CFPs and CFRs: Information theory in biology

Sun Jun 29 09:45:56 EDT 1997

Please distributed to interested friends and colleagues:

Call For Papers (CFPs) and Call For Referees (CFRs)

Complexity and information-theoretic approaches to biology
----------------------------------------------------------

This is a Call For Papers and Call For Referees 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 (dld at cs.monash.edu.au) and Klaus Prank.
Stream submission deadline (details below): 21 July 1997.
       ~~~~~~~~~~~~~~~~~~~

WWW site:  http://www.cs.monash.edu.au/~dld/PSB-3/PSB-3.Info.CFPs.html .

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 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 PSB-98 :
-----------------------------------------------------
Q1. How can my paper be included in PSB's hardbound proceedings?

   PSB publishes peer-reviewed full papers in an archival proceedings.  Each
   accepted paper will be allocated 12 pages in the proceedings volume.
   Paper authors are required to register (and pay) for the conference by
   the time they submit their camera-ready copy, or the paper will not be
   published.

Q2. How does a PSB publication compare to a journal publication?

   PSB papers are strenuously peer reviewed, and must report significant
   original material.  PSB expects to be included in Indicus Medicus,
   Medline and other indexing services starting this year.  All accepted
   full papers will be indexed just as if they had appeared in a journal.
   It is too early to assess the impact of a PSB paper quantitatively, but
   we will take every action we can to improve the visibility and
   significance of PSB publication.

Q3. If I do not want to submit a full paper to PSB, but wish to participate?

   Authors who do not wish to submit a full paper are welcome to submit one
   page abstracts, which will be distributed at the meeting separately from
   the archival proceedings, and are also welcome to display standard or
   computer-interactive posters.  

Q4. What are the paper submission deadlines?

   Papers will be due July 14, although session chairs can to adjust this
   deadline at their discretion.  Results will be announced August 22, and
   camera ready copy will be due September 22.  Poster abstracts will be
   accepted until October 1, and on a space available basis after that.
   Poster space is limited, especially for interactive posters that require
   computer or network access.

Q5. Where should I send my submission?

   All full papers must be submitted to the central PSB address so that we
   can track the manuscripts.   Physical submittors should send five copies
   of their paper to:

      PSB-98
      c/o Section on Medical Informatics
      Stanford University Medical School, MSOB X215
      Stanford, CA 94305-5479  USA

   Electronic submission of papers is welcome.  Format requirements for
   electronic submission will be available on the web page
   (http://www.cgl.ucsf.edu/psb) or from Russ Altman
   (altman at smi.stanford.edu).  Electronic papers will be submitted directly
   to Dr. Altman.

   We prefer that all one page abstracts be submitted electronically.
   Please send them to us in plain ascii text or as a Microsoft Word file.
   If this is impossible, please contact Dr. Altman as soon as possible.

Q6. How can I obtain travel support to come to PSB?

   We have been able to offer partial travel support to many PSB attendees
   in the past, including most authors of accepted full papers who request
   support.  However, due to our sponsoring agencies' schedules, we are
   unable to offer travel awards before the registration (and payment)
   deadlines for authors.  We recognize that this is inconvenient, and we
   are doing our best to rectify the situation.  NO ONE IS GUARANTEED TRAVEL
   SUPPORT.  Travel support applications will be available on our web site
   (see Q7).

Q7.  How can I get more information about the meeting?

   Check our web page: http://www.cgl.ucsf.edu/psb or send email to the
   conference chair: hunter at nlm.nih.gov

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.

 IMPORTANT DATES:

 Full paper submissions due    (NEW deadline):   July   21, 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

More information about the  "Complexity and information-theoretic approaches to
biology"  stream, including a sample list of relevant papers is available on
the WWW at  http://www.cs.monash.edu.au/~dld/PSB-3/PSB-3.Info.CFPs.html .

For further information about the above stream,
e-mail Dr. David Dowe, dld at cs.monash.edu.au ,
http://www.cs.monash.edu.au/~dld/ ,  Fax: +61 3 9905-5146
on or before 2 July  (or after 19th July)

or

Dr. Klaus Prank, ndxdpran at rrzn-serv.de ,
http://sun1.rrzn-user.uni-hannover.de/~ndxdpran/ ,
on or after 3 July.