Related papers: A Minimal OO Calculus for Modelling Biological Sys…
Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the…
The main goal of concept-oriented programming (COP) is describing how objects are represented and accessed. It makes references (object locations) first-class elements of the program responsible for many important functions which are…
Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to…
Type qualifiers offer a lightweight mechanism for enriching existing type systems to enforce additional, desirable, program invariants. They do so by offering a restricted but effective form of subtyping. While the theory of type qualifiers…
We present some first steps in the more general setting of the interpretation of dependent type theory in Ludics. The framework is the following: a (Martin-Lof) type A is represented by a behaviour (which corresponds to a formula) in such a…
The optical model is a fundamental tool to describe scattering processes in nuclear physics. The basic input is an optical model potential, which describes the refraction and absorption processes more or less schematically. Of special…
Biochemical molecules interact through modification and binding reactions, giving raise to a combinatorial number of possible biochemical species. The time-dependent evolution of concentrations of the species is commonly described by a…
We address the problem of answering Web ontology queries efficiently. An ontology is formalized as a Deductive Ontology Base (DOB), a deductive database that comprises the ontology's inference axioms and facts. A cost-based query…
In object systems, classes take the role of modules, and interfaces consist of methods. Because methods are encapsulated in objects, interfaces in object systems do not allow abstracting over \emph{where} methods are implemented. This…
Within the diverse interdisciplinary life sciences domains, semantic, workflow, and methodological ambiguities can prevent the appreciation of explanations of phenomena, handicap the use of computational models, and hamper communication…
The objective of this paper is to develop a functional programming language for quantum computers. We develop a lambda calculus for the classical control model, following the first author's work on quantum flow-charts. We define a…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
We present a unifying framework for type systems for process calculi. The core of the system provides an accurate correspondence between essentially functional processes and linear logic proofs; fragments of this system correspond to…
We develop algebraic models of simple type theories, laying out a framework that extends universal algebra to incorporate both algebraic sorting and variable binding. Examples of simple type theories include the unityped and simply-typed…
Classical models of computation have been successful in capturing the very essence of individual computing devices. Although they are useful to understand computability power and limitations in the small, such models are not suitable to…
We introduce a formalism based on a combinatorial notion of cell complex subject to an inclusion-reversing duality operation. Our main goal is to open the way for a functorial definition of field theories in a context where no manifold or…
In this work, we use a labelled deduction system based on the concept of computational paths (sequence of rewrites) as equalities between two terms of the same type. We also define a term rewriting system that is used to make computations…
We present a type inference algorithm for lambda-terms in Elementary Affine Logic using linear constraints. We prove that the algorithm is correct and complete.
In this paper, we present a brief tutorial on reduced order model (ROM) closures. First, we carefully motivate the need for ROM closure modeling in under-resolved simulations. Then, we construct step by step the ROM closure model by…
This paper details a simple approach to the implementation of Optimality Theory (OT, Prince and Smolensky 1993) on a computer, in part reusing standard system software. In a nutshell, OT's GENerating source is implemented as a BinProlog…