MLSB09, the Third International Workshop on Machine Learning in Systems Biology will be held in Ljubljana, Slovenia on September 5-6 2009 at the Jožef Stefan Institute.

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. You can download the call for papers from here.
Complete workshop proceedings can be downloaded from here .
The lectures were recorded by and can be seen here:
The Workshop was organized as "core - event" of Patterns Analysis, Statistical Modelling and Computational Learning - Network of Excellence 2 (PASCAL 2).


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.


We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. A non-exhaustive list of topics suitable for this workshop are:

Methods Applications
Machine Learning Algorithms Sequence Annotation
Bayesian Methods Gene Expression and post-transcriptional regulation
Data integration/fusion Inference of gene regulation networks
Feature/subspace selection Gene prediction and whole genome association studies
Clustering Metabolic pathway modeling
Biclustering/association rules Signaling networks
Kernel Methods Systems biology approaches to biomarker identification
Probabilistic inference Rational drug design methods
Structured output prediction Metabolic reconstruction
Systems identification Protein function and structure prediction
Graph inference, completion, smoothing Protein-protein interaction networks
Semi-supervised learning Synthetic biology


MLSB09 Chairs

Saso Dzeroski Jozef Stefan Institute, Slovenia
Pierre Geurts GIGA-Research, University of Ličge, 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 (Universitŕ 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 King (Aberystwyth University, UK)
Neil Lawrence (University of Manchester, UK)
Elena Marchiori (Vrije Universiteit Amsterdam, The Netherlands)
Yves Moreau (Katholieke Universiteit Leuven, Belgium)
William 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 Organizing Committee

Ivica Slavkov (Jozef Stefan Institute, Slovenia)
Dragi Kocev (Jozef Stefan Institute, Slovenia)
Tina Anzic (Jozef Stefan Institute, Slovenia)


For further information, please contact