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Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
Laboratory experiments play a key role in deciphering the chemistry of the interstellar medium (ISM) and the role that product complex organic molecules (COMs) may play in the origins of life. However, to date, most studies in experimental…
These lecture notes give an introduction to the theory of interacting particle systems. The main subjects are the construction using generators and graphical representations, the mean field limit, stochastic order, duality, and the relation…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
Recommender systems research is concerned with many aspects of recommender system behavior and effects than simply its effectiveness, and simulation can be a powerful tool for uncovering these effects. In this brief position paper, I…
This document is both a synthesis of current notions about complex systems, and a practical approach description. A disambiguation is proposed and exposes possible reasons for controversies related to causation and emergence. Theoretical…
We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…
It has been argued that reduction procedures are closely connected to the question about identity of proofs and that accepting certain reductions would lead to a trivialization of identity of proofs in the sense that every derivation of the…
Decision tree induction systems are being used for knowledge acquisition in noisy domains. This paper develops a subjective Bayesian interpretation of the task tackled by these systems and the heuristic methods they use. It is argued that…
Understanding realistic complex systems requires confronting significant conceptual, theoretical and experimental limitations rooted in the persistence of views that originated in the mechanics of simple moving bodies. We define the…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
This chapter serves as an introduction to systems engineering focused on the broad issues surrounding realizing complex integrated systems. What is a system? We pose a number of possible definitions and perspectives, but leave open the…
The aim of quantum system identification is to estimate the ingredients inside a black box, in which some quantum-mechanical unitary process takes place, by just looking at its input-output behavior. Here we establish a basic and general…
The aim of this short paper is to give a practical introduction to functional interpretation of proofs for computer scientists interested in synthesis.
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
Two possible realizations of the formal neuron are considered as quantum system. The first type complies with classical system. The second type vastly increases the possible problems.
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
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…