Measuring Coverage of Prolog Programs Using Mutation Testing

Testing is an important aspect in professional software development, both to avoid and identify bugs as well as to increase maintainability. However, increasing the number of tests beyond a reasonable amount hinders development progress. To decide on the completeness of a test suite, many approaches to assert test coverage have been suggested. Yet, frameworks for logic programs remain scarce. In this paper, we introduce a framework for Prolog programs measuring test coverage using mutations. We elaborate the main ideas of mutation testing and transfer them to logic programs. To do so, we discuss the usefulness of different mutations in the context of Prolog and empirically evaluate them in a new mutation testing framework on different examples.Comment: 16 pages, Accepted for presentation in WFLP 201

Proof Relevant Corecursive Resolution

Resolution lies at the foundation of both logic programming and type class context reduction in functional languages. Terminating derivations by resolution have well-defined inductive meaning, whereas some non-terminating derivations can be understood coinductively. Cycle detection is a popular method to capture a small subset of such derivations. We show that in fact cycle detection is a restricted form of coinductive proof, in which the atomic formula forming the cycle plays the role of coinductive hypothesis. This paper introduces a heuristic method for obtaining richer coinductive hypotheses in the form of Horn formulas. Our approach subsumes cycle detection and gives coinductive meaning to a larger class of derivations. For this purpose we extend resolution with Horn formula resolvents and corecursive evidence generation. We illustrate our method on non-terminating type class resolution problems.Comment: 23 pages, with appendices in FLOPS 201

Coinductive soundness of corecursive type class resolution

This work has been supported by the EPSRC grant “Coalgebraic Logic Programming for Type Inference” EP/K031864/1-2, EU Horizon 2020 grant “RePhrase: Refactoring Parallel Heterogeneous Resource-Aware Applications - a Software Engineering Approach” (ICT-644235), and by COST Action IC1202 (TACLe), supported by COST (European Cooperation in Science and Technology)Horn clauses and first-order resolution are commonly used to implement type classes in Haskell. Several corecursive extensions to type class resolution have recently been proposed, with the goal of allowing (co)recursive dictionary construction where resolution does not terminate. This paper shows, for the first time, that corecursive type class resolution and its extensions are coinductively sound with respect to the greatest Herbrand models of logic programs and that they are inductively unsound with respect to the least Herbrand models. We establish incompleteness results for various fragments of the proof system.Postprin

Planning intervention using dynamic assessments: A case study

Dynamic assessments (DA) of language have been shown to be a useful addition to the battery of tests used to diagnose language impairments in children, and to evaluate their skills. The current article explores the value of the information gained from a DA in planning intervention for a child with language impairment. A single case study was used to demonstrate the detailed qualitative information that can be derived from a DA procedure, and how that information may be used to elicit greater gains from intervention. The participant was a boy, aged 9, with a previously diagnosed language impairment. He was receiving language therapy regularly in a language resource base attached to his school. The CELF-3(UK) was used to monitor changes in his language, before and after two periods of intervention. The initial baseline phase consisted of regular ongoing language therapy. The second phase of therapy was modified by the speech and language therapist after receiving a report of the child’s performance on the Dynamic Assessment of Sentence Structure (DASS; Hasson et al., 2012), and observations of the child’s metalinguistic and metacognitive awareness. Greater gains observed in the second phase of therapy reflected the good modifiability shown by the child’s performance on the DASS

Effect of response format for clinical vignettes on reporting quality of physician practice

<p>Abstract</p> <p>Background</p> <p>Clinical vignettes have been used widely to compare quality of clinical care and to assess variation in practice, but the effect of different response formats has not been extensively evaluated. Our objective was to compare three clinical vignette-based survey response formats – open-ended questionnaire (A), closed-ended (multiple-choice) questionnaire with deceptive response items mixed with correct items (B), and closed-ended questionnaire with only correct items (C) – in rheumatologists' pre-treatment assessment for tumor-necrosis-factor (TNF) blocker therapy.</p> <p>Methods</p> <p><b><it>Study design</it></b>: Prospective randomized study. <b><it>Setting</it></b>: Rheumatologists attending the 2004 French Society of Rheumatology meeting. Physicians were given a vignette describing the history of a fictitious woman with active rheumatoid arthritis, who was a candidate for therapy with TNF blocking agents, and then were randomized to receive questionnaire A, B, or C, each containing the same four questions but with different response formats, that asked about their pretreatment assessment. <b><it>Measurements</it></b>: Long (recommended items) and short (mandatory items) checklists were developed for pretreatment assessment for TNF-blocker therapy, and scores were expressed on the basis of responses to questionnaires A, B, and C as the percentage of respondents correctly choosing explicit items on these checklists. <b><it>Statistical analysis</it></b>: Comparison of the selected items using pairwise Chi-square tests with Bonferonni correction for variables with statistically significant differences.</p> <p>Results</p> <p>Data for all surveys distributed (114 As, 118 Bs, and 118 Cs) were complete and available for analysis. The percentage of questionnaire A, B, and C respondents for whom data was correctly complete for the short checklist was 50.4%, 84.0% and 95.0%, respectively, and was 0%, 5.0% and 5.9%, respectively, for the long version. As an example, 65.8%, 85.7% and 95.8% of the respondents of A, B, and C questionnaires, respectively, correctly identified the need for tuberculin skin test (p < 0.0001).</p> <p>Conclusion</p> <p>In evaluating clinical practice with use of a clinical vignette, a multiple-choice format rather than an open-ended format overestimates physician performance. The insertion of deceptive response items mixed with correct items in closed-ended (multiple-choice) questionnaire failed to avoid this overestimation.</p

Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up

During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by Geobacter sulfurreducens, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of G. sulfurreducens, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of G. sulfurreducens cells grown in the 100-ml serum bottles. However, it significantly improved the growth behavior of cells grown in the 5-liter bioreactor by reducing the lag phase from 24 h to 6 h, while providing higher yield than in the 100-ml serum bottles

Hybrid Rules with Well-Founded Semantics

A general framework is proposed for integration of rules and external first order theories. It is based on the well-founded semantics of normal logic programs and inspired by ideas of Constraint Logic Programming (CLP) and constructive negation for logic programs. Hybrid rules are normal clauses extended with constraints in the bodies; constraints are certain formulae in the language of the external theory. A hybrid program is a pair of a set of hybrid rules and an external theory. Instances of the framework are obtained by specifying the class of external theories, and the class of constraints. An example instance is integration of (non-disjunctive) Datalog with ontologies formalized as description logics. The paper defines a declarative semantics of hybrid programs and a goal-driven formal operational semantics. The latter can be seen as a generalization of SLS-resolution. It provides a basis for hybrid implementations combining Prolog with constraint solvers. Soundness of the operational semantics is proven. Sufficient conditions for decidability of the declarative semantics, and for completeness of the operational semantics are given

Analysis of clinical uncertainties by health professionals and patients: an example from mental health

<p>Abstract</p> <p>Background</p> <p>The first step in practising Evidence Based Medicine (EBM) has been described as translating clinical uncertainty into a structured and focused clinical question that can be used to search the literature to ascertain or refute that uncertainty. In this study we focus on questions about treatments for schizophrenia posed by mental health professionals and patients to gain a deeper understanding about types of questions asked naturally, and whether they can be reformulated into structured and focused clinical questions.</p> <p>Methods</p> <p>From a survey of uncertainties about the treatment of schizophrenia we describe, categorise and analyse the type of questions asked by mental health professionals and patients about treatment uncertainties for schizophrenia. We explore the value of mapping from an unstructured to a structured framework, test inter-rater reliability for this task, develop a linguistic taxonomy, and cross tabulate that taxonomy with elements of a well structured clinical question.</p> <p>Results</p> <p>Few of the 78 Patients and 161 clinicians spontaneously asked well structured queries about treatment uncertainties for schizophrenia. Uncertainties were most commonly about drug treatments (45.3% of clinicians and 41% of patients), psychological therapies (19.9% of clinicians and 9% of patients) or were unclassifiable.(11.8% of clinicians and 16.7% of patients). Few naturally asked questions could be classified using the well structured and focused clinical question format (i.e. PICO format). A simple linguistic taxonomy better described the types of questions people naturally ask.</p> <p>Conclusion</p> <p>People do not spontaneously ask well structured clinical questions. Other taxonomies may better capture the nature of questions. However, access to EBM resources is greatly facilitated by framing enquiries in the language of EBM, such as posing queries in PICO format. People do not naturally do this. It may be preferable to identify a way of searching the literature that more closely matches the way people naturally ask questions if access to information about treatments are to be made more broadly available.</p

Extended RDF: Computability and Complexity Issues

ERDF stable model semantics is a recently proposed semantics for ERDF ontologies and a faithful extension of RDFS semantics on RDF graphs. In this paper, we elaborate on the computability and complexity issues of the ERDF stable model semantics. Based on the undecidability result of ERDF stable model semantics, decidability under this semantics cannot be achieved, unless ERDF ontologies of restricted syntax are considered. Therefore, we propose a slightly modified semantics for ERDF ontologies, called ERDF #n- stable model semantics. We show that entailment under this semantics is, in general, decidable and also extends RDFS entailment. Equivalence statements between the two semantics are provided. Additionally, we provide algorithms that compute the ERDF #n-stable models of syntax-restricted and general ERDF ontologies. Further, we provide complexity results for the ERDF #nstable model semantics on syntax-restricted and general ERDF ontologies. Finally, we provide complexity results for the ERDF stable model semantics on syntax-restricted ERDF ontologies