Category Theory and Model-Driven Engineering: From Formal Semantics to Design Patterns and Beyond

There is a hidden intrigue in the title. CT is one of the most abstract mathematical disciplines, sometimes nicknamed "abstract nonsense". MDE is a recent trend in software development, industrially supported by standards, tools, and the status of a new "silver bullet". Surprisingly, categorical patterns turn out to be directly applicable to mathematical modeling of structures appearing in everyday MDE practice. Model merging, transformation, synchronization, and other important model management scenarios can be seen as executions of categorical specifications. Moreover, the paper aims to elucidate a claim that relationships between CT and MDE are more complex and richer than is normally assumed for "applied mathematics". CT provides a toolbox of design patterns and structural principles of real practical value for MDE. We will present examples of how an elementary categorical arrangement of a model management scenario reveals deficiencies in the architecture of modern tools automating the scenario.Comment: In Proceedings ACCAT 2012, arXiv:1208.430

New Directions in Categorical Logic, for Classical, Probabilistic and Quantum Logic

Intuitionistic logic, in which the double negation law not-not-P = P fails, is dominant in categorical logic, notably in topos theory. This paper follows a different direction in which double negation does hold. The algebraic notions of effect algebra/module that emerged in theoretical physics form the cornerstone. It is shown that under mild conditions on a category, its maps of the form X -> 1+1 carry such effect module structure, and can be used as predicates. Predicates are identified in many different situations, and capture for instance ordinary subsets, fuzzy predicates in a probabilistic setting, idempotents in a ring, and effects (positive elements below the unit) in a C*-algebra or Hilbert space. In quantum foundations the duality between states and effects plays an important role. It appears here in the form of an adjunction, where we use maps 1 -> X as states. For such a state s and a predicate p, the validity probability s |= p is defined, as an abstract Born rule. It captures many forms of (Boolean or probabilistic) validity known from the literature. Measurement from quantum mechanics is formalised categorically in terms of `instruments', using L\"uders rule in the quantum case. These instruments are special maps associated with predicates (more generally, with tests), which perform the act of measurement and may have a side-effect that disturbs the system under observation. This abstract description of side-effects is one of the main achievements of the current approach. It is shown that in the special case of C*-algebras, side-effect appear exclusively in the non-commutative case. Also, these instruments are used for test operators in a dynamic logic that can be used for reasoning about quantum programs/protocols. The paper describes four successive assumptions, towards a categorical axiomatisation of quantitative logic for probabilistic and quantum systems

Abstract Hidden Markov Models: a monadic account of quantitative information flow

Hidden Markov Models, HMM's, are mathematical models of Markov processes with state that is hidden, but from which information can leak. They are typically represented as 3-way joint-probability distributions. We use HMM's as denotations of probabilistic hidden-state sequential programs: for that, we recast them as `abstract' HMM's, computations in the Giry monad $\mathbb{D}$, and we equip them with a partial order of increasing security. However to encode the monadic type with hiding over some state $\mathcal{X}$ we use $\mathbb{D}\mathcal{X}\to \mathbb{D}^2\mathcal{X}$ rather than the conventional $\mathcal{X}{\to}\mathbb{D}\mathcal{X}$ that suffices for Markov models whose state is not hidden. We illustrate the $\mathbb{D}\mathcal{X}\to \mathbb{D}^2\mathcal{X}$ construction with a small Haskell prototype. We then present uncertainty measures as a generalisation of the extant diversity of probabilistic entropies, with characteristic analytic properties for them, and show how the new entropies interact with the order of increasing security. Furthermore, we give a `backwards' uncertainty-transformer semantics for HMM's that is dual to the `forwards' abstract HMM's - it is an analogue of the duality between forwards, relational semantics and backwards, predicate-transformer semantics for imperative programs with demonic choice. Finally, we argue that, from this new denotational-semantic viewpoint, one can see that the Dalenius desideratum for statistical databases is actually an issue in compositionality. We propose a means for taking it into account

K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources

The integration of heterogeneous data sources and software systems is a major issue in the biomed ical community and several approaches have been explored: linking databases, on-the- fly integration through views, and integration through warehousing. In this paper we report on our experiences with two systems that were developed at the University of Pennsylvania: an integration system called K2, which has primarily been used to provide views over multiple external data sources and software systems; and a data warehouse called GUS which downloads, cleans, integrates and annotates data from multiple external data sources. Although the view and warehouse approaches each have their advantages, there is no clear winner . Therefore, users must consider how the data is to be used, what the performance guarantees must be, and how much programmer time and expertise is available to choose the best strategy for a particular application

Data access and integration in the ISPIDER proteomics grid

Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources