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Both scientists and children make important structural discoveries, yet their computational underpinnings are not well understood. Structure discovery has previously been formalized as probabilistic inference about the right structural form…
In this paper we apply the constructor-theoretic approach to the theory of constructed emotions, showing that core affect valence and knowledge can be considered as two different observables, leading to information or superinformation…
The word "complexity" is most often used as a meta--linguistic expression referring to certain intuitive characteristics of a natural system and/or its scientific description. These characteristics may include: sheer amount of data that…
We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic…
How does one formalize the structure of structures necessary for the foundations of physics? This work is an attempt at conceptualizing the metaphysics of pregeometric structures, upon which new and existing notions of quantum geometry may…
In the manuscript titled "Computation environment (1)", we introduced a notion called computation environment as an interactive model for computation and complexity theory. In this model, Turing machines are not autonomous entities and find…
Life is fundamentally a scientific enigma. The interplay between chaos, entropy dynamics, and Prigogine's dissipative systems offers profound insights into the emergence, stabilization, and eventual collapse of far-from-equilibrium systems.…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
In social systems, meaning can be communicated in addition to underlying processes of the information exchange. Meaning processing incurs on information processing with hindsight, while information processing recursively follows the time…
Learning-based signal processing systems increasingly support high-stakes medical decisions using heterogeneous biomedical signals, including medical images, physiological time series, and clinical records. Despite strong predictive…
Categories provide a coarse grained description of the world. A fundamental question is whether categories simply mirror an underlying structure of nature, or instead come from the complex interactions of human beings among themselves and…
Building taxonomies is often a significant part of building an ontology, and many attempts have been made to automate the creation of such taxonomies from relevant data. The idea in such approaches is either that relevant definitions of the…
Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A…
We develop a general formalism for representing and understanding structure in complex systems. In our view, structure is the totality of relationships among a system's components, and these relationships can be quantified using information…
Understanding causal heterogeneity is essential for scientific discovery in domains such as biology and medicine. However, existing methods lack causal awareness, with insufficient modeling of heterogeneity, confounding, and observational…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
"Standard" information theory says nothing about the semantic content of information. Nevertheless, applications such as evolutionary theory demand consideration of precisely this aspect of information, a need that has motivated a largely…
In this introductory article we present the basics of an approach to implementing computational interpreting of natural language aiming to model the meanings of words and phrases. Unlike other approaches, we attempt to define the meanings…
This paper addresses the open question formulated as: Which levels of abstraction are appropriate in the synthetic modelling of life and cognition? within the framework of info-computational constructivism, treating natural phenomena as…