- Comp-neuro - lists.cnsorg.org

Python Package: Echo State Networks

by Fabrizio Damicelli

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 realms of "Biologically-inspired Neural Networks", "Shallow Learning" and "Recurrent Neural Networks" in general. "echoes": Machine Learning with Echo State Networks, a scikit-learn compatible package. Code Repository: https://github.com/fabridamicelli/echoes A few interesting features: - scikit-learn compatible, i.e. scikit-learn tools such as GridSearchCV should work out-of-the-box - It is light-weight and fast (`numba` accelerated), i.e. many experiments can be simply run on a laptop - Flexible and customizable, e.g. use arbitrary connectivity, add custom activations, visualize neurons activity, etc. - Installation and getting started is easy: `pip install echoes` - Example notebooks: https://github.com/fabridamicelli/echoes/tree/master/examples/notebooks - Documentation: https://fabridamicelli.github.io/echoes/ As of today, a few people already trust it and the package registers >18K total downloads, ~500/month (pypi.org<http://pypi.org/>) and has been used already in a few research projects: - Hadaeghi et. al. (2021) Spatio-temporal feature learning with reservoir computing for T-cell segmentation in live-cell Ca2+ fluorescence microscopy: www.nature.com/articles/s41598-021-87607-y#Sec4<http://www.nature.com/articles/s41598-021-87607-y#Sec4> - Damicelli et.al<http://et.al/>. (2021) Brain Connectivity meets Reservoir Computing: www.biorxiv.org/content/10.1101/2021.01.22.427750v1.abstract<http://www.biorxiv.org/content/10.1101/2021.01.22.427750v1.abstract> - Fakhar et. al. (2022) Causal Influences Decouple From Their Underlying Network Structure In Echo State Networks: arxiv.org/abs/2205.11947<http://arxiv.org/abs/2205.11947> Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/echoes/issues) All the best, Fabrizio

Sept. 9, 2022

Postdoc / Junior Scientist / Research fellow positions in Complex Networks, Prague, Czech Republic

by Magda Pokorna

The following positions are open in the department of Complex Systems at the Institute of Computer Science, Czech Academy of Sciences, Prague, Czech Republic. Applications for all positions will be reviewed on a rolling basis*with a first cut-off point on *30. **9**. 2022.** 1. *Postdoctoral / Junior Scientist position in Multimodal Neuroimaging Machine Learning, Prague, Czech Republic* A Postdoc or Junior Scientistposition is available to join the _Complex Networks and Brain Dynamics group <http://cobra.cs.cas.cz/>_for the project: /*“Predicting functional outcome in schizophrenia from multimodal neuroimaging and clinical data“*/funded by the Czech Health Research Council.The project involves the development of tools to predict the functional outcome of schizophrenia from multimodal neuroimaging, clinical and cognitive measurements taken early after disease onset. To overcome limitations due to high dimensionality of data, we combine robust machine-learning tools, data-driven feature selection and theory-based brain network priors. The project is carried out in collaboration with the National Institute of Mental Health, using its unique large rich imaging, cognitive and biochemical data of early stage schizophrenia patients. *For more information, conditions and application* see https://www.cs.cas.cz/job-offer/postdoctoral-junior-scientist-position-Hlin…. 2. *Researc**h Fellow / Postdoc positions in Complex Networks and Brain Dynamics, Prague, Czech Republic* We are looking for new team members to join the _Complex Networks and Brain Dynamics group <http://cobra.cs.cas.cz/>_to work on its interdisciplinary projects. The group is part of the Department of Complex Systems, Institute of Computer Science of the Czech Academy of Sciences - based in Prague, Czech Republic, _https://www.cs.cas.cz/ <https://www.cs.cas.cz/>_.We focus on the development and application of methods of analysis and modelling of real-world complex networked systems, with particular interest in the structure and dynamics of human brain function. Our main research areas are neuroimaging data analysis (fMRI & EEG, iEEG, anatomical and diffusion MRI), brain dynamics modelling, causality and information flow inference, nonlinearity and nonstationarity, graph theory, machine learning and multivariate statistics; with applications in neuroscience, climate research, economics and general communication networks. *More information about the group at *_*http://cobra.cs.cas.cz/* <http://cobra.cs.cas.cz/>_*. **For more information, conditions and application* see https://www.cs.cas.cz/job-offer/research-fellow-postdoc-position-Hlinka1-20…. *Do not hesitate to contact the **group leader**/ Principal Investigator for informal inquiries: Ing. Mgr. Jaroslav Hlinka, Ph.D. *_*hlinka[at]cs.cas.cz* <mailto:hlinka@cs.cas.cz>_*, *_*http://www.cs.cas.cz/hlinka/*_

Sept. 9, 2022

Postdoctoral Position at UConn in Systems and Computational Neuroscience

by Ian Stevenson

The Physiological Acoustics Lab (http://escabilab.uconn.edu) at the University of Connecticut seeks applicants for a postdoctoral position in systems and computational neuroscience. We are seeking highly motivated and creative applicants that can lead a project on perception and neural coding of speech and vocalizations in the presence of competing natural environmental noises (e.g., restaurant noise, busy street, construction noise etc.). The broad project goal is to study the neural basis for listening in noisy environments and to devise a general computational theory that accounts for perception and physiology. The project will use a variety of experimental approaches including human perception, awake animal electrophysiology, large scale neural recording, and computational modeling. UConn has a vibrant neuroscience community and there are opportunities for collaboration between departments and institutes. The primary appointment is in Biomedical Engineering, but the work will be conducted in collaboration with the Behavioral Neuroscience division in the Psychology department (Statistical Neuroscience Lab, http://stevenson.lab.uconn.edu; Sensory Perception and Neuroscience Lab, http://read.lab.uconn.edu) as well as Electrical and Computer Engineering and Biomedical Engineering. Qualifications: A PhD in Neuroscience, Biomedical Engineering, Electrical Engineering, Computational Neuroscience, or a related field is required. The ideal candidate will have an interdisciplinary research background in computational and systems neuroscience with prior research experience in awake animal neurophysiology. A strong analytic background in neural data analysis is desirable, particularly modeling neural systems and analyzing datasets from large-scale multi-channel neural recordings. Experience with acoustic signal processing, sound recognition, and machine learning is also desirable. Appointment: The position is funded through an R01 grant and salaries follow NIH post-doctoral scale and are based on experience. Applicants should email escabi(a)engr.uconn.edu a single PDF file containing: 1) resume including past research experience and published work 2) one page statement of prior research experience 3) one page statement of future research interests and objectives 4) names of at least two individuals who can provide reference letters Ian Stevenson Associate Professor University of Connecticut Department of Psychological Sciences stevenson.lab.uconn.edu

Sept. 8, 2022

Job: ML Engineer to extend ReservoirPy library for health data (Reservoir Computing)

by Xavier Hinaut

We are looking for an engineer for at least one year to work with the open source ReservoirPy library on health data. You will be working in Bordeaux, France in the Mnemosyne computational neuroscience group https://team.inria.fr/mnemosyne <https://team.inria.fr/mnemosyne> in collaboration with other Bordeaux teams involved in biostatistics and machine learning. More info and online application: https://jobs.inria.fr/public/classic/en/offres <https://jobs.inria.fr/public/classic/en/offres> * ReservoirPy ReservoirPy [1, 2, 3] is a simple user-friendly library based on Python scientific modules. It provides a flexible interface to implement efficient Reservoir Computing (RC) [5] architectures with a particular focus on Echo State Networks (ESN) [4]. Advanced features of ReservoirPy allow to improve computation time efficiency on a simple laptop compared to basic Python implementation. Some of its features are: offline and online training, parallel implementation, sparse matrix computation, fast spectral initialization, advanced learning rules (e.g. Intrinsic Plasticity) etc. It also makes possible to easily create complex architectures with multiple reservoirs (e.g. deep reservoirs), readouts, and complex feedback loops. Moreover, graphical tools are included to easily explore hyperparameters with the help of the hyperopt library. It includes several tutorials exploring exotic architectures and examples of scientific papers reproduction. Github: https://github.com/reservoirpy/reservoirpy <https://github.com/reservoirpy/reservoirpy> Documentation: https://reservoirpy.readthedocs.io <https://reservoirpy.readthedocs.io/> Related projects: https://github.com/reservoirpy <https://github.com/reservoirpy> Twitter: https://twitter.com/reservoirpy <https://twitter.com/reservoirpy> * Deadline: 20th of September 2022 For informal questions send an email to xavier dot hinaut at inria dot fr. Online application: https://jobs.inria.fr/public/classic/en/offres <https://jobs.inria.fr/public/classic/en/offres> * Contract Engineer contract of 1 year, with possibility to extend the contract to more years or to continue in the team as PhD student. * Benefits package - Subsidized meals - Partial reimbursement of public transport costs - Possibility of partial teleworking and flexible organization of working hours - Professional equipment available (videoconferencing, loan of computer equipment, etc.) - Social, cultural and sports events and activities - Access to vocational training - Social security coverage [1] Trouvain N, Pedrelli L, Dinh TT, Hinaut X (2020). Reservoirpy: an efficient and user-friendly library to design echo state networks. International Conference on Artificial Neural Networks, 494-505. https://hal.inria.fr/hal-02595026v2/document <https://hal.inria.fr/hal-02595026v2/document> [2] Trouvain, N., Rougier, N. P., & Hinaut, X. (2022). Create Efficient and Complex Reservoir Computing Architectures with ReservoirPy. In FROM ANIMALS TO ANIMATS 16: The 16th International Conference on the Simulation of Adaptive Behavior (SAB2022). https://hal.inria.fr/hal-03761440/document <https://hal.inria.fr/hal-03761440/document> [3] Nathan Trouvain, Xavier Hinaut. reservoirpy: A Simple and Flexible Reservoir Computing Tool in Python. 2022. HAL preprint hal-03699931. https://hal.inria.fr/hal-03699931/document <https://hal.inria.fr/hal-03699931/document> [4] Jaeger, H., & Haas, H. (2004). Harnessing nonlinearity: Predicting chaotic systems and saving energy in wireless communication. science, 304(5667), 78-80. [5] Lukoševičius, M., & Jaeger, H. (2009). Reservoir computing approaches to recurrent neural network training. Computer Science Review, 3(3), 127-149. Xavier Hinaut Inria Research Scientist www.xavierhinaut.com -- +33 5 33 51 48 01 Mnemosyne team, Inria, Bordeaux, France -- https://team.inria.fr/mnemosyne & LaBRI, Bordeaux University -- https://www4.labri.fr/en/formal-methods-and-models & IMN (Neurodegeneratives Diseases Institute) -- http://www.imn-bordeaux.org/en --- Our Reservoir Computing library: https://github.com/reservoirpy/reservoirpy

Sept. 6, 2022

Multiple Vacancies at the University for Melbourne

by Uwe Aickelin

Hi, Hope this message finds you well. Please consider sharing this with any interested researchers. The University of Melbourne’s School of Computing and Information Systems is recruiting for 4x open positions. Application deadlines: Sep 26, 2022 (Australian Eastern Daylight Time) Lecturer/Senior Lecturer in machine learning: https://go.unimelb.edu.au/282e Lecturer/Senior Lecturer in theory of computing: https://go.unimelb.edu.au/f82e Lecturer/Senior Lecturer in information systems: https://go.unimelb.edu.au/482e Senior Lecturer/Associate Professor in fairness: https://go.unimelb.edu.au/h82e (These are continuing positions equiv. US tenure track research & teaching / faculty positions at a range of levels.) We’re excited to invite applications from individuals passionate about research, training, teaching, and engagement, to join us at Australia’s premier university, situated in one of the world’s most liveable cities. Best, Uwe Aickelin -- Professor Uwe Aickelin | Head of School of Computing and Information Systems Faculty of Engineering and Information Technology Level 3, Melbourne Connect – 700 Swanston Street The University of Melbourne, Victoria 3010 Australia T: +61 3 8344 3635 E: uwe.aickelin(a)unimelb.edu.au<mailto:uwe.aickelin@unimelb.edu.au> http://aickelin.com/ | http://linkedin.com/in/aickelin

Sept. 6, 2022

Neo community review extended to Sep 29 - call for comments and feedback

by Malin Sandström

Dear all, INCF is asking for your help to review the Neo object model <https://www.incf.org/sbp/neo>for electrophysiology data, to assess its value as a community standard. Participating is simple; read the INCF SBP committee review report <https://f1000research.com/documents/11-658> on F1000 and leave your feedback in the comments! You can comment to express your support, to point out possibilities for improvement - or both. We are especially interested in hearing from Neo users and from tool developers who have implemented support for Neo or use Neo as part of their workflow. Please give us your feedback in a comment as soon as possible, but latest September 29: f1000research.com/documents/11-658 More information: Neo <https://www.incf.org/sbp/neo> is an object model for handling electrophysiology data in multiple formats. It is suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. Neo has been implemented as a Python package for working with electrophysiology data, together with support for reading a wide range of neurophysiology file formats (including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, Igor Pro), and support for writing to a subset of these formats plus non-proprietary formats including Kwik and HDF5. Read more about Neo: Project page <https://neuralensemble.org/neo/> Documentation <https://neo.readthedocs.io/en/stable/> Github <https://github.com/NeuralEnsemble/python-neo> Paper <https://www.frontiersin.org/articles/10.3389/fninf.2014.00010/full> -- Malin Sandström, PhD Community Engagement Officer malin.sandstrom(a)incf.org ORCID: 0000-0002-8464-2494 International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org

Sept. 6, 2022

3rd SMILES workshop in less than one week! (12 sept.)

by Xavier Hinaut

The 3rd SMILES (Sensorimotor Interaction, Language and Embodiment of Symbols) Workshop will take place both on site and virtually at ICDL 2022 conference. **9am-6pm UTC+1 (London time) on September 12, 2022** * Invited talks: - Joanna Raczaszek-Leonardi (University of Warsaw, Poland) - Joel Z Leibo (DeepMind, London, UK) - Lorijn Zaadnoordijk (Trinity College Dublin, Ireland) - Martin Butz & Christian Gumbsch (University of Tübingen, Germany) - Ida Momennejad (Microsoft Research NYC, USA) * Important info: - Registration: https://forms.gle/No8xFFkmfKXXdNMm7 (if you come onsite, you also need to register here: https://icdl2022.qmul.ac.uk/?page_id=50 ) - Workshop website: https://sites.google.com/view/smiles-workshop/ - Onsite venue: Graduate Center, Queen Mary University of London, UK. More info here: https://icdl2022.qmul.ac.uk/?page_id=103 - Venue online: via Zoom and Discord group. - Join our Discord: https://discord.gg/sBZbdSWRvJ (expires after 100 hits) - Follow us on Twitter: https://twitter.com/SMILESconf * Workshop Short Description On the one hand, models of sensorimotor interaction are embodied in the environment and in the interaction with other agents. On the other hand, recent Deep Learning development of Natural Language Processing (NLP) models allow to capture increasing language complexity (e.g. compositional representations, word embedding, long term dependencies). However, those NLP models are disembodied in the sense that they are learned from static datasets of text or speech. How can we bridge the gap from low-level sensorimotor interaction to high-level compositional symbolic communication? The SMILES workshop will address this issue through an interdisciplinary approach involving researchers from (but not limited to): - Sensori-motor learning, - Symbol grounding and symbol emergence, - Emergent communication in multi-agent systems, - Chunking of perceptuo-motor gestures (gestures in a general sense: motor, vocal, ...), - Compositional representations for communication and action sequence, - Hierarchical representations of temporal information, - Language processing and language acquisition in brains and machines, - Models of animal communication, - Understanding composition and temporal processing in neural network models, and - Enaction, active perception, perception-action loop. * More info - contact: smiles.conf(a)gmail.com - organizers: Xavier Hinaut, Clément Moulin-Frier, Silvia Pagliarini, Joni Zhong, Michael Spranger, Tadahiro Taniguchi, Anne Warlaumont. - ICDL conference website: https://icdl2022.qmul.ac.uk/ Xavier Hinaut on behalf of the SMILES workshop organisers: - Clément Moulin-Frier, Inria and Ensta ParisTech, Bordeaux, France - Anne Warlaumont, UCLA, Los Angeles, USA - Silvia Pagliarini, UCLA, Los Angeles, USA - Michael Spranger, Sony AI and Sony CSL, Tokyo, Japan - Tadahiro Taniguchi, Ritsumeikan University, Kyoto, Japan - Junpei Zhong, Hong Kong Polytechnic University, Hong Kong, China Xavier Hinaut Inria Research Scientist www.xavierhinaut.com <http://www.xavierhinaut.com/> -- +33 5 33 51 48 01 Mnemosyne team, Inria, Bordeaux, France -- https://team.inria.fr/mnemosyne <https://team.inria.fr/mnemosyne> & LaBRI, Bordeaux University -- https://www4.labri.fr/en/formal-methods-and-models <https://www4.labri.fr/en/formal-methods-and-models> & IMN (Neurodegeneratives Diseases Institute) -- http://www.imn-bordeaux.org/en <http://www.imn-bordeaux.org/en> --- Our new release of Reservoir Computing library: https://github.com/reservoirpy/reservoirpy <https://github.com/reservoirpy/reservoirpy>

Sept. 5, 2022

2 year independent Postdoc position in human centered AI (German required)

by Laurenz Wiskott

The Institute for Neural Computation of the Faculty of Computer Science is looking for a Postdoc (m,f,x) for 2 years, full-time, TVL E13 The Institute for Neural Computation is part of the Faculty of Computer Science at the Ruhr-University Bochum, see https://www.ini.rub.de/. It focuses on the dynamics and learning of perception and behavior on a functional level but is otherwise very diverse, ranging from neurophysiology and psychophysics over computational neuroscience to machine learning and technical applications. There is an open position for a postdoc in the group of Prof. Dr. Laurenz Wiskott to be filled October 1st. The project is part of the competence center HUMAINE for human-centered artificial intelligence, see https://humaine.info/, and will be developed in close collaboration with colleagues at RUB and application partners in industry, among others. We offer: * An interesting interdisciplinary environment in the field of Artificial Intelligence / Machine Learning. * Opportunity to develop an independent research profile and your own research group. * Opportunity to pursue further scientific qualification. * Diverse and interesting contacts at the university, in transfer, and in industry. * A lot of room for own ideas and initiatives. Your opportunities: * Acquiring and maintaining industry contacts. * Scientific advice for companies to help them introduce AI in work processes. * Advising corresponding PhD and student projects. * Coordination of events and teaching of advanced training courses about human-centered AI for developers and decision makers in industry Your profile: * Very good PhD in mathematics, computer science, engineering, or a related field * Solid knowledge in Artificial Intelligence / Machine Learning. * Good programming and mathematical skills * Good command of German. * Good organizational and communicative abilities. * Advantageous: + Experience in industry cooperations and interdisciplinary projects. + Programming skills in Python. Our offerings: * Challenging and varied tasks with a high degree of personal responsibility * Support from and cooperation with competent colleagues * A dynamic environment * Fair and flexible working hours * Support in reconciling family and work/academics (including childcare placement, holiday offers, mobile children's room) Additional information: The load of teaching will be calculated according to § 3 of Lehrverpflichtungsverordnung (state of North Rhine-Westphalia). Contact details for your application: Prof. Dr. Laurenz Wiskott, Phone: +49 234 32 27997 Travel expenses for interviews cannot be refunded. For information on the collection of personal data in the application process see: https://www.ruhr-uni-bochum.de/en/information-collection-personal-data-appl…. We are looking forward to receiving your application with the specification ANR: 800 until 30.09.2022, send by e-mail to the following address: laurenz.wiskott(a)rub.de extent: full-time duration: temporary beginning: as soon as possible application deadline: 30.09.2022 The Ruhr-Universität Bochum is one of Germany’s leading research universities, addressing the whole range of academic disciplines. A highly dynamic setting enables researchers and students to work across the traditional boundaries of academic subjects and faculties. To create knowledge networks within and beyond the university is RUB’s declared aim. The Ruhr-Universität Bochum stands for diversity and equal opportunities. For this reason, we favour a working environment composed of heterogeneous teams, and seek to promote the careers of individuals who are underrepresented in our respective professional areas. The Ruhr-Universität Bochum expressly requests job applications from women. In areas in which they are underrepresented they will be given preference in the case of equivalent qualifications with male candidates. Applications from individuals with disabilities are most welcome.

Sept. 5, 2022

WWNeuRise online seminars Sept-Oct 2022

by William Podlaski

WorldWideNeuRise will host several online talks throughout Sept-Oct 2022 on various topics in systems neuroscience from the following early career researchers. The first session will be on Wednesday, 7 September, 5pm CET, featuring: Pantelis Vafeidis (Rangel Lab, Caltech) - "Learning static and dynamic mappings with local self-supervised plasticity" Anna Kutschireiter (Spiden AG) - "The secret Bayesian life of ring attractors" Followed by two more sessions (talk titles TBA): Wednesday, 21 September, 5pm CET Kevin Berlemont (Wang Lab, NYU) Gabriel Stine (Shadlen Lab, Columbia University) Wednesday, 12 October, 5pm CET William de Cothi (Barry Lab, UCL) Brianna Vandrey (Nolan Lab, University of Edinburgh) For more information, please visit our website (https://neurise.github.io/) find us on WorldWideNeuro (https://www.world-wide.org/Neuro/WWNeuRise/) or follow us on Twitter (https://twitter.com/WWNeuRise) We are always searching for PhD students and postdocs to give talks in our upcoming seminars on any topic in systems neuroscience. On our website ( https://neurise.github.io/) you can find an application form to directly apply, as well as a recommendation form, where you can suggest individuals from your lab, institute, or otherwise who you think might have an interesting story to tell! We are looking forward to seeing you at our upcoming seminars! The organising committee, Alon Baram (Behrens Lab, University of Oxford) Wesley Clawson (Levin Lab, Tufts University) Lucie Descamps (Kentros Lab, Norwegian University of Science and Technology) Gily Ginosar (Ulanovsky Lab, Weizmann Institute) Loreen Hertäg (Clopath Lab, Imperial College London) Joram Keijser (Sprekeler Lab, TU Berlin) Bill Podlaski (Machens Lab, Champalimaud Research)

Sept. 3, 2022

Academia and the World Beyond: Navigating Life after a PhD

by Christopher Madan

Hi everyone, Many PhD students and postdocs are unsure of what their options are, apart from academia. Even within academia, the responsibilities beyond research often haven't been sufficiently discussed. A book I have been working on for a few years has just come out, where I've interviewed 22 individuals about their post-PhD careers, both in academic and non-academic positions. All of them discuss their career journey, day-to-day life in their current position, and advice for current PhD students. You can find out more about the book on my website or directly from the publisher. https://engra.me/books/academiabeyond https://link.springer.com/book/10.1007/978-3-030-82606-2 Best, ~ Chris --- Christopher R Madan, PhD [he/him] | http://www.cmadan.com<http://www.cmadan.com/>, http://engra.me<http://engra.me/> Assistant Professor @ University of Nottingham Author of "An Introduction to MATLAB for Behavioral Researchers" | http://engra.me/books/matlab/ and "Academia and the World Beyond: Navigating Life after a PhD" | http://engra.me/books/academiabeyond 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.

Sept. 1, 2022