Related papers: A Minimal OO Calculus for Modelling Biological Sys…
Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types, leading to a gap between classes mentioned in biomedical…
The aim of this review is to highlight the possibility to apply the mathematical formalism and methodology of quantum theory to model behaviour of complex biosystems, from genomes and proteins to animals, humans, ecological and social…
The complexity of large-scale distributed systems, particularly when deployed in physical space, calls for new mechanisms to address composability and reusability of collective adaptive behaviour. Computational fields have been proposed as…
A common framework is provided that comprises classical ordinal item response models as the cumulative, sequential and adjacent categories models as well as nominal response models and item response tree models. The taxonomy is based on the…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
Just as the $\lambda$-calculus uses three primitives (abstraction, application, variable) as the foundation of functional programming, inheritance-calculus uses three primitives (record, definition, inheritance) as the foundation of…
Representation theorems for formal systems often take the form of an inductive translation that satisfies certain invariants, which are proved inductively. Theory morphisms and logical relations are common patterns of such inductive…
Factorization models express a statistical object of interest in terms of a collection of simpler objects. For example, a matrix or tensor can be expressed as a sum of rank-one components. However, in practice, it can be challenging to…
We rely on the strength of linguistic and philosophical perspectives in constructing a framework that offers a unified explanation for presuppositions and existential commitment. We use a rich ontology and a set of methodological principles…
A method for extracting positive information from negative goals is proposed. It makes use of typed existence properties between arguments of a predicate to rewrite negative goals in a logic program. A typed existence property is a…
In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers <> but also extainers ><,…
This paper argues that certain ontology design problems are profitably addressed by treating ontologies as theories and by defining a set of operations that create new ontologies, including their constraints, out of other ontologies. The…
On the topic of probabilistic rewriting, there are several works studying both termination and confluence of different systems. While working with a lambda calculus modelling quantum computation, we found a system with probabilistic…
Many calculi exist for modelling various features of object-oriented languages. Many of them are based on $\lambda$-calculus and focus either on statically typed class-based languages or dynamic prototype-based languages. We formalize…
In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the…
Many type systems have been presented in the literature for variants of the pi-calculus, but none of them are able to handle composite subjects such as those found in the language epi, which features polyadic synchronisation. The purpose of…
The main novelty of this paper is to consider an extension of the Calculus of Constructions where predicates can be defined with a general form of rewrite rules. We prove the strong normalization of the reduction relation generated by the…
In many areas of systems biology, including virology, pharmacokinetics, and population biology, dynamical systems are commonly used to describe biological processes. These systems can be characterized by estimating their parameters from…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
The method for a problem solution of expenditures reduction of computing resources and time is developed at a pattern recognition, with the way of construction of the minimum tests sets or separate minimum tests on Boolean matrixes is…