User-friendly Syntax Research Articles

A Constrained Factor Mixture Model for Detecting Careless Responses that is Simple to Implement

Using constrained factor mixture models (FMM) for careless response identification is still in its infancy. Existing models have overly restrictive statistical assumptions that do not identify all types of careless respondents. The current paper presents a novel constrained FMM model with more reasonable assumptions that capture both longstring and random careless respondents. We provide a comprehensive comparison of the statistical assumptions between the proposed model and two previous constrained models. The proposed model was evaluated using both real data ( N = 1,455) and statistical simulation. The results showed that the model had a superior fit, stronger convergent validity with other indicators of careless responding, more accurate parameter recovery and more accurate identification of careless respondents when compared to its predecessors. The proposed model does not require additional data collection effort, and thus researchers can routinely use it to control careless responses. We provide user-friendly syntax with detailed explanations online to facilitate its use.

Testing the Nonlinearity Assumption Underlying the Use of Reverse-Keyed Items: A Logical Response Perspective.

Researchers often assume a strong, linear relationship between regular- and reverse-keyed items, with responses on regular-keyed items (e.g., agree) perfectly mirroring those on reverse-keyed items (e.g., disagree). The current research challenges this received view and propounds a possible nonlinear relationship, partly due to the logical tendency of midlevel respondents to disagree with both types of items. In four examples (reported human height, job satisfaction, positive-negative affect, and self-esteem; total N = 50,544), a nonlinear model consistently explained additional item variance beyond a linear model. We further demonstrate that this relationship is moderated by item characteristics such as item extremity (job satisfaction) and item softening (self-esteem). Suboptimal modeling of the relationship may result in the apparent bidmensionality of a construct that characterizes regular- and reverse-keyed items as separate factors. User-friendly syntax for the examination of nonlinearity is provided to enhance the accessibility of the procedure.

Executable biochemical space for specification and analysis of biochemical systems.

Computational systems biology provides multiple formalisms for modelling of biochemical processes among which the rule-based approach is one of the most suitable. Its main advantage is a compact and precise mechanistic description of complex processes. However, state-of-the-art rule-based languages still suffer several shortcomings that limit their use in practice. In particular, the elementary (low-level) syntax and semantics of rule-based languages complicate model construction and maintenance for users outside computer science. On the other hand, mathematical models based on differential equations (ODEs) still make the most typical used modelling framework. In consequence, robust re-interpretation and integration of models are difficult, thus making the systems biology paradigm technically challenging. Though several high-level languages have been developed at the top of rule-based principles, none of them provides a satisfactory and complete solution for semi-automated description and annotation of heterogeneous biophysical processes integrated at the cellular level. We present the second generation of a rule-based language called Biochemical Space Language (BCSL) that combines the advantages of different approaches and thus makes an effort to overcome several problems of existing solutions. BCSL relies on the formal basis of the rule-based methodology while preserving user-friendly syntax of plain chemical equations. BCSL combines the following aspects: the level of abstraction that hides structural and quantitative details but yet gives a precise mechanistic view of systems dynamics; executable semantics allowing formal analysis and consistency checking at the level of the language; universality allowing the integration of different biochemical mechanisms; scalability and compactness of the specification; hierarchical specification and composability of chemical entities; and support for genome-scale annotation.

A logical specification language for ontologies in the system “Binary Model of Knowledge”

Abstract We describe the language LLS-1 for logical specifying ontologies written in “Binary Model of Knowledge” (BMK). BMK is the system intended for specifying heavy-weight ontologies by means of conceptual-type languages. The language LLS-1 has a user-friendly syntax in style of the Manchester syntax for OWL. We also determine a deduction method for LLS-1.

RFuzzy: Syntax, semantics and implementation details of a simple and expressive fuzzy tool over Prolog

We present the RFuzzy framework, a Prolog-based tool for representing and reasoning with fuzzy information. The advantages of our framework in comparison to previous tools along this line of research are its easy, user-friendly syntax, and its expressivity through the availability of default values and types. In this approach we describe the formal syntax, the operational semantics and the declarative semantics of RFuzzy (based on a lattice). A least model semantics, a least fixpoint semantics and an operational semantics are introduced and their equivalence is proven. We provide a real implementation that is free and available. (It can be downloaded from http://babel.ls.fi.upm.es/software/rfuzzy/.) Besides implementation details, we also discuss some actual applications using RFuzzy.

CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks

Model checking has proven to be a useful analysis technique not only for concurrent systems, but also for genetic regulatory networks ( Grns). Applications of model checking in systems biology have revealed that temporal logics should be able to capture both branching-time and fairness properties (needed for specifying multistability and oscillation properties, respectively). At the same time, they should have a user-friendly syntax easy to employ by non-experts. In this paper, we define Computation Tree Regular Logic ( Ctrl), an extension of Ctl with regular expressions and fairness operators that attempts to match these criteria. Ctrl subsumes both Ctl and Ltl, and has a reduced set of temporal operators indexed by regular expressions. We also develop a translation of Ctrl into Hennessy–Milner Logic with Recursion ( HmlR), an equational variant of the modal μ -calculus. This has allowed us to obtain an on-the-fly model checker with diagnostic for Ctrl by directly reusing the verification technology available in the Cadp toolbox. We illustrate the application of the Ctrl model checker by analyzing the Grn controlling the carbon starvation response of Escherichia coli.

Maude MSOS Tool

Modular structural operational semantics (MSOS) is a new framework that allows structural operational semantics (SOS) specifications to be made modular in the sense of not imposing the redefinition of transition rules, which is the case in SOS specifications, when an extension is made. Maude MSOS tool (MMT) is an executable environment for MSOS implemented in Full Maude as a realization of a semantics-preserving mapping between MSOS and rewriting logic (RWL). The modular SOS definition formalism (MSDF) is the specification language supported by MMT. MSDF syntax is quite close to MSOS mathematical notation and user-friendly by allowing several syntactic components to be left implicit. MMT joins the support for modularity with a user-friendly syntax together with the efficient execution and analysis of the Maude engine. We have used MMT in several different examples from programming languages semantics and concurrent systems. This paper reports on the development of MMT and its application to these two classes of specifications.

Synchronized regular expressions

Text manipulation is one of the most common tasks for everyone using a computer. The increasing number of textual information in electronic format that every computer user collects everyday also increases the need of more powerful tools to interact with texts. Indeed, much work has been done to provide simple and versatile tools that can be useful for the most common text manipulation tasks. Regular Expressions (RE), introduced by Kleene, are well known in the formal language theory. RE have been extended in various ways, depending on the application of interest. In almost all the implementations of RE search algorithms (e.g. the egrep [15] UNIX command, or the Perl [20] language pattern matching constructs) we find backreferences, i.e. expressions that make reference to the string matched by a previous subexpression. Generally speaking, it seems that all kinds of synchronizations between subexpressions in a RE can be very useful when interacting with texts. In this paper we introduce the Synchronized Regular Expressions (SRE) as an extension of the Regular Expressions. We use SRE to present a formal study of the already known backreferences extension, and of a new extension proposed by us, which we call the synchronized exponents. Moreover, since we are dealing with formalisms that should have a practical utility and be used in real applications, we have the problem of how to present SRE to the final users. Therefore, in this paper we also propose a user-friendly syntax for SRE to be used in implementations of SRE-powered search algorithms.

Synchronized Regular Expressions

Text manipulation is one of the most common tasks for everyone using a computer. The increasing number of textual information in electronic format that every computer user collects everyday stresses the need of more powerful tools to interact with texts. Indeed, much work has been done to provide nonprogramming tools that can be useful for the most common text manipulation issues. Regular Expressions (RE), introduced by Kleene, are well–known in the formal language theory. RE received several extensions, depending on the application of interest. In almost all the implementations of RE search algorithms (e.g. the egrep [A] UNIX command, or the Perl [17] language pattern matching constructs) we find backreferences (as defind in [1]), i.e. expressions that make reference to the string matched by a previous subexpression. Generally speaking, it seems that all the kinds of synchronizations between subexpressions in a RE can be very useful when interacting with texts. Therefore, we introduce the Synchronized Regular Expressions (SRE) as a derivation of the Regular Expressions. We use SRE to present a formal study of the already known backreferences extension, and of a new extension proposed by us, which we call the synchronized exponents. Moreover, since we are talking about formalisms that should have a practical utility and can be used in the real world, we have the problem of how to present SRE to the final users. Therefore, in this paper we also propose a user–friendly syntax for SRE to be used in implementations of SRE–powered search algorithms.

User-friendly syntax: design and presentation

A user-friendly programming system should have a user-friendly syntax; natural and systematic, easy to understand and use. Syntax should allow substitution of semantically similar constructs by each other. Syntax should also be flexible and allow several variants of syntactic notations to reduce the burden of memorizing rigid syntactic notations and to make it possible for a user to think more about ‘what’ instead of ‘how’. Nowadays programming languages, e.g. Ada, do not obey these principles. Their complexity is mainly caused by their nonsystematic and rigid syntax. This together with unformal and ambiguous presentation of syntax makes Ada difficult to use and Ada parsers inefficient. Uniform, natural and flexible syntax, where several variants of syntactic notations and abbreviations are allowed and minor syntactic errors automatically corrected, can be introduced by systematic top-down design using multi-level grammars. Systematic design and presentation allows greatly improved syntax without increasing size of the syntax grammar and the complexity of the parser.