Related papers: Algorithmic complexity in computational biology: b…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Evolutionary complexity is here measured by the number of trials/evaluations needed for evolving a logical gate in a non-linear medium. Behavioural complexity of the gates evolved is characterised in terms of cellular automata behaviour. We…
Axiomatic approach has demonstrated its power in mathematics. The main goal of this preprint is to show that axiomatic methods are also very efficient for computer science. It is possible to apply these methods to many problems in computer…
The complexity of a computational problem is traditionally quantified based on the hardness of its worst case. This approach has many advantages and has led to a deep and beautiful theory. However, from the practical perspective, this…
The quest for quantum computers is motivated by their potential for solving problems that defy existing, classical, computers. The theory of computational complexity, one of the crown jewels of computer science, provides a rigorous…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around 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…
Many proposed applications of neural networks in machine learning, cognitive/brain science, and society hinge on the feasibility of inner interpretability via circuit discovery. This calls for empirical and theoretical explorations of…
Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of…
The ethical consequences of, constraints upon and regulation of algorithms arguably represent the defining challenges of our age, asking us to reckon with the rise of computational technologies whose potential to radically transforming…
Computational psychiatry is a field aimed at developing formal models of information processing in the human brain, and how alterations in this processing can lead to clinical phenomena. Despite significant progress in the development of…
The cryptanalysis of various cipher problems can be formulated as NP-Hard combinatorial problem. Solving such problems requires time and/or memory requirement which increases with the size of the problem. Techniques for solving…
Accelerator physics relies on numerical algorithms to solve optimization problems in online accelerator control and tasks such as experimental design and model calibration in simulations. The effectiveness of optimization algorithms in…
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent,…
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…
This paper argues that the requirement of applicableness of quantum linearity to any physical level from molecules and atoms to the level of macroscopic extensional world, which leads to a main foundational problem in quantum theory…
Human societies continuously transform scattered information into collective judgments and coordinated action, whether through markets discovering prices, governments allocating resources, communities enforcing norms, or science converging…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
With the relentless rise of computer power, there is a widespread expectation that computers can solve the most pressing problems of science, and even more besides. We explore the limits of computational modelling and conclude that, in the…
In this paper the author presents some non-conventional thoughts on the complexity of the Universe and the algorithmic reproducibility of the human brain, essentially sparked off by the notion of algorithmic complexity. We must warn that…