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Computation, Volume 2, Issue 3 (September 2014), Pages 61-130

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Research

Open AccessArticle Universal Dimensions of Meaning Derived from Semantic Relations among Words and Senses: Mereological Completeness vs. Ontological Generality
Computation 2014, 2(3), 61-82; doi:10.3390/computation2030061
Received: 23 May 2014 / Revised: 18 June 2014 / Accepted: 27 June 2014 / Published: 15 July 2014
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Abstract
A key to semantic analysis is a precise and practically useful definition of meaning that is general for all domains of knowledge. We previously introduced the notion of weak semantic map: a metric space allocating concepts along their most general (universal) semantic [...] Read more.
A key to semantic analysis is a precise and practically useful definition of meaning that is general for all domains of knowledge. We previously introduced the notion of weak semantic map: a metric space allocating concepts along their most general (universal) semantic characteristics while at the same time ignoring other, domain-specific aspects of their meanings. Here we address questions of the number, quality, and mutual independence of the weak semantic dimensions. Specifically, we employ semantic relationships not previously used for weak semantic mapping, such as holonymy/meronymy (“is-part/member-of”), and we compare maps constructed from word senses to those constructed from words. We show that the “completeness” dimension derived from the holonym/meronym relation is independent of, and practically orthogonal to, the “abstractness” dimension derived from the hypernym-hyponym (“is-a”) relation, while both dimensions are orthogonal to the maps derived from synonymy and antonymy. Interestingly, the choice of using relations among words vs. senses implies a non-trivial trade-off between rich and unambiguous information due to homonymy and polysemy. The practical utility of the new and prior dimensions is illustrated by the automated evaluation of different kinds of documents. Residual analysis of available linguistic resources, such as WordNet, suggests that the number of universal semantic dimensions representable in natural language may be finite. Their complete characterization, as well as the extension of results to non-linguistic materials, remains an open challenge. Full article
Open AccessArticle Cultural Collapse and System Survival Due to Environmental Modification
Computation 2014, 2(3), 83-101; doi:10.3390/computation2030083
Received: 3 March 2014 / Revised: 19 June 2014 / Accepted: 25 June 2014 / Published: 29 July 2014
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Abstract
We consider a simple mathematical approach to the rise and fall of societies based on population growth and its effects on the environment, both beneficial and detrimental. We find that in any simple model of population dynamics with environmental coupling, stable cultures [...] Read more.
We consider a simple mathematical approach to the rise and fall of societies based on population growth and its effects on the environment, both beneficial and detrimental. We find that in any simple model of population dynamics with environmental coupling, stable cultures are impossible. Populations inevitably grow or decline exponentially. Further, if the parameters defining a civilisation are allowed to evolve towards an evolutionarily stable state, the only possible solutions are those where each culture ultimately declines. However, computer simulation with multiple competing cultures show that while each eventually collapses, some are always extant and the system is robust. In this broad class of models, individual death is a requirement for system survival. Full article
Open AccessArticle Investigation of the Ergopeptide Epimerization Process
Computation 2014, 2(3), 102-111; doi:10.3390/computation2030102
Received: 16 August 2013 / Revised: 10 July 2014 / Accepted: 22 July 2014 / Published: 8 August 2014
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Abstract
Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational [...] Read more.
Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that “folding” the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations. Full article
(This article belongs to the Section Computational Chemistry)
Figures

Open AccessArticle On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention
Computation 2014, 2(3), 112-130; doi:10.3390/computation2030112
Received: 6 May 2014 / Revised: 29 July 2014 / Accepted: 14 August 2014 / Published: 28 August 2014
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Abstract
Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models leads to a complex modeling problem. A discussion of the relationship between [...] Read more.
Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models leads to a complex modeling problem. A discussion of the relationship between biological processes, existing models for duplicate gene retention and data is presented. Existing models are then extended in deriving two new birth/death models for phylogenetic application in a gene tree/species tree reconciliation framework to enable probabilistic inference of the mechanisms from model parameterization. The goal of this work is to synthesize a detailed discussion of modeling duplicate genes to address biological questions, moving from previous work to future trajectories with the aim of generating better models and better inference. Full article
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)

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