12,978 research outputs found
Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system
Biology has taken strong steps towards becoming a computer science aiming at
reprogramming nature after the realisation that nature herself has reprogrammed
organisms by harnessing the power of natural selection and the digital
prescriptive nature of replicating DNA. Here we further unpack ideas related to
computability, algorithmic information theory and software engineering, in the
context of the extent to which biology can be (re)programmed, and with how we
may go about doing so in a more systematic way with all the tools and concepts
offered by theoretical computer science in a translation exercise from
computing to molecular biology and back. These concepts provide a means to a
hierarchical organization thereby blurring previously clear-cut lines between
concepts like matter and life, or between tumour types that are otherwise taken
as different and may not have however a different cause. This does not diminish
the properties of life or make its components and functions less interesting.
On the contrary, this approach makes for a more encompassing and integrated
view of nature, one that subsumes observer and observed within the same system,
and can generate new perspectives and tools with which to view complex diseases
like cancer, approaching them afresh from a software-engineering viewpoint that
casts evolution in the role of programmer, cells as computing machines, DNA and
genes as instructions and computer programs, viruses as hacking devices, the
immune system as a software debugging tool, and diseases as an
information-theoretic battlefield where all these forces deploy. We show how
information theory and algorithmic programming may explain fundamental
mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and
Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George
Ellis (eds.), Cambridge University Pres
Speech and crosstalk detection in multichannel audio
The analysis of scenarios in which a number of microphones record the activity of speakers, such as in a round-table meeting, presents a number of computational challenges. For example, if each participant wears a microphone, speech from both the microphone's wearer (local speech) and from other participants (crosstalk) is received. The recorded audio can be broadly classified in four ways: local speech, crosstalk plus local speech, crosstalk alone and silence. We describe two experiments related to the automatic classification of audio into these four classes. The first experiment attempted to optimize a set of acoustic features for use with a Gaussian mixture model (GMM) classifier. A large set of potential acoustic features were considered, some of which have been employed in previous studies. The best-performing features were found to be kurtosis, "fundamentalness," and cross-correlation metrics. The second experiment used these features to train an ergodic hidden Markov model classifier. Tests performed on a large corpus of recorded meetings show classification accuracies of up to 96%, and automatic speech recognition performance close to that obtained using ground truth segmentation
PhysicsGP: A Genetic Programming Approach to Event Selection
We present a novel multivariate classification technique based on Genetic
Programming. The technique is distinct from Genetic Algorithms and offers
several advantages compared to Neural Networks and Support Vector Machines. The
technique optimizes a set of human-readable classifiers with respect to some
user-defined performance measure. We calculate the Vapnik-Chervonenkis
dimension of this class of learning machines and consider a practical example:
the search for the Standard Model Higgs Boson at the LHC. The resulting
classifier is very fast to evaluate, human-readable, and easily portable. The
software may be downloaded at: http://cern.ch/~cranmer/PhysicsGP.htmlComment: 16 pages 9 figures, 1 table. Submitted to Comput. Phys. Commu
Gene Expression and its Discontents: Developmental disorders as dysfunctions of epigenetic cognition
Systems biology presently suffers the same mereological and sufficiency fallacies that haunt neural network models of high order cognition. Shifting perspective from the massively parallel space of gene matrix interactions to the grammar/syntax of the time series of expressed phenotypes using a cognitive paradigm permits import of techniques from statistical physics via the homology between information source uncertainty and free energy density. This produces a broad spectrum of possible statistical models of development and its pathologies in which epigenetic regulation and the effects of embedding environment are analogous to a tunable enzyme catalyst. A cognitive paradigm naturally incorporates memory, leading directly to models of epigenetic inheritance, as affected by environmental exposures, in the largest sense. Understanding gene expression, development, and their dysfunctions will require data analysis tools considerably more sophisticated than the present crop of simplistic models abducted from neural network studies or stochastic chemical reaction theory
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