Related papers: Some Remarks on Input Choices for Biochemical Syst…
As the field of recommender systems has developed, authors have used a myriad of notations for describing the mathematical workings of recommendation algorithms. These notations ap-pear in research papers, books, lecture notes, blog posts,…
These lecture notes concern the basics of the theory of process behaviour. First the concept of a (labelled) transition system receives ample treatment and then the following issues concerning process behaviour are elaborated in the setting…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
An inductive logic can be formulated in which the elements are not propositions or probability distributions, but information systems. The logic is complete for information systems with binary hypotheses, i.e., it applies to all such…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
In this paper we present a minimal object oriented core calculus for modelling the biological notion of type that arises from biological ontologies in formalisms based on term rewriting. This calculus implements encapsulation, method…
This paper presents the methodology for the system requirements and architecture w.r.t. their decomposition and refinement. It also introduces ideas of refinement layers and of refinement-based verification.
These are notes for a very rapid introduction to the basics of exterior differential systems and their connection with what is now known as Lie theory, together with some typical and not-so-typical applications to illustrate their use.
This work proposes a taxonomy for diagnosis computation methods which allows their standardized assessment, classification and comparison. The aim is to (i) give researchers and practitioners an impression of the diverse landscape of…
The paper is devoted to the introduction of natural deduction systems for some weak subintuitionistic logics, along with proofs of normalization theorems for these systems.
Over the last 20 years a large number of automata-based specification theories have been proposed for modeling of discrete,real-time and probabilistic systems. We have observed a lot of shared algebraic structure between these formalisms.…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
This document provides a brief overview of different metrics and terminology that is used to measure the performance of binary classification systems.
Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a…
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
Information theory and the framework of information dynamics have been used to provide tools to characterise complex systems. In particular, we are interested in quantifying information storage, information modification and information…
The recent usage of technical systems in human-centric environments leads to the question, how to teach technical systems, e.g., robots, to understand, learn, and perform tasks desired by the human. Therefore, an accurate representation of…
We discuss the possibility of making the {\it initial} definitions of mutually different (possibly interacting, or even entangled) systems in the context of decoherence theory. We point out relativity of the concept of elementary physical…
In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the…