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To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
We present the guarded lambda-calculus, an extension of the simply typed lambda-calculus with guarded recursive and coinductive types. The use of guarded recursive types ensures the productivity of well-typed programs. Guarded recursive…
A clear definition of system dynamics modeling can provide shared understanding and clarify the impact of the field. We introduce a set of characteristics that define quantitative system dynamics, selected to capture core philosophy,…
Ecology studies biodiversity in its variety and complexity. It describes how species distribute and perform in response to environmental changes. Ecological processes and structures are highly complex and adaptive. In order to quantify…
Critical systems require high reliability and are present in many domains. They are systems in which failure may result in financial damage or even loss of lives. Standard techniques of software engineering are not enough to ensure the…
Logically constrained term rewriting is a relatively new formalism where rules are equipped with constraints over some arbitrary theory. Although there are many recent advances with respect to rewriting induction, completion, complexity…
The infrastructure upon which the functioning of society depends is composed of complex ecosystems of systems. Consequently, we must reason about the properties of such ecosystems, which requires that we construct models of them. There are…
In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy)…
We present a solution to the problem of understanding a system that produces a sequence of temporally ordered observations. Our solution is based on generating and interpreting a set of temporal decision rules. A temporal decision rule is a…
The domain of explainable AI is of interest in all Machine Learning fields, and it is all the more important in clustering, an unsupervised task whose result must be validated by a domain expert. We aim at finding a clustering that has high…
We present a new type system combining occurrence typing, previously used to type check programs in dynamically-typed languages such as Racket, JavaScript, and Ruby, with dependent refinement types. We demonstrate that the addition of…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
Systems thinking is a way of making sense about the world in terms of multilevel, nested, interacting systems, their environment, and the boundaries between the systems and the environment. In this paper we discuss the evolution of systems…
Given a machine learning (ML) model and a prediction, explanations can be defined as sets of features which are sufficient for the prediction. In some applications, and besides asking for an explanation, it is also critical to understand…
We present an extension of System F with call-by-name exceptions. The type system is enriched with two syntactic constructs: a union type for programs whose execution may raise an exception at top level, and a corruption type for programs…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Inspired by Kobayashi's type system for lock freedom, we define a behavioral type system for ensuring progress in a language of binary sessions. The key idea is to annotate actions in session types with priorities representing the urgency…
Modern Learning Classifier Systems can be characterized by their use of rule accuracy as the utility metric for the search algorithm(s) discovering useful rules. Such searching typically takes place within the restricted space of co-active…
We introduce a categorical language in which it is possible to talk about DNA sequencing, alignment methods, CRISPR, homologous recombination, haplotypes, and genetic linkage. This language takes the form of a class of limit-sketches whose…
A rewriting system is a set of equations over a given set of terms called rules that characterize a system of computation and is a powerful general method for providing decision procedures of equational theories, based upon the principle of…