Simplifying the mosaic description of DNA sequences

By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share compositional similarity with one or more distant (non--neighbouring) domains. We thus obtain a coarse--grained description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly reducing its organizational complexity. This procedure gives a new means of evaluating genomic complexity as one examines organisms ranging from bacteria to human. The mosaic organization of DNA sequences could have originated from the insertion of fragments of one genome (the parasite) inside another (the host), and we present numerical experiments that are suggestive of this scenario.Comment: 16 pages, 1 figure, Accepted for publication in Phys. Rev.

Artificial Immune Systems - Models, algorithms and applications

Copyright © 2010 Academic Research Publishing Agency.This article has been made available through the Brunel Open Access Publishing Fund.Artificial Immune Systems (AIS) are computational paradigms that belong to the computational intelligence family and are inspired by the biological immune system. During the past decade, they have attracted a lot of interest from researchers aiming to develop immune-based models and techniques to solve complex computational or engineering problems. This work presents a survey of existing AIS models and algorithms with a focus on the last five years.This article is available through the Brunel Open Access Publishing Fun

From holism to compositionality: memes and the evolution of segmentation, syntax, and signification in music and language

Steven Mithen argues that language evolved from an antecedent he terms “Hmmmmm, [meaning it was] Holistic, manipulative, multi-modal, musical and mimetic”. Owing to certain innate and learned factors, a capacity for segmentation and cross-stream mapping in early Homo sapiens broke the continuous line of Hmmmmm, creating discrete replicated units which, with the initial support of Hmmmmm, eventually became the semantically freighted words of modern language. That which remained after what was a bifurcation of Hmmmmm arguably survived as music, existing as a sound stream segmented into discrete units, although one without the explicit and relatively fixed semantic content of language. All three types of utterance – the parent Hmmmmm, language, and music – are amenable to a memetic interpretation which applies Universal Darwinism to what are understood as language and musical memes. On the basis of Peter Carruthers’ distinction between ‘cognitivism’ and ‘communicativism’ in language, and William Calvin’s theories of cortical information encoding, a framework is hypothesized for the semantic and syntactic associations between, on the one hand, the sonic patterns of language memes (‘lexemes’) and of musical memes (‘musemes’) and, on the other hand, ‘mentalese’ conceptual structures, in Chomsky’s ‘Logical Form’ (LF)

Symbol Emergence in Robotics: A Survey

Humans can learn the use of language through physical interaction with their environment and semiotic communication with other people. It is very important to obtain a computational understanding of how humans can form a symbol system and obtain semiotic skills through their autonomous mental development. Recently, many studies have been conducted on the construction of robotic systems and machine-learning methods that can learn the use of language through embodied multimodal interaction with their environment and other systems. Understanding human social interactions and developing a robot that can smoothly communicate with human users in the long term, requires an understanding of the dynamics of symbol systems and is crucially important. The embodied cognition and social interaction of participants gradually change a symbol system in a constructive manner. In this paper, we introduce a field of research called symbol emergence in robotics (SER). SER is a constructive approach towards an emergent symbol system. The emergent symbol system is socially self-organized through both semiotic communications and physical interactions with autonomous cognitive developmental agents, i.e., humans and developmental robots. Specifically, we describe some state-of-art research topics concerning SER, e.g., multimodal categorization, word discovery, and a double articulation analysis, that enable a robot to obtain words and their embodied meanings from raw sensory--motor information, including visual information, haptic information, auditory information, and acoustic speech signals, in a totally unsupervised manner. Finally, we suggest future directions of research in SER.Comment: submitted to Advanced Robotic

Generalised additive multiscale wavelet models constructed using particle swarm optimisation and mutual information for spatio-temporal evolutionary system representation

A new class of generalised additive multiscale wavelet models (GAMWMs) is introduced for high dimensional spatio-temporal evolutionary (STE) system identification. A novel two-stage hybrid learning scheme is developed for constructing such an additive wavelet model. In the first stage, a new orthogonal projection pursuit (OPP) method, implemented using a particle swarm optimisation(PSO) algorithm, is proposed for successively augmenting an initial coarse wavelet model, where relevant parameters of the associated wavelets are optimised using a particle swarm optimiser. The resultant network model, obtained in the first stage, may however be a redundant model. In the second stage, a forward orthogonal regression (FOR) algorithm, implemented using a mutual information method, is then applied to refine and improve the initially constructed wavelet model. The proposed two-stage hybrid method can generally produce a parsimonious wavelet model, where a ranked list of wavelet functions, according to the capability of each wavelet to represent the total variance in the desired system output signal is produced. The proposed new modelling framework is applied to real observed images, relative to a chemical reaction exhibiting a spatio-temporal evolutionary behaviour, and the associated identification results show that the new modelling framework is applicable and effective for handling high dimensional identification problems of spatio-temporal evolution sytems