November 2021 - Comp-neuro - lists.cnsorg.org

Call for Papers: Reproducibility in Neuroscience
by Alberto Antonietti 15 Nov '21

15 Nov '21

Are you interested in making neuroscience more reproducible? Have you already tried to replicate a study? Are you bothered by the "Data and code are available upon reasonable request"? If your answer to one of the previous questions is "yes", then you could be interested in this call for papers. With this research topic, we aim to stimulate neuroscientists from all fields to design and publish works that rigorously attempt to reproduce landmarks or controversial studies: https://www.frontiersin.org/research-topics/26709/reproducibility-in-neuros… We are inviting papers on both: - "Results reproducibility", i.e., obtain the same results from an independent study with procedures as closely matched to the original study as possible; - "Inferential reproducibility", i.e. draw the same conclusions from either an independent replication, using different research methodologies, of a study or a reanalysis of the original data. Are you interested in making neuroscience more reproducible? Have you already tried to replicate a study? Are you bothered by the "Data and code are available upon reasonable request"? If your answer to one of the previous questions is "yes", then you could be interested in this call for papers. With this research topic, we aim to stimulate neuroscientists from all fields to design and publish works that rigorously attempt to reproduce landmarks or controversial studies: https://www.frontiersin.org/research-topics/26709/reproducibility-in-neuros… We are inviting papers on both: - "Results reproducibility", i.e., obtain the same results from an independent study with procedures as closely matched to the original study as possible; - "Inferential reproducibility", i.e. draw the same conclusions from either an independent replication, using different research methodologies, of a study or a reanalysis of the original data. We will consider both confirmatory and negative results, the unique criteria will be the rigorousness, fairness, and soundness of the replication study. Authors are required to make all materials and methods used to conduct their research available to other researchers. Data and codes used to analyze results must comply with FAIR principles and should preferably be uploaded to an online repository providing a global persistent identifier (e.g., OSF, Harvard Dataverse, Zenodo). Authors are also strongly encouraged to subject their codes to an independent audit at codecheck.org.uk. I’m very pleased to be launching a new article collection, Reproducibility in Neuroscience, together with an expert editorial team: - Alberto Antonietti - Blue Brain Project, Ecole polytechnique fédérale de Lausanne (EPFL), Geneva, Switzerland - Nele A Haelterman - Baylor College of Medicine, Houston, United States - Reeteka Sud - National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India - Nafisa M Jadavji - Midwestern University, Glendale, AZ, United States - Denes Szucs - University of Cambridge, Cambridge, United Kingdom We’re now in the process of putting together a group of top researchers whose work we’d like to feature in this collection, and we would like you to participate. The research topic is hosted by Frontiers in Integrative Neuroscience, you can find all information here: https://www.frontiersin.org/research-topics/26709/reproducibility-in-neuros… Important notice on Publishing Fee (APC) support: If Frontiers publishing fees are too high for your funding situation, you are eligible for full or partial APC fee support. In order to apply to fee support, please complete the fee support application form online, and allow up to two weeks for Frontiers to review and reply to your request: https://frontiers.qualtrics.com/jfe/form/SV_51IljifwFBXUzY1 More information can be found at: https://www.frontiersin.org/about/fee-policy Please get in touch if you have any questions - looking forward to hearing from you. Alberto On behalf of the Topic Editors. We will consider both confirmatory and negative results, the unique criteria will be the rigorousness, fairness, and soundness of the replication study. Authors are required to make all materials and methods used to conduct their research available to other researchers. Data and codes used to analyze results must comply with FAIR principles and should preferably be uploaded to an online repository providing a global persistent identifier (e.g., OSF, Harvard Dataverse, Zenodo). Authors are also strongly encouraged to subject their codes to an independent audit at codecheck.org.uk. I’m very pleased to be launching a new article collection, Reproducibility in Neuroscience, together with an expert editorial team: - Alberto Antonietti - Blue Brain Project, Ecole polytechnique fédérale de Lausanne (EPFL), Geneva, Switzerland - Nele A Haelterman - Baylor College of Medicine, Houston, United States - Reeteka Sud - National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India - Nafisa M Jadavji - Midwestern University, Glendale, AZ, United States - Denes Szucs - University of Cambridge, Cambridge, United Kingdom We’re now in the process of putting together a group of top researchers whose work we’d like to feature in this collection, and we would like you to participate. The research topic is hosted by Frontiers in Integrative Neuroscience, you can find all information here: https://www.frontiersin.org/research-topics/26709/reproducibility-in-neuros… Important notice on Publishing Fee (APC) support: If Frontiers publishing fees are too high for your funding situation, you are eligible for full or partial APC fee support. In order to apply to fee support, please complete the fee support application form online, and allow up to two weeks for Frontiers to review and reply to your request: https://frontiers.qualtrics.com/jfe/form/SV_51IljifwFBXUzY1 More information can be found at: https://www.frontiersin.org/about/fee-policy Please get in touch if you have any questions - looking forward to hearing from you. Alberto On behalf of the Topic Editors -- Questa email è stata esaminata alla ricerca di virus da AVG. http://www.avg.com

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Research Fellow "Machine Learning for Science" in Tübingen
by Philipp Berens 14 Nov '21

14 Nov '21

We have several positions to fill as Research Fellow "Machine Learning for Science" with potential runtime until 12/2025. We are searching at the postdoctoral level, for details see: https://www.nature.com/naturecareers/job/machine-learning-for-science-resea… Best Philipp -- -- Professor of Data Science for Vision Research Institute for Ophthalmic Research, University of Tübingen Cluster of Excellence "Machine Learning - New Perspectives for Science" www.berenslab.org

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PhD Position - A framework for automated inference, quality assessment and model enhancement of physics-based simulation models
by Philipp Benner 13 Nov '21

13 Nov '21

Dear colleagues, We are looking for a PhD student for the following project: For the design of safety critical components and structures, it is vital to ensure that integrity and reliability are maintained under all environmental conditions and feasible parameter settings. Physics based simulation models such as the Finite Element Method provide means to explore the behavior of a structure for many more scenarios than what can be measured experimentally. The development of an appropriate model either on the structural level or for the constitutive behavior of the materials involved is a complex task. The modelling assumptions can only be validated based on experimental data, which are either provided by databases with lab tests under different conditions on the material scale, or using monitoring techniques for a structural modelling problem. The challenge is that simulation models usually have multiple parameters that jointly influence the simulation results , i.e. there is not a one to one mapping between a single parameter and a single data set. As a consequence, an inverse problem has to be solved. The goal of this proposal is to 1. automate the procedure of calibrating model parameters based on experimental data including objective measures of the model quality 2. identify model discrepancies - which is particularly difficult for large datasets - by combining using Gaussian process models with physics based models 3. and suggest model improvements based on a dictionary type of learning procedure. All of the procedures are implemented in a Bayesian framework to account for measurement and model uncertainties. The validation of the developed methods is initially performed using virtual experiments allowing to directly prescribe model deficiencies and compare the identified models to the ground truth. The implementation of the models is done in an open source framework. As a consequence, the procedures are planned to be validated in parallel projects on real data sets. Details: https://www.bam.de/umantis/EN/952.html Kind regards, Philipp Benner

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PostDoc validation of safety-critical ML methods
by Philipp Benner 13 Nov '21

13 Nov '21

Dear colleagues, We have another exciting postdoc position: The digitization of engineering and materials science offers a wide range of options for optimizing manufacturing processes and testing procedures. Machine learning methods in particular show great potential here, e.g. in the prediction of material properties, the optimization of process parameters or as meta models for complex physical models in the context of a digital twin. The application of machine learning methods to safety-critical issues requires robust, explainable and generalizable models that can in particular also provide estimators for the accuracy of the model prediction. In the field of engineering, the dimensionality of the input data is also relatively large, combined with a relatively small number of data records. The aim is to develop methods that make it possible to apply ML methods taking into account statistical methods for safety-critical questions, and in particular to integrate additional information from physical models (described by partial differential equations). This sub-project is a collaboration between Department 7.7 “Modeling and Simulation” and Section S.3 “eScience”. The position is embedded in the additive manufacturing competence center and is financed by the QI-Digital (quality infrastructure) project. The project is integrated into an international research environment and requires active networking with industry and research. Further information: https://www.bam.de/umantis/EN/1024.html <https://www.bam.de/umantis/DE/1024.html> Kind regards, Philipp Benner

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COSYNE 2022: Abstract submission closes soon
by Tomas Hromadka 12 Nov '21

12 Nov '21

==================================================== Computational and Systems Neuroscience 2022 (Cosyne) MAIN MEETING 17 - 20 March 2022 Lisbon, Portugal WORKSHOPS 21 - 22 March 2022 Cascais, Portugal www.cosyne.org ==================================================== ---------------------------------------------------- MEETING ANNOUNCEMENT ---------------------------------------------------- The annual Cosyne meeting provides an inclusive forum for the exchange of empirical and theoretical approaches to problems in systems neuroscience, in order to understand how neural systems function. The MAIN MEETING is single-track. A set of invited talks is selected by the Executive Committee, and additional talks and posters are selected by the Program Committee, based on submitted abstracts. The WORKSHOPS feature in-depth discussion of current topics of interest, in a small group setting. All abstract submissions will be reviewed double blind. The deadline for Abstract submission is 20 November 2021. Cosyne topics include but are not limited to: neural basis of behavior, sensory and motor systems, circuitry, learning, neural coding, natural scene statistics, dendritic computation, neural basis of persistent activity, nonlinear receptive field mapping, representations of time and sequence, reward systems, decision-making, synaptic plasticity, map formation and plasticity, population coding, attention, neuromodulation, and computation with spiking networks. We would like to foster increased participation from experimental groups as well as computational ones. Please circulate widely and encourage your students and postdocs to apply. IMPORTANT DATES Abstract submission is now open Abstract submission deadline: 20 November 2021 When preparing an abstract, authors should be aware that not all abstracts can be accepted for the meeting. Abstracts will be selected based on the clarity with which they convey the substance, significance, and originality of the work to be presented. COSYNE SPEAKERS Eugenia Chiappe (Champalimaud Centre for the Unknown) Albert Compte (IDIBAPS, Barcelona) Sandeep Robert Datta (Harvard Medical School) André Fenton (New York University) Kate Jeffery (University College London) Ann Hermundstad (Janelia Research Campus, HHMI) Michael A. Long (New York University) Christian Machens (Champalimaud Centre for the Unknown) Asya Rolls (Technion - Israel Institute of Technology) Susanne Schreiber (Humboldt-Universität zu Berlin) Maryam Shanechi (University of Southern California) Scott Waddell (University of Oxford) Martha White (University of Alberta) ORGANIZING COMMITTEE General Chairs: Anne-Marie Oswald (U Pittsburgh) and Srdjan Ostojic (Ecole Normale Superieure Paris) Program Chairs: Laura Busse (LMU Munich) and Tim Vogels (IST Austria) Workshop Chairs: Anna Schapiro (U Penn) and Blake Richards (McGill) Tutorial Chair: Kanaka Rajan (Mount Sinai) DEIA Committee: Gabrielle Gutierrez (Columbia) and Stefano Recanatesi (U Washington) Undergraduate Travel Chairs: Angela Langdon (Princeton) and Sashank Pisupati (Princeton) Development Chair: Michael Long (NYU) Social Media Chair: Grace Lindsay (Columbia) Audio-Video Media Chair: Carlos Stein Brito (EPFL) Poster Design: Maja Bialon PROGRAM COMMITTEE Laura Busse (U Munich) Tim Vogels (IST Austria) Athena Akrami (UCL) Omri Barak (Technion) Brice Bathellier (Paris) Bing Brunton (U Washington) Yoram Burak (Hebrew University) SueYeon Chung (Columbia) Christine Constantinople (NYU) Victor de Lafuente (UNAM Mexico) Jan Drugowitsch (Harvard) Alexander Ecker (Göttingen) Tatiana Engel (Cold Spring Harbor) Annegret Falkner (Princeton) Kevin Franks (Duke) Jens Kremkow (Berlin) Andrew Leifer (Princeton) Sukbin Lim (Shanghai) Scott Linderman (Stanford) Emilie Mace (MPI Neurobiology) Mackenzie Mathis (EPFL Lausanne) Ida Momennejad (Microsoft) Jill O'Reilly (Oxford) Il Memming Park (Stony Brook) Adrien Peyrache (McGill Montréal) Yiota Poirazi (FORCE) Nathalie Rochefort (Edinburgh) Cristina Savin (NYU) Daniela Vallentin (MPI Ornithology) Brad Wyble (Penn State) EXECUTIVE COMMITTEE Stephanie Palmer (U Chicago) Zachary Mainen (Champalimaud) Alexandre Pouget (U Geneva) Anthony Zador (CSHL) CONTACT meeting [at] cosyne.org COSYNE MAILING LISTS Please consider adding yourself to Cosyne mailing lists (groups) to receive email updates with various Cosyne-related information and join in helpful discussions. See Cosyne.org -> Mailing lists for details.

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Two postdoctoral positions at Harvard
by Cengiz Pehlevan 11 Nov '21

11 Nov '21

Dear colleagues, We have two postdoctoral positions at Harvard that may be of interest. 1) The George F. Carrier Postdoctoral Fellowship. This prestigious independent position at Applied Mathematics is open to candidates with a wide range of interests, including neuroscience and machine learning. Even though the listed deadline has passed, we are still accepting applications. Details are here: https://academicpositions.harvard.edu/postings/10697 <https://academicpositions.harvard.edu/postings/10697> 2) Postdoctoral Fellow in the Theory of Representation Learning in Artificial and Natural Systems. We are looking for exceptional junior scientists to work collaboratively with a group of faculty from Computer Science (Boaz Barak), Statistics (Lucas Janson), Electrical Engineering (Demba Ba) and Applied Mathematics (Cengiz Pehlevan) towards a theory of representations in artificial and natural systems. Details are here (towards the bottom of the page): https://academicpositions.harvard.edu/postings/10730 <https://academicpositions.harvard.edu/postings/10730> Best wishes, Cengiz

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Postdoctoral fellowships at the Neuromathematics Center in Sao Paulo State, Brazil
by Antonio Roque 11 Nov '21

11 Nov '21

*Postdoctoral Fellowships inAcquisition, processing and quantitative analysis of neurobiological data* The Research, Innovation and Dissemination Center for Neuromathematics (NeuroMat), hosted by the University of São Paulo (USP), Brazil, and funded by the São Paulo Research Foundation (FAPESP), is offering three post-doctoral fellowships for recent PhDs with outstanding research potential. The fellowship will involve collaborations with research teams and laboratories associated with NeuroMat. The research to be developed by the post-doc fellows shall be strictly related to ongoing research lines developed by the NeuroMat team. The project may be developed at USP (São Paulo or Ribeirão Preto) or at UNICAMP (Campinas). We seek candidates capable of developing independent research in one of the research lines below. 1. Stochastic modeling of neurobiological data. 2. Acquisition, processing and quantitative analysis of neurobiological data. Candidates to the first research line are required to have a strong background in probability theory with emphasis on stochastic processes. Candidates to the second research line are required to have a strong background in neuroscience with previous experience in neurophysiological data acquisition, processing and analysis, and knowledge of computer programming. The initial appointment is for one year, with a possible extension to up to three years, conditional on research progress. The fellowship is competitive at an international level, and fellows benefit from extra funds for travel and research expenses plus limited support for relocation expenses. Application Instructions: Applicants should complete and submit the application form. The following documents and information are requested (please see the form for further details): - Summary of the CV, in the format required by FAPESP (see fapesp.br/en/6351 for instructions); - List of publications, with links to those available online. - A summary of the research plan for the next year, up to 5 pages in length. This document must explicitly state for which of the two aforementioned profiles the candidate has applied. It should also address how this research plan fits within the framework of the NeuroMat research program. Timetable: Candidates are encouraged to apply at their earliest convenience until December 12, 2021. Appointments are expected to start by February or March 2022. The initial period of the position lasts for 12 months, with possible renewals for up to three years. This opportunity is open to candidates of any nationality. The selected candidates will be awarded FAPESP Postdoctoral fellowships in the amount of BR 7,373 monthly and a research contingency fund, equivalent to 15% of the annual value of the fellowship, which should be spent on items directly related to the research activity. More details on FAPESP's postdoctoral fellowships are available at http://www.fapesp.br/en/5427. -- Dr. Antonio C. Roque Professor Associado Departamento de Fisica FFCLRP, Universidade de Sao Paulo 14040-901 Ribeirao Preto-SP Brazil - Brasil E-mails: antonior(a)usp.br <antonior(a)ffclrp.usp.br> aroquesilva(a)gmail.com URL: www.sisne.org Tels: +55 16 3315-3768 <+55%2016%203315-3768> (sala/office); +55 16 3315-3859 <+55%2016%203315-3859> (lab) FAX: +55 16 3315-4887 <+55%2016%203315-4887>

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ERC-funded Postdoc position in computational neuroscience and modelling of salamander locomotor circuits, EPFL, Lausanne, Switzerland
by Auke Ijspeert 11 Nov '21

11 Nov '21

The Biorobotics laboratory (Biorob, https://www.epfl.ch/labs/biorob/) at EPFL (Lausanne, Switzerland) has one open postdoc position in computational neuroscience and modeling of salamander locomotor circuits. The position is part of the Salamandra project, a Synergy grant funded by the ERC that started in September 2021, together with Prof. Andras Simon (Karolinska Institute, Sweden) and Prof. Dimitri Ryczko (U. Sherbrooke, Canada). See some info here: https://actu.epfl.ch/news/salamanders-provide-a-model-for-spinal-cord-rege-… The goals of the position are (i) to develop numerical models and simulations of the locomotor circuits in the spinal cord of the salamander, (ii) to analyze their dynamics when coupled to a simulated mechanical model of the body (interactions between central and peripheral mechanisms), and (iii) to investigate their regenerative properties after spinal cord lesions. The models will likely be based on integrate-and-fire neuron models, but other models could also be investigated (e.g. rate-based). The position is fully funded for 2 years (and can be extended to 4 years in total). EPFL is one of the leading Institutes of Technology in Europe and offers extremely competitive salaries and research infrastructure. *Requirements:* Candidates should have a Ph.D. and a strong publication record in computational neuroscience. An ideal candidate would have prior experience in: * Numerical models of oscillatory (spinal) circuits * Movement and locomotion control * Integrate-and-fire neural models (or similar neuron models) * Good management skills are a plus. Fluency in oral and written English is required. *How to apply for the position:* Postdoctoral applications should consist of a motivation letter (explaining why you are interested in the project, and why you feel qualified for it), a full CV, two or three relevant publications, and the email addresses of two or more referees. PDF files are preferred. Please send your application and any inquiry by email to auke.ijspeert(a)epfl.ch. Information concerning the type of research carried out by the lab can be found at https://www.epfl.ch/labs/biorob/ . *Deadline and starting date:* Applications are requested starting from now**, and will then be processed as they arrive until the position is closed. The ideal starting date is *early 2022* (with some flexibility). *Contact:* Information concerning the type of research carried out by the lab can be found at https://www.epfl.ch/labs/biorob/ . You should send your application and any inquiry by email to auke.ijspeert(a)epfl.ch -- ----------------------------------------------------------------- Prof Auke Jan Ijspeert Biorobotics Laboratory EPFL-STI-IBI-BIOROB, ME D1 1226, Station 9 EPFL, Ecole Polytechnique Fédérale de Lausanne CH 1015 Lausanne, Switzerland Office: ME D1 1226 Tel: +41 21 693 2658 Fax: +41 21 693 3705 www:http://biorob.epfl.ch Email:Auke.Ijspeert@epfl.ch -----------------------------------------------------------------

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Dec 13, 14 Workshop: The free energy principle of the brain: experiments and verification
by Hideaki Shimazaki 11 Nov '21

11 Nov '21

Dear colleagues, We are pleased to invite you to *an online two-day workshop on the free energy principle and active inference, focusing on its experimental verification and biological implementation*. The time is set for EU/UK and East Asia. Please visit our website for registration (free): https://sites.google.com/view/free-energy-workshop Workshop title: *The free energy principle of the brain: Experiments and verification* Date: 2021 Dec 13 (Mon) and 14 (Tue) Place: Online (Registration required) Invited Speakers and Titles: *Takuya Isomura* (RIKEN CBS) Active inference and the emergence of sentient behaviour *Hitoshi Okamoto* (RIKEN CBS) Zebrafish as a model animal for studying active inference *Beren Millidge *(U Oxford) The FEP, Predictive Coding, and Backpropagation in the Brain *Rafal Bogacz* (U Oxford) Dopamine: precision of action selection or prediction error *Naoki Honda* (Hiroshima U) Decoding reward-curiosity conflict in probabilistic bandit task *Miguel Aguilera* (Sussex U) When can we interpret organisms as performing Bayesian inference? *Jun Tani *(OIST) Cognitive Neurorobotics Study Using the Free Energy Principle *Ken-ichi Amemori *(Kyoto U) Neuroscientific and computational basis of anxiety in primates: conflict decision and risk aversion *Rosalyn Moran* (King's Colledge London) Active Inference from Neurobiology to Blackjack We are looking forward to your active participation! Sincerely, Hideaki on behalf of organizers Hideaki Shimazaki, CHAIN Hokkaido University Masatoshi Yasuda, CHAIN Hokkaido University Mark Miller, CHAIN Hokkaido University Takuya Isomura, RIKEN CBS Naoki Honda, Hiroshima U Christopher Buckley, Sussex U --- Hideaki Shimazaki, Ph.D Center for Human Nature, Artificial Intelligence, and Neuroscience (CHAIN) Hokkaido University https://www.neuralengine.org

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A Dendrites Virtual Workshop hosted at Emory University Dec. 7.
by Jaeger, Dieter 10 Nov '21

10 Nov '21

Dear Colleagues: We are pleased to invite you to our virtual workshop entitled "Are dendrites necessary for cortical computation?” to be held on Tuesday, December 7, 10:00am - 1:00 pm EST. This workshop is in the series of Emory University Initiative in Theory And Modeling of Living Systems (TMLS, http://livingtheory.emory.edu) virtual workshops, exploring provocative questions on the interface of biology and physical sciences. See https://www.youtube.com/c/EmoryTMLS for recordings of previous workshops in the program. Abstract: Many network models for modeling cortical function are built with single compartment units using a variety of more or less simple integrate and fire dynamics. On the other hand, many biologically oriented research groups place great emphasis on the complex and detailed properties of active processing in pyramidal neuron dendrites. The question to be addressed in this workshop is whether essential computational properties of biological cortical networks rely on dendritic processing, and if so, which? Finally, could such properties be formalized in simpler ways than using full biophysical detail and substantially add to the function of more abstract network modeling? Six exciting speakers will present their thoughts on the matter, and the audience will be able to interact with them in real time, asking questions through the YouTube comments interface. Free registration is requested at: https://forms.gle/9HzNgrYbJPYBUfSw9<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.gle…> We expect to stream the workshop live at the TMLS YouTube channel https://www.youtube.com/c/EmoryTMLS and we will send information, updates/changes to all registered participants before the workshop begins. Confirmed Speakers and Titles: Dieter Jaeger, Emory University, Introduction Claudia Clopath, Imperial College London Brent Doiron, University of Chicago “Cell specific inhibitory plasticity in assembly formation” Bartlett Mel, University of Southern California "How to optimize a dendrite for binary subunit pooling” Yiota Poirazi, IMBB-FORTH Crete “Dendritic solutions to logical operations in models of human neurons” Andreas Stöckel, University of Waterloo. “Passive Dendrites as a Computational Resource in the Neural Engineering Framework” Xiao-Jing Wang, New York University “Dendritic gating in the whole neocortex” Please feel free to forward this announcement to anyone that you think might be interested. Hope to see you there! Thank you, Dieter Jaeger (workshop organizer) Dieter Jaeger Professor, Department of Biology Emory University djaeger(a)emory.edu<mailto:djaeger@emory.edu> https://scholarblogs.emory.edu/jaegerlab/

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