DM: Information-theoretic data-mining in biology: CFPs

[David L Dowe]

   Dear "Data miners",

      Below is a fairly long Call For Papers (CFPs) and Call For 
Reviewers
(CFRs) with a fairly tight deadline (apologies about that) of July 21 
for
a conference stream in Hawaii on

Information-theoretic data-mining in biology.


More follows:

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 (dld@cs.monash.edu.au) and Klaus 
Prank.

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@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@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,
e-mail    Dr. David Dowe, dld@cs.monash.edu.au ,
or e-mail Dr. Klaus Prank, ndxdpran@rrzn-serv.de .



This page was put together by
Dr. David Dowe,
Dept. of Computer Science, Monash University, Clayton, Vic. 3168, 
Australia
e-mail: dld@cs.monash.edu.au
Fax: +61 3 9905-5146
http://www.cs.monash.edu.au/~dld/

and

Dr. Klaus Prank,
Abteilung Klinische Endokrinologie
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30623 Hannover
Germany
e-mail: ndxdpran@rrzn-serv.de
Tel.: +49 (511) 532-3827
Fax.: +49 (511) 532-3825
http://sun1.rrzn-user.uni-hannover.de/~ndxdpran/