Information-theoretic approaches to biology
This is the Call For Papers for the
4th Pacific Symposium on BioComputing
conference track on
"Information-theoretic approaches to biology".
PSB99 will be held from 4-9 January, 1999, in Mauni Lani,
on the Big Island of Hawaii.
Track Organisers: David L. Dowe
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
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
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.
(See an example
Link to Sample list of relevant papers (in ASCII).
Further comments re PSB99 :
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 http://www.cgl.ucsf.edu/psb/cfp.html for more information, including submission requirements.
Full paper submissions
cfp.html for details) due :
July 13, 1998
Notification of paper acceptance: August 22, 1998
Final camera-ready paper deadline: September 22, 1998
Poster abstracts due: October 1, 1998
Conference: January 4 - 9, 1999
For PSB99 reviewers only :
PSB99 review form (in plain ASCII text).
For further information,
e-mail Dr. David Dowe, firstname.lastname@example.org ,
or e-mail Dr. Klaus Prank, email@example.com .
This page ( http://www.csse.monash.edu.au/~dld/PSB99/PSB99.Info.CFPs.html )
was put together by
Dr. David Dowe,
School of Comp. Sci. and Softw. Eng., 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 in March 1998) and was last updated no earlier than Fri 24th Apr. 1998.
David L. Dowe,
Monash University, Australia,
Mar 1998, 24 Apr 1998, 7 May 1998, etc.
Copying is not permitted without expressed permission from
David L. Dowe.