May 2025 - Comp-neuro - lists.cnsorg.org

Python Package Release: Echo State Network 1.0.0
by Fabrizio Damicelli May 26, 2025

May 26, 2025

Dear Community, I'd like to announce the new release (version 1.0.0) of the Python Package "echoes": Machine Learning with Echo State Networks, a scikit-learn compatible package. Code Repository: https://github.com/fabridamicelli/echoes Especially in the realms of "Biologically-inspired Neural Networks", "Shallow Learning" and "Recurrent Neural Networks" in general. A few interesting features: - Installation and getting started is easy: `pip install echoes` * API follows scikit-learn standard (eg fit/predict). - It is light-weight and fast (`numba` accelerated), run your experiments on a laptop - Flexible and customizable, e.g. use arbitrary connectivity, add custom activations, visualize neurons activity, etc. * Example notebooks: https://github.com/fabridamicelli/echoes/tree/master/examples/notebooks - Documentation: https://fabridamicelli.github.io/echoes/ As of today the package registers already ~40K total downloads, ~600/month (pypi.org) and has been used already in a few research projects: - Hadaeghi et. al. (2021) Spatio-temporal feature learning with reservoir computing for T-cell segmentation in live-cell Ca2+ fluorescence microscopy: www.nature.com/articles/s41598-021-87607-y#Sec4 - Fakhar et. al. (2022) Causal Influences Decouple From Their Underlying Network Structure In Echo State Networks: arxiv.org/abs/2205.11947 - Damicelli et.al. (2021) Brain Connectivity meets Reservoir Computing: www.biorxiv.org/content/10.1101/2021.01.22.427750v1.abstract<http://www.biorxiv.org/content/10.1101/2021.01.22.427750v1.abstract> Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/echoes/issues) All the best, Fabrizio

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World wide VVTNS series (fifth season): Wednesday, May 28, 2025, at 11:00 am EDT| Nischal Mainali, ELSC, The Hebrew University
by David Hansel May 25, 2025

May 25, 2025

[image: VVTNS.png] https://www.wwtns.online <https://streaklinks.com/A9c7PbbpKY7PxB6PaAJWGD3-/https%3A%2F%2Fwww.wwtns.on…> - on twitter: wwtns@TheoreticalWide You are cordially invited to the lecture Nischal Mainali ELSC, The Hebrew University Mathematical regularities of irregular hippocampus place codes The lecture will be held on zoom on Wednesday, May 28, 2025, at *11:00 am EDT * To receive the link: https://www.wwtns.online/register-page *Abstract: *Measurements from hippocampal place cells in small enclosures have led classical view of highly stereotyped neural tuning functions with smooth, unimodal tuning fields that uniformly tile the environment. However, recent experiments conducted in large spaces across multiple species have revealed a much more irregular neural code than suggested by the classical view. Indeed, place cells in large environments typically fire in multiple locations, and the multiple firing fields of individual cells, as well as those of the entire population, vary considerably in size and shape. We recently showed that a simple mathematical model, wherein firing fields are generated by thresholding realizations of a random Gaussian process, accounts for the statistical properties of place fields in precise quantitative detail. This model captures the observed statistics of field sizes and positions and generates new quantitative predictions on field shapes and topologies. Moreover, these statistics are universal across species, but sensitive to the size and dimensionality of the environment. We quantitatively verified these predictions using multiple recent datasets from bats and rodents in one, two, and three dimensions, across both small and large environments. Collectively, these findings imply that common mechanism underlie the diverse statistical features observed in different experiments and suggest that synaptic projections to CA1 are predominantly random. *About VVTNS : Launched as the World Wide Theoretical Neuroscience Seminar (WWTNS) in November 2020 and renamed in homage to Carl van Vreeswijk in Memoriam (April 20, 2022), 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.* ᐧ

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Open PhD positions in the Institute of Machine Learning and Neural Computation at TU Graz
by Ozan Özdenizci May 25, 2025

May 25, 2025

Dear all, We have two open PhD positions in the Institute of Machine Learning and Neural Computation at Graz University of Technology, Austria. The candidates will join my research group with a focus at the intersection of AI safety and resource-efficient machine learning. These positions will be part of the Bilateral AI Cluster of Excellence program funded by the Austrian Science Fund, and candidates will be working in collaboration with our partner institutes JKU Linz, AAU Klagenfurt, ISTA, TU Vienna, and WU Vienna. For more information and details on how to apply: https://www.tugraz.at/institute/iml/institute/open-positions/bilai-jobs Best regards,  Ozan Özdenizci -- Dr. Ozan Özdenizci Assistant Professor Institute of Machine Learning and Neural Computation Graz University of Technology Inffeldgasse 16b/I, 8010 Graz, Austria

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Webinar for (soon-to-be) postdocs in computational neuroscience 3 June 11 am/5 pm CEST
by Sacha van Albada May 24, 2025

May 24, 2025

In the context of the Henriette Herz Scouting Programme of the Humboldt Foundation, I have a postdoc position available in the field of computational neuroscience. As a low-threshold introduction that does not immediately require a formal application, I am organizing two webinars on Tuesday 3 June, one at 11 am CEST and one at 5 pm CEST, where a colleague and I will briefly present our work and institute, followed by an `Ask Me Anything’ session where my group members and I answer questions. For potential attendees to decide if this is of interest to them, some keywords describing my research are: spiking network models based on anatomical and physiological data, large-scale simulations of cerebral cortex, mean-field theory, comparison with electrophysiological data. The precise research topic can be jointly decided. The candidate should not have previous links to Germany in terms of citizenship, studies, or research stays. Also those in the final stages of their PhDs are welcome. The funding period is 2 years for those who defended the PhD less than 4 years ago and 18 months for those who defended 4-12 years ago. I encourage you to register for internal planning purposes: 11 am CEST session: please register at https://events.hifis.net/event/2649/ and dial in at https://uni-koeln.zoom.us/j/93354865935?pwd=XaRxMWaWObqQJnCNEfmWxEuS1gKovn.1 5 pm CEST session: please register at https://events.hifis.net/event/2674/ and dial in at https://uni-koeln.zoom.us/j/96811002333?pwd=7mdYFayNSsmulys5GVN5Jn2j2jWxwL.1 Hoping to meet/see many of you there! Sacha van Albada -- Prof. Sacha Jennifer van Albada Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience Jülich Research Centre Jülich, Germany Tel. +49 2461 61-96808 Mobile +49 170 2352748 Fax +49 2461 61-9460 Computational Neuroanatomy Institute of Zoology University of Cologne Cologne, Germany Tel. +49-221-470-3829 Fax +49-221-470-4889 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellv. Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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WashU CTCN Postdoc Fellows
by Goodhill, Geoffrey May 24, 2025

May 24, 2025

POSTDOCTORAL FELLOWSHIPS AVAILABLE AT WASHINGTON UNIVERSITY IN ST LOUIS The Center for Theoretical and Computational Neuroscience (ctcn.wustl.edu) at Washington University in St Louis invites applications from outstanding Postdoctoral Fellows to work at the interface between theoretical and experimental neuroscience labs at WashU. Deadline for applications is July 1st 2025. The CTCN is a joint initiative between the Schools of Medicine, Engineering, and Arts and Sciences, and provides a hub for neuroscientists to collaborate with mathematicians, physicists and engineers to find creative solutions to some of the most difficult problems currently facing neuroscience and artificial intelligence. Each CTCN Postdoctoral Fellow is based in at least two labs, but also has the opportunity to seek out new collaborations which help build new connections within the WashU community. We are looking for people with drive, independence and outstanding prior achievement, who are committed to leveraging interdisciplinary collaboration to drive forward the field of theoretical and computational neuroscience. Washington University in St Louis is ranked in the top 10 worldwide for Neuroscience and Behavior. Salary for CTCN Fellows is significantly above standard NIH postdoc rates, and funds for conference travel are included. In addition, WashU offers excellent benefits and comprehensive access to career development, professional and personal support. The St Louis metropolitan area has a population of almost 3M and is rich in culture, green spaces and thriving music and arts scenes, with a highly accessible cost of living. For more details on this prestigious Fellowship opportunity, including how to apply, please see https://ctcn.wustl.edu/postdoc-fellows Professor Geoffrey J Goodhill CTCN Director Washington University School of Medicine 660 S. Euclid Avenue St. Louis, MO 63110 g.goodhill(a)wustl.edu<mailto:g.goodhill@wustl.edu> https://neuroscience.wustl.edu/people/geoffrey-goodhill-phd

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Interesting event: Meeting of the Minds: Western Science Meets Eastern Wisdom
by Thijs Hoedemakers_Werk May 23, 2025

May 23, 2025

Dear members of Comp-neuro, There is an event which might be of interest (see description below). Kind regards, Thijs __________________________________ Meeting of the Minds: Western Science Meets Eastern Wisdom On Friday, June 13, science and Buddhist wisdom come together in an inspiring dialogue between Prof. Dr. Heleen Slagter and Lama Jigmé Namgyal. Prof. Slagter, known for her groundbreaking research on attention, consciousness, and the effects of meditation on the brain, will share her scientific insights into how the mind works and how contemplative practices like meditation can transform awareness. Lama Jigmé Namgyal, an authentic Tibetan Buddhist teacher, meditation instructor, and end-of-life guide, has dedicated his life to studying the human mind and meditation. He will reflect on scientific findings through the lens of the centuries-old Tibetan wisdom tradition. This "Meeting of the Minds" promises a captivating dialogue where Western science and Eastern wisdom meet, complement each other, and at times challenge one another. Attendees will have a unique opportunity to explore how these different perspectives on consciousness, the mind, and human potential can enrich each other through a respectful exchange of ideas. There will be opportunities for audience interaction, making the experience both engaging and educational. The Speakers Prof. Heleen Slagter, a leading cognitive neuroscience researcher, is known for her work on the neural basis of core cognitive functions such as attention and their plasticity. Her research focuses on how the brain selects, suppresses, and processes information, and how practices like meditation can enhance these mechanisms. Meditation promotes greater awareness, adaptability, and cognitive flexibility, and Prof. Slagter will explain the scientific background behind these changes. Lama Jigmé Namgyal’s expertise in Tibetan Buddhist philosophy and meditation provides a spiritual perspective in this scientific conversation. For years, he has studied the transformative power of the mind from a Tibetan Buddhist viewpoint, where mindfulness, meditation, and the understanding of impermanence contribute to clarity and inner peace. His experience in guiding people through the dying process offers unique insights into the continuity of consciousness and the Tibetan view of life after death. This evening offers a fascinating exchange between two disciplines—neuroscience and Tibetan Buddhist wisdom—that can deepen our understanding of the human mind and consciousness. Practical Information (Temple & Online) * Date: Friday, June 13 * Time: Doors open at 19:00, Dialogue from 19:30 to 22:30 (with a short break) (CET) * Location: Phuntsok Chö Ling, Oostkousdijk 17B, 3024 CL Rotterdam * Online: Online participation also available * Price: €25 (non-members), €20 (members) (Temple & Online) * Registration link: click here<https://my.phuntsokcholing.org/shop/event?wsID=259>

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Late-breaking poster abstract submission for the 32nd Annual Computational Neuroscience Meeting ends on June 15
by Rubchinsky, Leonid L May 22, 2025

May 22, 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 ***********************

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Open PhD positions in Barcelona
by Diego Vidaurre May 22, 2025

May 22, 2025

Dear all, I am opening two PhD positions in Barcelona. These will be to work at the intersection between machine-learning methods development, computational neuroscience and clinical applications. The first project has a focus on how we can integrate across multiple sources of data to effectively model disease trajectories of neurodegeneration. The second will exploit primarily brain data to model disease networks and comorbidity. Please see more details here: https://www.crm.cat/call/89/phd-student-ref-2025-009-p04632-/107/ https://www.crm.cat/call/88/phd-student-ref-2025-008-p04632-/105/ Feel free to get in contact informally, and please disseminate Many thanks. d

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Epilepsy Workshop - OCNS 2025
by Guillaume Girier May 21, 2025

May 21, 2025

Computational Strategies in Epilepsy Modeling and Seizure Control Workshop CNS*2025 in Florence, Italy on July 08-09, 2025 We are happy to announce our Epilepsy workshop at the 34th Annual Computational Neuroscience Meeting in Florence. The event will take place on the morning of July 8th and all day of July 9th. To participate, you must be registered for at least the workshops on the organizer's website: https://www.cnsorg.org/cns-2025. For presentation abstracts and workshop schedule see: https://brady.cs.cas.cz/ocns-epilepsy-workshop. *Abstract* Epilepsy remains a complex neurological condition, necessitating innovative approaches to understanding and mitigating seizure activity. This workshop is designed to bring together computational neuroscientists and researchers with experimental and clinical background to explore cutting-edge strategies in epilepsy modeling and seizure control. For the general content structure, we plan to start from a modeler's perspective and then progressively move towards more data-driven approaches. The first session will explore seizure mechanisms through biophysical and neural mass models at different temporal and spatial scales, investigating, among others, ionic dynamics and network plasticity. It aims to understand seizure initiation, progression, and duration. The second session will focus on the application of computational models to EEG data recorded in epileptic patients. First, it will discuss the promising advances in seizure monitoring using wearable devices and long-term EEG recordings, particularly focusing on the use of data features inspired by concepts derived from mathematical modeling in epilepsy. Then, it will move on to advanced parameter inference methods to tailor models to individual data samples in order to provide mechanistic insight. The third session will examine stimulation-based strategies to terminate or prevent seizures. There will be a focus on recent advancements in closed-loop and low-frequency electrical stimulation to control seizures. On top of model-based approaches, this session will also include the clinical perspective on stimulation treatment and data-driven studies. *Our speakers are:* - *Piotr Suffczynski*, *Department of Biomedical Physics, University of Warsaw, Poland* - *Elif Köksal-Ersöz*, *Centre de Recherche en Neurosciences de Lyon - Inserm / CNRS, France* - *Louisiane Lemaire*, *MathNeuro team, University of Montpellier, France* - *Viktor Sip*, *Institut de Neurosciences des Systèmes, Aix-Marseille Université, INSERM, France* - *Brian Litt*, *Department of Neurology and Bioengineering, University of Pennsylvania, Philadelphia, USA* - *Christian Meisel*, *Department of Neurology and Berlin Institute of Health, Universitätsmedizin Berlin, Germany* - *Isa Dallmer-Zerbe*, *Institute of Computer Science of the Czech Academy of Sciences, Czech Republic* - *Dominic Dunstan*, *Department of Mathematics & Statistics, University of Exeter, Exeter, United Kingdom* - *Levin Kuhlmann*, *Department of Data Science and AI, Faculty of Information Technology, Monash University, Australia* - *Guillaume Girier*, *Institute of Computer Science of the Czech Academy of Sciences, Czech Republic* - *Matthew Szuromi*, *Boston University, USA* - *Laila Weyn*, *Department of Information Technology (INTEC), Ghent University/IMEC, Belgium* - *Daria Nesterovich Anderson**, **Faculty of Engineering, University of Sydney, Australia* We will be delighted to welcome you. GIRIER Guillaume, Postdoc Researcher, Complex networks and Brain Dynamics Group COBRA project: http://cobra.cs.cas.cz BRADY project: https://brady.cs.cas.cz/ girier(a)cs.cas.cz | *Personal website <https://sites.google.com/view/guillaumegirier/>*

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CompSysBio2025: Advanced Lecture Course on Computational Systems Biology - Aussois (FR), 5-10 October 2025
by Anton Crombach May 19, 2025

May 19, 2025

We are excited to announce the 5th Advanced Lecture Course on Computational Systems Biology which will be held between October 5-10, 2025 ( [ https://project.inria.fr/compsysbio2025/ | https://project.inria.fr/compsysbio2025/ ] ) at Aussois (France). Pre-registrations are open and abstracts may be submitted. The main Course emphasis is methodological. One goal is to illustrate the wealth and diversity of Systems Biology issues for scientists from Computer Science, Mathematics and Physics. Another goal is to allow biologists motivated by Systems Biology to go deeper into methodological issues in order to facilitate their contacts with scientists from the formal sciences. Sessions are preferentially organized around methodological issues: multi-scale and spatio-temporal modeling, genetic and molecular networks, dynamical and stochastic systems, machine learning and AI for systems biology, with a constant eye on biological relevance ( [ https://project.inria.fr/compsysbio2025/program/ | https://project.inria.fr/compsysbio2025/program/ ] ). This will be complemented by blackboard teaching and hands-on sessions in parallel classes bearing on specific topics or methods ( [ https://project.inria.fr/compsysbio2025/blackboard-teaching-and-computer-pr… | https://project.inria.fr/compsysbio2025/blackboard-teaching-and-computer-pr… ] ). The Course will be an opportunity for participants to interact directly with 23 prominent scientists ( [ https://project.inria.fr/compsysbio2025/invited-speakers/ | https://project.inria.fr/compsysbio2025/invited-speakers/ ] ) in this rapidly growing field. The conference center is located in a lovely authentic village, Aussois, nestled in the heart of the French National Park of Vanoise, a huge and beautiful natural space where flora and fauna are protected, located in the French Alps. In order to facilitate casual interactions during the conference, there will be time for hiking in the afternoon to discover such wonderful landscape. Participants are strongly encouraged to submit an abstract of their current work to be presented as a poster in order to facilitate scientific interactions. Some abstracts will be selected for short talks by the Scientific Committee. Fellowships are available for students and will be awarded to cover registration fees on the basis of the submitted abstract. The School is free of charge for CNRS employees (researchers, PhD students, postdocs, engineers, etc.). Please spread the word to anybody that might be interested in CompSysBio2025 ! Best regards The Organisation Committee of CompSysBio2025 CompsysBio2025 is sponsored by CNRS, CECAM, LBMC, PEPR Maths-Vives, PEPR Cell-ID, GDR BIMMM and Labex Persyval-Lab Key dates Abstract submission until July 31st 2025 Registration until August 31st 2025

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