相关论文: A formal model of autocatalytic sets emerging in a…

In this article, I develop a formal model of free will for complex systems based on emergent properties and adaptive selection. The model is based on a process ontology in which a free choice is a singular process that takes a system from…

The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal…

Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of…

We consider an unsupervised classifying agent that evolves by enforcing self-consistency of its labels under continual exposure to a data-generating environment. Because the agent's predictions feed back into its own regularized updates,…

We study an autocatalytic system consisting of several interacting chemical species. We observe a strong dependence of the concentrations of the chemicals on the size of the system. This dependence is caused by the discrete nature of the…

Systems of interacting species, such as biological environments or chemical reactions, are often described mathematically by sets of coupled ordinary differential equations. While a large number $\beta$ of species may be involved in the…

Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…

Research in the field of automated vehicles, or more generally cognitive cyber-physical systems that operate in the real world, is leading to increasingly complex systems. Among other things, artificial intelligence enables an…

The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…

Autocatalytic chemical reaction networks can collectively replicate or maintain their constituents despite degradation reactions only above a certain threshold, which we refer to as the decay threshold. When the chemical network has a…

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…

This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…

The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…

At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…

In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy)…

Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…

The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis,…

The recent surge in Generative Artificial Intelligence (AI) has introduced exciting possibilities for computational chemistry. Generative AI methods have made significant progress in sampling molecular structures across chemical species,…

This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…

Designing plausible network models typically requires scholars to form a priori intuitions on the key drivers of network formation. Oftentimes, these intuitions are supported by the statistical estimation of a selection of network evolution…