[Socbin] Call for papers: Machine Learning in Systems Biology

[Juho Rousu]

[apologies for multiple postings]



************************** Call for Papers *****************************
						
			   MLSB 09

Third International Workshop on Machine Learning in Systems Biology

		5-6 September 2009, Ljubljana, Slovenia

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      		http://mlsb09.ijs.si/



MOTIVATION


Molecular biology and all the biomedical sciences are undergoing a
true revolution as a result of the emergence and growing impact of a
series of new disciplines/tools sharing the "-omics" suffix in their
name.  These include in particular genomics, transcriptomics,
proteomics and metabolomics, devoted respectively to the examination
of the entire systems of genes, transcripts, proteins and metabolites
present in a given cell or tissue type.

The availability of these new, highly effective tools for biological
exploration is dramatically changing the way one performs research in
at least two respects.  First, the amount of available experimental
data is not a limiting factor any more; on the contrary, there is a
plethora of it.  Given the research question, the challenge has
shifted towards identifying the relevant pieces of information and
making sense out of it (a "data mining" issue). Second, rather
than focus on components in isolation, we can now try to understand
how biological systems behave as a result of the integration and
interaction between the individual components that one can now monitor
simultaneously (so called "systems biology").

Taking advantage of this wealth of "genomic" information has become a
conditio sine qua non for whoever ambitions to remain competitive in
molecular biology and in the biomedical sciences in general. Machine
learning naturally appears as one of the main drivers of progress in
this context, where most of the targets of interest deal with complex
structured objects: sequences, 2D and 3D structures or interaction
networks. At the same time bioinformatics and systems biology have
already induced significant new developments of general interest in
machine learning, for example in the context of learning with
structured data, graph inference, semi-supervised learning, system
identification, and novel combinations of optimization and learning
algorithms.

The Workshop is organized as "core - event" of Pattern Analysis,
Statistical Modelling and Computational Learning - Network of Excellence
2 (PASCAL 2, http://www.pascal-network.org/)


OBJECTIVE


The aim of this workshop is to contribute to the cross-fertilization
between the research in machine learning methods and their
applications to systems biology (i.e., complex biological and medical
questions) by bringing together method developers and
experimentalists. We encourage submissions bringing forward methods
for discovering complex structures (e.g. interaction networks,
molecule structures) and methods supporting genome-wide data analysis.


LOCATION AND CO-LOCATION


The workshop will take place 5-6 September 2009 at the Jozef Stefan
Institute, Ljubljana, Slovenia. It will immediately precede ECML PKDD
2009, taking place 7-11 September 2009 in Bled, Slovenia (Bled is 30
miles from Ljubljana, transport will be organized).


SUBMISSIONS INSTRUCTIONS


We invite you to submit an extended abstract of maximum 8 pages,
formatted according to the Springer Lecture Notes in Computer Science
style. Each extended abstract must be submitted online via the Easychair
submission system: http://www.easychair.org/conferences/?conf=mlsb09

The extended abstracts will be reviewed by the scientific programme
committee. The papers will be selected for oral or poster presentation
according to their originality and relevance to the workshop topics.

Electronic versions of the extended abstracts will be accessible to the
participants prior to the conference and will be made publicly available
on the conference web site after the conference.

The accepted papers will be published in Journal of Machine Learning 
(JMLR) Workshop and Conference Proceedings (http://jmlr.csail.mit.edu/).


KEY DATES


01 June: deadline for submission of extended abstracts for oral
presentation
03 July: notification for oral presentations
03 August: deadline for submission of abstracts for poster presentations
10 August: notification for posters & camera ready versions due
5-6 September: workshop


TOPICS


A non-exhaustive list of topics suitable for this workshop is given
below:

Methods

Machine learning algorithms
Bayesian methods
Data integration/fusion
Feature/subspace selection
Clustering
Biclustering/association rules
Kernel methods
Probabilistic inference
Structured output prediction
Systems identification
Graph inference, completion, smoothing
Semi-supervised learning

Applications

Sequence annotation
Gene expression and post-transcriptional regulation
Inference of gene regulation networks
Gene prediction and whole genome association studies
Metabolic pathway modeling
Signaling networks
Systems biology approaches to biomarker identification
Rational drug design methods
Metabolic reconstruction
Protein function and structure prediction
Protein-protein interaction networks
Synthetic biology


CONFIRMED INVITED SPEAKERS

Ross D. King, Aberystwyth University, UK
William Stafford Noble, University of Washington, USA
Diego di Bernardo, University of Naples "Federico II", Italy


MLSB09 PROGRAM CHAIRS


Sašo Džeroski, Jozef Stefan Institute, Ljubljana, Slovenia
Pierre Geurts, Department of EE and CS & GIGA-Research, University of
Liège, Belgium
Juho Rousu, Department of Computer Science, University of Helsinki,
Finland


SCIENTIFIC PROGRAM COMMITTEE


Florence d'Alché-Buc, University of Evry, France
Saso Dzeroski, Jozef Stefan Institute, Slovenia
Paolo Frasconi, Università degli Studi di Firenze, Italy
Cesare Furlanello, Fondazione Bruno Kessler, Trento, Italy
Pierre Geurts, University of Liège, Belgium
Mark Girolami, University of Glasgow, UK
Dirk Husmeier, Biomathematics & Statistics Scotland, UK
Samuel Kaski, Helsinki University of Technology, Finland
Ross D. King, Aberystwyth University, UK
Neil Lawrence, University of Manchester, UK
Elena Marchiori, Vrije Universiteit Amsterdam, The Netherlands
Yves Moreau, Katholieke Universiteit Leuven, Belgium
William Stafford Noble, University of Washington, USA
Gunnar Rätsch, FML, Max Planck Society, Tübingen
Juho Rousu, University of Helsinki, Finland
Céline Rouveirol, University of Paris XIII, France
Yvan Saeys, University of Gent, Belgium
Guido Sanguinetti, University of Sheffield, UK
Ljupco Todorovski, University of Ljubljana, Slovenia
Koji Tsuda, Max Planck Institute, Tuebingen
Jean-Philippe Vert, Ecole des Mines, France
Louis Wehenkel,  University of Liège, Belgium
Jean-Daniel Zucker, University of Paris XIII, France
Blaz Zupan, University of Ljubljana, Slovenia


LOCAL ORGANIZATION

Ivica Slavkov, Dragi Kocev, Tina Anžič, Jozef Stefan Institute,
Ljubljana, Slovenia