March 2024 - Comp-neuro - lists.cnsorg.org

Late-breaking poster abstract submission for the 32nd Annual Computational Neuroscience Meeting ends on June 15
by Rubchinsky, Leonid L March 10, 2025

March 10, 2025

Dear Colleagues, We would like to remind that the late-breaking poster abstracts submission at CNS*2023 ends on June 15. CNS*2023, 32nd Annual Computational Neuroscience Meeting, will be in Leipzig, Germany, on July 15-19, 2023. The information about the meeting and abstract submission can be found here: Registration: https://ocns.memberclicks.net/cns-2023-registration Abstract submission: https://www.cnsorg.org/cns-2023-abstract-submission CNS*2023 information: https://www.cnsorg.org/cns-2023 With kind regards, Leonid Rubchinsky OCNS Vice President *********************** Leonid Rubchinsky, PhD Professor Department of Mathematical Sciences, Indiana University Purdue University Indianapolis Stark Neurosciences Research Institute, Indiana University School of Medicine 402 N. Blackford St Indianapolis, IN 46202-3216 lrubchin(a)iupui.edu http://www.math.iupui.edu/~lrubchin ***********************

2 7

Save the date: UK Neural Computation meeting July 8-10th, Sheffield
by Mark Humphries Jan. 24, 2025

Jan. 24, 2025

Save the date! The UK Neural Computation meeting is in Sheffield for 2024, the gathering of the UK’s computational and systems neuroscience community 8 July: ECR day 9-10 July: main meeting 11 invited speakers, 4 talks from abstracts and loads of posters Abstract submission and registration opening soon Please spread the word! More details: https://neuralcomputation.uk/ Enquiries: uknc24(a)sheffield.ac.uk<mailto:uknc24@sheffield.ac.uk> Organisers Hannes Saal (Sheffield) Stuart Wilson (Sheffield) Mark Humphries (Nottingham) This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

1 6

Postdoctoral Researcher position at Goettingen Campus Institute for Dynamics of Biological Networks, University of Goettingen
by von Behren, Christina Dec. 16, 2024

Dec. 16, 2024

Dear Scientists, The Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN)<https://www.uni-goettingen.de/de/608362.html> invites applications for a position of Postdoctoral Researcher in Computational Biophysics (all genders welcome) The position will be full-time (currently 39,8 hours/week), German pay grade 13 TV-L, starting as soon as possible. The CIDBN Department "Physics of Biological Systems", headed by Prof. Fred Wolf, offers a fixed-term contract until June 30, 2025 with the perspective of an extension commensurate with building a competitive track record at the frontier of computational biophysics and neural circuit theory. Information is processed in brain circuits through the coordinated action of large-scale circuits of neurons and synapses. Ultimately, it is the nano-scale molecular architecture of neuronal synapses that can make or break the power of neural circuit computation. Progress in a broad suite of nanoscopy techniques is currently uncovering the molecular-level design of synapses subserving functions such as working memory or sensory coding. The spatio-temporal operation of these nano-machines and the efficiency of their design, however, remain to be understood and are core research aims of the Göttingen Collaborative Research Centre (CRC) 1286 "Quantitative Synaptology"<https://www.sfb1286.de/?lang=en>. We are inviting applications from theoretical biophysicists, molecular systems biologists, or computational scientists with an ambition to pioneer computational studies of synaptic functional design. We offer a stimulating environment of theoretical neuroscientists, neural data-scientists, and cutting-edge experimentalists associated with CRC 1286. In addition, the institute provides dedicated support for high-performance computing. We are dedicated to supporting the growth of original research personalities at the frontier of computational science and neural circuit theory. The successful applicant will hold an excellent PhD in physics, applied mathematics, computer science, or equivalent, and have a strong interest in high-performance computing in neuroscience or cellular systems biology. We expect excellent analytical and coding skills, interest in working in a transdisciplinary team as well as excellence in scientific writing and reasoning. Experience in non-equilibrium statistical physics, stochastic dynamics, membrane biophysics, ion-channel and biochemical kinetics, buffered Ca-diffusion, and Ca-exocytosis coupling would be advantageous. The Göttingen Campus is a leading center of neuroscience in Europe hosting numerous internationally renowned research institutions, including the University, the University Medical Center, two life science Max Planck Institutes, the European Neuroscience Institute, the German Primate Center, and the Bernstein Center for Computational Neuroscience Göttingen. The CIDBN is a newly founded transdisciplinary institute whose mission is to foster frontier research at the border of the exact and biological sciences. The University of Göttingen is an equal opportunities employer and places particular emphasis on fostering career opportunities for women. Qualified women are therefore strongly encouraged to apply. The university has committed itself to being a family-friendly institution and supports their employees in balancing work and family life. The mission of the University is to employ a greater number of severely disabled persons. Applications from severely disabled persons with equivalent qualifications will be given preference. Please send your e-mail application in one single PDF-document, including a letter of motivation, your curriculum vitae with a list of publications, copies of your certificates and contact information of two references to cidbn(a)uni-goettingen.de<mailto:cidbn@uni-goettingen.de> (subject: Postdoc CIDBN). The position remains open until filled. Georg-August-Universität Göttingen Göttingen Campus Institute for Dynamics of Biological Networks Heinrich-Düker-Weg 12, 37073 Göttingen. If you have any questions, please contact Prof. Fred Wolf via e-mail: fred.wolf(a)ds.mpg.de<mailto:fred.wolf@ds.mpg.de>. Please note: With submission of your application, you accept the processing of your applicant data in terms of data-protection law. Further information on the legal basis and data usage is provided in the Hinweisblatt zur Datenschutzgrundverordnung (DSGVO) https://www.uni-goettingen.de/hinweisdsgvo <https://www.uni-goettingen.de/hinweisdsgvo%20> Best regards, Christina von Behren ------ Goettingen Campus Institute for Dynamics of Biological Networks Bernstein Center for Computational Neuroscience Goettingen University of Goettingen Heinrich-Dueker-Weg 12 37073 Goettingen Germany Tel.: +49-(0)551-39-26674

2 1

Python Package: SER model
by Fabrizio Damicelli Aug. 8, 2024

Aug. 8, 2024

Dear Computational Neuroscience Community, I would like to point you to a potentially useful Python Package that might be of interest for your research, especially in the realm dynamical models and spreading dynamics on networks. "ser": S(usceptible)E(xcited)R(efractory) model on graphs, a dynamical model of spreading excitations. Code Repository: https://github.com/fabridamicelli/ser As of today, a few people already trust it and the package registers >11K total downloads, ~500/month (pypi.org) and has been used already in a few research projects. A few interesting features: - It is light-weight and fast (`numba` accelerated), i.e. many experiments can be simply run on a laptop - Installation and getting started is easy: `pip install ser` - Example notebooks: https://github.com/fabridamicelli/ser/blob/main/examples The SER model is a classical cellular automaton model used to study all sorts of complex systems, ranging from forest fire dynamics to self-organized criticality in the brain. Despite of the simplicity of its setup, it is capable of generating complex emergent dynamics with absolutely non-trivial higher-order statistical properties. To learn more about the SER model and its applications, you might want to check out these references: - Messe et al. (2018). Toward a theory of coactivation patterns in excitable neural networks. doi.org/10.1371/journal.pcbi.1006084 - Haimovici et al. (2013). Brain Organization into Resting State Networks Emerges at Criticality on a Model of the Human Connectome. doi.org/10.1103/PhysRevLett.110.178101 - Damicelli et al. (2019). Topological reinforcement as a principle of modularity emergence in brain networks. doi.org/10.1162/netn_a_00085 Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/ser/issues) All the best, Fabrizio Damicelli

1 2

Fully-funded PhD in machine-learning for analysing subject's decisions (Nottingham, UK)
by Mark Humphries April 22, 2024

April 22, 2024

A fully-funded PhD is available with Dr Silvia Maggi and Professor Mark Humphries (University of Nottingham) and Dr Hazem Toutonji (University of Sheffield). Decision-making happens in dynamic environments. Understanding how subjects respond to such a fast-changing world requires approaches that can track subject's choice strategies at the resolution of single trials. We recently developed a Bayesian inference algorithm (Maggi et al., 2023, bioRxiv) that enables trial-resolution tracking of learning and exploration during learning. This project will build on this work to solve crucial problems of determining which of a set of behavioural strategies a subject is using and how to incorporate evidence uncertainty into its detection of the learning of strategies and transitions between them. Using the extended algorithm on datasets of rodents and humans performing decision tasks will let us test a range of hypotheses for how correct decisions are learnt and what innate strategies are used. Application deadline: November 30th 2023 PhD start date: February 1st 2024 Please send all queries to Silvia (silvia.maggi(a)nottingham.ac.uk) or Mark (mark.humphries(a)nottingham.ac.uk) Full details and how to apply here: https://www.findaphd.com/phds/project/cognitive-flexibility-in-dynamic-deci… Professor Mark Humphries | Professor of Computational Neuroscience Lab: humphries-lab.org<https://www.humphries-lab.org/> Twitter: @markdhumphries Public blog: https://medium.com/the-spike Book: "The Spike: An Epic Journey Through the Brain in 2.1 Seconds" (Princeton UP) out now in paperback: https://press.princeton.edu/books/paperback/9780691241487/the-spike This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

1 1

Postdoc in Machine Learning for Neuroscience, Edinburgh
by Matthias Hennig April 3, 2024

April 3, 2024

We are looking for a postdoctoral researcher to develop new machine learning approaches for the analysis of large-scale extracellular recordings. The position is part of a wider effort to enable new discoveries with state-of-the-art electrode arrays and recording devices, and jointly supervised by Matthias Hennig and Matt Nolan. It offers a great opportunity to work with theoretical and experimental neuroscientists innovating open source tools and software for systems neuroscience. Based in Edinburgh - vibrant neuroscience community and a great place to live. More information and application details: https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/job/10003 Feel free to contact me for more information (m.hennig(a)ed.ac.uk) Best, Matthias -- Matthias H Hennig http://homepages.inf.ed.ac.uk/mhennig/ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

3 2

Postdoctoral Research Fellow in Biocomputation at the University of Hertfordshire, UK
by Volker Steuber April 2, 2024

April 2, 2024

Post Title: Research Fellow in Biocomputation SBU/Department: School of Physics, Engineering and Computer Science ________________________________ FTE: 1 FTE (working 37 hours per week) Duration of Contract: Fixed term Contract (3 years) Salary: UH7 £36,333 pa with potential to progress to £43,155 pa on achieving designated skills and experience Annual Leave: 35 days plus standard public holidays and an additional 4 days including the closure of our office between Christmas and New Year Location: College Lane Campus, Hatfield, UK Closing Date: 14th June 2023 Interview Date: To be confirmed Reference Number: 048016 Date advert placed: 17th May 2023 Main duties and responsibilities We are seeking a full-time Research Fellow to join the Biocomputation Research Group in the School of Physics, Engineering and Computer Science at the University of Hertfordshire to conduct high-quality research in Computational Neuroscience. The successful candidate’s research will involve synergistic collaborations with a multidisciplinary team to investigate brain processes using methodologies such as computational modelling, machine learning and AI. Research to be conducted could, e.g., comprise modelling brain circuits like the olfactory bulb or the cerebellum and simulating and analysing their function. Additional impact could arise in machine learning, AI, data science, neurorobotics and neuromorphic computing. The successful candidate will be expected to establish a programme of research in collaboration with colleagues at UH and partner organisations in the UK and abroad. Leading the preparation and publication of research manuscripts is a key aspect of the role. Contributions to the preparation of research proposals and applications for funding to external bodies, such as the European Commission and the UK Research and Innovation (UKRI) are expected. The postholder will create opportunities to maximise research activities, capturing relevant evidence to support impact and engaging with external partners and stakeholders. Skill and experience required * Strong theoretical, computational and programming background in computational modelling and/or machine learning and/or data science and/or AI. * Background and expertise in computational neuroscience (e.g. spiking neural networks, brain function and anatomy, analysis of brain data). * Demonstrated experience to conduct independent research in computational neuroscience or a related field, e.g., through published research papers or monographs. * Applicants must be proficient in both written and oral English * The applicants must be able to work independently and in a structured manner and demonstrate good collaborative skills. Qualifications required • An undergraduate honours degree (or equivalent) in Computer Science, Physics, Mathematics, Neuroscience, or a related discipline and a PhD (or expectation that one will soon be awarded) in a relevant discipline. An appointment to this role may require an Academic Technology Approval Scheme (ATAS) certificate. Contact Details/Informal Enquiries: Professor Volker Steuber, v.steuber(a)herts.ac.uk Professor Michael Schmuker, m.schmuker(a)herts.ac.uk Apply through: https://www.jobs.herts.ac.uk/go/048016 Our vision is to transform lives: UH is committed to Equality, Diversity and Inclusion and building a diverse community. We welcome applications from suitably qualified and eligible candidates regardless of their protected characteristics and recognise there are different ways applicants may achieve the criteria in this document. We offer a range of employee benefits including generous annual leave, flexible location opportunities within the UK, discounted Sports Village memberships and free Active Staff sessions, personal and professional development and family-friendly policies. Volker Steuber Professor of Computational Neuroscience Biocomputation Research Group School of Physics, Engineering and Computer Science University of Hertfordshire College Lane, Hatfield, AL10 9AB, UK biocomputation.herts.ac.uk<http://biocomputation.herts.ac.uk>

1 2

World wide VVTNS series: Wednesday, April 3 at 11am (EDT),Manuel Beiran Columbia University | Prediction of neural activity in connectome-constrained recurrent networks
by David Hansel March 31, 2024

March 31, 2024

Important: North America moved to daylight savings time on March 10 Please check the time in your country ------------------- [image: VVTNS.png] https://www.wwtns.online - on twitter: wwtns@TheoreticalWide You are cordially invited to the lecture given by Manuel Beiran Columbia University on the topic of "Prediction of neural activity in connectome-constrained recurrent networks *"* The lecture will be held on zoom on *April 3, 2024*, at *11:00 am EDT * To receive the zoom link: https://www.wwtns.online/register-page *Abstract: *In this talk, I will explain a theory of connectome-constrained neural networks in which a “student” network is trained to reproduce the activity of a ground-truth “teacher”, representing a neural system for which a connectome is available. Unlike standard paradigms with unconstrained connectivity, here both networks have the same connectivity but they have different biophysical parameters, reflecting uncertainty in neuronal and synaptic properties. We find that the connectome is often insufficient to constrain the dynamics of networks that perform a specific task, illustrating the difficulty of inferring function from connectivity alone. However, recordings from a small subset of neurons can remove this degeneracy, producing dynamics in the student that agree with the teacher. Our theory can prioritize which neurons to record from to most efficiently unmeasured network activity. The analysis shows that the solution spaces of connectome-constrained and unconstrained models are qualitatively different, and provides a framework to determine when such models yield consistent dynamics. *About VVTNS : Created as the World Wide Neuroscience Seminar (WWTNS) in November 2020 and renamed in homage to Carl van Vreeswijk in Memoriam (April 20, 2022), its aim is to be a platform to exchange ideas among theoreticians. Speakers have the occasion to talk about theoretical aspects of their work which cannot be discussed in a setting where the majority of the audience consists of experimentalists. The seminars, **held on Wednesdays at 11 am ET,** are 45-50 min long followed by a discussion. The talks are recorded with authorization of the speaker and are available to everybody on our YouTube channel.* -- 'Life is good ..' (Carl van Vreeswijk, 1962-2022) --------------------------------------- David Hansel Directeur de Recherche au CNRS Co-Group leader Cerebral Dynamics Plasticity and Learning lab., CNRS 45 rue des Saints Pères 75270 Paris Cedex 06 Tel (Cell): +33 607508403 - Fax (33).1.49.27.90.62 ᐧ

1 0

Research Summit on Fundamental Challenges for AI. Mountain View, April 15th.
by Battleday, Ruairidh March 29, 2024

March 29, 2024

We are most excited to announce the AE Spring Summit on Fundamental Challenges for AI (Computer History Museum, Mountain View; April 15th). www.algopreneurship.org This is a day of keynote talks and panels by leading AI researchers on what the open problems for the development of AI algorithms are, and promising scientific and engineering strategies for solving them. We have invited speakers and representatives from the following five technical stakeholder groups to this Summit: - Academia - Tech - FROs / nonprofits - Start-up - VCs / Funders By soliciting answers and discussions from scientists and leaders at these different groups we hope to also examine what their different roles will be in the next period of AI research, and to foster the sharing of research between them. This should be an exciting and productive day, and we have made lower-priced tickets available for students and early-stage researchers. Lunch and a reception will be provided. We look forward to seeing some of you there, and please feel free to share news about the event on social media. The Thinking About Thinking <http://www.thinkingaboutthinking.org> Team Twitter / X: https://bit.ly/springsummitaix LinkedIn: https://bit.ly/springsummitaiLI -- Dr Ruairidh McLennan Battleday BMBCh (Oxon) PhD Postdoctoral Research Fellow Center for Brain Science, Harvard University Center for Brains, Minds, and Machines, MIT

1 0

Doctoral studies in the computational neuroscience of decision-making
by Paul Cisek March 28, 2024

March 28, 2024

Doctoral studies in the computational neuroscience of decision-making Department of Neuroscience, University of Montreal Applications are invited for doctoral studies in computational neuroscience, in the laboratory of Paul Cisek at the University of Montreal. Our research investigates the neural mechanisms of embodied decision-making and action planning in humans and non-human primates using computational models of the nervous system integrated with behavioral experiments, transcranial magnetic stimulation, and multi-electrode recording in multiple regions of the cerebral cortex and basal ganglia. New projects will use virtual reality to study naturalistic behavior in humans and non-human primates and develop theoretical models of how distributed cortical and subcortical circuits govern continuous interaction with a dynamic environment. We are currently seeking a PhD student whose primary project will involve mathematical models that capture and explain data from previous and current experiments and make testable predictions for future work. Students with a strong background in mathematics, engineering, computer science, or physics, coupled with a keen interest in theoretical neuroscience are encouraged to apply. Prior experience in neurophysiology, behavioral neuroscience and/or computational modeling of neural systems is desirable. Interested candidates are asked to send a curriculum vita, copies of academic transcripts, a statement of research interests and the names and contact information for two references, to Paul Cisek (paul.cisek(a)umontreal.ca<mailto:paul.cisek@umontreal.ca>). Applications will be accepted until the position is filled, but preference will be given to applications received before April 30, 2024. Paul Cisek, PhD Département de neurosciences Université de Montréal Physical: 2960 chemin de la tour, local 4117 Montréal, QC H3T 1J4 CANADA Mailing: CP 6128 Succursale centre-ville, Montréal, QC H3C 3J7 CANADA e-mail: paul.cisek(a)umontreal.ca<mailto:paul.cisek@umontreal.ca> Web: www.cisek.org/pavel<http://www.cisek.org/pavel>

1 0