Logical relations for coherence of effect subtyping

A coercion semantics of a programming language with subtyping is typically defined on typing derivations rather than on typing judgments. To avoid semantic ambiguity, such a semantics is expected to be coherent, i.e., independent of the typing derivation for a given typing judgment. In this article we present heterogeneous, biorthogonal, step-indexed logical relations for establishing the coherence of coercion semantics of programming languages with subtyping. To illustrate the effectiveness of the proof method, we develop a proof of coherence of a type-directed, selective CPS translation from a typed call-by-value lambda calculus with delimited continuations and control-effect subtyping. The article is accompanied by a Coq formalization that relies on a novel shallow embedding of a logic for reasoning about step-indexing

Towards a Java Subtyping Operad

The subtyping relation in Java exhibits self-similarity. The self-similarity in Java subtyping is interesting and intricate due to the existence of wildcard types and, accordingly, the existence of three subtyping rules for generic types: covariant subtyping, contravariant subtyping and invariant subtyping. Supporting bounded type variables also adds to the complexity of the subtyping relation in Java and in other generic nominally-typed OO languages such as C# and Scala. In this paper we explore defining an operad to model the construction of the subtyping relation in Java and in similar generic nominally-typed OO programming languages. Operads, from category theory, are frequently used to model self-similar phenomena. The Java subtyping operad, we hope, will shed more light on understanding the type systems of generic nominally-typed OO languages.Comment: 13 page

A Type Language for Calendars

Time and calendars play an important role in databases, on the Semantic Web, as well as in mobile computing. Temporal data and calendars require (specific) modeling and processing tools. CaTTS is a type language for calendar definitions using which one can model and process temporal and calendric data. CaTTS is based on a "theory reasoning" approach for efficiency reasons. This article addresses type checking temporal and calendric data and constraints. A thesis underlying CaTTS is that types and type checking are as useful and desirable with calendric data types as with other data types. Types enable (meaningful) annotation of data. Type checking enhances efficiency and consistency of programming and modeling languages like database and Web query languages

Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context