May 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

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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>

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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.

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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

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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

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Fw: New conference on subcortical sensory circuits, 2023, EMBL, Germany
by Maria Leite May 30, 2023

May 30, 2023

[Apologies if you receive multiple copies of this Call for Participation] Dear colleagues, we invite you to participate in the Conference on Subcortical sensory circuits: visual, auditory, somatosensory, and beyond Date: November 28- December 1, 2023 Location: EMBL ATC, Heidelberg, Germany Conference website: https://www.embl.org/about/info/course-and-conference-office/events/ssc23-0… This conference will focus on different subcortical circuits involving various sensory modalities and revisit their increasingly complex and interconnected contributions to perception, behavior, and cognition. The meeting will take place at EMBL Headquarters in Heidelberg, Germany, and features many exciting speakers such as keynotes Karel Svoboda, Allen Institute, USA and Sabine Kastner, Princeton University, USA. Abstract Submission: Nearly half of the talks will be selected from the submitted abstracts. The submission can be made by visiting the conference website and the deadline is September 5. Registration: The registration for the conference is already open. Financial Support: Financial assistance in the form of fee waivers and travel grants is available.

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Survey of user experiences in modeling
by Anton Arkhipov May 30, 2023

May 30, 2023

Dear Colleagues, Our NIH BRAIN Initiative-sponsored project (1U24NS124001) is conducting an annual survey of the needs and experiences of users in neuroscience modeling. Would you be so kind to help us by filling out this brief survey? https://www.surveymonkey.com/r/2023NeuralModelingSoftware It will take only 5 minutes, and the results will help guide future development of software and documentation for the community. Whether you use our tools or not, an expert or novice in modeling, we’d love to hear from you! Thank you so much. If you have any questions, please feel free to reach out by email. Best regards, Anton. Anton Arkhipov Investigator E: antona(a)alleninstitute.org<mailto:antona@alleninstitute.org> [Text Description automatically generated] alleninstitute.org<https://alleninstitute.org> brain-map.org

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Postdoc positions in ML/Neuro at Tübingen University
by Jakob Macke May 26, 2023

May 26, 2023

Dear colleagues, We have several openings for Postdoctoral Researchers to work at the intersection of Machine Learning and Computational Neuroscience funded by the ERC Consolidator Grant “DeepCoMechTome: Using deep learning to understand computations in neural circuits with Connectome-constrained Mechanistic Models“. The goal of DeepCoMechTome is to develop simulation-based machine learning tools that will make it possible to build neural network models that are both biologically realistic and computationally powerful. Some relevant prior work can be found in https://www.biorxiv.org/content/10.1101/2023.03.11.532232v1. We are looking for candidates with a strong quantitative background and PhD in a relevant discipline, ideally in computational neuroscience, machine learning or numerical simulation, a genuine interest in collaborative work at the interface of machine learning and neuroscience, and strong programming skills (ideally Python and relevant deep learning frameworks). Our research group (https://www.mackelab.org <https://www.mackelab.org/>) develops methods in machine learning and artificial intelligence to accelerate scientific discovery, with a particular focus on neuroscience. We aim to provide an interdisciplinary, collaborative and supportive work environment which emphasizes diversity and inclusion. We are embedded in Tübingen’s internationally renowned research community in artificial intelligence and computational neuroscience, including the Cyber Valley Initiative, the Tübingen AI Center, the ELLIS initiative, the Excellence Cluster Machine Learning, the Bernstein Center for Computational Neuroscience, the Hertie Institute for AI in Brain Health and dedicated MSc Programs in Machine Learning and Computational Neuroscience. We are situated in the AI Research Building, in close proximity to the Max Planck Institutes for Intelligent Systems and Biological Cybernetics, and participate in the two International Max Planck Research Schools (IMPRS) `Intelligent Systems’ and`Mechanisms of Mental Function and Dysfunction’. The University of Tübingen is committed to equal opportunity, diversity and inclusion. In case of equal qualification and experience, physically challenged applicants are given preference. The University of Tübingen aims at increasing the share of women in science and highly encourages female scientists to apply. We also explicitly encourage scientists from outside Germany to apply. Please submit your application materials to mls-jobs(a)inf.uni-tuebingen.de <mailto:mls-jobs@inf.uni-tuebingen.de>, including a CV with publication list, a statement of research interests (max. two pages), contact details of two referees, and a link to a code repository (or work samples). Application deadline is June 20, 2023. Candidates are encouraged to send their application material early, as we will start reviewing applications before the deadline. Initial fixed-term contracts will be for 3 years at level E13 TV-L with possible extensions, starting date is flexible. Part-time positions are possible. Hiring is carried out by the Central Administration. For further details and instructions, see www.mackelab.org/jobs <http://www.mackelab.org/jobs>. Best, Jakob Macke Prof. Dr. Jakob Macke Machine Learning in Science; Cluster of Excellence "Machine Learning”, University of Tübingen Adjunct Senior Research Scientist, Department of Empirical Inference; Max Planck Institute for Intelligent Systems Tübingen Director, Bernstein Center for Computational Neuroscience www.mackelab.org <http://www.mackelab.org/>

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Fully funded PhD Opportunity: Brain Dynamics and Motor Skill Learning in Surgery - deadline 8 June 2023
by aomurtag May 25, 2023

May 25, 2023

An exciting PhD studentship position available in the Engineering department at Nottingham Trent University, United Kingdom, for highly competitive candidates with excellent qualifications. Application deadline: 8th of June 2023. Project title: Brain Dynamics and Motor Skill Learning in Surgery The project involves the use of EEG and fNIRS recordings from task performing human subjects and Matlab programming and signal analysis in order to discover patterns related to cognitive load and motor skill. For more information: NTU link: https://lnkd.in/gfbiYQRM Find-a-phd link: https://lnkd.in/gQgPrUiE Application instructions: https://lnkd.in/grUFevV5

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Call for Abstracts for the Bernstein Conference 2023 in Berlin - Contributed talks and posters
by Bernstein Communication May 25, 2023

May 25, 2023

Call for Abstracts for the Bernstein Conference 2023 in Berlin - Contributed talks and posters +++ The Bernstein Network Computational Neuroscience invites proposals for Contributed Talks of the Bernstein Conference 2023 in Berlin. +++ ____ Each year the Bernstein Network invites the international computational neuroscience community to the annual Bernstein Conference for intensive scientific exchange. It has established itself as one of the most renown conferences worldwide in this field, attracting students, postdocs and PIs from around the world to meet and discuss new scientific discoveries. www.bernstein-conference.de ____ IMPORTANT DATES * Bernstein Conference: September 26 - 29, 2023 * Deadline for submission of abstracts to be considered for Contributed Talks: June 21, 2023 * Deadline for poster abstract submission: July 19, 2023 ____ ABSTRACTS We invite the computational neuroscience community to submit their abstracts: Submitted abstracts can either be considered as contributed talks or posters. All accepted abstracts will be published online and will be citable via Digital Object Identifiers (DOI). Further information can be found here: https://bernstein-network.de/bernstein-conference/abstract-submission/<https://bit.ly/BC_submission> ____ INVITED SPEAKERS Keynote Marlene Cohen (University of Chicago, USA) Invited Talks Tiago Branco (Sainsburry Wellcome Center, UK) Stefano Fusi (Columbia University, USA) Ann Kennedy (Northwestern University, USA) Julija Krupic (University of Cambridge, UK) Wiktor Mlynarski (Institute of Science and Technology, Austria / LMU Munich, Germany) Adrien Peyrache (McGill University, Canada) Kanaka Rajan (Icahn School of Medicine at Mount Sinai, USA) Christopher Summerfield (University of Oxford and Deepmind, UK) Julia Veit (Albert-Ludwigs-Univesität Freiburg, Germany) ____ CONFERENCE COMMITTEE Robert Gütig (Conference Chair) Tatjana Tchumatchenko (Program Chair) Srdjan Ostojic (Program Vice Chair) Anna Levina (Workshop Chair) Maria Eckstein (Workshop Vice Chair) & Athena Akrami, Ann Hermundstad, Mehrdad Jazayeri, Christian Leibold, Ashok Litwin-Kumar, Ida Momennejad, Nicole Rust, Andrew Saxe, Daniela Vallentin, Friedemann Zenke. ____ For any further questions, please contact: bernstein.conference(a)fz-juelich.de -- Dr. Dorthe Kaufhold Scientific Management and Coordination Bernstein Network Computational Neuroscience | Bernstein Coordination Site Branch Office of the Forschungszentrum Jülich at the University of Freiburg Hansastr. 9a | 79104 Freiburg, Germany phone: +49 761 203-9589 mail: bernstein.communication(a)fz-juelich.de<mailto:bernstein.communication@fz-juelich.de> web: www.bernstein-network.de<http://www.bernstein-network.de> Twitter: BernsteinNeuro Mastodon: BernsteinNetwork(a)mastodon.world<mailto:BernsteinNetwork@mastodon.world> LinkedIn: Bernstein Network Computational Neuroscience, Germany ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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