Complexity and information-theoretic approaches to biology
This is the Call For Papers for the 3rd Pacific Symposium on BioComputing (PSB-3, 1998) conference stream on
"Complexity and information-theoretic approaches to biology".
PSB-98 will be held from 5-9 January, 1998, in Hawaii, at the Ritz Carlton Kapalua on Maui.
Stream Organisers: David L. Dowe
Specific technical area to be covered by this stream:
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 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).
This stream invites all original papers of a biological nature which use notions of information and/or 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 couple of 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 complexity.
In problems of prediction, as well as using "yes"/"no" predictions,
we would encourage the authors to consider also using
where the score assigned to a probabilistic prediction is given according to
the negative logarithm of the stated probability of the event.
Link to Sample list of relevant papers (in ASCII).
Link to list of Frequently Asked Questions (FAQs) re PSB-98 (in ASCII).
Further comments re PSB-98 :
PSB'98 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.
Full paper submissions due
(NEW deadline): July 28, 1997
Poster abstracts due: August 10, 1997
Notification of paper acceptance: August 22, 1997
Camera-ready copy due: September 22, 1997
Conference: January 5 - 8, 1998
For further information,
e-mail Dr. David Dowe, firstname.lastname@example.org ,
or e-mail Dr. Klaus Prank, email@example.com .
This page was put together by
Dr. David Dowe,
Dept. of Computer Science, Monash University, Clayton, Vic. 3168, Australia
firstname.lastname@example.org (Fax: +61 3 9905-5146)
Dr. Klaus Prank,
Abteilung Klinische Endokrinologie,
Medizinische Hochschule Hannover,
email@example.com (Tel: +49 (511) 532-3827 Fax: +49 (511) 532-3825)
(and was started on Sun 23rd Mar. 1997) and was last updated on Sun 29th Jun. 1997.
David L. Dowe,
Monash University, Australia,
23 Mar 1997, 29 Jun 1997, 7 May 1998, etc.
Copying is not permitted without expressed permission from
David L. Dowe.