April 2023 - Comp-neuro - lists.cnsorg.org

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

Postdoc Position in Moral Artificial Intelligence (Jointly sponsored by Duke and CMU)
by Dr Jana Schaich Borg, Ph.D. March 11, 2024

March 11, 2024

Postdoc available in our interdisciplinary Moral AI group! Description: We have an opening for a joint two-year postdoctoral position at the School of Computer Science at Carnegie Mellon University and the Social Science Research Institute, Duke Institute for Brain Sciences, and Kenan Institute for Ethics at Duke University (with the possibility of renewal for a third year). The postdoc can be employed through any of these departments in either University, depending on their preference. The candidate is expected to live in either Pittsburgh or Durham depending on their chosen home department, but will be asked to travel occasionally to the other location. The focus of the position is on conducting impactful research on moral artificial intelligence, addressing problems such as: Designing artificial intelligence systems to model and predict human moral judgments Designing effective elicitation mechanisms and interfaces to capture moral preferences Developing techniques for implementing and evaluating AI systems that are based on these modeled preferences, and assessing the dynamic impact of these systems on the preferences and behavior of users who interact with them Qualifications: Applicants should hold a Ph.D. in computer science, statistics, mathematics, computational neuroscience, computational cognitive science, or related technical fields and have expertise in Machine Learning and AI / statistics / data science. Additional background in moral psychology, moral philosophy, (AI or other) ethics, HCI, social decision-making and/or social science is preferred, but not required. Interested applicants should apply online <https://apply.interfolio.com/113237> <https://apply.interfolio.com/113237> (https://apply.interfolio.com/113237) or contact Dr. Jana Schaich Borg via email (js524(a)duke.edu) including a CV and statement of research interests, and the name of three referees that can provide letters of recommendation. We are strongly committed to a diverse academic environment and place high priority on attracting underrepresented candidates.

2 4

Call for Visiting Scholars in Theoretical Sciences at OIST (Application by August 15)
by Kenji Doya Oct. 21, 2023

Oct. 21, 2023

We are pleased to announce Visiting Scholars in Theoretical Sciences at OIST for a flexible term of 1 to 12 months as below. ***** As part of an initiative to develop a vibrant program in theoretical sciences, OIST invites applications for Visiting Scholars in the Theoretical Sciences. The Okinawa Institute of Science and Technology (OIST) is a research institution with a Ph.D. program. Outstanding graduate students and faculty are being attracted internationally. OIST is beautifully situated on the tropical island of Okinawa, Japan. Applicants should have a Ph.D. in a relevant field and be independent researchers, i.e., should have an academic standing equivalent to senior postdoc, junior group leader, or faculty member at a research-intensive institution. The position has a flexible term of 1 to 12 months taken continuously starting between October 2021 and March 2022 with a preference for longer-term visitors. The appointment may be taken while on leave or sabbatical from another university and comes with housing, research funds, and moving allowance. Successful candidates will be eligible to apply for support with salary, where this is necessary to facilitate the visit. No teaching duties come with the position. OIST is an institution with no departments, aiming to eliminate barriers between people working in different fields. It provides a family-friendly working environment including the multilingual Child Development Center and has proactive policies designed to promote a culture of diversity. OIST is an equal opportunity, affirmative action educator, and employer. Further details can be found at https://www.oist.jp/. Applicants should submit a CV including a list of publications, a brief description of their research to date and proposed research while visiting OIST, and the desired period of visit. All visits are subject to the availability of funding. Applications received by August 15, 2021, are guaranteed full consideration. If you have any questions, please send inquiries to: tsvp(a)oist.jp To apply, please go to our Interfolio page, http://apply.interfolio.com/88541 ---- Kenji Doya <doya(a)oist.jp> Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna, Okinawa 904-0495, Japan Phone: +81-98-966-8594; Fax: +81-98-966-2891 https://groups.oist.jp/ncu

1 3

Faculty position at Cold Spring Harbor Laboratory in computational neuroscience
by Benjamin Cowley Aug. 28, 2023

Aug. 28, 2023

Hi all, Cold Spring Harbor Laboratory has an open search for a faculty position in computational/theoretical neuroscience. Applications are due Nov. 15, 2022. https://www.cshl.edu/about-us/careers/faculty-positions/ Here is the job description: Cold Spring Harbor Laboratory (CSHL) is seeking to fill a faculty position in the area of COMPUTATIONAL/THEORETICAL NEUROSCIENCE. Of particular interest to this search are candidates with expertise in computational and theoretical neuroscience, machine learning, and artificial intelligence. The successful candidate will have an outstanding record of research achievement and an innovative research program. They will join a highly interactive and collaborative neuroscience group working on neural circuits, neural development, neurogenetics, theoretical and computational neuroscience, artificial intelligence, synaptic function, brain disorders, rodent cognition, perception, and social behavior. Preference will be given to applicants at the Assistant Professor level, but outstanding candidates at all career stages will be considered. Cold Spring Harbor Laboratory is a world-renowned research and educational institution with programs in cancer, neuroscience, plant biology, genomics, and quantitative biology. Located on the North Shore of Long Island 30 miles from New York City, the Laboratory has a rich and successful research environment rooted in interdisciplinary collaboration as well as an innovative graduate school that attracts talented students each year. CSHL is committed to fostering a diverse work environment that values best practices in mentorship, equity, and inclusion. Successful candidates will be expected to establish productive research programs while mentoring diverse groups of students and postdocs. Applications are strongly encouraged from groups historically underrepresented in science, including women and U.S. racial/ethnic minority populations. To apply, please submit a cover letter, CV, description of research accomplishments, statement of future research plans, and a statement of diversity & mentoring to: https://cshl.peopleadmin.com/postings/20153 Position ID 03299-R; letters of reference will be requested separately. The statement of diversity & mentoring should describe a candidate’s mentoring philosophy, contributions to equity and inclusion in science, and prior training (as applicable) in mentoring, academic management/leadership, and antidiscrimination/antiracism. We will begin considering applications on a rolling basis on October 5, 2022, and applications will be considered until *November 15*. Inquiries regarding the search should be directed to: CSHLfacultyjobs(a)cshl.edu

1 2

Endowed professorship "AI-based Modeling in Neurology"
by Philipp Berens May 10, 2023

May 10, 2023

Dear all, we are currently advertising an Endowed professorship "AI-based Modeling in Neurology" (https://www.academics.com/jobs/endowed-professor-w3-of-ai-based-modeling-in…) at the University of Tübingen. We are looking for candidates that perform innovative research on artificial intelligence (AI) methods for modelling the healthy and diseased brain from a translational and clinical perspective. This can include the development and use of brain simulations to better understand healthy brain function and the effects of neurological diseases (e.g. epilepsy, Alzheimer's, Parkinson's) and integrating simulations and clinical neurodata (e.g. functional MRI imaging, EEG, electrophysiology) with the help of machine learning. Tübingen offers a first-rate environment at the intersection of neuroscience and AI/ML research with the Excellence Cluster for Machine Learning in Science, the Tübingen AI Center, the Max Planck Institutes for Intelligent Systems and Biological Cybernetics, the Hertie Institute for Clinical Brain Research and many other institutions! We are looking forward to your application by May 19th. Best Philipp -- Professor of Data Science, Director Hertie Institute for AI in Brain Health Medical Faculty of the University of Tübingen www.berenslab.org

1 1

PhD position on dynamic RSA, CIMeC, Uni Trento, Italy
by Moritz Wurm April 28, 2023

April 28, 2023

Dear all, We are seeking for a highly motivated PhD student to join the Action Recognition and Concepts Group <https://www.cimec.unitn.it/en/929/action-recognition-and-concepts-group> at CIMeC (Center for Mind/Brain Sciences), University of Trento, Italy. The research project will focus on a MEG-based dynamic extension to representational similarity analysis (dynamic RSA <https://doi.org/10.1101/2022.09.02.506366>) that we have recently developed in our lab to investigate predictive representations of temporally extended unfolding events. The successful candidate should have a background in cognitive neuroscience (preferably M/EEG or fMRI, MVPA/RSA) and strong programming skills (preferably Matlab). Deadline to apply is May 31. Please get in touch with me (moritz.wurm(a)unitn.it <mailto:moritz.wurm@unitn.it>) as soon as possible if you are interested or have questions. Find more information on CIMeC’s doctoral program here <https://www.unitn.it/drcimec/>. All the best, Moritz Wurm -- Moritz Wurm, PhD Center for Mind/Brain Sciences (CIMeC), University of Trento Corso Bettini 31, 38068 Rovereto (TN), Italy moritz.wurm(a)unitn.it +39 0461-28 8632 https://sites.google.com/site/moritzfwurm

1 0

Assistant Professor position at Maastricht University
by Jolivet, Renaud (MACSBIO) April 28, 2023

April 28, 2023

My department - Systems Biology at Maastricht University - has an opening for an Assistant Professor in Plant Systems, Computational or Synthetic Biology (https://www.academictransfer.com/en/327187/assistant-professor-plant-system…) This is part of a cluster hire for a new centre and the search is broad. We are particularly interested by people who develop computational methods that can be applied to plants, but also to humans and animals, and we would be particularly interested by a candidate developing methods useful in neuroscience. Please contact me directly if interested. — Prof. Renaud B. Jolivet Chair of Neural Engineering and Computation Maastricht University ERA Forum Stakeholder Representative, European Commission Chair of the Science and Technology Committee, EBRAINS Member of the Board of Directors, Organization for Computational Neurosciences 2023 Neurotech Fellow, Foresight Institute User Team Leader, ISOLDE, CERN +41798302129 (mobile) ‭+31433881741 (office)‬ r.jolivet(a)maastrichtuniversity.nl<mailto:renaud.jolivet@unige.ch> twitter.com/RenaudJolivet<https://twitter.com/RenaudJolivet>

1 0

PhD Position in Computational Neuroscience, NI group @ Technische Universität Berlin, Germany
by Klaus Obermayer April 26, 2023

April 26, 2023

*Neural Information Processing Group @ Technische Universität Berlin* *PhD Position in Computational Neuroscience (salary level TV-L E13 100%)* *Modelling Neural Dynamics and the Effects of Transcranial Electrical Stimulation* *Faculty IV - Institute of Software Engineering and Theoretical Computer Science / Neural Information Processing Group* *Reference number: *IV-215/23 (starting at the earliest possible date / for 5 years) *Working field: *Participation in the projects of the our research group in the field of computational neuroscience on modelling neural dynamics and the effects of transcranial electrical stimulation; collaboration with theoretical and experimental / clinical research groups of the Collaborative Research Center 1315 „Mechanisms and Disturbances of Memory Consolidation" (https://www.sfb1315.de/, cf. project B03) and the Bernstein Center for Computational Neuroscience Berlin (https://www.bccn-berlin.de/) assistance in the maintenance of the computer infrastructure of the research group; teaching tutorials for introductory courses in programming and algorithms & architectures for non-CS students. For information about our research group see https://www.tu.berlin/en/ni. *Requirements: *Successfully completed university degree (Master, Diplom, or equivalent) in Computational Neuroscience, Computer Science, Electrical Engineering, Mathematics, Physics, or related fields; in-depth knowledge in dynamical systems, very good command of the German and English languages, the ability to teach in both German and English is required; very good programming skills and competences in the operating system UNIX; experience in modelling neural systems, teaching experience, and experience in server administration (UNIX) are desirable. Please send your application with the usual documents exclusively by e-mail to Prof. Dr. Klaus Obermayer at *klaus.obermayer(a)tu-berlin.de*, quoting the *reference number*. *Closing date* for applications for full consideration 12/05/23. Applications will be accepted until the position is filled.

1 0

PhD position Radboud University Donders Institute
by peter.delooff＠ru.nl April 26, 2023

April 26, 2023

Dear list, Apologies for any cross postings, but we have a PhD position available from a collaboration between the Donders Institute, RadboudUMC and Tilburg University that might be of interest to you. For additional information, please visit: https://werkenbijfivoor.nl/vacatures/details/phd-student-in-digital-phenoty… PhD Student in Digital Phenotyping and implementation with wearables in Forensic Psychiatry We are seeking a highly motivated PhD student to join our interdisciplinary team of researchers in the field of forensic psychiatry and digital phenotyping. The successful candidate will work with the team on developing several stress, sleep, and physical activity algorithms based on data from the Healthy Brain Study (HBS). The HBS is a prospective longitudinal cohort study that utilizes careful digital phenotyping in 1000 healthy participants. HBS combines bio-sampling, neuro-imaging and ecological momentary assessments to carefully assess several physiological, cognitive, affective and behavioural outcomes in both the laboratory and in real life with wearables. The PhD student will work on integrating these algorithms in an existing open source application for wearables in collaboration with patients and staff members from Forensic Psychiatry that will provide tailored, personalized insights and can be implemented in treatment settings. The PhD student will also carefully design several single case experiments to assess the efficacy and value of the open source application in (forensic) psychiatric treatment. This project is a collaboration between Donders Institute Radboud, Tilburg University, Fivoor, and de Borg and will be embedded in the infrastructure of the Donders Institute, providing a unique and stimulating learning environment for young researchers, including a high-profile graduate school and in-house methodological expert courses. All the best,

1 0

Announcement of EITN Fall school in Computational Neuroscience
by DESTEXHE Alain April 25, 2023

April 25, 2023

Hi All, In the name of the organizers, I'd like to announce the next edition of the EITN Fall School in Computational Neuroscience, in Paris in September 20-29, 2023. This school is intended for PhD students (although we do accept postdocs or Master students occasionally), and is structured in 4 scales of modeling: cellular, network, populations and whole-brain models. Each scale is associated with courses and tutorials on simulation tools such as Neuron, NEST, BRIAN, TVB, etc. The students form 4 groups to work on a modeling project, with the help of tutors. The course ends with the student presentations of the results obtained. This 10-day intensive course selects students on the basis of their excellence and need to follow this training. Students interested should send CV and a motivation letter to eitn(a)services.cnrs.fr (deadline end of June 2023). More details can be found at https://eitn.cnrs.fr/events/eitn-fall-school-2023 Thanks and see (some of) you soon, Alain --------------- EITN Fall School in Computational Neuroscience 2023 Paris, 20-29 September 2023 The EITN Fall School in Computational Neuroscience consists of a 10-day course in theoretical and computational neuroscience, from cellular to whole-brain levels. The course is structured in thematic days with lectures, tutorials, and project work.The course is typically aimed for PhD students, young postdocs, or master students interested to learn more about techniques of computational neuroscience, and the use of various simulation environments for model building. The students will form thematic groups to work on predefined subjects, with the help of tutors.The course will cover cellular models, models of brain signals, circuit models and networks, mean-field models, and whole-brain models. There will be lectures and tutorials associated to these topics. Organizers: Sacha Van Albada (Julich), Albert Gidon (U Berlin), Hermann Cuntz (Ernst Strüngmann Institute, Frankfurt), Alain Destexhe (CNRS), Matteo di Volo (University Lyon 1), Spase Petkoski (Aix-Marseille Univ.), Gorka Zamora-Lopez (Universitat Pompeu Fabra) Why join? 10 days of intensive training in computational neuroscience provided by researchers from all over Europe. A complete program: • Cellular models, and models of brain signals • Circuit models and networks • Mean-field models • Whole-brain models Hands-on learning schedule based on: • Morning classes and tutorials • Group projects in the afternoon • Free time in the evenings to visit Paris How to apply? This training has a limited capacity of 20 students, therefore a selection will be performed by a scientific organizing committee. Applications are open until 30 June 2023. Send your application by email at eitn(a)services.cnrs.fr<mailto:eitn@services.cnrs.fr> → You will receive a confirmation your application has be received within 5 working days (or on the day application period closes (whichever comes the soonest). If not, please consider a technical issue and submit your application again. Contact eitn(a)services.cnrs.fr<mailto:eitn@services.cnrs.fr> for any question or assistance. Selection criteria include: • Working or studying in neuroscience or related • Experience in python programming would help • Priority is given to PhD students as the primary target of this training, although Master students and post-docs are welcome to apply as well Practical information: If selected, registration fee to attend the training is 400€ If selected, you will need to bring your own laptop with a few pre-installed programs. The tuition fee includes lunch, coffee, access to conference facilities and internet connection during the course days (Sunday not included). Location : Institut Supérieur Clorivière, 119 Bd Diderot, 75012 Paris This training is design to be attended in-person in Paris. It will not be recorded nor accessible remotely. Download flyer.pdf<http://eitn.cnrs.fr/wp-content/uploads/2023/04/Flyer.pdf> <http://eitn.cnrs.fr/wp-content/uploads/2023/04/Flyer.pdf> Preliminary list of Faculty and Speakers: Jan Antolik Nicolas Brunel Hermann Cuntz Gustavo Deco Damien Depannemaecker Alain Destexhe Matteo di Volo Gaute Einevoll Albert Gidon Moritz Helias Viktor Jirsa Marja-Leena Linne Jorge Mejias Spase Petkoski Maria Sacha Marcel Stimberg Bartosz Telenczuk Federico Tesler Sacha Van Albada Romain Veltz Gorka Zamora-Lopez <https://eitn.cnrs.fr/events/eitn-fall-school-2023>

1 0