Leveraging Semantics to Improve Reproducibility in Scientific Workflows

Reproducibility of published results is a cornerstone in scientific publishing and progress. Therefore, the scientific community has been encouraging authors and editors to publish their contributions in a verifiable and understandable way. Efforts such as the Reproducibility Initiative [1], or the Reproducibility Projects on Biology [2] and Psychology [3] domains, have been defining standards and patterns to assess whether an experimental result is reproducible.

Towards measuring the complexity of introducing semantics into a company

The Semantics Difficulty Model (SDM) is a model that measures the difficult of introducing semantics technology into a company. SDM manages three descriptions of stages, which we will refer to as ?snapshots?: a company semantic snapshot, data snapshot and semantic application snapshot. Understanding a priory the complexity of introducing semantics into a company is important because it allows the organization to take early decisions, thus saving time and money, mitigating risks and improving innovation, time to market and productivity. SDM works by measuring the distance between each initial snapshot and its reference models (the company semantic snapshots reference model, data snapshots reference model, and the semantic application snapshots reference model) with Euclidian distances. The difficulty level will be "not at all difficult" when the distance is small, and becomes "extremely difficult" when the the distance is large. SDM has been tested experimentally with 2000 simulated companies with arrangements and several initial stages. The output is measured by five linguistic values: "not at all difficult, slightly difficult, averagely difficult, very difficult and extremely difficult". As the preliminary results of our SDM simulation model indicate, transforming a search application into integrated data from different sources with semantics is a "slightly difficult", in contrast with data and opinion extraction applications for which it is "very difficult".

Federating queries in SPARQL 1.1: syntax, semantics and evaluation

Given the sustained growth that we are experiencing in the number of SPARQL endpoints available, the need to be able to send federated SPARQL queries across these has also grown. To address this use case, the W3C SPARQL working group is defining a federation extension for SPARQL 1.1 which allows for combining graph patterns that can be evaluated over several endpoints within a single query. In this paper, we describe the syntax of that extension and formalize its semantics. Additionally, we describe how a query evaluation system can be implemented for that federation extension, describing some static optimization techniques and reusing a query engine used for data-intensive science, so as to deal with large amounts of intermediate and final results. Finally we carry out a series of experiments that show that our optimizations speed up the federated query evaluation process.

Deriving the full-reducing Krivine machine from the small-step operational semantics of normal order

We derive by program transformation Pierre Crégut s full-reducing Krivine machine KN from the structural operational semantics of the normal order reduction strategy in a closure-converted pure lambda calculus. We thus establish the correspondence between the strategy and the machine, and showcase our technique for deriving full-reducing abstract machines. Actually, the machine we obtain is a slightly optimised version that can work with open terms and may be used in implementations of proof assistants.

A syntactic and functional correspondence between reduction semantics and reduction-free full normalisers

Olivier Danvy and others have shown the syntactic correspondence between reduction semantics (a small-step semantics) and abstract machines, as well as the functional correspondence between reduction-free normalisers (a big-step semantics) and abstract machines. The correspondences are established by program transformation (so-called interderivation) techniques. A reduction semantics and a reduction-free normaliser are interderivable when the abstract machine obtained from them is the same. However, the correspondences fail when the underlying reduction strategy is hybrid, i.e., relies on another sub-strategy. Hybridisation is an essential structural property of full-reducing and complete strategies. Hybridisation is unproblematic in the functional correspondence. But in the syntactic correspondence the refocusing and inlining-of-iterate-function steps become context sensitive, preventing the refunctionalisation of the abstract machine. We show how to solve the problem and showcase the interderivation of normalisers for normal order, the standard, full-reducing and complete strategy of the pure lambda calculus. Our solution makes it possible to interderive, rather than contrive, full-reducing abstract machines. As expected, the machine we obtain is a variant of Pierre Crégut s full Krivine machine KN.

Selections from science and sanity; an introduction to non-Aristotelian systems and general semantics,

"Limited edition for experimental use by teachers and study group leaders."

An algebraic definition of Knuthian semantics /

"Contract no. E(04-3)-34, PA 214."

Control statement syntax and semantics of a language for parallel processors,

"Supported in part by the Advanced Research Projects Agency ... under Contract no. US AF 30(602) 4144."

LINGOL, a readable formalism for programming language semantics /

"UILU-ENG 77 1766."

Introducing reference semantics via refinement

Two types of semantics have been given to object-oriented formal specification languages. Value semantics denote a class by a set of values representing its objects. Reference semantics denote a class by a set of references, or pointers, to values representing its objects. While adopting the former facilitates formal reasoning, adopting the latter facilitates transformation to object-oriented code. In this paper, we propose a combined approach using value semantics for abstract specification and reasoning, and then refining to a reference semantics before transforming specification to code.

A partial-correctness semantics for modelling assembler programs

Previous work on formally modelling and analysing program compilation has shown the need for a simple and expressive semantics for assembler level programs. Assembler programs contain unstructured jumps and previous formalisms have modelled these by using continuations, or by embedding the program in an explicit emulator. We propose a simpler approach, which uses techniques from compiler theory in a formal setting. This approach is based on an interpretation of programs as collections of program paths, each of which has a weakest liberal precondition semantics. We then demonstrate, by example, how we can use this formalism to justify the compilation of block-structured high-level language programs into assembler.

Semantics of query-driven communication of exact values

We address the question of how to communicate among distributed processes valuessuch as real numbers, continuous functions and geometrical solids with arbitrary precision, yet efficiently. We extend the established concept of lazy communication using streams of approximants by introducing explicit queries. We formalise this approach using protocols of a query-answer nature. Such protocols enable processes to provide valid approximations with certain accuracy and focusing on certain locality as demanded by the receiving processes through queries. A lattice-theoretic denotational semantics of channel and process behaviour is developed. Thequery space is modelled as a continuous lattice in which the top element denotes the query demanding all the information, whereas other elements denote queries demanding partial and/or local information. Answers are interpreted as elements of lattices constructed over suitable domains of approximations to the exact objects. An unanswered query is treated as an error anddenoted using the top element. The major novel characteristic of our semantic model is that it reflects the dependency of answerson queries. This enables the definition and analysis of an appropriate concept of convergence rate, by assigning an effort indicator to each query and a measure of information content to eachanswer. Thus we capture not only what function a process computes, but also how a process transforms the convergence rates from its inputs to its outputs. In future work these indicatorscan be used to capture further computational complexity measures. A robust prototype implementation of our model is available.

Compositional semantics of dataflow networks with query-driven communication of exact values

We develop and study the concept of dataflow process networks as used for exampleby Kahn to suit exact computation over data types related to real numbers, such as continuous functions and geometrical solids. Furthermore, we consider communicating these exact objectsamong processes using protocols of a query-answer nature as introduced in our earlier work. This enables processes to provide valid approximations with certain accuracy and focusing on certainlocality as demanded by the receiving processes through queries. We define domain-theoretical denotational semantics of our networks in two ways: (1) directly, i. e. by viewing the whole network as a composite process and applying the process semantics introduced in our earlier work; and (2) compositionally, i. e. by a fixed-point construction similarto that used by Kahn from the denotational semantics of individual processes in the network. The direct semantics closely corresponds to the operational semantics of the network (i. e. it iscorrect) but very difficult to study for concrete networks. The compositional semantics enablescompositional analysis of concrete networks, assuming it is correct. We prove that the compositional semantics is a safe approximation of the direct semantics. Wealso provide a method that can be used in many cases to establish that the two semantics fully coincide, i. e. safety is not achieved through inactivity or meaningless answers. The results are extended to cover recursively-defined infinite networks as well as nested finitenetworks. A robust prototype implementation of our model is available.