Related papers: The Core & Periphery Hypothesis: A Conceptual Basi…
This paper proposes a theory of encapsulation, establishing a relationship between encapsulation and information hiding through the concept of potential structural complexity (P.S.C.), the maximum possible number of source code dependencies…
The safe integration of machine learning modules in decision-making processes hinges on their ability to quantify uncertainty. A popular technique to achieve this goal is conformal prediction (CP), which transforms an arbitrary base…
At present, there is a great deal of confusion regarding complexity and its measures (reviews on complexity measures are found in, e.g. Lloyd, 2001 and Shalizi, 2006 and more references therein). Moreover, there is also confusion regarding…
This paper proposes an extension of the traditional Central Dogma of molecular biology to a more dynamic model termed the Central Dogma Cycle (CDC) and a broader network called the Central Dogma Cyclic Network (CDCN). While the Central…
In this paper, we make the case that a scientific theory of deep learning is emerging. By this we mean a theory which characterizes important properties and statistics of the training process, hidden representations, final weights, and…
A fascinating hypothesis is that human and animal intelligence could be explained by a few principles (rather than an encyclopedic list of heuristics). If that hypothesis was correct, we could more easily both understand our own…
Concept-based Models are a class of inherently explainable networks that improve upon standard Deep Neural Networks by providing a rationale behind their predictions using human-understandable `concepts'. With these models being highly…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
Until presently, most approaches for understanding physiological or pathological phenomena have been based on the assumption that these processes start from individual cells, a concept introduced primarily by Virchow in the 19th century.…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Starting from the hypothesis that both physics, in particular space-time and the physical vacuum, and the corresponding mathematics are discrete on the Planck scale we develop a certain framework in form of a class of ' cellular networks'…
Entropy is arguably one of the most powerful concepts to understand the world, from the behavior of molecules to the expansion of the universe, from how life emerges to how hybrid complex systems like cities come into being and continue…
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an…
Cell formation problem is among the first obstacles the designer of cellular production systems must overcome. This paper presents a critical analysis of the various criteria and constraints considered in the literature. The objective is to…
The theory of cellular automata in operational probabilistic theories is developed. We start introducing the composition of infinitely many elementary systems, and then use this notion to define update rules for such infinite composite…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
Human mobility is a fundamental process underpinning socioeconomic life and urban structure. Classic theories, such as egocentric activity spaces and central place theory, provide crucial insights into specific facets of movement, like…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are `sloppy', i.e., exhibit behavior controlled by a relatively small number of parameter…