January 2024 - Comp-neuro - lists.cnsorg.org

Announcing Open Source Brain v2.0: NetPyNE, NWB Explorer and JupyterLab; ModelDB models and DANDI Archive datasets

by Padraig Gleeson

<Apologies for cross posting> We would like to announce a major new version of the Open Source Brain platform (v2.0) we have been working on which has a range of new features for you to try: https://v2.opensourcebrain.org. You can create cloud based, persistent workspaces which contain models and data from a number of sources (https://v2.opensourcebrain.org/repositories) including: - All *OSBv1* projects incorporating NeuroML and PyNN models - All *ModelDB* entries - All *BRAIN Initiative DANDI Archive* datasets containing NWB files Inbuilt applications which can open these workspaces include: *- NetPyNE UI*, a 3D graphical application for neuronal simulations (NeuroML compliant) *- NWB Explorer* for opening and visualising data in NWB files *- JupyterLab*, a full interactive Python environment, with a number of computational neuroscience, data analysis and machine learning packages preinstalled. Full documentation is at https://docs.opensourcebrain.org and a Guided Tour introducing the main features of the platform is here <https://docs.opensourcebrain.org/OSBv2/Guided_tour.html>. We are very keen for new users to try out our platform. Please note that you will require a different username/password for OSBv2 from OSBv1. We are also very happy to make dedicated resources available on the platform to support classes/tutorials/computational neuroscience schools. The Open Source Brain Initiative aims to: - Make neuroscience experimental data and computational models from around the world easily findable in a single location - Provide a free to use, collaborative, web based, interactive computing platform that integrates state of the art software tools for accessing and working with large scale data sets and computational models. - Encourage the use of standards for making research outputs more FAIR (Findable, Accessible, Interoperable and Reusable): OSBv2 supports NeuroML for models and NWB for data. Please get in contact if you would like to help us with any of these goals! Regards, The OSB Team

Jan. 17, 2024

CFP COMPLEX NETWORKS 2024 Istanbul Turkey December 10 - 12, 2024

by Hocine Cherifi

13 *th **International Conference on Complex Networks & Their Applications* Istanbul, Turkey December 10 - 12, 2024 COMPLEX NETWORKS 2024 <https://complexnetworks.org/> We encourage researchers from diverse disciplines to share their insights, engage in discussions, and contribute to the vibrant field of complex networks. Join us in Istanbul for a stimulating exchange of ideas and collaborations that transcend disciplinary boundaries. Submission Deadline: September 3, 2024 Submission Categories: Full papers (not previously published up to 12 pages) and Extended Abstracts (about published or unpublished research up to 4 pages) are welcome. · *Papers *will be included in the conference *proceedings edited by Springer* · *Extended abstracts* will be published in the *Book of Abstracts (with ISBN)* Publication Opportunities: Extended versions will be invited for publication in *special issues of international journals:* o PLOS <https://journals.plos.org/plosone/> one <https://journals.plos.org/plosone/> o PLOS COMPLEX SYSTEMS <https://journals.plos.org/complexsystems/> o Applied Network Science <https://appliednetsci.springeropen.com/> edited by Springer o Social Network Analysis and Mining <https://link.springer.com/journal/13278> edited by Springer o Advances in Complex Systems <https://www.worldscientific.com/toc/acs/24/02> edited by World Scientific o Entropy <https://www.mdpi.com/journal/entropy> edited by MDPI o Complex Systems <https://www.complex-systems.com/about/> *TOPICS* *Topics include, but are not limited to: * o Models of Complex Networks o Structural Network Properties and Analysis o Complex Networks and Epidemics o Community Structure in Networks o Community Discovery in Complex Networks o Motif Discovery in Complex Networks o Network Mining o Network embedding methods o Machine learning with graphs o Dynamics and Evolution Patterns of Complex Networks o Link Prediction o Multilayer Networks o Network Controllability o Synchronization in Networks o Visual Representation of Complex Networks o Large-scale Graph Analytics o Social Reputation, Influence, and Trust o Information Spreading in Social Media o Rumour and Viral Marketing in Social Networks o Recommendation Systems and Complex Networks o Financial and Economic Networks o Complex Networks and Mobility o Biological and Technological Networks o Mobile call Networks o Bioinformatics and Earth Sciences Applications o Resilience and Robustness of Complex Networks o Complex Networks for Physical Infrastructures o Complex Networks, Smart Cities and Smart Grids o Political networks o Supply chain networks o Complex networks and information systems o Complex networks and CPS/IoT o Graph signal processing o Cognitive Network Science o Network Medicine o Network Neuroscience o Quantifying success through network analysis o Temporal and spatial networks o Historical Networks We look forward to your submissions and your participation in COMPLEX NETWORKS 2024! The Organizers Join us at COMPLEX NETWORKS 2024 <https://www.complexnetworks.org/> *-------------------------* Hocine CHERIFI University of Burgundy Franche-Comté Laboratoire* I*nterdisciplinaire *C*arnot de *B*ourgogne - ICB UMR 6303 CNRS Editor in Chief Plos Complex Systems <https://plos.org/complex-systems-research-journal/#:~:text=PLOS%20Complex%2….> Founding & Adisory Editor Applied Network Science <https://appliednetsci.springeropen.com/> Editorial Board member PLOS One <https://journals.plos.org/plosone/>, IEEE ACCESS <https://ieeeaccess.ieee.org/?http%3A%2F%2Fieeeaccess_ieee_org%2F>, Scientific Reports <https://www.nature.com/srep/>, Journal of Imaging <https://www.mdpi.com/journal/jimaging>, Quality and Quantity <https://www.springer.com/journal/11135/>, Computational Social Networks <https://computationalsocialnetworks.springeropen.com/>, Complex Systems <https://www.complex-systems.com/>

Jan. 17, 2024

ACDL 2024, 7th Advanced Course on Data Science & Machine Learning - From Deep Learning to Generative AI | June 10-14 | Riva del Sole Resort & SPA - Italy -> Early Registration: by February 23

by Giuseppe Nicosia

* Apologies for multiple copies. Please forward to anybody who might be interested, thanks * #ACDL2024, An Interdisciplinary Course: From Deep Learning to Generative AI ACDL 2024 is a full-immersion 5-day course in Tuscany on cutting-edge advances in AI, Deep Learning, LLMs, Data Sc. & Generative AI with lectures delivered by world-renowned experts. If you want to learn NLP, Generative AI Transformers, Diffusion Models, Large language models, Vision - Large-scale vision models, Vision and language, Beyond vision and language, Multimodal Foundation Models and much more then take part in ACDL 2024! ;-) Riva del Sole Resort & SPA - Tuscany, Italy, June 10-14 https://acdl2024.icas.events acdl(a)icas.cc EARLY REGISTRATION: by February 23 (AoE) https://acdl2024.icas.events/registration/ Oral Presentation Submission Deadline: by February 23 (AoE) LECTURERS: Each Lecturer will hold up to four lectures on one or more research topics. https://acdl2024.icas.events/lecturers/ * Joseph Sifakis, Verimag Laboratory, Grenoble, France *Turing Award* Lecture(s) "Testing systems intelligence - A systems engineering perspective" * Gabriel Barth-Maron, DeepMind, London, UK 4 Lessons on "Multimodal Foundation Models" * Sven Giesselbach, Fraunhofer Institute - IAIS, Germany 5 Lessons on "Introduction on Foundation Models" * Ramin Hasani, MIT, USA 4 Lessons on "Continuous Neural Networks / Liquid Neural Networks" * Nora Kassner, DeepMind, London, UK "Large Language Models: Life after Pre-training" "Large Language Models: Evaluation" "Large Language Models: Reasoning and Factuality" "Large Language Models: Retrieval augmentation and Tool-use" * Petros Koumoutsakos, Harvard University, USA “Machine Learning for Modeling and Control of Complex Systems” 1/2 “Machine Learning for Modeling and Control of Complex Systems” 2/2 “Solving forward and inverse problems with and without neural networks” “Bayesian Uncertainty Quantification” * Maria Liakata, The Alan Turing Institute, UK 4 Lessons on "Longitudinal Language Processing with User Generated Content" * Panos Pardalos, University of Florida, USA Lectures 1-2 TBA Topics: Data Science, Application to Neuroscience * Jakub M. Tomczak, Eindhoven University of Technology, The Netherlands 4 Lessons on “Deep Generative Modelling” * Rianne van den Berg, Microsoft Research Amsterdam, The Netherlands 3 Lessons on "Diffusion Models" * Pascal Van Hentenryck, Georgia Institute of Technology, USA 3 Lessons on "Fusing Machine Learning and Optimization for Engineering" * Max Welling, University of Amsterdam, The Netherlands 3 Lessons on "Generalized Belief Propagation Algorithms for Tensor Network Contractions" More Lecturers TBA TUTORIAL SPEAKERS: TBA Each Tutorial Speaker will hold more than four lessons on one or more research topics. PAST LECTURERS: https://acdl2024.icas.events/past-lecturers/ ACDL 2024 VENUE: Riva del Sole Resort & SPA Località Riva del Sole‚ Castiglione della Pescaia (Grosseto) CAP 58043‚ Tuscany‚ Italy p: +39-0564-928111 e: booking.events(a)rivadelsole.it w: https://www.rivadelsole.it/en/ https://acdl2024.icas.events/venue/ PAST EDITIONS: https://acdl2024.icas.events/past-editions/ REGISTRATION: https://acdl2024.icas.events/registration/ CERTIFICATE & 8 ECTS: PhD students, Postdocs, Industry Practitioners, Junior and Senior Academics, and will be typical profiles of the ACDL attendants. The Course will involve a total of 36-40 hours of lectures, according to the academic system the final achievement will be equivalent to 8 ECTS points for the PhD Students (and some strongly motivated master student) attending the Course. At the end of the course, a formal certificate will be delivered indicating the 8 ECTS points. TO PARTICIPATE IN ACDL 2024, all attendants must (1/2) register for the course (by February 23, 2024) and (2/2) book accommodation at the course venue, Riva del Sole Resort & SPA‚ (by April 23, 2024); all attendants must stay at the Riva del Sole Resort & SPA. Once accommodation has been booked at Riva del Sole Resort & SPA‚ the participant must send this information (including the Booking Number) to the ACDL organizing committee (acdl(a)icas.cc) ACDL is a residential course, so all lecturers and participants must reside in the same Hotel (Riva del Sole Resort & SPA). No exceptions are made. For privacy reasons, the Hotel cannot match people. If you have someone to share the apartment with, please send to the Hotel ( booking.events(a)rivadelsole.it) the name, surname and email address. Otherwise the solution is to book an apartment in single use. Anyone interested in participating in ACDL 2024 should register as soon as possible. See you in Riva del Sole in June! Giuseppe Nicosia & Panos Pardalos - ACDL 2024 Directors. ACDL 2024 Scientific & Organizing Committees. https://acdl2024.icas.events acdl(a)icas.cc 7th Advanced Course on Data Science & Machine Learning - ACDL 2024, 10-14 June, Riva del Sole Resort & SPA, Castiglione della Pescaia (Grosseto) – Tuscany, Italy. An Interdisciplinary Course: Big Data, Deep Learning & AI without Borders Early Registration: by February 23, 2024 (AoE) The Course is equivalent to 8 ECTS points for the PhD Students and the Master Students attending the Course. https://acdl2024.icas.events/ 10th International Conference on Learning, Optimization and Data – LOD 2024, 22–25 September, Riva del Sole Resort & SPA, Castiglione della Pescaia (Grosseto) Tuscany, Italy https://lod2024.icas.events/ lod(a)icas.cc Submission Deadline: March 23 4th Advanced Course and Symposium on Artificial Intelligence and Neuroscience – ACAIN 2024, 22–25 September Riva del Sole Resort & SPA, Castiglione della Pescaia (Grosseto) Tuscany, Italy https://acain2024.icas.events/ acain(a)icas.cc Symposium Submission Deadline: March 23 Early Registration Deadline for the Course: March 23 The Course is equivalent to 8 ECTS points for the PhD Students and the Master Students attending the Course. ICAS - The Interdisciplinary Centre of Advanced Studies https://icas.cc/

Jan. 17, 2024

PhD position: Effects of music on sleep EEG

by Martin Dresler

Hi, Within the Lullabyte.org consortium, one additional PhD position needs to filled, combining neuroscience, musicology and AI. The project will investigate the effects of generative music on sleep, as measured by wearable sleep EEG. The position will be integrated into the highly collaborative and interdisciplinary European Marie Curie Network Lullabyte.org, working on the intersection of musicology, sleep research, and AI. It will be mostly based at Endel.io in Berlin, with secondments to the Technical University Dresden and the Donders Institute in Nijmegen/NL. Requirements: training in both music and neuroscience, with a master degree or equivalent in one of the following (or related) fields: musicology, music technology, computer music, neuroscience, psychology. Application until 24-01-2024, starting date as soon as possible. Please send your applications including a brief (1-2 pages) motivation letter, CV, and contact information for two references to miriam.akkermann(a)tu-dresden.de Cheers, Martin Donders Sleep & Memory Lab, Radboud University Medical Center Kapittelweg 29, 6525 EN Nijmegen, Netherlands https://dreslerlab.org

Jan. 17, 2024

Effort and time trade-offs during foraging : PhDD position.

by Ahmed El Hady

Imagine that you need to catch a bus to return home after work. Will you decide to run as fast as possible to catch the first incoming bus? Or will you walk slowly to save your energy after an exhausting day, at the risk of missing this first bus and arriving late at home? Foraging tasks are emerging as crucial models for naturalistic decision making in rodents . On mechanistic level, those tasks give us the opportunity to understand how individual sensitivities to time and effort drive variability in the strategy of rodents facing an explore vs exploit dilemma. If those questions are of interest to you , there is an opening for a PhD position at the Centuri Turing Center for living systems in Marseille where the project is advised by David Robbe ( INMED, Marseille) , Eloy Christophe ( IRPHE, Marseille) and Ahmed El Hady ( Cluster for Advanced Study of Collective Behavior, Konstanz ). The project will combine theoretical and experimental approaches to understand how foraging strategies vary in terms of their sensitivities to time and effort during a variety of experimental conditions. We are looking for a candidate with a strong quantitative background, capable to developing numerical simulation/model (i.e. strong programing skills) and with a strong taste for animal behavior and cognition For more details and application procedure , please check the website : https://centuri-livingsystems.org/phd2024-19/ Please do not hesitate to get in touch in case you have any questions, Ahmed El hady Dr. Ahmed El Hady Group Leader Cluster for Advanced Study of Collective Behavior Max Planck Institute of Animal Behavior Universitätsstraße 10, 78464 Konstanz Room ZT 907 Postbox 687 Tel.: +49 7531 88-4742

Jan. 16, 2024

Postdoc position in Montreal (McGill)

by Becket Ebitz

Do you want to know what mice think about when they are on mushrooms? Are you interested in using computational models to compare how mice and humans think? The Behavioural Neurogenomics Lab (https://www.bagotlab.org) at McGill University is looking for a highly motivated computational neuroscience postdoc to lead a newly funded collaboration examining the neural bases of effects of stress and psychedelics on reward processing in mice and humans. This is a fully funded position intersecting computational modeling, neural circuit interrogation and robust behavioural paradigms. Based in Montreal, the candidate will work closely with the Noise Lab at Universite de Montreal (https://ebitzlab.com/) and the Mayo Lab ( https://profiles.ucalgary.ca/leah-mayo) at University of Calgary to develop new approaches for the comparative study of the neural processing of reward. The candidate must have a PhD in computational neuroscience, psychology, cognitive science or a quantitative discipline as well as fluency in Matlab or Python and experience in statistical data analysis and an interest in translational or comparative research. Ideally, the candidate would have some background in cognitive and/or reinforcement learning models, generalized linear models, hidden Markov models or probabilistic graphical models. Anticipated start date April 1, 2024 for an initial term of 1 year with the possibility of renewal. Come join an exciting, diverse team in a unique city with a supportive, and highly collaborative environment! To apply, please send a PDF of your CV to rosemary.bagot(a)mcgill.ca with a list of three potential references to contact. In your email, please describe 1) why you are interested in the position and 2) how your prior experience relates to this research opportunity.

Jan. 16, 2024

Overlapping versus non-overlapping community models

by Greg Rosenbaum

I’ve been reading a lot about network community structure, in the context of large-scale brain networks. One of my favorite papers on the subject was Betzel and Bassett (2016) <https://www.sciencedirect.com/science/article/pii/S1053811916306152>. However, most papers I’ve read, including Betzel and Bassett (2016), partition a network into disjoint communities. I’ve also encountered some publications that use overlapping communities instead, such as Najafi et al. (2016) <https://www.sciencedirect.com/science/article/abs/pii/S1053811916300957.>. This seems like an important choice. I think I agree with Najafi et al. (2016) that overlapping communities can reveal more about brain structure. For example, consider a case of two overlapping communities. They will share a common core – their intersection. Due to how communities are generated, the intersection would necessarily be highly coherent and form a community in its own right at a different resolution. In other words, we’d have two systems that share the same structure, reusing it for different purposes. This kind of reuse is a core principle in system architecture. It makes sense to see it in the brain. However, the two papers I’ve cited are pretty old at this point. Has there developed a consensus about what kind of community model is best suited for studying the brain?

Jan. 16, 2024

[Meetings] Deadline reminder: 2024 Nengo Summer School Call For Applications

by Michael Furlong

Dear colleagues, Please note that the deadline for application submission to the Nengo Summer School, February 1st, 2024, is approaching. [All details about this school can be found online at https://www.nengo.ai/summer-school] The Centre for Theoretical Neuroscience at the University of Waterloo is excited to announce our 9th annual Nengo summer school on large-scale brain modelling and neuromorphic computing. This two-week school will teach participants to use the Nengo simulation package to build state-of-the-art cognitive and neural models to run both in simulation and on neuromorphic hardware. Summer school participants will be given on-site access to neuromorphic hardware and will learn to run high-level applications using Nengo! More generally, Nengo provides users with a versatile and powerful environment for designing cognitive and neural systems and has been used to build what is currently the world's largest functional brain model, Spaun, which includes spiking deep learning, reinforcement learning, adaptive motor control, and cognitive control networks. For a look at the last in-person summer school, check out this short video: https://youtu.be/vRcN5-0wdQE We welcome applications from all interested graduate students, postdocs, professors, and industry professionals with a relevant background. ***Application Deadline: February 1, 2024*** Format: A combination of tutorials and project-based work. Participants are encouraged to bring their own ideas for projects, which may focus on testing hypotheses, modelling neural or cognitive data, implementing specific behavioural functions with neurons, expanding past models, or providing a proof-of-concept of various neural mechanisms. Hands-on tutorials, work on individual or group projects, and talks from invited faculty members will make up the bulk of day-to-day activities. A project demonstration event will be held on the last day of the school, with prizes for strong projects! Participants will have the opportunity to learn how to: * interface Nengo with various kinds of neuromorphic hardware (e.g. BrainDrop, SpiNNaker) * build perceptual, motor, and sophisticated cognitive models using spiking neurons * model anatomical, electrophysiological, cognitive, and behavioural data * use a variety of single cell models within a large-scale model  * integrate machine learning methods into biologically oriented models * interface Nengo with cameras and robotic systems * implement modern nonlinear control methods in neural models * and much more… Date and Location: June 2nd to June 14th, 2024 at the University of Waterloo, Ontario, Canada. Applications: Please visit http://www.nengo.ai/summer-school, where you can find more information regarding costs, travel, lodging, along with an application form listing required materials. If you have any questions about the school or the application process, please contact Michael Furlong (michael.furlong(a)uwaterloo.ca) The school is partly supported by ABR, Inc. We look forward to hearing from you!

Jan. 15, 2024

Postdoc in neural data analysis at the University of Edinburgh

by Angus Chadwick

Dear all, We invite applications for a Postdoctoral Research Associate to work on an exciting project developing novel methodologies for analysis of large-scale neural recordings over learning. This project is part of an international collaboration between the labs of Dr Angus Chadwick (University of Edinburgh), Prof Alex Cayco-Gajic (École Normalé Supérieure) and Prof Matthew Perich (Université de Montréal). The successful candidate will build upon a method recently developed by the host lab (Dr Chadwick) together with collaborator Prof Cayco-Gajic (Pellegrino, Cayco-Gajic* and Chadwick*, NeurIPS 2023). The project involves development of novel data-analytic methodologies and application to cutting-edge neural datasets collected during motor and perceptual learning tasks. In particular, the candidate will build upon the recent line of work by the supervisory team: https://arxiv.org/abs/2308.11567 https://www.sciencedirect.com/science/article/pii/S0896627322009059 https://www.sciencedirect.com/science/article/abs/pii/S0959438823000843 The role is based primarily at the Institute for Adaptive and Neural Computation at the University of Edinburgh. Funding is available to undertake extended research visits to the labs of international collaborators at École Normale Supérieure and Université de Montréal. This is a full-time position, with an initial appointment of 18 months, and available to start immediately. There full job ad can be viewed here: https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1… To apply, please email Dr Angus Chadwick at angus dot chadwick at ed.ac.uk with a CV and contact details for two references. Informal inquiries are also encouraged. Applications will be considered until the position is filled, with priority for those submitted before 9th February 2024. Best wishes, Angus Chadwick The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

Jan. 15, 2024

Call for Cosyne workshop contributed short talks

by Cristina Savin

Hello all We invite the community to submit short abstracts on relevant recent results documenting limitations of current tools, unexpected negative results and/or potential new ideas to overcome them. We will select a small number of contributed talks from these submissions as part of our Cosyne “I can't believe it's not better!” workshop. Submissions from junior researchers are particularly welcome. Deadline: January 31st Details about the workshop and the abstract submission process can be found on our workshop webpage: https://cosyne2024-icbinb.github.io/ We look forward to seeing many of you in Cascais! Cristina Savin and Alex Williams

Jan. 15, 2024