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

SEBIO: A Semantic BioInformatics Platform for the New E-Science

Knowledge integration and exchange of data within and among organizations is a universally recognized need in bioinformatics and genomics research through the e-science field. The main problem looming over the lack of integration is the fact that the current Web is an environment primarily developed for human users and micro-array data resources lack widely accepted standards; this leads to a tremendous data heterogeneity. Using semantic technologies as a key technology for interoperation of various datasets enables knowledge integration of the vast amount of biological and biomedical data. In this paper, we aim at providing a semantically-enhanced bioinformatics platform (SEBIO), which handles these issues effectively. We will describe the problems arisen and the solutions applied so far. For that, the SEBIO approach is unfolded and its main components explained, to see in more detail how perfectly it copes with the aforementioned difficulties