Related papers: An evolutionary approach to Function
This article critically examines the foundational principles of contemporary AI methods, exploring the limitations that hinder its potential. We draw parallels between the modern AI landscape and the 20th-century Modern Synthesis in…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
This paper describes work carried out on a model for the evolution of graph classes in complex objects. By defining evolution rules and propagation strategies on graph classes, we aim to define a user-definable means to manage data…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…
The question whether an ontology can safely be replaced by another, possibly simpler, one is fundamental for many ontology engineering and maintenance tasks. It underpins, for example, ontology versioning, ontology modularization,…
Machine intelligence can develop either directly from experience or by inheriting experience through evolution. The bulk of current research efforts focus on algorithms which learn directly from experience. I argue that the alternative,…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies…
The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive…
Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is…
This paper presents a high-level conceptual framework to help orient the discussion and implementation of open-endedness in evolutionary systems. Drawing upon earlier work by Banzhaf et al., three different kinds of open-endedness are…
A common method of making a theory more understandable, is by comparing it to another theory which has been better developed. Radical interpretation is a theory which attempts to explain how communication has meaning. Radical interpretation…
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.…
We consider two, apparently similar, models of biological evolution which have been claimed to exhibit self-organized critical behaviour. A careful reanalysis of these models, including several new analytic results for one of them, suggests…
The paper discusses the role of interpretations, understood as multifunctions that preserve and reflect logical consequence, as refinement witnesses in the general setting of pi-institutions. This leads to a smooth generalization of the…
In the paper "Bellman function for extremal problems in $\mathrm{BMO}$", the authors built the Bellman function for integral functionals on the $\mathrm{BMO}$ space. The present paper provides a development of the subject. We abandon the…
Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…
This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect…
The importance of molecular-scale forces in sculpting biological form and function has been acknowledged for more than a century. Accounting for forces in biology is a problem that lies at the intersection of soft condensed matter physics,…