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

Python Package: SER model
by Fabrizio Damicelli 08 Aug '24

08 Aug '24

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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Late-breaking poster abstract submission for the 32nd Annual Computational Neuroscience Meeting ends on June 15
by Rubchinsky, Leonid L 31 May '24

31 May '24

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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Fully-funded PhD in machine-learning for analysing subject's decisions (Nottingham, UK)
by Mark Humphries 22 Apr '24

22 Apr '24

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

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Postdoctoral Research Fellow in Biocomputation at the University of Hertfordshire, UK
by Volker Steuber 02 Apr '24

02 Apr '24

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. 11 Mar '24

11 Mar '24

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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Full time Lecturer in Computational/Cognitive Neuroscience (Manchester, UK)
by Caroline Lea-Carnall 14 Dec '23

14 Dec '23

The University of Manchester wishes to appoint a full-time Lecturer in Computational Neuroscience / Experimental Psychology / Cognitive Neuroscience (Teaching and Research) to join the Division of Psychology, Communication and Human Neuroscience at the University of Manchester. The successful applicant will have a research profile that has a strong fit to key research themes in the Division. Candidates with demonstrable skills and interests in applying computational approaches to central research questions in experimental psychology and/or cognitive neuroscience are particularly encouraged to apply. The successful applicant will contribute to undergraduate and masters level teaching with a particular focus on contemporary technical research skills (e.g. Python, GitHub, advanced statistical analysis in R). Application deadline: 11th December 2023 Full details and how to apply here: https://www.jobs.manchester.ac.uk/Job/JobDetail?isPreview=Yes&jobid=27033&a… Caroline Lea-Carnall, PhD | Lecturer in Neuroscience | School of Health Sciences | Faculty of Biology, Medicine and Health The University of Manchester | Room 3.07d, Zochonis Building | Oxford Road | Manchester M13 9PG

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Postdoc Fellow Position in EEG at UCL
by Fabrizi, Lorenzo 30 Nov '23

30 Nov '23

🔬🧠👶 Exciting opportunity! Postdoc research fellow wanted to join a new collaborative research project at UCL's Medawar Pain and Somatosensory Labs, UCLH and Birkbeck BabyLab/ToddlerLab<https://cbcd.bbk.ac.uk/toddlerlab>, led by Dr. Lorenzo Fabrizi<https://profiles.ucl.ac.uk/1290>, Dr. Judith Meek<https://www.uclh.nhs.uk/our-services/find-consultant/dr-judith-meek> and Prof. Emily Jones<https://cbcd.bbk.ac.uk/people/scientificstaff/emily-jones>. Investigate the connection between early sensory experiences and long-term sensory processing in preterm-born neonates and children. Use EEG and novel sensory testing to identify individuals at risk of sensory challenges. Collaborate with experts in preterm brain imaging and neurodevelopment. Requires a background in Medical Physics, Bioengineering, Computational Neuroscience, or related fields, proficiency in brain imaging and programming, and strong communication skills. Apply here<https://www.ucl.ac.uk/work-at-ucl/search-ucl-jobs/details?jobId=17017&jobTi…>. Deadline 2nd of January 2024. Lorenzo Fabrizi, PhD Associate Professor Medical Research Foundation Fellow Neuroscience, Physiology and Pharmacology Department Room G17A, Medawar Building Bloomsbury Campus University College London Gower St, London WC1E 6BT office tel. 02031081888 (int. 51888)

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Postdoctoral Position in modelling the impact of interoceptive signals on neural dynamics and human cognition. ENS Paris
by Boris 30 Nov '23

30 Nov '23

Postdoctoral Position in modelling the impact of interoceptive signals on neural dynamics and human cognition. Group for Neural Theory and LNC2, Ecole Normale Superieure, Paris. A post-doctoral position in theoretical neuroscience is open to explore the impact of cardiac inputs on cortical dynamics. Understanding the role of internal states in human cognition has become a hot topic, with a wealth of experimental results but limited attempts at analyzing the computations that underlie the link between bodily organs and brain. Our particular focus is on elucidating how the different mechanisms for heart-to-cortex coupling (e.g., phase-resetting, gating, phasic arousal,..) can account for human behavioral and neural data, from somatosensory detection to more high-level concepts such as self-relevance, using data-based dynamical models. The ideal candidate should have a doctoral degree in a quantitative discipline and previous experience with computational approaches to neural functions, excellent programming skills coupled with an interest for, and a willingness to learn about, interoception and its influences on neural dynamics and cognition. The candidate will have a unique opportunity to join the project at its very inception and take a key role in the technical and conceptual development. The position is available for 3 years. The postdoctoral fellow will be based at the Group for Neural Theory <https://gnt.dec.ens.fr/en> and LNC2 <https://lnc2.dec.ens.fr/en> , in Boris Gutkin’s team <https://lnc2.dec.ens.fr/en/teams/mathematics-neural-circuits> with strong interactions with Catherine Tallon-Baudry’s team. LNC2 is located in the center of Paris within the Cognitive Science Department <https://cognition.ens.fr/en> at Ecole Normale Supérieure <https://www.ens.psl.eu/en>, with numerous opportunities to interact with the Paris scientific community at large, in a stimulating and supportive work environment. Group for Neural Theory provides a rich environment and local community for theoretical neuroscience. Lab life is in English, speaking French is not a requirement. Salary according to experience and French regulations with health and social benefits. Informal enquiries and applications (CV, motivation letter and contacts for reference) should be sent boris.gutkin(a)gmail.com <mailto:boris.gutkin@gmail.com> and catherine.tallon-baudry(a)ens.psl.eu <mailto:catherine.tallon-baudry@ens.psl.eu>. Applications will be evaluated on the fly, the position remaining open until filled.

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Fully-funded PhD in machine learning for medical imaging (Indiana University, US)
by chigurupatisreekar＠gmail.com 28 Nov '23

28 Nov '23

The Garyfallidis Research Group (grg.luddy.indiana.edu) at the Luddy School of Informatics, Computing, and Engineering has open PhD positions on the topic of artificial general intelligence for medical applications. The appointment starts Fall 2024. The PhD student will join a dynamic and interdisciplinary team that includes engineers, neuroscientists, and cognitive scientists. The PhD applicants will work with Prof. Eleftherios Garyfallidis on various areas of research, including machine learning, medical imaging and/or scientific visualization. Prof. Garyfallidis' team collaborates with more than 300 research labs across the US. His research group is also the headquarters for the DIPY and FURY organizations deploying research software in thousands of labs across the globe. Minimum Qualifications: A BSc (or equivalent) is required in engineering, computer science, statistics, physics, mathematics or neuroscience or related fields; and solid programming skills necessary to handle big data and develop large scale simulations. Knowledge of Python and C is a plus. Knowledge of graphic shaders is a bonus. Previous experience in open-source development is not required but good to have. Questions and CV should be sent to elef(a)indiana.edu. Interviews will take place after officially applying here https://graduate.indiana.edu/admissions/apply.html#/login The specific track is Neuroengineering. Note that the deadline for Fall 2024 is December 15 2023. Indiana University is an R01 (research level 1) university with multiple campuses. We are situated on the Bloomington campus that has over 50K students. The GRG is part of a new engineering department that focuses entirely on building intelligent systems. Students receive a fellowship (working as research assistants or teaching assistants) for the first 4 years of the PhD program. The students are encouraged to get internships in industry during the summer months (optional). This fellowship package guarantees recipients a full stipend, fee remission, and student health insurance during a 4 year period as you work towards the Ph.D. degree. Lab: https://grg.luddy.indiana.edu Twitter: https://twitter.com/dipymri

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Two postdoc openings on computational analysis and modelling of dynamic functional connectivity in Alzheimer's Disease (Strasbourg, FunSy team, France)
by Demian Battaglia 27 Nov '23

27 Nov '23

We are happy to announce two postdoc openings in the group of Dr. Demian Battaglia, within the newly created Functional System Dynamics team at University of Strasbourg. The recruited postdocs will work as well in close collaboration with Dr. Romain Goutagny in Strasbourg and Dr. Viktor Jirsa at the Institute for Systems Neuroscience in Marseille. Both positions will focus on investigating the link between dynamics of large-scale functional connectivity and cognition: first, by assessing that the maintenance of a structured and fluid dynamics of Functional Connectivity is a predictor of cognitive performance and of its resilience despite progressing neurodegeneration; second by showing that interventions aiming at restoring "healthy" brain dynamics can rescue cognitive performance. POSITION START: as early as possible (ideally, before April 2024) POSTDOC DURATION: 24 months - TWO POSITIONS AVAILABLE Specifically the first position will delve with the study of dynamic Functional Connectivity variations and their correlation with variations of cognitive performance in longitudinal studies of aging and Alzheimer's disease cohorts (human resting state fMRI, physiological markers, cognitive profiling...). The second position will delve with the characterization of the effects of non-invasive visual gamma flickering stimulation (vGENUS) on electrophysiological activity in AD mutant mice and the modelling of the mechanisms behind these effects via virtual mouse mean-field whole-brain simulations. We are seeking for candidates, with previous experience in computational neuroscience or computer science, physics or mathematics training with strong motivation to transit toward neuroscience. Previous experience with whole-brain modelling or dynamic functional connectivity analyses would be a plus, although not strictly required. Interested candidates could have hybrid data analysis/computational modelling projects. We expect fluent programming skills (e.g., Python, C/C++, Matlab), good communication skills in English (oral and written), the ability to work well in an international team, curiosity and open-mindedness (more than applying existing methods, we tend to forge original ones, shaped by the specific scientific questions we work on). The candidate will integrate the Functional System Dynamics team (FunSy, https://funsyteam.org) at University of Strasbourg, which is a mixed theoretical and experimental group focusing on the functional roles of multi-scale system's level dynamics. FunSy research aims at linking dynamics to information processing, behavior and cognition in the healthy and pathological brain, exploring projects in rodent, non-human primate or human neuroscience as well as pure theory. The present postdoc openings are funded by the Foundation "Vaincre Alzheimer" and the French National Priority Research Investment Program "PEPR Digital Health". Strict interactions are to be expected with other partners in this initiative ("Brain Health Trajectories"), with frequent visits at Viktor Jirsa's lab at Aix-Marseille University, or other researchers at Neurospin in Saclay (Paris South) or Grenoble. Strasbourg University is home of an emergent and active community in neuroscience, from molecules and cells to whole brain imaging and behavior, in relation with clinics. The proximity with Germany and Switzerland is an asset allowing interactions with transnational computational neuroscience centers. Strasbourg, one of European Union's capitals, is a fascinating city with a rich student and cultural life, well connected via high-speed train to important European cities (e.g. less than two hours from Paris) DEADLINE FOR APPLICATION: December 24th 2023 Please send your application, including CV, motivation letter and representative publications (preprints accepted) electronically to Dr. Demian Battaglia. In addition, contacts of at least two academic references must be communicated (contact email or recommendation letter attachments). Pre-selected candidates will be interviewed over Zoom or invited to give a talk if possible. We wish to promote the recruitment of strong candidates from minority groups in STEM research. Feel free to inquire for additional requests of information. CONTACT: Demian Battaglia (dbattaglia(a)unistra.fr or demian.battaglia(a)univ-amu.fr)

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