Important Dates


• February 5, 2014: Start of the challenge (development period).

• May 5, 2014: End of challenge.

• May 20, 2014: All teams must turn in fact sheets. The three top ranking teams must turn in their code to qualify for prizes. The post-challenge verifications start.

• June 1, 2014: End of the post challenge verifications. Release of the official ranking.


• June 30 (extended deadline), 2014: ECML workshop paper submission deadline.

• July (5) 10, 2014: : ECML workshop paper acceptance notification

• July 25, 2014 : ECML workshop paper camera ready deadline

• September 15 or 19, 2014: ECML workshop, Nancy, France. Discussion of the results.

Neural Connectomics Workshop

From Imaging to Connectivity

September 15, 2014 - Nancy, France


Understanding the brain structure and some of its alterations caused by disease, is key to accompany research on the treatment of epilepsy and Alzheimer’s disease and other neuropathologies, as well as gaining understanding of the general functioning of the brain and its learning capabilities. At the neural level, recovering the exact wiring of the brain (connectome) including nearly 100 billion neurons, having on average 7000 synaptic connections to other neurons, is a daunting task. The goal of this workshop is to bring together researchers in machine learning and neuroscience to discuss progress and remaining challenges in this exciting and rapidly evolving field. We aim to attract machine learning and computer vision specialists interested in learning about a new problem, as well as computational neuroscientists who may be interested in modeling connectivity data. We will discuss also the results of the First ChaLearn Neural Connectomics Challenge.

ECML connectomics workshop group picture

Download the call for papers.

Invited speakers:

Elisha Moses, Weizmann Institute of Science, Israel: Keynote on "Dynamics in Small Neuronal Networks".

Florin Popescu, Fraunhofer Institute, Berlin, Germany: Keynote on "causal discovery in time series" .

Jordi Soriano, University of Barcelona, Spain: Tutorial on "Activity, connectivity and other challenges in living neuronal networks". [slides PDF][slides PPTX]

Topics of interest to the workshop include, but are not limited to:

• building connectomes from EM data

• building connectomes from fMRI data

• building connectomes from neurophysiology data

• bridging neuroanatomy and neurophysiology

• connectomics and learning

• neuroimaging technology advances

• network reconstruction algorithms

• causality in time series

• feature selection vs. causal discovery

• generative vs. discriminative modeling

• sharing data

• sharing code

• organizing new challenges

• establishing ground truth, benchmarking

• quantitative metrics of evaluation

• theoretical understanding

Accepted Papers

New : files of the papers and slides have been added

Paper accepted for Oral Presentation :

    • "Supervised Neural Network Structure Recovery", Ildefons Magrans de Abril and Ann Nowé [pdf file...] [slides]
    • "NeuralConnectivity Reconstruction from Calcium Imaging Signal using Random Forest with Topological Features", Wojciech Czarnecki and Rafal Jozefowicz [pdf file...] [slides]
    • "Signal Correlation Prediction Using Convolutional Neural Networks", Lukasz Romaszko [pdf file...] [slides]
    • "Simple connectome inference from partial correlation statistics in calcium imaging", Antonio Sutera, Arnaud Joly, Vincent François-Lavet, Zixiao Aaron Qiu, Gilles Louppe, Damien Ernst and Pierre Geurts [pdf file...] [slides]
    • "Reconstruction of Excitatory Neuronal Connectivity via Metric Score Pooling and Regularization", Chenyang Tao, Wei Lin and Jianfeng Feng [pdf file...][slides]
    • "SuperSlicing Frame Restoration for Anisotropic ssTEM", Dmitry Laptev and Joachim Buhmann [pdf file...] [slides]

Note 1 : Accepted papers for Oral Presentation are encouraged to prepare a poster for discussion.

Note 2 : For the final version of the papers the papers could be longer than 6 pages (6 to 12 pages).


Paper accepted for Poster Presentation:

    • "Inferring Causation from Correlation in Sparse Networks", Alexander Niederbühl, Volker Pernice and Stefan Rotter [pdf file...]
    • "Efficient combination of pairwise feature networks", Pau Bellot and Patrick Meyer [pdf file...]
    • "Predicting Spiking Activities in DLS Neurons with Linear-Nonlinear-Poisson Model", Sisi Ma [pdf file...]
    • "Large-Scale Automated Identification of Mouse Brain Cells in Confocal Light Sheet Microscopy Images", Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone and Giulio Iannello [pdf file...]
    • "Mapping neuronal activity with cellular resolution on a brain-wide scale", Ludovico Silvestri, Nikita Rudinskiy, Marco Paciscopi, Irene Costantini, Leonardo Sacconi, Paolo Frasconi, Bradley Hyman and Francesco Pavone [pdf file...] [slides...]

We would like you to submit your final paper version, together with its Latex sources, by: July 30, 2014 together with a cover letter answering the remarks of the reviewers. Please use the JMLR Workshop and Conference Proceedings format:


Challenge participants, please include a summary *result table* with:

- your team name

- your final private leaderboard performance

- the performance of the winner

- any other result of potential interest you wish to compare with.

The schedule of the workshop could be found here [pdf file]

Proceedings published by Springer [Proceedings DRAFT pdf]

Organizers - Contact:

Vincent Lemaire, Orange, France

Demian Battaglia, Aix Marseille Université, France

Isabelle Guyon, ChaLearn, California, USA

Jordi Soriano, University of Barcelona, Spain

Organizing committee (confirmed):

• Javier M. Buldú (URJC, Madrid, Spain)

• Mario Chavez (UPMC, France)

• Frederick Eberhardt (Caltech, Los Angeles, USA)

• Seth Flaxman (CMU)

• Sergio Gomez (URV, Tarragona, Spain)

• Alice Guyon (UPMC, Sophia Antipolis, France)

• Antti Hyttinen (University of Helsinki, Finland)

• Sisi Ma (NYU, New-York, USA)

• Adam Packer (UCL, London, UK)

• Jonas Peters (ETH Zuerich, Swtzerland)

• Florin Popescu (Fraunhofer Institute, Berlin, Germany)

• Bisaka Ray (NYU, New-York, USA)

• Alex Roxin (FCBR, Barcelona, Spain)

• Mehreen Saeed (Lahore Univ., Pakistan)

• Alexander Statnikov (New York University, USA)

• Miguel Valencia (Univ. De Navarra, Spain)

• Joshua Vogelstein (Duke Univ, North Carolina, USA)

• Gorka Zamora (BCCN, Berlin, Germany)

• Kun Zhang (Max Plank Institute for Intelligent Systems, Germany


To register to the workshop you have to register to ECML 2014 (this is a ECML decision).

Go to to do the registration.

Fee Includes:

• Admission to all scientific sessions, workshops and tutorials on Monday and Friday

• Admission to the technical programme on Tuesday, Wednesday and Thursday

• Conference materials

• Welcome Cocktail;

• Conference Dinner;

• Perhaps : Two buffet diners during the evening of the poster days