February 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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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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MBL Methods in Computational Neuroscience Course
by Stephen A. Baccus March 25, 2023

March 25, 2023

Applications are open for the Methods in Computational Neurosciencecourse at the Marine Biology Laboratory in Woods Hole, MA. The course will run from July 26 to August 23, 2023. The online application form and additional information can be found at: https://www.mbl.edu/education/advanced-research-training-courses/course-off… The course application deadline is *March 31*. The course covers a range of topics in computational neuroscience including neuronal biophysics, neural coding & information processing, circuit dynamics, learning & memory, motor control, and cognitive processing & disease. In addition, numerous tutorials and problem sets will cover a broad range of computational and mathematical modeling methods. The course strongly emphasizes the collaboration between theory and experiment in solving neuroscience problems, and lectures will be given by a mixture of theorists and experimentalists. The final weeks of the course are primarily reserved for work on projects that students design in collaboration with the resident faculty. 2023 Course Directors: Stephen Baccus, Stanford University Xiao Jing Wang, New York University 2023 Faculty: Larry Abbott, Columbia University Emery Brown, MIT Nicolas Brunel, Duke University Randy Buckner, Harvard University Anne Churchland, UCLA Claudia Clopath, Imp. College London Marlene Cohen, U. of Pittsburgh Shaul Druckmann, Stanford University Uri Eden, Boston University Bard Ermentrout, U. of Pittsburgh Adrienne Fairhall, U. of Washington Michale Fee, MIT Loren Frank, UCSF Stefano Fusi, Columbia University Surya Ganguli, Stanford University Paul Glimcher, New York University Mark Goldman, UC Davis Nancy Kopell, Boston University Eve Marder, Brandeis University John Murray, Yale University Srdjan Ostojic, ENS - PSL Yiota Poirazi, IMBB-FORTH David Redish, U. Minnesota Terry Sejnowski, Salk Institute Sebastian Seung, Princeton University Reza Shadmehr, Johns Hopkins Univ. Haim Sompolinsky, Hebrew University Nelson Spruston, Janelia Res., HHMI Nao Uchida, Harvard University Byron Yu, Carnegie Mellon University Greg Wayne, DeepMind

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PhD position in Natural Language Processing and Machine Learning at IT University of Copenhagen (deadline April 1st)
by Stefan Heinrich Feb. 28, 2023

Feb. 28, 2023

Full-time PhD position at IT University of Copenhagen, under the umbrella of the Pioneer Centre for AI, Denmark, starting in Summer-Autumn 2023. Topic: Modelling compositional language structures across languages. The origin of language development of human beings can at least be traced back to two sources: the survival needs for communication and the unique wiring of human brains. The two factors can co-develop with each other through life-span. Nevertheless, languages from the whole world are with tremendous diversity. Yet, given the fact that all human brains share very similar structures and connection patterns, which presumably afford for similar ways to encode and decode information from the external world, there likely exist some hidden common structures, like some word orders or numbers of phonemes in a language, that are shared at least within, or even across, language families. An important constraint for these similar structures comes from the theory that the brain is processing language embodied in all our senses and via processing streams that are also involved in a range of other cognitive functions from specific motor control up to general problem-solving. This suggests that language comprehension and production, in fact, developed on top of existing information processing schemes, which in turn might have similarly shaped how the different language families have developed. A particular mechanism that was recently hypothesized to give rise to the structure of the brain’s sequence processing is temporal compositionality and chunking, which seemingly operate on language sequences as well. With this PhD project, we want to identify and describe the specific, latent temporal encoding structures that may constrain the temporal features of spoken language. In this project, the candidate will study structure patterns in spoken language and investigate how to build a model that can extract temporal characteristics of speech across different languages. Since the project is interdisciplinary, active collaboration within the Pioneer Centre for AI, as well as with experts in computational neuroscience and developmental psychology in Germany and Japan are planned. Application details: The ideal candidate should have a Masters in Computer Science, Computational Neuroscience, Computational Linguistics, Developmental Psychology, Cognitive Science or related fields, as well as a strong interest in interdisciplinary research, at the intersection of Natural Language Processing, Machine Learning, and Psycholinguistics. The salary scale will be in accordance with the Ministry of Finance’s agreement with the Danish Confederation of Professional Associations for a full-time position. As a PhD Student at the Pioneer Centre for AI you will have extraordinary access to computing resources, international researchers across disciplines, courses and events at the centre and meaning collaboration with industry, the public sector etc. ITU is a teaching and research-based tertiary institution concerned with information technology (IT) and the opportunities it offers. The University offers an informal working environment, a varied everyday life, and a highly motivated, competent, diverse, and international faculty. Copenhagen has a strong educational system, a rich cultural life, universal healthcare, good childcare, and a well-functioning infrastructure. The city is also among the world’s most liveable cities according to the Economist Global Liveability Index. Candidates will work together with Stefan Heinrich (stehe(a)itu.dk) and Barbara Plank (bapl(a)itu.dk) and are encouraged to get in contact for details. Link to further application information: https://www.aicentre.dk/phd-openings - and application link: https://candidate.hr-manager.net/ApplicationInit.aspx?cid=119&ProjectId=181… Application deadline: 01 April 2023, at 23:59 CET. -- *************************** Dr. Stefan Heinrich Assistant Professor Computer Science Department IT University of Copenhagen https://stefanheinrich.net/ ***************************

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Tenure-track position in computational neuroscience
by Asohan Amarasingham Feb. 28, 2023

Feb. 28, 2023

Dear Colleagues, The Department of Psychology at the City College of New York (CCNY) of the City University of New York (CUNY) is currently soliciting applications for a tenure-track assistant professorship in computational neuroscience. Review of applications will begin on March 3, 2023. Please consider submitting an application. Best regards, Asohan Amarasingham FACULTY VACANCY ANNOUNCEMENT The Department of Psychology at the City College of New York (CCNY) invites applications for a full-time, tenure-track faculty position in computational neuroscience at the rank of Assistant Professor to begin in Fall 2023. The CCNY Psychology Department is a vibrant, diverse department located in Harlem, serving over 2000 undergraduate majors, with master's programs in General Psychology and Mental Health Counseling, a doctoral program in Clinical Psychology, and is affiliated with Ph.D. programs in Psychology and Neuroscience at the CUNY Graduate Center. The ideal candidate will use an innovative combination of computational, data-analytic, and/or modeling techniques to better understand how the brain gives rise to cognitive phenomena. All areas of relevance to cognitive neuroscience are of interest, including but not limited to: sensation, perception, emotion, memory, language, learning and reward, and consciousness. Successful applicants will be encouraged to participate in all programs the Department offers and to pursue interdisciplinary collaborations within and across the program, the department, and other departments at the College, including the Grove School of Engineering, the CUNY School of Medicine, and many related programs at the CUNY Graduate Center, including the CUNY Advanced Science Research Center, the Initiative for Theoretical Sciences, and allied doctoral and master's programs that span the sciences. They will be responsible for teaching, research, and mentorship/advisement duties. They also will share responsibility for committee and department assignments including administrative, supervisory, and other functions. QUALIFICATIONS A Ph.D. in psychology, neuroscience, applied mathematics, computer science, engineering, or a similarly allied field is required. The candidate is expected to maintain an active program of research, publish theoretical and empirical research in top-tier journals, be committed to both undergraduate and graduate education, and provide mentoring/advisement to students. Potential for obtaining external grant support is essential. Also required is the ability to teach successfully, demonstrated scholarship or achievement, and the ability to cooperate with others for the good of the institution. COMPENSATION CUNY offers faculty a competitive compensation and benefits package covering health insurance, pension and retirement benefits, paid parental leave, and savings programs. We also provide mentoring and support for research, scholarship, and publication as part of our commitment to ongoing faculty professional development. HOW TO APPLY Only applications submitted through CUNYfirst will be considered for this position. If you are viewing this job posting externally, please apply as follows: * Go to www.cuny.edu <http://www.cuny.edu/> and click on "Employment" * Click "Search job listings" * Click on "More options to search for CUNY jobs" * Search for Job Opening ID number 25407 Click on the "Apply Now" button and follow the instructions. Applications, including the following must be uploaded to the CUNYfirst job application website as a single PDF document: 1. Cover Letter 2. Curriculum Vitae 3. Statement of research interest and goals 4. Selected Publications 5. Three (3) confidential letters of recommendation sent to kwok(a)ccny.cuny.edu<mailto:hkwok@ccny.cuny.edu>

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NEST Conference 2023 – Save the date & registration
by Hans Ekkehard Plesser Feb. 27, 2023

Feb. 27, 2023

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2023. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We particularly encourage young scientists to participate in the conference! This year's conference will take place as a virtual event on 15-16 June 2023. Register now! For more information please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and colleagues -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Call for applications - MSc Neuroscience, Uni Freiburg (Germany)
by Carsten Mehring Feb. 27, 2023

Feb. 27, 2023

MSc program in Neuroscience - University of Freiburg, Germany We are inviting applications for the interdisciplinary MSc program in Neuroscience at the University of Freiburg, Germany. The program provides theoretical and practical training in neuroscience, covering both the foundations and latest research in the field. It is taught by lecturers from an international scientific community from multiple faculties and neuroscience research centres. The modular course structure caters to the specific backgrounds and research interests of each individual student and we offer specialisations in neural circuits and behavior, computational neuroscience and neurotechnology. All courses are taught in English. We welcome applications with a background in natural sciences, mathematics, behavioural sciences, computer science, medicine or engineering sciences. The deadline for applications for the October 2023 entry is the 31st of March 2023. Further details can be found on our homepage http://www.mscneuro.uni-freiburg.de <http://www.mscneuro.uni-freiburg.de/> With kind regards Carsten Mehring — Bernstein Center Freiburg & Faculty of Biology University of Freiburg

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post-doc position on interacting neuronal assemblies at University of Genova
by Paolo Massobrio Feb. 27, 2023

Feb. 27, 2023

We are seeking highly motivated candidates for a post-doctoral position (1 year) at the Neuroengineering and NeuroTechnology Lab, <http://www.unige.it/> University of Genova, Genova, ITALY. The candidate will be involved in the funded PNRR Italian Project Mnesys (https://mnesys.eu/) a large neuroscience and neuropharmacology consortium coordinated by University of Genova which involves 25 partners. Among the topics of the project, the one which will involve the candidate deals with both computational and experimental staffs. In particular, the candidate will work with experimental models of brain-on-a-chip where different neuronal populations (e.g., cortical-hippocampal; cortical-thalamic; cortical-cerebellar, .) interact originating complex neuronal dynamics. Depending on the candidate attitude, she/he will be involved in the development of large-scale computational models of such interconnected neuronal networks or the development of advanced algorithms to infer functional and dynamical properties originated by the interactions of these ensembles. Requirements: Candidates must have: 1) a PhD in bioengineering, computational neuroscience, physics, engineering, mathematics or a related field; 2) Excellent programming skills in Python, Matlab, C++/C#, 3) a published record of research in the field of computational neuroscience and/or neuroengineering; 4) experience in electrophysiological data analysis and/or modeling. Deadline for submitting the application is March 13th, 2023. The selected candidates will be contacted for a further interview during the following week. The earliest possible starting date is April 1st, 2023, and the position will last for 1 year (possible extension). Our research group has a long tradition in studying the interactions between neuronal populations coupling to Micro-Electrode Arrays (MEAs). See for example the following papers: 1. F. Callegari, M. Brofiga, P. Massobrio. Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays. PLoS Computational Biology, 2023. 2. M. Brofiga, M. Pisano, M. Tedesco, A. Boccaccio, P. Massobrio. Functional inhibitory connections modulate the electrophysiological activity patterns of cortical-hippocampal ensembles, Cerebral Cortex, 2022. 3. P. Massobrio, V. Pasquale, S. Martinoia. Self-organized criticality in cortical assemblies occurs in concurrent scale-free and small-world networks, Scientific Reports, 2015. 4. T. Kanagasabapathi, P. Massobrio, R. A. Barone, M. Tedesco, S. Martinoia, W. J. Wadman, M. M. J. Decre. Functional connectivity and dynamics of cortical-thalamic networks co-cultured in a dual compartment device. Journal of Neural Engineering, 2012. Our labs are located in Genova <https://www.visitgenoa.it/en/iat> , a beautiful town in northern Italy, both from historical (its historical center is the largest of Europe) and naturalistic point of view (sea and mountains coexist creating a unique landscape). Genova is only 1.30h away from Milan by train and connected by plane to Rome (1.00h), London (2h) and Paris (1.30h). Applications must include an extended CV, a motivation letter, the most relevant papers, and names and addresses of two references. If you are interested, please send your application to: Paolo Massobrio e-mail: paolo.massobrio(a)unige.it <mailto:paolo.massobrio@unige.it> Tel: +39-010-3352761 _________________________________ Paolo Massobrio, PhD Associate Professor of Bioengineering Neuroengineering and Neurotechnology Lab Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS) University of Genova Via Opera Pia 13, 16145, Genova, ITALY Phone: +39 010 3352761 URL: <http://www.dibris.unige.it/> www.dibris.unige.it E-mail: <mailto:paolo.massobrio@unige.it> paolo.massobrio(a)unige.it

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