- Comp-neuro - lists.cnsorg.org

Methods of Information Theory workshop at CNS*2017

by Joseph Lizier

Dear all, Please note that the final schedule and speaker abstracts are available for the following workshop at CNS*2017 in Antwerp this week: Workshop on Methods of Information Theory in Computational Neuroscience 19 and 20 July 2017 Methods originally developed in Information Theory have found wide applicability in computational neuroscience. Beyond these original methods there is a need to develop novel tools and approaches that are driven by problems arising in neuroscience. A number of researchers in computational/systems neuroscience and in information/communication theory are investigating problems of information representation and processing. While the goals are often the same, these researchers bring different perspectives and points of view to a common set of neuroscience problems. Often they participate in different fora and their interaction is limited. The goal of the workshop is to bring some of these researchers together to discuss challenges posed by neuroscience and to exchange ideas and present their latest work. The workshop is targeted towards computational and systems neuroscientists with interest in methods of information theory as well as information/communication theorists with interest in neuroscience. Program: Wed 19 July (Room C.101): * 09:00 Raul Vicente, University of Tartu -- "Estimating and applying partial information decomposition to complex systems" * 09:45 Jil Meier, Delft University of Technology -- "The epidemic spreading model and the direction of information flow in brain networks" * 11:00 Karl Friston, University College London -- "Active inference and artificial curiosity" * 11:45 Taro Toyoizumi, RIKEN Brain Science Institute -- "A Local Learning Rule for Independent Component Analysis" * 14:00 Fleur Zeldenrust, Radboud Universiteit -- "Estimating the information extracted by a single spiking neuron from a continuous input time series" * 14:30 Pedro Martinez Mediano, Imperial College London -- "Integrated Information Theory Without the Hot Air" * 15:00 Mehrdad Salmasi, Ludwig-Maximilians-University Munich "Information rate of a synapse during short-term depression" * 16:00 Tatjana Tchumatchenko, Max Planck Institute for Brain Research, Frankfurt -- "Information coding of mean and variance modulating signals in cortical neurons" * 16:45 Renaud Jolivet, University of Geneva -- "Energy-efficient information transfer at synapses" * 17:30 Rodrigo Cofre, University of Geneva and Universidad de Valparaíso -- "Information Entropy Production and Large deviations of Maximum Entropy Processes from Spike Trains" Thu 20 July (Room C.101): * 09:00 Lionel Barnett, University of Sussex -- "Information Transfer in Continuous and Discrete Time" * 09:45 Joseph T. Lizier, The University of Sydney "An estimator for transfer entropy between spike trains" * 11:00 Viola Priesemann, Max Planck Institute for Dynamics and Self-organization, Goettingen -- "Quantifying Information Storage and Modification in Neural Recordings" * 11:45 Demain Battaglia, Aix-Marseille University -- "Discrete information processing states in anesthetized rat recordings" * 14:00 Selin Aviyente, Michigan State University "Directed Information: Application to EEG during cognitive control" * 14:45 Adrià Tauste, Universitat Pompeu Fabra -- "Directed information flow within the thalamo-cortical network" * 16:00 Daniele Marinazzo, University of Ghent -- "Synergy and redundancy in dynamical systems: towards a practical and operative definition" * 16:45 Lubomir Kostal, Academy of Sciences of the Czech Republic -- "Reference frame independence as a constraint on the mutual information decomposition" * 17:30 Robin Ince, University of Glasgow -- "Quantifying representational interactions in neuroimaging and electrophysiological data using information theory" Organisers: Joseph T. Lizier -- chair, The University of Sydney Viola Priesemann, Max Planck Institute for Dynamics and Self-organisation Justin Dauwels, Nanyang Technological University Taro Toyoizumi, RIKEN Brain Science Institute Alexander G. Dimitrov, Washington State University Lubomir Kostal, Academy of Sciences of the Czech Republic Michael Wibral, Goethe University, Frankfurt

July 16, 2017

CNS2017 workshop on "Neuronal Oscillations: mechanisms and functionality"

by Frances Skinner

Please post: Dear all, We invite you to attend our workshop an CNS2017 tthis year. "Neurona*l Oscillations: mechanisms and functionality"* Oscillations at various frequency ranges have been observed in several brain structures (hippocampus, entorhinal cortex, olfactory bulb and others). They are believed to be important for cognitive functions such as learning, memory, navigation and attention. These rhythms have been studied at the single cell level, as the result of the interaction of a neuron’s intrinsic properties, at the network level, as the result of the interaction between the participating neurons and neuronal populations in a given brain region, and at higher levels of organization involving several of these regions. Recent advances in this field have benefited from the interaction between experiment and theory, and models with varying levels of detail. The purpose of this workshop is to bring together modelers, experimentalists and theorists with the goal of sharing and discussing their current results and ideas on the underlying mechanisms that govern the generation of these rhythms at various levels of organization, and their functional implications. An additional goal is to discuss what we mean by an explanation in the context of this workshop. To this end, speakers will be encouraged to address this issue from the perspective of Aristotle's four causes (efficient, material, formal and final causes) <http://plato.stanford.edu/archives/spr2015/entries/aristotle-causality/>. Please see 'What is computational neuroscience? (XVI) What is an explanation?' <http://romainbrette.fr/2013/06/>. Speakers: Day 1: F Skinner, J White, M Bezaire, V Cutsuridis, J Guzman, L Rubchinsky, D Levenstein, F Battaglia, M Bartos, J Mejias Day 2: C. Borgers, C Canavier, M Cunningham, J Lefebvre, A Peyrache, H Rotstein, B Pesaran, A Saudargiene For more details, please visit http://vassiliscutsuridis.com/workshop/CNS2017web.htm Thank you, Frances (on behalf of the organizers) -- Frances Skinner, PhD Krembil Research Institute/UHN and Univ Toronto www.skinnerlab.org

July 14, 2017

postdoc in Barcelona to do single cell recordings in humans

by Quian Quiroga, Rodrigo (Prof.)

*** Apologies for multiple postings*** Dear all, Please see below details of a postdoc position at the Barcelona ßeta Brain Research Center to study memory mechanisms by performing single cell recordings in humans in collaboration with Hospital del Mar. Cheers, Rodrigo Postdoc Position Barcelona ßeta Brain Research Center (BBRC) The Barcelona ßeta Brain Research Center (BBRC) offers a fully funded postdoc position at the research group headed by Professor Rodrigo Quian Quiroga. The group is part of a new Research Program on Memory, complementary to ongoing research at BBRC dealing with the Prevention of Alzheimer Disease. The group is associated to the epilepsy group headed by Dr. Gerardo Conesa at Hospital del Mar, a health center close to BBRC. Research will involve the study single cell recordings in humans. These recordings are performed in epileptic patients for curative surgery. In particular, the project will investigate concept cells (a.k.a. Jennifer Aniston neurons) – that means, neurons in the hippocampus and surrounding areas that selectively fire to specific concepts, like different pictures and the written or spoken name of a particular person (e.g. Quian Quiroga et al, Nature 2005; Quian Quiroga Nature Reviews Neuroscience 2012), which are involved in declarative memory functions. The successful candidate will contribute to performing recordings with patients at the Hospital del Mar and the analysis of the data to investigate the role of these neurons in memory formation, consolidation, long-term coding and recall. Candidates should have excellent quantitative skills (data processing, and programming, preferably in Matlab) and ideally, a strong background in neuroscience and experience with neurophysiology recordings. They should be able to work both independently and as part of a research team within the BBRC. The position is initially offered for 2 years, with the possibility to extend it for another 2 years. Salary will be competitive, depending on experience. The closing date for the applications is Monday 25th August 2017. Start date will be in October 2017. For application details and further particulars see: https://fpmaragall.org/en/wp-content/uploads/sites/3/2014/07/Postdoc_Neural… Informal inquiries are welcome and should be submitted electronically to: rh(a)fpmaragall.org Rodrigo Quian Quiroga Centre for Systems Neuroscience University of Leicester www.le.ac.uk/csn

July 14, 2017

CNS meeting 2017 workshop on "Recent methods and analyses for neuronal population recordings"

by Valentina Pasquale

Dear all, I would like to remind you about the WORKSHOP "RECENT METHODS AND ANALYSES FOR LARGE-SCALE NEURONAL POPULATION RECORDINGS" | JULY 19TH-20TH IN ANTWERP @ CNS MEETING 2017 http://www.computational-neuroscience-of-sensory-systems.org/workshop-on-re… Abstract: Understanding how assemblies of neurons encode information requires recording large populations of cells in the brain. In recent years, progress in population calcium imaging and multichannel electrophysiology opened the possibility to record from hundreds or even thousands of neurons simultaneously. While these techniques offer unprecedented chances to monitor large neural circuits, they also push for the design of new algorithms to gather and process information from such high-dimensional datasets. The workshop "Recent methods and analyses for large-scale neuronal population recordings", which will be held on July 19th-20th in Antwerp at the CNS meeting 2017, will gather leading experimentalists and theoreticians to discuss latest computational methods and analyses used to process such large-scale neuronal population recordings, both in vivo and in vitro. Focusing on high-density electrophysiology and calcium imaging, it will review recent advances in neuroinformatics research, including spike sorting techniques and characterization of neural assemblies' spatio-temporal activity. Organizers: Valentina Pasquale (IIT), Michela Chiappalone (IIT), Pierre Yger (Institut de la Vision, France) Speakers: July 19th * Matthias Hennig (University of Edinburgh, Scotland) * Felix Franke (ETH Zurich, Switzerland) * Nick Steinmetz (University College London, UK) * Pierre Yger (Institut de la Vision, France) * Thomas Deneux (UNIC, CNRS, France) * Marius Pachitariu (University College London, UK) * Stephen J. Eglen (University of Cambridge, UK) * Adrien Peyrache (McGill University, Canada) July 20th * George Dimitriadis (Sainsbury Welcome Centre, UK) * Gaute Einevoll (NMBU, Norway) * Yannick Bornat (IMS Bordeaux, France) * Ulisse Ferrari (Institut de la Vision, France) * Sonja Grün (Forschungszentrum Jülich, Germany) * Valentina Pasquale (Istituto Italiano di Tecnologia, Italy) * Arno Onken (Istituto Italiano di Tecnologia, Italy) * Paolo Bonifazi (Ikerbasque, Bilbao, Spain) For further information, please visit: http://www.computational-neuroscience-of-sensory-systems.org/workshop-on-re… Best, Valentina Pasquale valentina.pasquale(a)iit.it<mailto:valentina.pasquale@iit.it> ISTITUTO ITALIANO DI TECNOLOGIA Optical Approaches to Brain Function Lab Via Morego, 30 16163 Genova t: +39 010 71781 475 f: +39 010 71781 230 www.iit.it<http://www.iit.it/>

July 14, 2017

Open PhD position computational neuroscienceB

by Claudius Gros

I would like to brink your attention our PhD-program in Computational Neurosciences / Complex Dynamical Systems at the Institute of Theoretical Physics, Goethe University Frankfurt, Germany Field(s): computational neurosciences, complex systems, theory neural networks, simulated robotics, dynamical systems. Application deadline: August 11, 2017 Contact: Prof. Claudius Gros, cgr[(a)]itp.uni-frankfurt.de We are developing new models and generative principles for the brain using a range of toolsets from dynamical systems theory and computational neurosciences. Examples are new objective functions and generating functionals for the sensori-motor loop, transient state dynamics and self-limiting Hebbian plasticity rules. Several subjects are available for the announced PhD thesis including the generation of transient state dynamics through short-term synaptic plasticity, the study of the stationarity principle for statistical learning and/or the generation of motor primitives through self-organized embodiment within the sensori-motor loop. The work will include analytic investigations and numerical simulations of neural networks and/or of simulated robots, using the toolset of dynamical systems theory. The candidate must have a Diploma/Master in physics, an excellent academic track record and good computational skills. Experience or strong interest in the fields of complex systems, computational neurosciences, dynamical systems theory and/or artificial or biological cognitive systems is expected. The degree of scientific research experience needs to be on the level of a German Diploma/Master The appointment will start summer/fall 2017, for up to three years. Interested applicants must submit a curriculum vitae, a list of publications and copies of the academic record. Name, affiliation and email of one or more potential references are to be given. Claudius Gros http://www.itp.uni-frankfurt.de/~gros General information on the University of Frankfurt and its employment policy. With its around 46000 students and 4600 employees, the Goethe University in Frankfurt is the largest university in the state of Hessen and an internationally renowned, important regional employer. Numerous quality and performance oriented internal reforms have been initiated in the recent years. The reorganized campuses for natural sciences and humanities offer an ideal environment for research and education. Since 2008, the Goethe University is a foundation under public law and enjoys full administrative autonomy. The fixed-term employment of the academic staff is subject to the provisions of the Temporary Science Employment Law (Wissenschaftszeitvertragsgesetz) and the Hessian Higher Education Act (Hessisches Hochschulgesetz). The University advocates gender equality and therefore strongly encourages women to apply. People with disabilities are given preference if equally qualified. ### ### Prof. Dr. Claudius Gros ### http://itp.uni-frankfurt.de/~gros ### ### Complex and Adaptive Dynamical Systems, A Primer ### A graduate-level textbook, Springer (2008/10/13/15) ### ### Mageia, das Buch der Farben ### http://www.buchderfarben.de ###

July 12, 2017

Vice Chancellor's 5-year Research Fellowship in Biocomputation, Mental Health and Wellbeing (University of Hertfordshire, U.K.)

by Steuber, Volker

Research Fellow: Biocomputation, Mental Health and Wellbeing University of Hertfordshire - School of Computer Science Location: Hatfield Salary: £32,004 to £38,183 Grade 7 p.a. Hours: Full Time Contract Type: Fixed-Term/Contract Placed on: 27th June 2017 Closes: 21st August 2017 Job Ref: 014834 FTE 1.0 FTE working 37 hours per week Duration of Contract: Fixed term contract 5 years from October 2017 Qualifications required: Very strong PhD degree in a quantitative research-oriented discipline, examples are computer science, mathematics, physics and neuroscience; excellent programming skills in at least one major computer language (essential), and very strong mathematical background, with particular emphasis on areas such as computer algebra, Krohn-Rhodes algebraic automata theory and language theory, discrete/continuous/constructive dynamical systems theory, group theory, algebraic topology, information theory, probability theory and statistics, and mathematical methods for computational intelligence. Background in computational neuroscience, including processing and analysis of EEG data, especially EEG microstates, is highly desirable. Experience writing high-quality research publications (essential) and grant applications (desirable), as well as excellent communication skills (essential). Successful history of working in multidisciplinary teams (highly desirable). Description of the research activity and area: Algorithms and Biocomputation are growing areas of research excellence at the University of Hertfordshire. This Fellowship targets the development and application of our novel computational and mathematical methods (e.g., automata-, language-theoretic and algebraic methods; computational mechanics and Krohn-Rhodes computational algebraic biology) to biological systems. The Research Fellow will support ongoing and future work characterizing the neurodynamical spatio-temporal structure of human mental states led by Professor Chrystopher L. Nehaniv and external collaborator Dr Elena Antonova (Institute of Psychiatry, Psychology and Neuroscience, King’s College London). Our current BIAL Foundation grant focuses on using EEG microstate ‘grammars’ to distinguish different mental states in expert meditators. EEG microstates are quasi-stable maps of electric potential landscapes of short duration, typically classed in a small number of discrete types analogous to ‘letters’ of an alphabet. The tendency for simple EEG microstate transitions between certain pairs of these discrete types has already been shown to characterize clinical populations (people with schizophrenia or Alzheimer’s vs. healthy controls). Our current research targets finer understanding of richer temporal neurodynamical structure and patterns, using these novel computational methods, toward harnessing their potential eventually for applications in Health and Wellbeing as a diagnostic tool for different clinical populations. The Fellow will reinforce the established collaboration with KCL, supporting validation and development of our methods toward their eventual application in clinical diagnosis and mental illness prevention, as well as in promotion of wellbeing. The Fellow will be expected to publish in high-impact journals and present conference papers together with Professor Nehaniv and Dr Antonova, to contribute to writing grant applications to national and international funding bodies [e.g., Wellcome Trust, EPSRC/BBSRC/MRC, European Commission, and other funding agencies], and contribute to REF outputs of the School of Computer Science. In accord with the CONCORDAT for professional development of researchers, the candidate may be afforded the opportunity to undertake a limited amount of appropriate teaching (upon mutual agreement). The Royal Society / Wolfson Biocomputation Research Laboratory at the University of Hertfordshire has a long history of interdisciplinary innovation in computational methods for systems biology and neural systems, as well as applications of bioinspired-methods to other fields. It enjoys close interdisciplinary links to the Adaptive Systems and Algorithms Research Groups, whose interests include mathematical computer science, compilers, security, networks, artificial Intelligence robotics, artificial life, language acquisition, human-robot interaction, etc., and have labs equipped with humanoid and non-humanoid robots, as well as 3D printing facilities. External research connections to UK, European and international partners (e.g. University of California, Berkeley; Univ. Debrecen and Renyi Institute, Hungary; Sardex, Italy; etc) are supported through numerous research council and EC-funded collaborations and projects. Skills and experience needed: The Fellow will have established him/herself as an independent researcher, capable of establishing a programme of research activity within the scope of the project. S/he will have excellent oral and written communication skills in both spoken and written English and a track record of publications in high impact journals. The Fellow will be expected to build capacity in the area of Biocomputation and participate in attracting external funding, previous success being a desirable attribute. S/he should be able to establish good working relationships, and work closely with members of the Centre for Computer Science and Informatics Research and the School of Computer Science, at the University of Hertfordshire and with partner organisations as appropriate. The fellow should have knowledge of research methodology appropriate for the subject area and knowledge of appropriate databases for the discipline and ability to conduct literature searches in the discipline using appropriate electronic resources. Contact Details: Informal enquiries can be made to Professor Chrystopher L. Nehaniv, email: C.L.Nehaniv(a)herts.ac.uk<mailto:C.L.Nehaniv@herts.ac.uk> tel: +44 1707 284470<tel:01707%20284470> The University offers a range of benefits including a pension scheme, professional development, family friendly policies, child care vouchers, a fee waiver of 50% for all children of staff under the age of 21 at the start of the course, discounted memberships at the Hertfordshire Sports Village and generous annual leave. To make a formal application, follow links and apply on-line: http://www.jobs.ac.uk/job/BCH822/research-fellow-biocomputation-mental-heal…

July 12, 2017

Postdoc Position: Learning Dynamics in Recurrent Networks

by Shouval, Harel

A postdoc position is available in the Shouval lab. The Postdoc will work on a project funded by the BRAIN grant: “Learning spatio-temporal statistics from the environment in recurrent networks”. In this project we will model both recurrent network models, and also the learning rules that allow them to learn their dynamics from environmental cues. This project is a collaboration between the lab of Harel Shouval at the University of Texas in Houston, and the lab of Nicolas Brunel at Duke. This is a two-year position and it can start immediately. The Shouval lab is a leader in developing models of synaptic plasticity and understanding their impact on learning and memory. The models we develop span from the molecular level and up to the systems level. In our some of our recent work we study the impact of synaptic plasticity on recurrent network dynamics and on incorporating reinforcement learning into biophysical plasticity models. We use both computational and analytical techniques to study these issues. The Shouval lab is located in the department of Neurobiology and Anatomy, in the UT medical school. Houston has a thriving Neuroscience community and it is an excellent environment for Theoretical and Computational Neuroscience. There is a high concentration of Theoretical Neuroscience labs at the different Houston area Universities (Baylor, Rice, UH, UT). Our Theoretical Neuroscience community is highly collaborative and there is a joint organization to foster these collaborations; the Gulf Coast Consortium in Theoretical and Computational Neuroscience (GCC-TCN). We hold an annual conference, joint graduate courses and a journal club. The ideal candidate will have a PhD in Computational Neuroscience with strong analytical and computational skills. I will also consider candidates with a background in the Physical or Computational Sciences who would like to become a Theoretical Neuroscientists. If you want to apply please send me your CV, and a brief cover letter that includes names of possible references. I will also be happy to answer any question you might have about the project or the position. Harel Shouval Professor Department of Neurobiology and Anatomy The University of Texas Medical School, Houston Director of the Neuroscience Graduate program Email: harel.shouval(a)gmail.com<mailto:harel.shouval@gmail.com> Web: https://med.uth.edu/nba/faculty/harel-shouval/

July 11, 2017

POSTDOCTORAL FELLOWSHIP IN COMPUTATIONAL MODELING OF BRAIN NETWORKS at Stanford University

by Aarthi Padmanabhan

The Stanford Cognitive and Systems Neuroscience Laboratory invites applications for a postdoctoral fellowship in human brain network analysis and modeling. We seek candidates with strong research backgrounds in one or more of the following areas: resting-state and task-evoked fMRI connectivity, structural HARDI-based connectivity, neurophysiological modeling of brain networks, Bayesian modeling, machine learning, and deep neural networks. Candidates must have strong computational skills and a PhD in computational neuroscience, computer science, physics, biomedical engineering or related fields. This is an exciting opportunity to work on multiple NIH- and Stanford-funded projects using multimodal (fMRI, optogenetic, DTI, EEG) brain imaging techniques in multiple clinical populations and normative groups. The successful candidate will develop a vigorous research program that contributes to, and complements, ongoing research studies. The candidate will have access to state-of-the-art brain imaging and HPC/GPU facilities. Please email a CV, statement of research interests and relevant background, and names of three referees to Drs. Vinod Menon and Aarthi Padmanabhan at scsnl.stanford+postdoc(a)gmail.com<mailto:scsnl.stanford@gmail.com> Aarthi Padmanabhan, PhD Scientific Research Director Stanford Cognitive and Systems Neuroscience Laboratory Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine

July 11, 2017

Neuroscience Gateway Workshop at SFN 2017 meeting

by Ted Carnevale

Using the Neuroscience Gateway Portal for Parallel Simulations Saturday, Nov. 11 from 9 AM to noon at downtown Washington DC location. This workshop combines didactic presentations and hands-on instruction on how to use the Neuroscience Gateway Portal (NSG) for computationally intensive simulations and data analysis. NSG eliminates most technical and adminstrative barriers to using high performance computing resources, and even gives away free CPU time on parallel supercomputers. Software currently installed on NSG includes BluePyOpt, Brian, CARLsim, Freesurfer, GENESIS, MATLAB, MOOSE, NEST, NEURON, PyNN, and the Virtual Personalized Multimodal Connectome Pipeline. The registration deadline for this workshop is Friday Oct. 27, but you should sign up early because space is limited. See https://www.neuron.yale.edu/neuron/static/courses/nsg2017/nsg2017.html for more information and a link to the registration form. --Ted

July 11, 2017

NEURON course at SFN 2017 meeting

by Ted Carnevale

Using NEURON to Model Cells and Networks Friday, Nov. 10 from 9 AM to 5 PM at a downtown Washington DC location. This course provides a practical introduction to building and using models of neurons and networks with NEURON. Covered topics include basic concepts, workflow for building and using models, speeding up simulations with parallel hardware from multicore personal computers to massively parallel supercomputers, using Python with NEURON, and modeling reactive diffusion with the RxD class. The registration deadline for this course is Friday Oct. 27, but you should sign up early because space is limited. See http://www.neuron.yale.edu/neuron/static/courses/dc2017/dc2017.html for more information and a link to the registration form. --Ted

July 11, 2017