Related papers: Regulated Multiset Rewriting Systems
While machine-learning models are flourishing and transforming many aspects of everyday life, the inability of humans to understand complex models poses difficulties for these models to be fully trusted and embraced. Thus, interpretability…
Human language and its governing rules present a number of analogies with the organization and structure of communication and information management in living organisms. This chapter will provide a short general introduction about grammar,…
Systematic and multifactor risk models are revisited via methods which were already successfully developed in signal processing and in automatic control. The results, which bypass the usual criticisms on those risk modeling, are illustrated…
Logically Constrained Term Rewriting Systems (LCTRSs) provide a general framework for term rewriting with constraints. We discuss a simple dependency pair approach to prove termination of LCTRSs. We see that existing techniques transfer to…
Multiset automata are a class of automata for which the symbols can be read in any order and obtain the same result. We investigate weighted multiset automata and show how to construct them from weighted regular expressions. We present…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Maximally parallel multiset rewriting systems (MPMRS) give a convenient way to express relations between unstructured objects. The functioning of various computational devices may be expressed in terms of MPMRS (e.g., register machines and…
One of the most important aims of the fields of robotics, artificial intelligence and artificial life is the design and construction of systems and machines as versatile and as reliable as living organisms at performing high level…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
We propose a notion of complexity for oriented conditional term rewrite systems satisfying certain restrictions. This notion is realistic in the sense that it measures not only successful computations, but also partial computations that…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Multistate models offer a powerful framework for studying disease processes and can be used to formulate intensity-based and more descriptive marginal regression models. They also represent a natural foundation for the construction of joint…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
In the former article "Formal mathematical systems including a structural induction principle" we have presented a unified theory for formal mathematical systems including recursive systems closely related to formal grammars, including the…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
In this paper we present a reformulation--framed as a constrained optimization problem--of multi-robot tasks which are encoded through a cost function that is to be minimized. The advantages of this approach are multiple. The…
This book explores an alternative to the current dominant paradigm where a discrete computer model is constructed as an attempt to approximate some continuum theory. We focus on a class of discrete computer models that are based on simple…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…