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Complexity and information-theoretic approaches to biology
----------------------------------------------------------
This is the second 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: July 14, 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 .
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
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
----------------------------------------------------------
This is the second 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: July 14, 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 .
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
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