Cajal Course in Computational Neuroscience

6th - 26th August 2017, Lisbon, Portugal - 2017-01-16


Registration for this years Cajal Course in Computational Neuroscience has opened. The course will be hosted at the Champalimaud Centre for the Unknown in Lisbon, Portugal and is directed by Gilles Laurent from the MPI for Brain Research in Frankfurt, Christians Machens from the Champalimaud Centre for the Unknown and Jakob Macke from the Research Center caesar.

The course is designed for graduate students and postdoctoral fellows from a variety of disciplines. The application deadline is the 20th of March 2017 at midnight, CET time. More information about the course and how to apply visit the official website. This course is part of the CAJAL Advanced Neuroscience Training Programme - an initiative by FENS, IBRO and The Gatsby Foundation - and is hosted by Champalimaud Foundation, Portugal. We are grateful to Google DeepMind for additional funding.

Four Abstracts at Cosyne!


The annual meeting on Computational and Systems Neuroscience is the most important conference for exchange of experimental and theoretical/computational approaches to problems in systems neuroscience. We are happy that all four of our submissions to the Cosyne Conference were successful this year, and will be presented at the conference. In addition, Artur and Jan-Matthis received travel grants.

On day 1 (February 23), Giacomo Bassetto will present his work on data-efficient receptive field estimation (I-27).

On day 2 (February 24), you are spoilt for choice between two posters from the group: In II-3, ``Flexible Bayesian inference for mechanistic models of neural dynamics’’ by Pedro Goncalves, Jan-Matthis Lueckmann, Giacomo Bassetto and Marcel Nonnenmacher, we are presenting an approach for making statistical inference possible and painless for any neuron model of your choice.

In II-77 ``Can serial dependencies in choices and neural activity explain choice probabilities?’’, Jan-Matthis Lueckmann’s work from our collaboration with Hendrikje Nienborg will investigate whether and how choice probabilities are affected by temporal dependencies.

On day 3 (February 25), check out Artur Speiser’s work with Srinivas Turaga and Evan Archer, on ``Amortized inference for fast spike prediction from calcium imaging data.’’– using deep learning to make generative-model based inference of action potentials much faster.

International Max Planck Research School Brain and Behavior

fully funded Phd positions in Bonn and Florida, deadline soon! - 2016-11-17

The International Max Planck Research School for Brain and Behavior is a fully funded graduate program in the neurosciences jointly hosted between caesar and the Max Planck Florida Institute for Neuroscience , USA, and in collaboration with partner universities in Bonn and Florida. The Ph.D. program is open to highly qualified and motivated candidates from all over the world who hold an outstanding diploma or master degree. We will be taking in our second cohort of students this year, the deadline is soon (December 1st)– apply at! Selection symposium will be in March next year, and positions will start in 2017.

Workshop at NIPS

Brains and Bits; Neuroscience Meets Machine Learning - 2016-08-26

Together with Allie Fletcher (UCLA), Eva Dyer and Konrad Koerding (Northwestern), Jascha Sohl-Dickstein (Google Research) and Joshua Vogelstein (John Hopkins), Jakob is organising a two-day workshop on Brains and Bits: Neuroscience Meets Machine Learning at NIPS 2016. It’s all happening on Friday-Saturday, December 9th-10th, 2016, in Barcelona. We have an exciting line-up of speakers from machine learning, computational neuroscience and computer-science:

  • Yoshua Bengio, Université de Montréal
  • Adrienne Fairhall, University of Washington
  • Demis Hassabis, Google DeepMind
  • Christos Papadimitriou,UC Berkeley
  • Terry Sejnowski, Salk Institute, UCSD
  • Anima Anandkumar, UC Irvine
  • Mitya Chklovskii, Simons Foundation
  • David Cox, Harvard
  • Sophie Denève, ENS
  • Emily Fox, University of Washington
  • Surya Ganguli, Stanford
  • Fred Hamprecht, Heidelberg
  • Jonathan Pillow, Princeton
  • Maneesh Sahani, Gatsby Unit, University College London

Deadline for submissions is 29/09/2016– we will have both posters and contributed talks!

More instructions and information on the workshop website.

CAJAL Course in Computational Neuroscience

at the Cajal Center for the Unknown, Lisbon, Portugal - 2016-08-02

Jan-Matthis, Pedro and Jakob are taking part in the CAJAL Course in Computational Neuroscience from August 7th to 27th at the Champalimaud Centre in Lisbon. Jan-Matthis will attend as a student, and Jakob and Pedro will be teaching. Congratulations to Jan-Matthis for being accepted to the course, and many thanks to the Boehringer Ingelheim Fonds for awarding a travel-grant to Jan-Matthis!

Deep Learning Summer School


From August 1st to 7th, Jan-Matthis is attending the deep learning summer school in Montreal, organized by the Canadian Institute For Advanced Research.

New Internship Student


Today Poornima Ramesh joined our group for an internship, on a DAAD Rise Scholarship. Welcome on board Poornima!

NVIDIA Hardware Grant


NVIDIA granted us a Titan X GPU for faster training of deep neural networks for analyzing behavioural data. Many thanks to NVIDIA, as well to Jan-Matthis for helping write the application.

Titisee conference

on building tools for quantifying brain and behaviour - 2016-04-15

Jakob is taking part in the 113th Titsee-conference by the Boehringer Ingelheim Fonds– looking forward to discussing `tools for quantifying brain and behaviour’ with an amazing group of scientists in the black forest.

Are neural systems really poised at criticality?

new preprint online - 2016-02-26

Large-scale recordings of neuronal activity make it possible to gain insights into the collective activity of neural ensembles. It has been hypothesized that neural populations might be optimized to operate at a `thermodynamic critical point’, and that this property has implications for information processing. Support for this notion has come from a series of studies which identified statistical signatures of criticality in the ensemble activity of retinal ganglion cells. What are the underlying mechanisms that give rise to these observations?

We just uploaded a new manuscript that challenges these findings. In the manuscript, we show that signatures of criticality arise even in simple feed-forward models of retinal population activity. In particular, they occur whenever neural population data exhibits correlations, and is randomly sub-sampled during data analysis. These results show that signatures of criticality are not necessarily indicative of an optimized coding strategy, and challenge the utility of analysis approaches based on equilibrium thermodynamics for understanding partially observed biological systems.

New paper on Bayesian estimation of psychometric functions

with Heiko Schuett, Stefan Harmeling and Felix Wichmann - 2016-02-25

The paper Painfree and accurate Bayesian estimation of psychometric functions for (potentially) overdispersed data with Heiko Schuett, Stefan Harmeling and Felix Wichmann was accepted at Vision Research. Psychometric functions play an essential role in much of behavioural neuroscience and psychophysics. In this paper, we describe efficient and accurate methods for estimating psychometric functions using Bayesian inference techniques. In contrast to previous methods, they dont require any parameter tuning or fickly MCMC, as the posterior is integrated numerically. In addition, the model also includes a term that captures `overdispersion’, which can result from fluctuations in the performance of a behaviour. A (hopefully) easy-to-use matlab implementation is available here

AWS Research Grant


Amazon Web Services awarded us an ‘AWS Research Grant’ to develop dimensionality reduction methods for massively parallel neural population data, and to evaluate them on Amazon AWS. Thanks to Hooram and Marcel who helped in preparing the application.

New International Max Planck Research School Brain and Behavior

fully funded Phd positions in Bonn and Florida - 2015-10-25

The new International Max Planck Research School for Brain and Behavior is a fully funded graduate program in the neurosciences jointly hosted between caesar and the Max Planck Florida Institute for Neuroscience (MPFI), USA. The Ph.D. program is open to highly qualified and motivated candidates from all over the world who hold an outstanding diploma or master degree. Application deadline is December 1; positions available starting September 2016.

Talk at Group for Neural Theory, ENS Paris


Jakob will be giving a talk about Marcels work at the Group for Neural Theory at Ecole Normale Superieure on Thursday, October 29th.

New Theory Reading Group

Enjoy Computational Neuroscience and Machine Learning on Thursday morning. - 2015-10-02

We are setting up an inter-disciplinary reading group focussed on computational neuroscience and machine learning. Be warned: We will not be afraid to read technical papers. We meet (roughly every second) Thursday morning in caesar near our offices. Everyone that is willing to actively contribute is welcome to attend, please send an email to Jakob to be added to the mailing list.

Paper accepted at NIPS!

Congratulations to Mijung and Gergo! - 2015-09-13

The paper `Unlocking neural population non-stationarities using hierarchical dynamics models’ by Mijung (Website) and Gergo Bohner was accepted at NIPS. There were 1838 submissions to NIPS this year, 403 of which were accepted at the conference. Pdf and code will follow soon. In this paper, we developed a model and inference procedure for tracking changes in the parameters of population models across trials. To illustrate the method, we used data that was kindly provided to us by Alexander Ecker.

Bernstein Conference in Heidelberg

Two talks and a poster - 2015-09-07

Giacomo, Piotr and Jakob are travelling to Heidelberg next week to attend the Bernstein Conference. Jakob will give a talk in the Workshop `Estimating Parameters and Unobserved State Variables from Neural Data’ on Monday, 14/09/15, and will present Marcel’s work on ‘Correlations and signatures of criticality in neural population models’ in a contributed talk in the main conference on Wednesday 16/09/15. Giacomo will present a poster on our joint work with Alex Ecker on Wednesday evening.

We are hiring!

Postdoc and graduate student positions available - 2015-07-24

We need you: We are hiring both graduate students and postdocs to join our group. If you have a background in a quantitative discpline and want to do graduate or postdoctoral research in computational neuroscience and machine learning, check out the advertisement!

Congratulations to Evan!


Evan Archer (Website), who did his graduate work with Jonathan Pillow at at UT Austin (now Princeton) and with Jakob in Tuebingen, successfully defended his thesis in Tuebingen. In his graduate work, Evan developed Bayesian methods for statistical modelling of neural population spike trains, including very flexible and efficient methods for density estimation, entropy estimation, and system identification both for single neurons and populations of neurons.

Evan is now a postdoc with John Cunningham and Liam Paninski at the Statistics Department and Grossman Center for the Statistics of Mind at Columbia University. Many congratulations to the very first ‘Dr. rer. nat.’ from the lab!

Visions in Science @ caesar


From September 24-26, Visions in Science, the annual interdisciplinary scientific event organized bythe Max Planck PhDnet is taking place at caesar. This year’s conference is themed ‘Branch and Connect’ and it will feature talks on neuroscience and network analysis.

Students attending summer schools


Marcel was accepted into the Advanced Course in Computational Neuroscience, which is part of the CAJAL Advanced Neuroscience Training Programme, and is held at the Champalimaud Foundation in Lisbon, Portugal, 9th-29th August 2015.

Jan-Matthis is going to a summer course in mining and modeling of neuroscience data, which is held at UC Berkeley between 6th and 17th July 2015. The course is organised by the Redwood Center for Theoretical Neuroscience, and is founded through CRCNS (Collaborative Research in Computational Neuroscience).

Welcome to our new Website

It is done - 2015-04-23

Today our new website went live. We will continue to update and expand content in the near future, so please bear with us as we are working on it.

Bonn Brain 3 at caesar


Jakob will give a talk at Bonn Brain3- the first general meeting of the Bonn neuroscience community at caesar on Friday, April 25 at 9am.

Computational and Systems Neuroscience (Cosyne) 2015


We are at Computational and Systems Neuroscience conference this year. We will present a poster with the title Correlations and signatures of criticality in neural population models together with the Bethge lab. It will be presented in the third poster session on Saturday the 7th of March beginning at 7:30pm.

Hope to see you there.

Workshop Causation from Correlation?

with the Junge Akademie - 2015-02-15

How and when can we infer causal relationships from observational data? Together with colleagues, Jakob organised an inter-disciplinary workshop on this topic for the `Junge Akademie’. Jakob and Jan-Matthis will attend, and more information will be posted on the Junge-Akademie website after the workshop.

Two papers accepted at NIPS

... one of which as a spotlight! - 2014-09-14

We had two papers accepted at NIPS this year– Evan’s paper Low-dimensional models of neural population activity in sensory cortical circuits was accepted for a poster presentation, and Patrick’s, Giacomo’s and Florian’s paper A Bayesian model for identifying hierarchically organised states in neural population activity for a spotlight. There were 1678 submissions to NIPS this year, 414 of which were accepted at the conference, and 62 of which for spotlights.