Machine Learning in Systems Biology: Submission deadline extended

MLSB 09
Third International Workshop on Machine Learning in Systems Biology
5-6 September 2009, Ljubljana, Slovenia
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.

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

For an oral presentation, please submit an extended abstract of maximum eight pages. Formatting instructions are available on the website of the workshop. Extended abstracts should be submitted online by 1 June 2009 via the Easychair submission system at
http://www.easychair.org/conferences/?conf=mlsb09.
The accepted submissions will be collected in the proceedings of the workshop.

KEY DATES

12 June: deadline for submission of extended abstracts for oral presentation
10 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

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

Special session on multiscale spectral embeddings

We invite you to apply to participate in a special session on spectral embeddings, as a part of the IEEE Workshop on Statistical Signal Processing (http://www.ssp2009.org/), which will be held in Cardiff, Wales, UK, Aug.31-Sept. 3, 2009.

The session will deal with various aspects and applications of spectral embeddings in machine learning and signal processing.

A participant can contribute an extended abstract of 4 pages that will be published as part of the conference proceedings or short abstract.

During the special session all participants will give a talk on their contribution

APPLICATION DEADLINE: 10 June 2009

To apply, please contact Dr. Yosi Keller at yosi.keller (at) gmail.com

We look forward to receiving your applications.

Sincerely,

The Organisers

Prof. Naoki Saito and Dr. Yosi Keller .

Special Issue “Music, Brain, & Cognition” of Connection Science Available

Dear Colleagues,

We would like to announce the Connection Science Special Issue “Music, Brain, & Cognition” Vol. 21 (2-3):
http://prod.informaworld.com/smpp/title~db=all~content=g911586331

This special issue aims to shed light on some of the key issues in current and future music research and technology. In the 90th, cognitive Musicology was envisaged to be composed from diverse disciplines such as brain research and artificial intelligence striving for a more scientific understanding of the phenomenon of music. One and a half decades following the special issue on Music and Creativity in Connection Science, edited by Griffith and Todd (1994), this issue, again, demonstrates how the horizons in the field have continued to expand.

Research activity in auditory neuroscience, applied to music in particular, is catching up with the scientific advances in vision research. The fast advancement of brain imaging methodology such as the electroencephalogram has further encouraged music research. Brain imaging grants access to music-related brain processes directly rather than circuitously via psychological experiments and verbal feedback by the subjects. Adaptability is an important topic on the agenda of roadmaps for the development of music technology. Adaptability helps transferring knowledge to new situations, users, or music styles. In music information retrieval, solutions have been developed to solve specialized tasks. But would such a system be useful to identify new styles or new musical concepts?

How is the perception of a musical event influenced by the context of previous musical development and high-level structure? The general success of Bayesian networks inspired cognitive science as well, developing models of concept learning, inference, and surprise. Bayesian networks have proven to be an approach well suited to address some of the most vital phenomena in music, such as beat, expectation, attention, tension, interestingness, and surprise.

We would like to thank the special editorial board, consisting of Klaus Obermayer, Eduardo Reck Miranda, Xavier Serra, and John Shawe- Taylor. We owe a great thanks to the 48 highly competent reviewers that have provided elaborated reviews often of original scientific value of their own.

Best,
David R. Hardoon and Hendrik Purwins

CONTENT:
*Editorial: Trends and perspectives in music cognition research and technology
(Hendrik Purwins; David R. Hardoon)

*Information dynamics: patterns of expectation and surprise in the
perception of music
(Samer Abdallah; Mark Plumbley)

*What/when causal expectation modelling applied to audio signals
(Amaury Hazan; Ricard Marxer; Paul Brossier; Hendrik Purwins; Perfecto Herrera; Xavier Serra)

*Genre classification using chords and stochastic language models
(Carlos Pérez-Sancho; David Rizo; José M. Iñesta)

*GLM and SVM analyses of neural response to tonal and atonal stimuli: new techniques and a comparison
(Simon Durrant; David R. Hardoon; André Brechmann; John Shawe- Taylor; Eduardo R. Miranda; Henning Scheich)

*From frequency to pitch, and from pitch class to musical key: shared principles of learning and perception
(Jamshed J. Bharucha)

*Model cortical responses for the detection of perceptual onsets and beat tracking in singing
(Martin Coath; Susan L. Denham; Leigh M. Smith; Henkjan Honing; Amaury Hazan; Piotr Holonowicz; Hendrik Purwins)

*Analysing musical performance through functional data analysis: rhythmic structure in Schumann’s Träumerei (Josué Almansa; Pedro Delicado)

*Exploiting functional relationships in musical composition (Amy K. Hoover; Kenneth O. Stanley)

*Predictive models for music (Jean-François Paiement; Yves Grandvalet; Samy Bengio)

Deadline Extension: BBCI Workshop 2009 on Advances in Neurotechnology (Berlin, July 8-10)

Due to several requests and the fact that June 1st is a national holiday in some countries, we have extended the poster submission deadline as well as the early registration deadline.

Call for Participation
Call for Poster Submissions

BBCI Workshop 2009
July 8-10, Berlin, Germany

http://bbci.agilemeetings.com

IMPORTANT DATES

* Submission Date: 2009-06-09 **extended**
* Notification of Acceptance: 2009-06-15 **extended**
* Workshop Date: 2009-07-08 – 2009-07-10

ORGANIZATION

* Bernstein Focus: Neurotechnology (BFNT-B) in cooperation with the
* Bernstein Center for Computation Neuroscience Berlin (BCCN-B) and the
* Berlin Institute of Technology (TUB)

Klaus-Robert Mueller, TUB and BFNT-B
Benjamin Blankertz, TUB and BFNT-B
John-Dylan Haynes, BCCN-B
Michael Tangermann, TUB
Steven Lemm, Fraunhofer FIRST
Matthias L. Jugel, BFNT-B

Andrea Gerdes, TUB/Workshop Secretary

DESCRIPTION

Different approaches to Brain-Computer Interfaces have been developed, each one with specific solutions that range from understanding and explaining cognitive functions to communicating with real and virtual environments by thought alone.

The Berlin BCI Workshop presents an overview, in-depth tutorials and discussions on the latest research at all levels of interaction. The research presented will cover invasive recording, with its high temporal and spatial resolution, semi-invasive ECoG, non-invasive EEG, with high temporal and low spatial resolution, non-invasive NIRS and fMRI measurement, with partially high spatial and low temporal resolution and potential combinations of the different methods.

The workshop programme includes one day full of tutorials on invasive BCI, electro-physiology and non-invasive BCI. The two other workshop days cover all aspects of invasive and non-invasive EEG, NIRS and fMRI, plus informative results of the “TOBI: Tools for Brain-Computer Interaction” project, aspects of Brain@Work (neurotechnology-based man-machine interaction for industrial applications) and our newly founded Bernstein Focus: Neurotechnology (Noninvasive Neurotechnologies for Man-Machine Interactions). The poster session following the tutorials will cross over into the BBCI barbecue, smoothing discussions with drinks and food.

SUBMISSION

Please send your posters (in PDF) or abstracts (max. 2 pages, PDF or plain text) to the poster chair Michael Tangermann , no later than 2009-06-09.

Maximum final poster size is A0 (width x height: 841mm × 1189mm).

CONFIRMED SPEAKERS

– Miguel Nicolelis, Duke University
– Gerwin Schalk, Wadsworth Center
– Theresa Vaughan, Wadsworth Center
– Niels Birbaumer, Eberhard-Karls-University Tuebingen
– Nikos K. Logothetis, MPI for Biological Cybernetics
– Gert Pfurtscheller, University of Graz
– Eberhard E. Fetz, University of Washington
– Christa Neuper, University of Graz
– Lars Kai Hansen, Technical University of Denmark
– Jack Gallant, University of California – Berkeley
– Rainer Goebel, Maastricht University
– Alexander Gail, Georg-August-Universitaet Goettingen
– Gert Pfurtscheller, University of Graz
– Theresa Vaughan, Wadsworth Center
– Eilon Vaadia, Hebrew University of Jerusalem
– Ruediger Rupp, Stiftung Orthopaedische Universitaetsklinik, Heidelberg
– Gabriel Curio, Charité Berlin
– John-Dylan Haynes, Bernstein Center for Computational Neuroscience
– Klaus-Robert Mueller, Berlin Institute of Technology
– Benjamin Blankertz, Berlin Institute of Technology
– Michael Tangermann, Berlin Institute of Technology

VENUE

Bernstein Center for Computational Neuroscience Berlin, located at the beautiful campus Mitte of the Charité – Universitätsmedizin Berlin.

http://www.bccn-berlin.de/

WORKSHOP FEES

Business: 300 EUR
Standard: 250 EUR

* Early Registration Discount (before 2009-06-18)

– Academic : 200 EUR
– Bernstein: 100 EUR
– Students : 50 EUR

FUNDING

The workshop is supported by the Bernstein Focus: Neurotechnology Berlin and an application for PASCAL funding is pending.

Postdoctoral Position, Kings College London

Area: interface between bio-informatics, applied mathematics, and statistical mechanics

Subject keywords:
data integration, machine learning, Bayesian analysis, gene arrays

Duration: 3 years

Starting date: Sept 2009

Closing date for applications: June 12th 2009

The aim of the project is to perform a Bayesian classification and regression analysis by integrating data representing tumour image traits (MRI scans, mammograms, FRET/FLIM, and PET images) with gene expression profiles, in order to predict clinical outcomes and treatment response for breast cancer patients. We also expect to study the gene regulation networks involved in the disease progression, possibly using additional public data sets.

The candidate will assess existing statistical and machine learning methods to extract and integrate information from gene array, image traits and biophysical experiments. He/she must be able to develop and implement new or improved algorithms to make the best use of available data. The candidate will also perform mathematical investigations of gene regulatory networks and their disruptions caused by cancer.

Ideally, the candidate for this position would have a very solid mathematical background, preferably in statistical mechanics and/or statistical (machine) learning theory, and have experience in and affinity for dealing with biological data. The candidate must have scientific programming experience, and be comfortable with communicating with scientists from different backgrounds (mathematicians, biologists, physicists, and physicians).

Application forms:
www.mth.kcl.ac.uk/~tcoolen/postdoc1/

Further information:

Dr E Blanc
MRC Centre for Developmental Neurobiology
and KCL Centre for Bioinformatics (KCBI)
eric.blanc (at) kcl.ac.uk

Prof ACC Coolen
Department of Mathematics
ton.coolen (at) kcl.ac.uk

Bats recognize the individual voices of other bats

Bats can use the characteristics of other bats’ voices to recognize each other, according to a study by researchers from the University of Tuebingen, Germany and the University of Applied Sciences in Konstanz, Germany. The study, published June 5 in the open-access journal PLoS Computational Biology, explains how bats use echolocation for more than just spatial knowledge.

The researchers first tested the ability of four greater mouse-eared bats to distinguish between the echolocation calls of other bats. After observing that the bats learned to discriminate the voices of other bats, they then programmed a computer model that reproduces the recognition behaviour of the bats. Analysis of the model suggests that the spectral energy distribution in the signals contains individual-specific information that allows one bat to recognize another.

Animals must recognize each other in order to engage in social behaviour. Vocal communication signals are helpful for recognizing individuals, especially in nocturnal organisms such as bats. Little is known about how bats perform strenuous social tasks, such as remaining in a group when flying at high speeds in darkness, or avoiding interference between echolocation calls. The finding that bats can recognize other bats within their own species based on their echolocation calls may therefore have some significant implications.

The full article is available at the following link
http://dx.plos.org/10.1371/journal.pcbi.1000400

###

FINANCIAL DISCLOSURE: This work was funded by SFB 550, by the Graduiertenkolleg Neurobiologie. It was supported in part by the IST Program of the European Community, under the PASCAL network of excellence, IST-2002-506778. This work was also supported by the human resources and mobility activity Marie Curie host fellowships for early stage research training under contract MEST-CT-2004-504321 PERACT by the European Union. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

COMPETING INTERESTS: The authors have declared that no competing interests exist.

CITATION: Yovel Y, Melcon ML, Franz MO, Denzinger A, Schnitzler H-U (2009) The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls. PLoS Comput Biol 5(6): e1000400. doi:10.1371/journal.pcbi.1000400

CONTACT:

Dr. Yossi Yovel
Weizmann institute of science (current affiliation)
phone: 97289346304
cell: 972506463642
email: yossiyovel (at) hotmail.com

The original press release can be found here.

SOKD-2009: Service-oriented knowledge discovery workshop at ECML/PKDD-2009

SoKD-09: Third Generation Data Mining: Towards Service-oriented Knowledge Discovery

2nd SoKD Workshop at ECML PKDD 2009
7 September 2009, Bled, Slovenia

Paper submission deadline is June 10.

See the Call for papers and other details at http://zulu.ijs.si/WEB/SoKD09/

You are invited to submit papers related to the topic of this workshop, which include:

– third generation data mining systems
– service-oriented knowledge discovery
– data mining services
– data mining ontologies
– ontologies as background knowledge used for learning
– information fusion
– knowledge mining, mining of patterns and models
– data mining workflows
– heterogenous data sources
– … and related topics

Proceedings of SoKD-08 can be found at
http://www.ecmlpkdd2008.org/workshop-papers-sokd

Attend KDD-09 (early reg deadline May 31) – The Data Mining and Knowledge Discovery conf., Paris

KDD-2009: The Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD’09)

Paris, France
June 28 – July 1, 2009.
http://www.kdd.org/kdd2009/

Register by May 31 to get the early registration rates!
http://www.kdd.org/kdd2009/registration.html

As the premier international conference on Data Mining and Knowledge Discovery, KDD 2009 provides a forum for academic researchers and industry and government innovators to share their results and experiences. Researchers and practitioners will gather to present academic and industrial papers, panels, implemented software demos, posters, workshops, tutorials, and insights from the popular KDD Cup competition.

New this year: a social networking platform where attendees can learn about the proceedings, collaborate on research papers, discuss individual sessions, receive real-time updates on the conference, and help organize social events in Paris using the site.

CONFERENCE VENUE
—————-

For the first time KDD will leave America and come to Europe; KDD 2009 will take place in beautiful downtown Paris, at the Marriott Paris Rive Gauche Hotel, 17 Boulevard St Jacques, 75014 Paris, France.

On Monday, June 29 the Conference reception will be held at the Hotel de Ville of Paris, in the main reception room, the Salle des Fetes, where Paris usually welcomes Heads of States and VIPs.

Please go to http://www.kdd.org/kdd2009/registration.html to register online for the conference. The early conference registration deadline is May 31 Find the hotel reservation code on
http://www.kdd.org/kdd2009/travel.html to enjoy the group rate for the hotel.

This year the organizers are introducing a new option besides full participation: “Workshops, Tutorials,and Evenings” (or, “Nights and Weekends”). This enables you to participate all day Sunday, for the workshops and/or tutorials, as well as the evenings (5pm+ Sunday-Tuesday),
which feature invited industry talks, receptions at the beautiful Paris Town Hall and Marriott Hotel, and technical poster sessions. (The option omits, however, the full technical program during the 3 days, Mon-Wed.)

If you have any registration questions direct them to:

Mandy Mann (mandy.mann at regmaster.com) or +1 407 971 4451.

For other questions, the KDD organizer contact information is at:
http://www.kdd.org/kdd2009/

CONFERENCE HIGHLIGHTS
——————–

a) INVITED SPEAKERS:

This year, KDD features five distinguished invited speakers:
– David J. Hand, “Mismatched Models, Wrong Results, and Dreadful Decisions: On choosing appropriate data mining tools”
– Heikki Mannila, “Randomization Methods in Data Mining”
– Stanley Wasserman, ““Network Science: An Introduction to Recent Statistical Approaches”
– Ravi Kumar, “Mining Web Logs: Applications and Challenges”
– Ashok N. Srivastava, “Data Mining at NASA: from Theory to Applications”

b) TUTORIALS: (all tutorials are free with conference registration)

9 diverse half-day tutorials will be presented on Sunday, June 28th.
http://www.kdd.org/kdd2009/tutorials.html

c) WORKSHOPS (all workshops are free with conference registration)

11 workshops, including 4 challenge workshops, will be held Sunday,
June 28th . http://www.kdd.org/kdd2009/workshops.html

The detailed Conference program will soon be available on the KDD-09 web
site.

d) KDD CUP

Based on challenge data provided by Orange Labs, this year’s competition focuses on predicting customer scores from large marketing databases from the French Telecom company, Orange.
10,000 Euros of prizes and travel grants — generously donated by Orange — will be distributed among the cup winners.
See progress on: http://www.kddcup-orange.com/

ENJOY PARIS
———–

While in Paris, enjoy the city! Register on http://www.kdd.org/kdd2009/travel.html#deals for special deals available to KDD participants on Saturday 27 June, Thursday 2 July, and Friday 3 July.

— KDD organizers http://www.sigkdd.org/kdd2009/organizers.html

Machine Learning Summer School 2009

University of Cambridge, UK
29 August – 10 September 2009
http://mlg.eng.cam.ac.uk/mlss09/

We invite you to apply to attend the 13th Machine Learning Summer School, which will be held at the University of Cambridge. The school will offer lectures and practicals given by leading researchers in the field on a wide range of topics in machine learning. We hope to attract international students, young researchers and industry practitioners with a keen interest in machine learning and a strong mathematical background.

APPLICATION DEADLINE: 1 June 2009

APPLICATION WEBSITE: http://mlg.eng.cam.ac.uk/mlss09/application.htm

We can offer a limited number of travel grants, and encourage students to apply even if they may not be able to meet the full costs of travel and attendance.

Confirmed Lecturers:
Christopher Bishop
Andrew Blake
David Blei
Philip Dawid
Zoubin Ghahramani
Simon Godsill
Geoffrey Hinton
Thomas Hofmann
Michael Jordan
Michael Littman
David MacKay
Thomas P. Minka
Iain Murray
Peter Orbanz
Carl Edward Rasmussen
Bernhard Schölkopf
John Shawe-Taylor
Yee Whye Teh
Josh Tenenbaum
Lieven Vandenberghe

This year’s MLSS is organised by the University of Cambridge, with Microsoft Research and PASCAL.

We look forward to receiving your applications.

Sincerely,

The Organisers
Zoubin Ghahramani, Carl Edward Rasmussen, Christopher M. Bishop, A. Philip Dawid, David J.C. Mackay, Peter Orbanz, Joaquin Quiñonero Candela

PASCAL Visual Object Classes Recognition Challenge 2009

We are running the PASCAL Visual Object Classes Recognition Challenge again this year. As in 2008 there are 20 object classes. Participants can recognize any or all of the classes, and there are classification, detection and pixel-wise segmentation competitions. (New for 2009, segmentation has been promoted from a “taster” to a full competition.)
There is also a “taster” competition on person layout (detecting head, hands, feet).

The development kit (Matlab code for evaluation, and baseline algorithms) and training data is now available at:

http://pascallin.ecs.soton.ac.uk/challenges/VOC/voc2009/index.html

where further details are given. The timetable of the challenge is:

* 15 May 2009: Development kit (training and validation data plus
evaluation software) made available.

* 15 June 2009: Test set made available.

* 7 September 2009. Deadline for submission of results.

* 3 October 2009: Workshop in association with ICCV 2009, Kyoto, Japan.

Mark Everingham
Luc Van Gool
Chris Williams
John Winn
Andrew Zisserman