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Final CFPs: Info theory in biology

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  • Final CFPs: Info theory in biology

    Information-theoretic approaches to biology

    This is the final Call For Papers and also a Call for Reviewers for
    the 4th Pacific Symposium on BioComputing (PSB99, 1999) conference track on
    "Information-theoretic approaches to biology".

    PSB-99 will be held from 4-9 January, 1999, in Mauni Lani on the
    Big Island of Hawaii.

    Submission deadline : 15th July 1998.

    Track Organisers: David L. Dowe ( and Klaus Prank.

    WWW site: .

    If you wish to submit to this track, please do so in the next fortnight.

    If you think you can review for this track, please e-mail your contact
    details (name, e-mail address, telephone, fax, WWW home page, research
    interests, etc.) to Dr. David Dowe ( and
    Dr. Klaus Prank(

    Specific technical area to be covered by this track:

    Approaches to biological problems using notions of information or complexity,
    including methods such as Algorithmic Probability, Minimum Message Length and
    Minimum Description Length. Two possible applications are (e.g.) protein
    folding and biological information processing.
    Kolmogorov (1965) and Chaitin (1966) studied the notions of complexity and
    randomness, with Solomonoff (1964), Wallace (1968) and Rissanen (1978) applying
    these to problems of statistical and inferential learning (and ``data mining'')
    and to prediction. The methods of Solomonoff, Wallace and Rissanen have
    respectively come to be known as Algorithmic Probability (ALP), Minimum Message
    Length (MML) and Minimum Description Length (MDL). All of these methods relate
    to information theory, and can also be thought of in terms of Shannon's
    information theory, and can also be thought of in terms of Boltzmann's
    thermo-dynamic entropy.

    An MDL/MML perspective has been suggested by a number of authors in the context
    of approximating unknown functions with some parametric approximation scheme
    (such as a neural network). The designated measure to optimize under this
    scheme combines an estimate of the cost of misfit with an estimate of the cost
    of describing the parametric approximation (Akaike 1973, Rissanen 1978,
    Barron and Barron 1988, Wallace and Boulton, 1968).

    This track invites all original papers of a biological nature which use
    notions of information and/or information-theoretic complexity, with no strong
    preference as to what specific nature. Such work has been done in problems of,
    e.g., protein folding and DNA string alignment. As we shortly describe in some
    detail, such work has also been done in the analysis of temporal dynamics in
    biology such as neural spike trains and endocrine (hormonal) time series
    analysis using the MDL principle in the context of neural networks and
    context-free grammar complexity.

    To elaborate on one of the relevant topics above, in the last three years
    or so, there has been a major focus on the aspect of timing in biological
    information processing ranging from fields such as neuroscience to
    endocrinology. The latest work on information processing at the single-cell
    level using computational as well as experimental approaches reveals previously
    unimagined complexity and dynamism. Timing in biological information processing
    on the single-cell level as well as on the systems level has been studied by
    signal-processing and information-theoretic approaches in particular in the
    field of neuroscience (see for an overview: Rieke et al. 1996). Using such
    approaches to the understanding of temporal complexity in biological
    information transfer, the maximum information rates and the precision of spike
    timing to the understanding of temporal complexity in biological information
    transfer, the maximum information rates and the precision of spike timing could
    be revealed by computational methods (Mainen and Sejnowski, 1995; Gabbiani and
    Koch 1996; Gabbiani et al., 1996).

    The examples given above are examples of some possible biological application
    domains. We invite and solicit papers in all areas of (computational) biology
    which make use of ALP, MDL, MML and/or other notions of information and
    information-theoretic complexity.

    In problems of prediction, as well as using "yes"/"no" predictions, we would
    encourage the authors to consider also using probabilistic prediction, where
    the score assigned to a probabilistic prediction is given according to the
    negative logarithm of the stated probability of the event.

    List of Frequently Asked Questions (FAQs) re PSB99 :

    Further comments re PSB-99 :
    PSB99 will publish accepted full papers in an archival Proceedings. All
    contributed papers will be rigorously peer-reviewed by at least three
    referees. Each accepted full paper will be allocated up to 12 pages in the
    conference Proceedings. The best papers will be selected for a 30-minute
    oral presentation to the full assembled conference. Accepted poster
    abstracts will be distributed at the conference separately from the
    archival Proceedings. To be eligible for proceedings publication, each full
    paper must be accompanied by a cover letter stating that it contains
    original unpublished results not currently under consideration elsewhere.
    See for more information.


    Full paper submissions due: July 15, 1998
    Poster abstracts due: August 22, 1998
    Notification of paper acceptance: September 22, 1998
    Camera-ready copy due: October 1, 1998
    Conference: January 4 - 9, 1999

    More information about the "Information-theoretic approaches to biology"
    track, including a sample list of relevant papers is available on
    the WWW at .

    More information about PSB99 is available from

    For further information,
    e-mail Dr. David Dowe,
    or e-mail Dr. Klaus Prank, .

    This page was put together by
    Dr. David Dowe,
    School of Computer Science and Softw. Eng.,
    Monash University, Clayton, Vic. 3168, Australia
    e-mail: Fax: +61 3 9905-5146


    Dr. Klaus Prank,
    Abteilung Klinische Endokrinologie
    Medizinische Hochschule Hannover
    Carl-Neuberg-Str. 1, D-30623 Hannover, Germany
    Tel.: +49 (511) 532-3827 Fax.: +49 (511) 532-3825

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