is possible. The case study shows how this result is successfully applied for the propagation of security constraints in enterprise modelling between business and IT models.

Structural characteristics of the hydrophobic patch of azurin and its interaction with p53: a site-directed spin labeling study

Site-directed spin labeling (SDSL) is a powerful tool for monitoring protein structure, dynamics and conformational changes. In this study, the domain-specific properties of azurin and its interaction with p53 were studied using this technique. Mutations of six residues, that are located in the hydrophobic patch of azurin, were prepared and spin labeled. Spectra of the six azurin mutants in solution showed that spin labeled residues 45 and 63 are in a very restricted environment, residues 59 and 65 are in a spacious environment and have free movement, and residues 49 and 51 are located in a relatively closed pocket. Polarity experiments confirmed these results. The changes observed in the spectra of spin labeled azurin upon interaction with p53 indicate that the hydrophobic patch is involved in this interaction. Our results provide valuable insight into the topographic structure of the hydrophobic domain of azurin, as well as direct evidence of its interaction with p53 in solution via the hydrophobic patch. Cytotoxicity studies of azurin mutants showed that residues along the hydrophobic patch are important for its cytotoxicity.

The Metaphysics of Mixed Inferences: Problems with Functionalist Accounts of Alethic Pluralism

Alethic pluralists argue truth is a metaphysically robust higher-order property that is multiply realized by a set of diverse and domain-specific subvening alethic properties. The higher-order truth property legitimizes mixed inferences and accounts for a univocal truth predicate. Absent of this higher-order property, pluralists lack an account of the validity of mixed inferences and an adequate semantics for the truth predicate and thereby appear forced to abandon the central tenets of alethic pluralism. I argue the use of many-valued logics to support pluralism fails to address the pluralist’s metaphysical problem regarding mixed inferences and mixed truth functional connectives. The high degree of heterogeneity of the alethic realizers (unlike the realizers for pain) challenges the plausibility of a single higher-order functional property. A functional property with such a heterogeneous base cannot be projectable at a theoretically significant level. The problem with mixed inferences and truth functions is but one symptom of the deeper projectability problem.

Safe functional reactive programming through dependent types

Functional Reactive Programming (FRP) is an approach to reactive programming where systems are structured as networks of functions operating on signals. FRP is based on the synchronous data-flow paradigm and supports both continuous-time and discrete-time signals (hybrid systems). What sets FRP apart from most other languages for similar applications is its support for systems with dynamic structure and for higher-order reactive constructs. Statically guaranteeing correctness properties of programs is an attractive proposition. This is true in particular for typical application domains for reactive programming such as embedded systems. To that end, many existing reactive languages have type systems or other static checks that guarantee domain-specific properties, such as feedback loops always being well-formed. However, they are limited in their capabilities to support dynamism and higher-order data-flow compared with FRP. Thus, the onus of ensuring such properties of FRP programs has so far been on the programmer as established static techniques do not suffice. In this paper, we show how dependent types allow this concern to be addressed. We present an implementation of FRP embedded in the dependently-typed language Agda, leveraging the type system of the host language to craft a domain-specific (dependent) type system for FRP. The implementation constitutes a discrete, operational semantics of FRP, and as it passes the Agda type, coverage, and termination checks, we know the operational semantics is total, which means our type system is safe.

An innovative approach for testing bioinformatics programs using metamorphic testing

BackgroundRecent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered.ResultsWe propose to use a novel software testing technique, metamorphic testing (MT), to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs), thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics.ConclusionThis paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work represents a significant step towards software reliability in bioinformatics.

8.3.1 Bridging the Chasm ‐ Tracing from Architectural Frameworks to SysML

AbstractA conspicuous disconnect exists between a MoDAF/DoDAF Architectural Model (MAF) and any subsequent Systems Engineering modeling activities. MAF permits the modeling of 'system‐of‐systems' and they both facilitate the capture of the high‐level properties of a system's interfaces. However, how is this critical information communicated to an organization contracted to develop the real system? How does an organization ensure traceability from MAF artifacts and any subsequent Systems Engineering artifacts? In addition to heavyweight and lightweight mapping, SysML offers bridges that provide traceability between artifacts in MAF and any subsequent system specification. The concepts used by the different languages are examined as well as mapping from MAF to SysML. Then this paper explores allocation and requirements traceability. Due to the inherent extensibility of a UML‐based model, properties not prescribed by MAF (‘Risk’) can be added to a MAF and the two approaches to flow‐down can be augmented with these domain specific properties.

HOTTest

Model-based testing is an effective black-box test generation technique for applications. Existing model-based testing techniques, however, fail to capture implicit domain-specific properties, as they overtly rely on software artifacts such as design documents, requirement specifications, etc., for completeness of the test model. This article presents a technique, HOTTest, which uses a strongly typed domain-specific language to model the system under test. This allows extraction of type-related system invariants, which can be related to various domain-specific properties of the application. Thus, using HOTTest, it is possible to automatically extract and embed domain-specific requirements into the test models. In this article we describe HOTTest, its principles and methodology, and how it is possible to relate domain-specific properties to specific type constraints. HOTTest is described using the example of HaskellDB, which is a Haskell-based embedded domain-specific language for relational databases. We present an example application of the technique and compare the results to some other commonly used Model-based test automation techniques like ASML-based testing, UML-based testing, and EFSM-based testing.

Structure-function relationships in UCP1, UCP2 and chimeras: EPR analysis and retinoic acid activation of UCP2.

Uncoupling proteins (UCPs) are composed of three repeated domains of approximately 100 amino acids each. We have used chimeras of UCP1 and UCP2, and electron paramagnetic resonance (EPR), to investigate domain specific properties of these UCPs. Questions include: are the effects of nucleotide binding on proton transport solely mediated by amino acids in the third C-terminal domain, and are the amino acids in the first two domains involved in retinoic or fatty acid activation? We first confirmed that our reconstitution system produced UCP1 that exhibited known properties, such as activation by fatty acids and inhibition of proton transport by purine nucleotides. Our results confirm the observations reported for recombinant yeast that retinoic acid, but not fatty acids known to activate UCP1, activates proton transport by UCP2 and that this activation is insensitive to nucleotide inhibition. We constructed chimeras in which the last domains of UCP1 or UCP2 were switched and tested for activation by fatty acids or retinoic acid and inhibition by nucleotides. U1U2 is composed of mUCP1 (amino acids 1-198) and hUCP2 (amino acids 211-309). Fatty acids activated proton transport of U1U2 and GTP mediated inhibition. In the other chimeric construct U2U1, hUCP2 (amino acids 1-210) and mUCP1 (amino acids 199-307), retinoic acid still acted as an activator, but no inhibition was observed with GTP. Using EPR, a method well suited to the analysis of the structure of membrane proteins such as UCPs, we confirmed that UCP2 binds nucleotides. The EPR data show large structural changes in UCP1 and UCP2 on exposure to ATP, implying that a putative nucleotide-binding site is present on UCP2. EPR analysis also demonstrated changes in conformation of UCP1/UCP2 chimeras following exposure to purine nucleotides. These data demonstrate that a nucleotide-binding site is present in the C-terminal domain of UCP2. This domain was able to inhibit proton transport only when fused to the N-terminal part of UCP1 (chimera U1U2). Thus, residues involved in nucleotide inhibition of proton transport are located in the two first carrier motifs of UCP1. While these results are consistent with previously reported effects of the C-terminal domain on nucleotide binding, they also demonstrate that interactions with the N-terminal domains are necessary to inhibit proton transport. Finally, the results suggest that proteins such as UCP2 may transport protons even though they are not responsible for basal or cold-induced thermogenesis.

A state space analysis of propose-and-revise

A central research topic in the area of knowledge engineering is the reuse of problem-solving methods for developing knowledge based systems. For being able to reuse a problem-solving method it is important to know under which restrictions a problem-solving method is appropriate to solve a given problem. This paper describes the problem-solving method propose-and-revise as well as the way this problem-solving method searches in its problem space for a solution. A quantitative analysis of the efficiency of this search process is given. Additionally, task and domain specific properties and restrictions and their influence on the efficiency of the search process are considered. For these purposes an instance of the problem-solving method is transformed to a corresponding instance of a Stanford Research Institute Problem Solver (STRIPS) planning system. Then the problem-solving method is considered as an additional control strategy for such a planning system. By this way the various insights and analysis results which are available in the area of planning systems may be exploited for the analysis of problem-solving methods.

Exploiting domain-specific properties: compiling parallel dynamic neural network algorithms into efficient code

Domain-specific constraints can be exploited to implement compiler optimizations that are not otherwise feasible. Compilers for neural network learning algorithms can achieve near-optimal colocality of data and processes and near-optimal balancing of load over processors, even for dynamically irregular problems. This is impossible for general programs, but restricting programs to the neural algorithm domain allows for the exploitation of domain-specific properties. The operations performed by neural algorithms are broadcasts, reductions, and object-local operations only; the load distribution is regular with respect to the (perhaps irregular) network topology; changes of network topology occur only from time to time. A language, compilation techniques, and a compiler implementation on the MasPar MP-1 are described and quantitative results for the effects of various optimizations used in the compiler are shown. Conservative experiments with weight pruning algorithms yield performance improvements of 27 percent due to load balancing and 195 percent improvement is achieved due to data locality, both compared to unoptimized versions. Two other optimizations-connection allocation and selecting the number of replicates-speed programs up by about 50 percent and 100 percent, respectively. This work can be viewed as a case study in exploiting domain-specific information; some of the principles presented here may apply to other domains as well.

Studies in Inductive Inference in Infancy

Imitation of events was used to explore the inductive generalizations that 14-month-olds have made about animals, vehicles, and household artifacts. In Experiment 1 infants generalized domain-specific properties such as drinking to animals but not to vehicles, whereas they generalized domain-neutral properties such as going into a building to exemplars from both domains. The next four experiments showed that infants tend to interpret animal events very broadly, for example, construing a dog merely as a land animal rather than as a differentiated kind in its own right. Infants were somewhat more selective in their construals of vehicles. Experiment 6 showed that 14-month-olds also generalize “basic-level properties” very broadly. For example, they chose a pan to demonstrate drinking almost as often as a cup and fed a bone to a bird as often as to a dog. By 20 months, their selections narrowed appropriately for artifacts, but were still overgeneralized for natural kinds. The experiments indicate that infants tend to generalize their early experiences broadly across domains, often across exemplars that have a variety of different surface characteristics. The data suggest that it is the conceptual meaning of objects, rather than their physical features, that controls early associative learning.

V. DOMAIN‐SPECIFIC PROPERTIES

Monographs of the Society for Research in Child DevelopmentVolume 63, Issue 1 p. 92-103 V. DOMAIN-SPECIFIC PROPERTIES First published: 03 February 2011 https://doi.org/10.1111/j.1540-5834.1998.tb02750.xAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Volume63, Issue1January 1998Pages 92-103 RelatedInformation

9] Lipase engineering: A widow into structure-function relationships

Utilization of genetic engineering techniques to create novel functional lipases has increased knowledge of structure-function relationships in this important class of enzymes. The examples of engineered lipases presented in this chapter addressed the investigation of domain-specific properties, heparin binding, and subunit orientation. Conclusions reached are credible because the designed lipases retained catalytic activity, implying native, or near-native, conformation. This approach has demonstrated vigor by determining the domain location of several important enzyme functions and by providing the first evidence that LPL subunits are arranged in a head-to-tail orientation. In conjunction with physical techniques, such as crystallography and nuclear magnetic resonance spectroscopy, the engineered lipase approach could reveal new insights into the mechanism by which lipolysis is accomplished. The studies described here represent only the first attempts to explore that subject; more sophisticated lipase engineering will be used in future as a window into structure-function relationships.