From ASIM.ROY at asu.edu Mon Sep 1 09:39:25 2008 From: ASIM.ROY at asu.edu (Asim Roy) Date: Mon Sep 1 14:40:34 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments In-Reply-To: Message-ID: Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" Jim Bower's response: And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Jim, would love to get some references for your statement:- "development probably recapitulating evolutionary history." This really is the kind of process in the brain that I am looking for. Just a few references would suffice. By the way, learning takes place during development too. Just ask anyone in cognitive science. Development is not disassociated from learning. And ANN never implied learning begins after development. That's a misconception. On the "blank slate" idea in ANN, just look at the phenomenon of adult neurogenesis. Our adult brains generate new cells in the thousands on a daily basis and they are part of the "blank slate" because they don't come with ready-made connections or anything. The process that you refer to as "development probably recapitulating evolutionary history" is called "learning" in ANN. It's that process that constructs networks out of these new cells and makes them operational. Asim -----Original Message----- From: comp-neuro-bounces@neuroinf.org [mailto:comp-neuro-bounces@neuroinf.org]On Behalf Of james bower Sent: Wednesday, August 27, 2008 9:05 AM To: CompNeuro List Subject: [Comp-neuro] Discussion - Kuhn - and brief comments A few brief comments -- given that school has started, and I now have to prepare to "influence" the latest next generation. First a BIG POINT: Klaus Stiefel: pre-paradigmatic " What he meant by that is a disagreement about the basic explainanda" No, Kuhn was focused on process to quote: "the early developmental stages of most sciences (are) characterized by continual competition between a number of distinct views of nature, each partially derived from, and all roughly compatible with, the dictates of scientific observation and method, (In pre-paradigmatic science) what differentiates these various schools (is) not one or another failure of method - they are all "scientific" - but what we shall come to call their incommensurable ways of seeing the world and practicing science within it" (pg 4 The Structure of Scientific Revolution.) If this discussion over the last two months doesn't make it clear that, as a field, we currently have "incommensurate ways of seeing the world and practicing science within it" I don't know what does. Kuhn goes on to say: "Men (sic) whose research is based on shared paradigms are committed to the same rules and standards for scientific practice." Again, this discussion makes it pretty clear to me that we have not yet reached that point. In fact, (and I would say reflecting this fact) the kind of discussion we have been having here seldom ever happens as we are content (and being pre-paradigmatic can get away with) agreeing to not discuss what we don't agree on, another characteristic of pre-paradigmatic science -- and the reason I don't mind starting these discussions. Bryan Bishop: "There's a few too many layers of folk psychology here," I agree, and have characterized all of biology as fundamentally folkloric in nature -- based on story telling, with few real definitions of anything. Something comp bio (neuro) will, I hope, eventually fix. And on to the approaches we don't agree on: Bryan Bishop: "I bet it becomes clear that trying to do "natural language processing" from statistical inferences doesn't get us as much hard science as the brain could provide." Of course, I agree -- and also agree that this field continues to be distorted by what is essential snake oil we sell to the Department of Defense about how studying the brain will help win wars. This rather self serving commitment to "neuro-morphic engineering" as it is now called, has been distorting our science for a while. In the last 8 years even more dramatically. Mario Negrello: "I'd say instead that some approaches gather more acolytes, and then overflow others in sheer voluminous quantity," Unfortunately, as just noted, very often related to who you are selling the science to (funders) and also, unfortunately, how 'easy' the methods are and therefore how many can jump on the bandwagon without much preparation (or even knowledge of the brain in this case) -- 20 years studying the realistic model of the Purkinje cell and counting. Bard Ermentrout: " I suspect that it would be too hard to adjust parameters for realistic models " Is hard bad? Or is the brain, in fact, hard? Igor Carron: "The groundwork of theory as you put it has, in nuclear technology, always been a way to acquire and use experimental findings." And this, in fact, is the value of theory -- not to capture 'truth' as many in comp neuro seem be believe, but to organize experimental studies -- the more the theory is removed from the actual structure of the brain - the more it exists by itself, disconnected from the ability to improve, or more importantly to refute it. Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Asim Roy: "Is there a way in computational neuroscience to verify any of these theories of learning? " Wrong question. Axel Hutt: " can (neuro)biology really treat a population of some thousand elements ? " We will need to figure out how - numerous groups are working on it. Anibalmastobiza: "cerebellum, usually considered as a center for motor processing and coordination just as it was for the basal ganglia that now we know that is also involve in cognition" While I appreciate the support, I have another question for cognitive neuroscientists, how come anything that lights up in a brain scan becomes a "cognitive center" seems weird to me. Jim ================================== Dr. James M. Bower Ph.D. Professor of Computational Neuroscience Research Imaging Center University of Texas Health Science Center - - San Antonio 8403 Floyd Curl Drive San Antonio Texas 78284-6240 Main Number: 210- 567-8100 Fax: 210 567-8152 Mobile: 210-382-0553 CONFIDENTIAL NOTICE: The contents of this email and any attachments to it may be privileged or contain privileged and confidential information. This information is only for the viewing or use of the intended recipient. If you have received this e-mail in error or are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of, or the taking of any action in reliance upon, any of the information contained in this e-mail, or any of the attachments to this e-mail, is strictly prohibited and that this e-mail and all of the attachments to this e-mail, if any, must be immediately returned to the sender or destroyed and, in either case, this e-mail and all attachments to this e-mail must be immediately deleted from your computer without making any copies hereof and any and all hard copies made must be destroyed. If you have received this e-mail in error, please notify the sender by e-mail immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080901/3f9f48ed/attachment.html From bernabe at imse.cnm.es Tue Sep 2 08:59:21 2008 From: bernabe at imse.cnm.es (Bernabe Linares-Barranco) Date: Tue Sep 2 11:27:55 2008 Subject: [Comp-neuro] pre/post-doc positions for EU project on neuro/nanotechnologies Message-ID: <48BCE449.1090903@imse.cnm.es> Dear comp-neuro list members, This is an announcement for: Pre and/or post-doctoral research fellowships at the Sevilla Microelectronics Institute, to work on an interdisciplinary EU project combining nanotechnologies and neural networks. Candidates will be working on developing device models for adaptive nano-devices and use them to propose and simulate large scale adaptive neural systems for specific applications. Interested candidates, please contact Bernabe Linares-Barranco (bernabe 'at' imse 'dot' cnm 'dot' es). -- ------------------------------------------------------------------------- Bernabe Linares-Barranco, PhD Full Professor (Profesor de Investigacion) CSIC Instituto Microelectronica Sevilla (IMSE) Phone: 34-95-505-6670/66 National Microelectronics Center, CNM-CSIC Fax: 34-95-505-6686 Ed. CICA, Av. Reina Mercedes s/n E-mail: Bernabe.Linares(AT)imse.cnm.es 41012 Sevilla, SPAIN URL: http://www.imse.cnm.es/~bernabe ------------------------------------------------------------------------- From bower at uthscsa.edu Tue Sep 2 05:03:30 2008 From: bower at uthscsa.edu (Jim Bower) Date: Tue Sep 2 11:31:01 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments In-Reply-To: <48B7FB0F.3030509@salk.edu> References: <48B7FB0F.3030509@salk.edu> Message-ID: First, humans knew for at least several thousand years before Newton the question: why or how do the planets wander (redundant in fact) and they also knew what data to collect (their position in the night sky). By the time of Newton, many astronomers also used telescopes. What they lacked was a formal agreed upon structural foundation (Newtonian mechanics), around which the field could be organized, and through which it could pose explicitly formulated questions. Indeed, the software projects you mention are a step in that direction (GENESIS was intended explicitly to be so). But only a small step. With respect to measurements -- I have already pointed out that the standard form in which experimentalists report their results (PST Histograms) are likely to be completely inappropriate for brains. As far as textbooks, specialized journals, learned societies, etc, are concerned -- just because we officially have them, doesn't mean that they are what they say they are -- or they do what Kuhn was talking about. I have suggested previously, that these are more modeled after physics - than appropriate for the study of the brain or biology as a whole. I have already made the point that there is a direct link between the development of the scientific journal and the nature of explanation and communication in physics. in biology we are still largely story tellers -- and have simply adapted the form of scientific publication invented by Newton and his colleagues to our story telling. Ironically enough, it was physics and not biology, that has lead the way in the use of the Internet for publishing. Further, the internet has allowed physicists to explore pre-review publication of scientific papers. Why? Because along with the story telling nature of biological publications comes the largely political process of peer review - which in recent years has gotten way way out of hand. I can not tell you how much heat we took in the early days of the computational neuroscience meetings, when we actually were willing to publish short papers that had not been thoroughly peer reviewed -- Why does a publication in biology require the approval of the dons? but not in physics? Because we don't yet have quantitatively defined paradigms, we have qualitatively (at best) supported opinions, whose propagation (and protection) is dependent on 'who says so'. How else is it possible for the cerebellum to remain a motor control device for 150 years? With respect to unmeasurable theories - it seems to me that string theory is doing pretty well -- why is that? Finally, and sad to say, this list serve is made up of those interested in the brain who are most likely to quantify their data and theories -- one should not be deluded into thinking that "most neuroscientists" get anywhere close. "Most neuroscientists" still regard modeling as a largely empty exercise of little relevance to them (at least judging by what they do and don't reference in their papers). I am afraid to say it is sometimes hard for me to disagree with them. The huge disconnect between experiment and modeling in neuroscience is explicit testament to our lack of real paradigmatic structure -- I do think that this is slowly changing, but tell me how many graduate schools of neuroscience have a required course in theory and modeling -- probably can count them on one hand. And how much modeling shows up in our textbooks? This disconnect is another reason why I think realistic modeling is a crucial technology for moving forward. Jim Bower On Aug 29, 2008, at 8:35 AM, Klaus M. Stiefel wrote: > Hi All, Dear Dr. Bower, > > "incommensurate ways of seeing the world and practicing science > within it" is basically what I meant by "basic explainanda". Modern > neuroscience is practiced so commensurate (= having a common > measure) that most neuroscientists buy their measuring equipment > (amplifiers ect.) from the same handful of international companies > and use the same set of equations and software (NEURON, GENESIS, > XPP). Especially in paradigmatic sciences, there will be a lack of > (deemed unnecessary and solved) discussion. > > Kuhn argues (SSR, chapter 2) that a science, once it is > paradigmatic, has textbooks, specialized journals, and professional > societies, like biology and neuroscience have many. A healthy > scientific disagreement like the one in this discussion is not > necessarily a sign of a pre-paradigmatic science. It might lead the > way to a paradigm change, though. > > One of the few people who I believe are outside of the main paradigm > of neuroscience is Roger Penrose, and his ideas about quantum > coherence in neurons. He has (rightfully, I believe) few followers, > and you won't see any devices to measure the quantum effects he is > talking about at the vendors' booths at SFN. > > Best, > > Klaus Stiefel >> >> Klaus Stiefel: pre-paradigmatic " What he meant by that is a >> disagreement about the basic explainanda" >> >> No, Kuhn was focused on process to quote: "the early developmental >> stages of most sciences (are) characterized by continual >> competition between a number of distinct views of nature, each >> partially derived from, and all roughly compatible with, the >> dictates of scientific observation and method, (In pre- >> paradigmatic science) what differentiates these various schools >> (is) not one or another failure of method - they are all >> "scientific" - but what we shall come to call their incommensurable >> ways of seeing the world and practicing science within it" (pg 4 >> The Structure of Scientific Revolution.) If this discussion over >> the last two months doesn't make it clear that, as a field, we >> currently have "incommensurate ways of seeing the world and >> practicing science within it" I don't know what does. Kuhn goes >> on to say: "Men (sic) whose research is based on shared paradigms >> are committed to the same rules and standards for scientific >> practice." Again, this discussion makes it pretty clear to me that >> we have not yet reached that point. In fact, (and I would say >> reflecting this fact) the kind of discussion we have been having >> here seldom ever happens as we are content (and being pre- >> paradigmatic can get away with) agreeing to not discuss what we >> don't agree on, another characteristic of pre-paradigmatic science >> -- and the reason I don't mind starting these discussions. >> > > > _______________________________________________ > Comp-neuro mailing list > Comp-neuro@neuroinf.org > http://www.neuroinf.org/mailman/listinfo/comp-neuro -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080901/8952ba5a/attachment.html From edauce at gmail.com Tue Sep 2 09:50:49 2008 From: edauce at gmail.com (Emmanuel Dauce) Date: Tue Sep 2 11:34:59 2008 Subject: [Comp-neuro] Neurocomp'08 registration deadline : September 15th! Message-ID: <205190660809020050m2d9cd651ya681a9a86660ca57@mail.gmail.com> Dear colleagues, The deadline for registration to Neurocomp'08 (Second french conference on Computational Neurosciences) is now approaching! * Registration deadline : Septembre 15, 2008 * Conference dates: October 8-11, 2008 * Conference Web Site : http://2008.neurocomp.fr * Registration Site : http://colloquedr12.dr20.cnrs.fr This international conference, whose aim is to gather the (not only) french Computational Neurosciences community, will this year take place in Marseille. The main conference will be held from wednesday 8th to friday 10th of October, on the campus of "La Timone" (end of metro line 1) The invited speakers are this year : - Ad Aertsen (Freiburg, Germany) - Gustavo Deco (Barcelona, Spain) - Gregor sch?ner (Bochum, Germany) - Andrew Schwartz (Pittsburgh, PA, USA) Two satellite workshops are organized on Saturday, October 11th : * ? Brain-machine interfaces (BMI) ? 9h00-13h00 * ? Computational Vision ? 9h00-13h00 The registration to the workshops has to be done by selecting th "workshop" option on the registration site of the main conference. Conference preliminary program : Mercredi 8 octobre 2008 *********************** La Timone - Amphi H1 *** A partir de 17h : Inscription + Apero bienvenue (18h00) *** *** 19h00 - 20h30 : Session inaugurale *** 19:00 - 19:10 : Introduction Fr?d?ric Alexandre 19:10 - 19:30 : Pr?sentation Neurocomp Thierry Vi?ville 19:30 - 20:30 : Titre ? confirmer Ad Aertsen (Freiburg, Allemagne) (Invited Talk) Jeudi 9 octobre 2008 ******************** La Timone - Amphi H1 *** 8h00 - 9h00 : Inscription + installation posters 1 *** *** 9h00 - 10h40 : Session 1 *** 9:00 - 10:00 : The Intrinsic Properties of the Brain: The Role of Fluctuations During Rest Gustavo Deco (Barcelone, Espagne) (Invited Talk) 10:00 - 10:20 : Interactions of motion and form in the visual cortex ? a neural model Cornelia Beck, Heiko Neumann (Talk 56) 10:20 - 10:40 : Functional properties of feed-forward inhibition Jens Kremkow, Laurent Perrinet, Ad Aertsen, Guillaume Masson (Talk 16) *** 10h40 - 11h00 : Caf? *** *** 11h00 - 12h15 : Session 2 - Neuron models *** 11:00 - 11:20 : Methods for comparing and constraining models of dendritic spines Skene Nathan, Nasuto Slawomir (Talk 67) 11:20 - 11:40 : Mod?lisation des rythmes rapides b?ta et gamma du bulbe olfactif Nicolas Fourcaud-Trocm? (Talk 39) 11:40 - 11:45 : A formalization of the computational impact of intrinsic plasticity J?r?mie Naud?, St?phane Genet, Hugues Berry, S?verine Mahon, Jeanne Paz, Bruno Delord (Spotlight 15) 11:45 - 11:50 : Noise induced tuned decrease in firing in neural models: inverse stochastic resonance Boris Gutkin, Henry Tuckwell, Juergen Jost (Spotlight 27) 11:50 - 11:55 : Estimation des param?tres du mod?le d'Hodgkin-Huxley par des m?taheuristiques Laure Buhry, Sylvain Saighi, Audrey Giremus, Eric Grivel, Sylvie Renaud (Spotlight 47) 11:55 - 12:00 : Nicotine control of dopamine signaling in the Ventral Tegmental Area Michael Graupner, Boris Gutkin (Spotlight 64) 12:00 - 12:05 : Stimulus-dependency in the power-law scaling of the subthreshold activity of V1 cells Olivier Marre, Sami El Boustani, S?bastien B?huret, Cyril Monier, Thierry Bal, Alain Destexhe, Yves Fr?gnac (Spotlight 32) 12:05 - 12:10 : Impact of cortical input on subthalamic activity during deep brain stimulation Julien Modolo, Anne Beuter (Spotlight 35) 12:10 - 12:15 : A unified and quantitative network model to describe spatial attention in area V4 Etienne Hugues, Jorge Jose (Spotlight 61) *** 12h15 - 13h15 : D?jeuner *** *** 13h15 - 14h30 : Poster Session *** *** 14h30 - 16h10 : Session 3 *** 14:30 - 15:30 : Titre ? confirmer Gregor Sch?ner (Invited Talk) 15:30 - 15:35 : On practical neural field parameters adjustment Fr?d?ric Alexandre, J?r?my Fix, Axel Hutt, Nicolas Rougier, Thierry Vi?ville (Spotlight 31) 15:35 - 15:40 : Detection de contours visuels par un modele de champ neuronal Mathieu Galtier, Olivier Faugeras (Spotlight 43) 15:40 - 15:45 : Impl?mentation d'un m?canisme de "covert attention" avec un r?seau de neurones impulsionnels Sylvain Chevallier, Philippe Tarroux (Spotlight 19) 15:45 - 15:50 : A model of neural mechanisms in monocular transparent motion perception Florian Raudies, Pierre Bayerl, Heiko Neumann (Spotlight 13) 15:50 - 15:55 : A simple mechanism to reproduce the neural solution of the aperture problem in monkey area MT Maria-Jose Escobar, Guillaume Masson, Pierre Kornprobst (Spotlight 41) 15:55 - 16:00 : A Model of Optimal Oculomotor Strategies in Reading for Normal and Damaged Visual Fields Jean-Baptiste Bernard, Fermin Moscoso del Prado Martin, Anna Montagnini, Eric Castet (Spotlight 11) 16:00 - 16:05 : Explicit uncertainty for eye movement selection Francis Colas, Fabien Flacher, Pierre Bessi?re, Beno?t Girard (Spotlight 12) 16:05 - 16:10 : Bayesian modelling of sensorimotor systems: Application to handwriting Estelle Gilet, Julien Diard, Pierre Bessi?re (Spotlight 45) *** 16h10 - 17h10 : Poster Session (continued) *** *** 17h10 - 18h30 : Session 4 - Functional and behavioral models *** 17:10 - 17:30 : A computational approach to the covert and overt deployment of spatial attention J?r?my Fix, Nicolas Rougier, Fr?d?ric Alexandre (Talk 40) 17:30 - 17:50 : Biophysical cortical column model for optical signal analysis Sandrine Chemla, Thierry Vi?ville, Frederic Chavane (Talk 46) 17:50 - 18:10 : Mod?lisation macroscopique du complexe Hippocampe-Cortex Entorhinal Fabrice Wendling, Etienne Labyt, Fabrice Bartolomei (Talk 9) 18:10 - 18:30 : 3D navigation with an insect-inspired autopilot Geoffrey Portelli, Julien Serres, Franck Ruffier, Nicolas Franceschini (Talk 22) Vendredi 10 octobre 2008 ************************ La Timone - Amphi H1 *** 8h00 - 9h00 : Installation posters 2 *** *** 9h00 - 10h00 : Session 5 *** 9:00 - 10:00 : Titre ? confirmer Andrew Schwartz (Invited Talk) 10:00 - 10:20 : Spike based inference in a network with divisive inhibition Sophie Den?ve, Timm Lochmann (Talk 20) 10:20 - 10:40 : Un mod?le computationnel de l?automatisation motrice Lionel Rigoux, Olivier Sigaud (Talk 74) *** 10h40 - 11h00 : Caf? *** *** 11h00 - 12h20 Session 6 - BCI and signal processing *** 11:00 - 11:20 : Maximum decoding abilities of temporal patterns and synchronized firings Boris Gour?vitch, Jos Eggermont (Talk 42) 11:20 - 11:40 : Reconstructing the cortical functional network during imagery tasks for boosting asynchronous BCI Michel Besserve, Jacques Martinerie, Line Garnero (Talk 70) 11:40 - 11:45 : Non-identity Learning Vector Quantization applied to evoked potential detection Nanying Liang, Laurent Bougrain (Spotlight 49) 11:45 - 11:50 : Adaptive classification of mental states for asynchronous brain computer interfaces Jean Le Pavec, Maureen Clerc (Spotlight 60) 11:50 - 11:55 : Independent component analysis reveals the unity of cognitive control Cl?mence Roger, Christian, G. B?nar, Franck Vidal, Thierry Hasbroucq, Boris Burle (Spotlight 63) 11:55 - 12:00 : Estimation of individual evoked potential by wavelet transform Moncef Benkherrat, Franck Vidal, Thierry Hasbroucq, Boris Burle (Spotlight 66) 12:00 - 12:05 : Letter perception: from item-level erps to computational models Arnaud Rey, St?phane Dufau, St?phanie Massol, Jonathan Grainger (Spotlight 38) 12:05 - 12:10 : Implementation of a bayesian Filter in a Photoreceptor Cell Audrey Houillon, Jacques Droulez (Spotlight 48) 12:10 - 12:15 : Quantifying Neural Correlations Using Lempel-Ziv Complexity Jean-Luc Blanc, Nicolas Schmidt, Loic Bonnier, Laurent Pezard, Annick Lesne (Spotlight 58) 12:15 - 12:20 : Motion integration modulated by form information ?milien Tlapale, Guillaume Masson, Pierre Kornprobst (Spotlight 68) *** 12h20 - 13h20 : D?jeuner *** *** 13h00 - 14h30 : Poster session *** *** 14h30 - 16h15 : Session 7 - Population coding and functional specialization *** 14:30 - 14:50 : Les groupes polychrones pour capturer l'aspect spatio-temporel de la m?morisation Regis Martinez, Helene Paugam-Moisy (Talk 69) 14:50 - 15:10 : Effects of intrinsic oscillations on weight dynamics under Spike timing-dependent plasticity Fabiano Baroni, Pablo Varona (Talk 62) 15:10 - 15:30 : Statistics of spikes trains, synaptic plasticity and Gibbs distributions. Bruno Cessac, Horacio Rostro, Juan-Carlos Vasquez, Thierry Vi?ville (Talk 29) 15:30 - 15:50 : Specialisation in recurrent neural networks with spike-timing-dependent plasticity Matthieu Gilson, David B. Grayden, Doreen A. Thomas, J. Leo van Hemmen, Anthony N. Burkitt (Talk 5) 15:50 - 15:55 : M?canisme d'auto-organisation corticale : un mod?le bas? sur la r?gle de plasticit? synaptique BCM Thomas Girod, Fr?d?ric Alexandre (Spotlight 34) 15:55 - 16:00 : Reliable recall of spontaneous activity patterns in chaotic cortical networks Pierre Yger, Olivier Marre, Andrew Davison, Yves Fr?gnac (Spotlight 28) 16:00 - 16:05 : Spike-Timing Dependent Plasticity and Regime Transitions in Random Recurrent Neural Networks Fr?d?ric Henry, Emmanuel Dauc? (Spotlight 24) 16:05 - 16:10 : Analyzing cortical network dynamics with respect to different connectivity assumptions Nicole Voges, Laurent Perrinet (Spotlight 25) 16:10 - 16:15 : To which extend is the ``neural code'' a metric ? Bruno Cessac, Horacio Rostro, Juan-Carlos Vasquez, Thierry Vi?ville (Spotlight 23) *** 16h15 - 17h00 : Poster session (continued) *** *** 17h00 - 18h30 Session 8 - Neural Interfaces *** 17:00 - 17:20 : Pr?sentation INCF (Invited Talk) 17:20 - 17:40 : Implementing entorhinal grid fields in biophysical neuronal models Michiel Remme, Mate Lengyel, Boris Gutkin (Talk 55) 17:40 - 18:00 : Tools for electrophysiology labs: a C coded dynamic-clamp on DSP board (aC/DC). Sofiane Boussa, Pasquier Jennifer, Leboulenger Fran?ois, Frank Le Foll, Alain Faure (Talk 71) 18:00 - 18:30 : Tour de table / Pr?sentation NeuroComp 09 *** 20h00 : Banquet *** -- -- Emmanuel Dauc? Centrale Marseille/UMR 6233 +33 491 05 47 30 / +33 491 17 22 88 http://emmanuel.dauce.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080902/7ed75324/attachment.html From Jean-Marc.Bollon at inrialpes.fr Mon Sep 1 17:30:10 2008 From: Jean-Marc.Bollon at inrialpes.fr (Jean-Marc Bollon) Date: Tue Sep 2 11:36:00 2008 Subject: [Comp-neuro] Probabilistic Reasoning and Decision Making in Sensory-Motor Systems - NEW BOOK Message-ID: <2C763D5F-0053-4554-80CB-F8FBF8759820@inrialpes.fr> Probabilistic Reasoning and Decision Making in Sensory-Motor Systems ****************************************************************************** Both living organisms and robotic systems must face the same central difficulty: How to survive being ignorant? How to use an incomplete and uncertain model of their environment to perceive, infer, decide, learn and act efficiently? Indeed, any model of a real phenomenon is incomplete: there are always some hidden variables, not taken into account in the model, that influence the phenomenon. The effect of these hidden variables is that the model and the phenomenon never behave exactly alike. Uncertainty is the direct and unavoidable consequence of incompleteness. A model may not foresee exactly the future observations of a phenomenon as these observations are biased by the hidden variables. It may neither predict exactly the consequences of its decisions. Probability theory, considered as an alternative to logic to model rational reasoning, is the perfect mathematical framework to face this difficult challenge. Learning is used in a first step to transform incompleteness into uncertainty, inference is then used to reason and take decisions based on the probability distributions constructed by learning. This so-called subjectivist approach to probability allows uncertain reasoning as complex and formal as the ones made using logic with exact knowledge. This book presents twelve different implementations of this approach to very different sensory-motor systems either by programming robots or by modeling living systems. Each of these works summarizes a PhD dissertation defended in different European universities. All these works use Bayesian Programming: a mathematical formalism, which defines in simple mathematical terms the way probability, can be used as an alternative to logic. Bayesian Programming also proposes a programming and modeling methodology as, to respect the mathematical formalism, the programmer should follow always the same steps to build his model. Finally, Bayesian Programming is a common language to understand and compare the different models. This language is used all along this book by all the authors and insures the global coherence of these twelve very different examples. More information : http://emotion.inrialpes.fr/BP/spip.php?article18 How to buy : http://www.springer.com/engineering/book/978-3-540-79006-8 http://www.amazon.com/Probabilistic-Reasoning-Decision-Sensory-Motor-Springer/dp/3540790063/ref=sr_1_7ie=UTF8&s=books&qid=1205844732&sr=1-7 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080901/50097767/attachment.html From harry.erwin at sunderland.ac.uk Tue Sep 2 10:43:27 2008 From: harry.erwin at sunderland.ac.uk (Harry Erwin) Date: Tue Sep 2 11:37:37 2008 Subject: [Comp-neuro] Summary of responses to calcium spike query Message-ID: <3DF1B21B-8018-415A-913C-22F6B535ED4E@sunderland.ac.uk> I've posted a summary of the responses at the end of the following article on my neuroscience wiki: Errors are my responsibility--I'll make corrections, additions, or deletions as my attention is drawn to them. The basic conclusion is that the membrane potential 'hump' in cells containing calcium T channels seems to be best modelled by having two channel open modes, similar to what Tsien suggests, with the first mode having a short time constant and the second a time constant for closing about 100 times longer. The second mode seems to involve binding of Ca++ with a regulation factor that then locks the channel open. Alain Destexhe's papers ten years ago are worth rereading. If you can't afford the computational cost of modelling this explicitly or only need a qualitative model, consider using the model in Grossberg, S. and Versace, M. (2008). Thanks to everyone for the help. -- Harry Erwin, PhD, Senior Lecturer of Computing, University of Sunderland. Computational neuroethologist: http://scat-he-g4.sunderland.ac.uk/~harryerw/phpwiki/index.php/AuditoryResearch From B.T.Vincent at dundee.ac.uk Tue Sep 2 11:28:09 2008 From: B.T.Vincent at dundee.ac.uk (Dr Ben Vincent) Date: Tue Sep 2 13:18:09 2008 Subject: [Comp-neuro] a paper available Message-ID: <48BD0729.9080804@dundee.ac.uk> Title: Is the early visual system optimised to be energy efficient? PDF: http://www.personal.dundee.ac.uk/~btvincen/vincent_etal_2005.pdf Cheers, Ben -- Dr Benjamin Vincent Lecturer School of Psychology University of Dundee http://www.personal.dundee.ac.uk/~btvincen/ From uta.noppeney at tuebingen.mpg.de Tue Sep 2 18:12:43 2008 From: uta.noppeney at tuebingen.mpg.de (Uta Noppeney) Date: Wed Sep 3 13:14:12 2008 Subject: [Comp-neuro] PhD/PostDoc - Computational Cognitive Neuroimaging Message-ID: <48BD65FB.1090503@tuebingen.mpg.de> PhD/PostDoc - Computational Cognitive Neuroimaging Applications are invited for a PhD or PostDoc position in the ?Cognitive Neuroimaging Group? (http://www.kyb.mpg.de/noppeneygroup/index.html) at the Max Planck Institute for Biological Cybernetics. Projects will combine fMRI and computational modelling to investigate the neural basis of category learning. The position is supervised by Dr Uta Noppeney, in collaboration with Prof Peter Dayan (Gatsby Computational Neuroscience Unit, UCL) and Prof Bernhard Sch?lkopf (machine learning department, MPI). The Max Planck Institute for Biological Cybernetics provides an excellent multi-disciplinary and interactive research environment combining expertise in neurophysiology, psychophysics, machine learning and development of MRI methodology. Applicants should combine interest in neuroscience with a strong mathematical and analytical background and have a master/diploma or equivalent degree in Neuroscience, Physics, Computer Science or related areas. The Ph.D./PostDoc position is funded by a MPI stipend. Applications including a CV, a statement of research interests, and the names and full contact details of two referees should be sent to: uta.noppeney@tuebingen.mpg.de The closing date for applications is 2 October 2008. From ASIM.ROY at asu.edu Tue Sep 2 21:50:42 2008 From: ASIM.ROY at asu.edu (Asim Roy) Date: Wed Sep 3 13:14:14 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments In-Reply-To: Message-ID: Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" Jim Bower's response: And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Jim, would love to get some references for your statement:- "development probably recapitulating evolutionary history." This really is the kind of process in the brain that I am looking for. Just a few references would suffice. By the way, learning takes place during development too. Just ask anyone in cognitive science. Development is not disassociated from learning. And ANN never implied learning begins after development. That's a misconception. On the "blank slate" idea in ANN, just look at the phenomenon of adult neurogenesis. Our adult brains generate new cells in the thousands on a daily basis and they are part of the "blank slate" because they don't come with ready-made connections or anything. The process that you refer to as "development probably recapitulating evolutionary history" is called "learning" in ANN. It's that process that constructs networks out of these new cells and makes them operational. Asim Roy Arizona State University -----Original Message----- From: comp-neuro-bounces@neuroinf.org [mailto:comp-neuro-bounces@neuroinf.org]On Behalf Of james bower Sent: Wednesday, August 27, 2008 9:05 AM To: CompNeuro List Subject: [Comp-neuro] Discussion - Kuhn - and brief comments A few brief comments -- given that school has started, and I now have to prepare to "influence" the latest next generation. First a BIG POINT: Klaus Stiefel: pre-paradigmatic " What he meant by that is a disagreement about the basic explainanda" No, Kuhn was focused on process to quote: "the early developmental stages of most sciences (are) characterized by continual competition between a number of distinct views of nature, each partially derived from, and all roughly compatible with, the dictates of scientific observation and method, (In pre-paradigmatic science) what differentiates these various schools (is) not one or another failure of method - they are all "scientific" - but what we shall come to call their incommensurable ways of seeing the world and practicing science within it" (pg 4 The Structure of Scientific Revolution.) If this discussion over the last two months doesn't make it clear that, as a field, we currently have "incommensurate ways of seeing the world and practicing science within it" I don't know what does. Kuhn goes on to say: "Men (sic) whose research is based on shared paradigms are committed to the same rules and standards for scientific practice." Again, this discussion makes it pretty clear to me that we have not yet reached that point. In fact, (and I would say reflecting this fact) the kind of discussion we have been having here seldom ever happens as we are content (and being pre-paradigmatic can get away with) agreeing to not discuss what we don't agree on, another characteristic of pre-paradigmatic science -- and the reason I don't mind starting these discussions. Bryan Bishop: "There's a few too many layers of folk psychology here," I agree, and have characterized all of biology as fundamentally folkloric in nature -- based on story telling, with few real definitions of anything. Something comp bio (neuro) will, I hope, eventually fix. And on to the approaches we don't agree on: Bryan Bishop: "I bet it becomes clear that trying to do "natural language processing" from statistical inferences doesn't get us as much hard science as the brain could provide." Of course, I agree -- and also agree that this field continues to be distorted by what is essential snake oil we sell to the Department of Defense about how studying the brain will help win wars. This rather self serving commitment to "neuro-morphic engineering" as it is now called, has been distorting our science for a while. In the last 8 years even more dramatically. Mario Negrello: "I'd say instead that some approaches gather more acolytes, and then overflow others in sheer voluminous quantity," Unfortunately, as just noted, very often related to who you are selling the science to (funders) and also, unfortunately, how 'easy' the methods are and therefore how many can jump on the bandwagon without much preparation (or even knowledge of the brain in this case) -- 20 years studying the realistic model of the Purkinje cell and counting. Bard Ermentrout: " I suspect that it would be too hard to adjust parameters for realistic models " Is hard bad? Or is the brain, in fact, hard? Igor Carron: "The groundwork of theory as you put it has, in nuclear technology, always been a way to acquire and use experimental findings." And this, in fact, is the value of theory -- not to capture 'truth' as many in comp neuro seem be believe, but to organize experimental studies -- the more the theory is removed from the actual structure of the brain - the more it exists by itself, disconnected from the ability to improve, or more importantly to refute it. Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Asim Roy: "Is there a way in computational neuroscience to verify any of these theories of learning? " Wrong question. Axel Hutt: " can (neuro)biology really treat a population of some thousand elements ? " We will need to figure out how - numerous groups are working on it. Anibalmastobiza: "cerebellum, usually considered as a center for motor processing and coordination just as it was for the basal ganglia that now we know that is also involve in cognition" While I appreciate the support, I have another question for cognitive neuroscientists, how come anything that lights up in a brain scan becomes a "cognitive center" seems weird to me. Jim ================================== Dr. James M. Bower Ph.D. Professor of Computational Neuroscience Research Imaging Center University of Texas Health Science Center - - San Antonio 8403 Floyd Curl Drive San Antonio Texas 78284-6240 Main Number: 210- 567-8100 Fax: 210 567-8152 Mobile: 210-382-0553 CONFIDENTIAL NOTICE: The contents of this email and any attachments to it may be privileged or contain privileged and confidential information. This information is only for the viewing or use of the intended recipient. If you have received this e-mail in error or are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of, or the taking of any action in reliance upon, any of the information contained in this e-mail, or any of the attachments to this e-mail, is strictly prohibited and that this e-mail and all of the attachments to this e-mail, if any, must be immediately returned to the sender or destroyed and, in either case, this e-mail and all attachments to this e-mail must be immediately deleted from your computer without making any copies hereof and any and all hard copies made must be destroyed. If you have received this e-mail in error, please notify the sender by e-mail immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080902/400fb7ec/attachment.html From gary at cs.ucsd.edu Wed Sep 3 17:30:06 2008 From: gary at cs.ucsd.edu (Garrison Cottrell) Date: Wed Sep 3 17:50:05 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments In-Reply-To: References: Message-ID: <9D6F59D2-B9C5-4581-AB2B-50E59A224FDC@cs.ucsd.edu> I hate to jump into this, but... Speaking as a true novice, I would like to point out that the neurogenesis that occurs on a daily basis is very specific to the dentate gyrus; if someone knows of "daily neurogenesis" elsewhere, I would like to hear about it. This is not the same as learning in an ANN - these new neurons have a specific function, which some of the best minds in our field are currently trying to figure out (see Aimone, J., Wiles, J., & Gage, F. (2006). Potential role for adult neurogenesis in the encoding of time in new memories. Nature Neuroscience, 9(6), 723-727. for one example). It is only if you don't have a good weight change rule (e.g., STDP) and/or you believe in localist encodings that you need neurogenesis to learn. (shields up! ;-)) g. On Sep 2, 2008, at 12:50 PM, Asim Roy wrote: > Asim Roy: "a "blank slate" simply implies a network whose > connection weights and other parameters have not been set yet -" > > Jim Bower's response: And, no such thing in biology, where > development doesn't end and learning begins - it is continuous, and > development probably recapitulating evolutionary history. Another > reason why the mainstream ANN models make no sense. > > > Jim, would love to get some references for your statement:- > "development probably recapitulating evolutionary history." This > really is the kind of process in the brain that I am looking for. > Just a few references would suffice. > > By the way, learning takes place during development too. Just ask > anyone in cognitive science. Development is not disassociated from > learning. And ANN never implied learning begins after development. > That's a misconception. > > On the "blank slate" idea in ANN, just look at the phenomenon of > adult neurogenesis. Our adult brains generate new cells in the > thousands on a daily basis and they are part of the "blank slate" > because they don't come with ready-made connections or anything. The > process that you refer to as "development probably recapitulating > evolutionary history" is called "learning" in ANN. It's that process > that constructs networks out of these new cells and makes them > operational. > > Asim Roy > Arizona State University > > > -----Original Message----- > From: comp-neuro-bounces@neuroinf.org [mailto:comp-neuro-bounces@neuroinf.org > ]On Behalf Of james bower > Sent: Wednesday, August 27, 2008 9:05 AM > To: CompNeuro List > Subject: [Comp-neuro] Discussion - Kuhn - and brief comments > > A few brief comments -- given that school has started, and I now > have to prepare to "influence" the latest next generation. > > First a BIG POINT: > > Klaus Stiefel: pre-paradigmatic " What he meant by that is a > disagreement about the basic explainanda" > > No, Kuhn was focused on process to quote: "the early developmental > stages of most sciences (are) characterized by continual competition > between a number of distinct views of nature, each partially derived > from, and all roughly compatible with, the dictates of scientific > observation and method, (In pre-paradigmatic science) what > differentiates these various schools (is) not one or another failure > of method - they are all "scientific" - but what we shall come to > call their incommensurable ways of seeing the world and practicing > science within it" (pg 4 The Structure of Scientific Revolution.) > If this discussion over the last two months doesn't make it clear > that, as a field, we currently have "incommensurate ways of seeing > the world and practicing science within it" I don't know what > does. Kuhn goes on to say: "Men (sic) whose research is based on > shared paradigms are committed to the same rules and standards for > scientific practice." Again, this discussion makes it pretty clear > to me that we have not yet reached that point. In fact, (and I > would say reflecting this fact) the kind of discussion we have been > having here seldom ever happens as we are content (and being pre- > paradigmatic can get away with) agreeing to not discuss what we > don't agree on, another characteristic of pre-paradigmatic science > -- and the reason I don't mind starting these discussions. > > Bryan Bishop: "There's a few too many layers of folk psychology > here," > > I agree, and have characterized all of biology as fundamentally > folkloric in nature -- based on story telling, with few real > definitions of anything. Something comp bio (neuro) will, I hope, > eventually fix. > > > > And on to the approaches we don't agree on: > > Bryan Bishop: "I bet it becomes clear that trying to do "natural > language processing" from statistical inferences doesn't get us as > much hard science as the brain could provide." > > Of course, I agree -- and also agree that this field continues to be > distorted by what is essential snake oil we sell to the Department > of Defense about how studying the brain will help win wars. This > rather self serving commitment to "neuro-morphic engineering" as it > is now called, has been distorting our science for a while. In the > last 8 years even more dramatically. > > Mario Negrello: "I'd say instead that some approaches gather more > acolytes, and then overflow others in sheer voluminous quantity," > > Unfortunately, as just noted, very often related to who you are > selling the science to (funders) and also, unfortunately, how 'easy' > the methods are and therefore how many can jump on the bandwagon > without much preparation (or even knowledge of the brain in this > case) -- 20 years studying the realistic model of the Purkinje > cell and counting. > > > Bard Ermentrout: " I suspect that it would be too hard to adjust > parameters for realistic models " > > Is hard bad? Or is the brain, in fact, hard? > > > Igor Carron: "The groundwork of theory as you put it has, in nuclear > technology, always been a way to acquire and use experimental > findings." > > And this, in fact, is the value of theory -- not to capture 'truth' > as many in comp neuro seem be believe, but to organize experimental > studies -- the more the theory is removed from the actual structure > of the brain - the more it exists by itself, disconnected from the > ability to improve, or more importantly to refute it. > > > Asim Roy: "a "blank slate" simply implies a network whose > connection weights and other parameters have not been set yet -" > > And, no such thing in biology, where development doesn't end and > learning begins - it is continuous, and development probably > recapitulating evolutionary history. Another reason why the > mainstream ANN models make no sense. > > > Asim Roy: "Is there a way in computational neuroscience to verify > any of these theories of learning? " > > Wrong question. > > > Axel Hutt: " can (neuro)biology really treat a population of some > thousand elements ? " > > We will need to figure out how - numerous groups are working on it. > > > Anibalmastobiza: "cerebellum, usually considered as a center for > motor processing and coordination just as it was for the basal > ganglia that now we know that is also involve in cognition" > > While I appreciate the support, I have another question for > cognitive neuroscientists, how come anything that lights up in a > brain scan becomes a "cognitive center" seems weird to me. > > > Jim > > > > > > > > > ================================== > > Dr. James M. Bower Ph.D. > > Professor of Computational Neuroscience > > Research Imaging Center > University of Texas Health Science Center - > - San Antonio > 8403 Floyd Curl Drive > San Antonio Texas 78284-6240 > > Main Number: 210- 567-8100 > Fax: 210 567-8152 > Mobile: 210-382-0553 > > CONFIDENTIAL NOTICE: > The contents of this email and any attachments to it may be > privileged or > contain privileged and confidential information. This information is > only > for the viewing or use of the intended recipient. If you have > received this > e-mail in error or are not the intended recipient, you are hereby > notified > that any disclosure, copying, distribution or use of, or the taking > of any > action in reliance upon, any of the information contained in this e- > mail, or > any of the attachments to this e-mail, is strictly prohibited and > that this > e-mail and all of the attachments to this e-mail, if any, must be > immediately returned to the sender or destroyed and, in either case, > this > e-mail and all attachments to this e-mail must be immediately > deleted from > your computer without making any copies hereof and any and all hard > copies > made must be destroyed. If you have received this e-mail in error, > please > notify the sender by e-mail immediately. > > > > > > > > > _______________________________________________ > Comp-neuro mailing list > Comp-neuro@neuroinf.org > http://www.neuroinf.org/mailman/listinfo/comp-neuro Gary Cottrell 858-534-6640 FAX: 858-534-7029 Computer Science and Engineering 0404 IF USING FED EX INCLUDE THE FOLLOWING LINE: CSE Building, Room 4130 University of California San Diego - 9500 Gilman Drive # 0404 La Jolla, Ca. 92093-0404 "Only connect!" -E.M. Forster "I am awaiting the day when people remember the fact that discovery does not work by deciding what you want and then discovering it." -David Mermin Email: gary@ucsd.edu Home page: http://www-cse.ucsd.edu/~gary/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080903/f08e1b8a/attachment.html From elli.chatzopoulou at incf.org Thu Sep 4 16:12:11 2008 From: elli.chatzopoulou at incf.org (INCF - Elli Chatzopoulou) Date: Thu Sep 4 16:42:22 2008 Subject: [Comp-neuro] INCF newsletter service Message-ID: <48BFECBB.3010406@incf.org> The INCF Secretariat has recently launched a bi-monthly Newletter service, publishing the latest developments and activities of the INCF and related neuroinformatics initiatives. The first two newsletters are available here: http://www.incf.org/news/newsletters The September-October INCF newsletter is featuring: -the latest news about the INCF Software Center -a presentation of the INCF German Node and the Bernstein Network -information about the upcoming INCF Neuroinformatics Congress -a short interview of Gaute Einevoll, coordinator of the INCF Norwegian Node You can subscribe to the INCF newsletter mailing list simply by sending a message to incf-info-subscribe@incf.org -- Elli Chatzopoulou, Ph.D. Scientific Information and Public Relations Officer International Neuroinformatics Coordinating Facility Secretariat Karolinska Institutet Nobels v?g 15A SE-171 77 Stockholm Sweden Email: elli.chatzopoulou@incf.org Phone: +46 8 524 87491 Mobile: +46 7 614 87491 Fax: +46 8 524 87150 web: www.incf.org From michele.giugliano at epfl.ch Thu Sep 4 09:25:13 2008 From: michele.giugliano at epfl.ch (Michele Giugliano) Date: Thu Sep 4 16:59:18 2008 Subject: [Comp-neuro] Post Doctoral Research Position in Neuroengineering Message-ID: <48BF8D59.8000806@epfl.ch> The EPFL and the Brain Mind Institute (http://bmi.epfl.ch) are seeking an outstanding and highly motivated Postdoctoral researcher for a challenging project with focus on the biophysical interactions between neuronal networks and conductive nanoparticles (see references below). The successful candidate is expected to join a new generation of neuro-nano engineers and neuroscientists, consolidating and developing unique interdisciplinary skills, at the interface among (neuro)biology, (nano)technology and (micro)electronics, mastering both the languages of ?neurons? (i.e. cellular electrophysiology and neurosciences) and of ?nanotechnology? (i.e. carbon nanotubes and conductive nanoparticles). Requirements/qualifications: Candidates must have strong experimental skills, but also interest and motivation to actively build on existing scientific collaborations and on-campus facilities. Preferred educational background is a PhD in Neuroscience, Bioengineering or Nanotechnology. Experience with patch-clamp recordings, cell / slice culturing and computational modeling is an advantage. The successful candidate should also possess a high degree of motivation, excellent written and verbal communication skills and a demonstrated ability to work independently and interact with a multi-disciplinary team of scientists. Environment: The Laboratory of Neural Microcircuitry at the Brain Mind Institute, based at the Swiss federal Institute of Technology (EPFL) The Dept. of Biomedical Sciences, University of Antwerp (Belgium) Contact: Interested applicants should submit a one-page description of past research experience, a resume of educational and research experience, including publications, and names of three people that could provide letters of reference, to Prof. Dr. M. Giugliano (email: michele .dot. giugliano .at. epfl .dot. ch) Theoretical Neurobiology, Dept. of Biomedical Sciences, University of Antwerp (Belgium) and Laboratory of Neural Microcircuitry, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne We do not respond to obvious mass mailing. Ref: Mazzatenta et al., Journal of Neuroscience, 2007 Sucapane et al., Journal of Nanoneuroscience, 2008 Giugliano et al., Drug Discovery Today: Disease Models, 2008 Giugliano et al., in "In Progress in Nanotechnology Neurosciences", 2008 (reprints available from http://www.giugliano.info) See also: Lovat et al., Nano Letters, 2005 Silva, Nat. Rev. Neurosci. 2006 Keefer et al., Nat. Nanotech., 2008 From stiefel at salk.edu Thu Sep 4 16:16:13 2008 From: stiefel at salk.edu (Klaus M. Stiefel) Date: Thu Sep 4 17:01:16 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments In-Reply-To: References: <48B7FB0F.3030509@salk.edu> Message-ID: <48BFEDAD.20702@salk.edu> An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080904/439d7b53/attachment.html From mnegrello at gmail.com Thu Sep 4 11:17:03 2008 From: mnegrello at gmail.com (Mario Negrello) Date: Thu Sep 4 17:04:25 2008 Subject: [Comp-neuro] Development, Evolution and Learning (was) Discussion - Kuhn - and brief comments References: <96C01CC6-88EE-4D66-B2D3-19778E326DCE@gmail.com> Message-ID: <6A80976B-6E85-4BC2-88B7-703C2BC08A8D@gmail.com> > > Asim said: > On the "blank slate" idea in ANN, just look at the phenomenon of > adult neurogenesis. Our adult brains generate new cells in the > thousands on a daily basis and they are part of the "blank slate" > because they don't come with ready-made connections or anything. The > process that you refer to as "development probably recapitulating > evolutionary history" is called "learning" in ANN. It's that process > that constructs networks out of these new cells and makes them > operational. I guess that this varies with your level of analysis. Developmental recapitulation of evolutionary history is about major brain development, hubs and tracts and gross architecture, those features that are morphologically conspicuous in the brain. Learning is different, it's fine tuning, when an already functional brain develops further functionality by interacting with a complex environment. Moreover, as was pointed out by Cottrell, the new neurons you mention do not sprout anywhere, but presumably, noly where there is a reason or a function for them to do. One of the stories i know about new neurons being generated relates to communication behavior in fish. Fish that produce aggressive calls, grow new cells to make their calls more potent. This was solidly shown in: Dunlap, K.D., et al 2006. Social interaction and cortisol treatment increase cell addition and radial glia fiber density in the diencephalic periventricular zone of adult electric fish, Apteronotus leptorhynchus, Hormones & Behavior 50:10-17. So, between cell addition and brain development there is a considerable distance. I do not suppose that by explaining mechanisms of learning, we shall also understand the functional entailments of particular architectures. For instance, Eugene Izhikevich in a talk in 'Dynamical Systems in Neuroscience' at the NYU in June 2008 (if memory serves me right), showed the last output of his mega brain model. The model has the gross architecture of a human brain as seen through DTI (diffusion tensor imaging), and the microarchitecture derived from rats and cats. What surprised me in terms of the results, was that he claimed that frequencies measured from the model resembled those known from their correspodent areas of the brain. Alpha in V1, Theta in hippocampus, and others. I take that to mean that many functional capabilities of the brain will be effectively only learneable if the proper architecture is there. Else, if it were only learning, there would be little reason for a cat to be unable to learn the things a human does. Surely, one can draw analogies from evolution, through development, until learning. One can amalgamate all and say that they are all 'metastable adaptations', or something. But so far, the clear divisions that appear between the study of each, are fully justified: we need theories for each. For all, later. Learning needs its story as much as development. Gruss, M. > > -----Original Message----- > From: comp-neuro-bounces@neuroinf.org [mailto:comp-neuro-bounces@neuroinf.org > ]On Behalf Of james bower > Sent: Wednesday, August 27, 2008 9:05 AM > To: CompNeuro List > Subject: [Comp-neuro] Discussion - Kuhn - and brief comments > > A few brief comments -- given that school has started, and I now > have to prepare to "influence" the latest next generation. > > First a BIG POINT: > > Klaus Stiefel: pre-paradigmatic " What he meant by that is a > disagreement about the basic explainanda" > > No, Kuhn was focused on process to quote: "the early developmental > stages of most sciences (are) characterized by continual competition > between a number of distinct views of nature, each partially derived > from, and all roughly compatible with, the dictates of scientific > observation and method, (In pre-paradigmatic science) what > differentiates these various schools (is) not one or another failure > of method - they are all "scientific" - but what we shall come to > call their incommensurable ways of seeing the world and practicing > science within it" (pg 4 The Structure of Scientific Revolution.) > If this discussion over the last two months doesn't make it clear > that, as a field, we currently have "incommensurate ways of seeing > the world and practicing science within it" I don't know what > does. Kuhn goes on to say: "Men (sic) whose research is based on > shared paradigms are committed to the same rules and standards for > scientific practice." Again, this discussion makes it pretty clear > to me that we have not yet reached that point. In fact, (and I > would say reflecting this fact) the kind of discussion we have been > having here seldom ever happens as we are content (and being pre- > paradigmatic can get away with) agreeing to not discuss what we > don't agree on, another characteristic of pre-paradigmatic science > -- and the reason I don't mind starting these discussions. > > Bryan Bishop: "There's a few too many layers of folk psychology > here," > > I agree, and have characterized all of biology as fundamentally > folkloric in nature -- based on story telling, with few real > definitions of anything. Something comp bio (neuro) will, I hope, > eventually fix. > > > > And on to the approaches we don't agree on: > > Bryan Bishop: "I bet it becomes clear that trying to do "natural > language processing" from statistical inferences doesn't get us as > much hard science as the brain could provide." > > Of course, I agree -- and also agree that this field continues to be > distorted by what is essential snake oil we sell to the Department > of Defense about how studying the brain will help win wars. This > rather self serving commitment to "neuro-morphic engineering" as it > is now called, has been distorting our science for a while. In the > last 8 years even more dramatically. > > Mario Negrello: "I'd say instead that some approaches gather more > acolytes, and then overflow others in sheer voluminous quantity," > > Unfortunately, as just noted, very often related to who you are > selling the science to (funders) and also, unfortunately, how 'easy' > the methods are and therefore how many can jump on the bandwagon > without much preparation (or even knowledge of the brain in this > case) -- 20 years studying the realistic model of the Purkinje > cell and counting. > > > Bard Ermentrout: " I suspect that it would be too hard to adjust > parameters for realistic models " > > Is hard bad? Or is the brain, in fact, hard? > > > Igor Carron: "The groundwork of theory as you put it has, in nuclear > technology, always been a way to acquire and use experimental > findings." > > And this, in fact, is the value of theory -- not to capture 'truth' > as many in comp neuro seem be believe, but to organize experimental > studies -- the more the theory is removed from the actual structure > of the brain - the more it exists by itself, disconnected from the > ability to improve, or more importantly to refute it. > > > Asim Roy: "a "blank slate" simply implies a network whose > connection weights and other parameters have not been set yet -" > > And, no such thing in biology, where development doesn't end and > learning begins - it is continuous, and development probably > recapitulating evolutionary history. Another reason why the > mainstream ANN models make no sense. > > > Asim Roy: "Is there a way in computational neuroscience to verify > any of these theories of learning? " > > Wrong question. > > > Axel Hutt: " can (neuro)biology really treat a population of some > thousand elements ? " > > We will need to figure out how - numerous groups are working on it. > > > Anibalmastobiza: "cerebellum, usually considered as a center for > motor processing and coordination just as it was for the basal > ganglia that now we know that is also involve in cognition" > > While I appreciate the support, I have another question for > cognitive neuroscientists, how come anything that lights up in a > brain scan becomes a "cognitive center" seems weird to me. > > > Jim > > > > > > > > > ================================== > > Dr. James M. Bower Ph.D. > > Professor of Computational Neuroscience > > Research Imaging Center > University of Texas Health Science Center - > - San Antonio > 8403 Floyd Curl Drive > San Antonio Texas 78284-6240 > > Main Number: 210- 567-8100 > Fax: 210 567-8152 > Mobile: 210-382-0553 > > CONFIDENTIAL NOTICE: > The contents of this email and any attachments to it may be > privileged or > contain privileged and confidential information. This information is > only > for the viewing or use of the intended recipient. If you have > received this > e-mail in error or are not the intended recipient, you are hereby > notified > that any disclosure, copying, distribution or use of, or the taking > of any > action in reliance upon, any of the information contained in this e- > mail, or > any of the attachments to this e-mail, is strictly prohibited and > that this > e-mail and all of the attachments to this e-mail, if any, must be > immediately returned to the sender or destroyed and, in either case, > this > e-mail and all attachments to this e-mail must be immediately > deleted from > your computer without making any copies hereof and any and all hard > copies > made must be destroyed. If you have received this e-mail in error, > please > notify the sender by e-mail immediately. > > > > > > > > > _______________________________________________ > Comp-neuro mailing list > Comp-neuro@neuroinf.org > http://www.neuroinf.org/mailman/listinfo/comp-neuro -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080904/1123ec64/attachment-0001.html From ASIM.ROY at asu.edu Thu Sep 4 21:38:55 2008 From: ASIM.ROY at asu.edu (Asim Roy) Date: Fri Sep 5 12:04:24 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments In-Reply-To: <9D6F59D2-B9C5-4581-AB2B-50E59A224FDC@cs.ucsd.edu> Message-ID: Here's something from Wikipedia on adult neurogenesis. The references are below. "Some authors (particularly Elizabeth Gould) have suggested that adult neurogenesis may also occur in other areas including primate neocortex (e.g., Shankle et al. 1999, Gould et al., 1999b; Zhao et al., 2003), although others, including Rakic (2002), have questioned the scientific evidence of these findings; in the broad sense, they suggest that the new cells may be glia. A recent paper by Ponti, Peretto, and Bonfanti found evidence of neuronal neurogenesis in the cerebellum of adult rabbits. [1] " Therefore adult neurogenesis may not be restricted to the dentate gyrus. The broader argument here is that the brains of humans and other animals have mechanisms and processes in place to use these new cells, when they occur, to either construct new networks or enhance existing networks. And so adult neurogenesis not only provides the most concrete biological evidence for the "blank slate" idea of ANN, but also the evidence that there are mechanisms and processes in place to utilize it. Given the fact that the brain goes through changes all the time (reconfiguration in terms of new connections, synaptic adjustments), the "blank slate" for learning need not always be from neurogenesis. Learning does take place even when neurogenesis is restricted, but it becomes harder, as shown by many studies, one of which is quoted below. To reiterate the broader point: the brain indeed has mechanisms and processes to work with "blank slates," but the "blank slate" need not always be from neurogenesis. Here's something from a study linking learning and neurogenesis in crickets, from Cayr, Scotto-Lomassese, Malaterre, Strambi and Strambi [2007]: "Since the discovery of adult neurogenesis, a major issue is the role of newborn neurons and the function-dependent regulation of adult neurogenesis. We decided to use an animal model with a relatively simple brain to address these questions. In the adult cricket brain as in mammals, new neurons are produced throughout life. This neurogenesis occurs in the main integrative centers of the insect brain, the mushroom bodies (MBs), where the neuroblasts responsible for their formation persist after the imaginal molt. The rate of production of new neurons is controlled not only by internal cues such as morphogenetic hormones but also by external environmental cues.....In search of a functional role for the new cells, we specifically ablated MB neuroblasts in young adults using brain-focused gamma ray irradiation. We developed a learning paradigm adapted to the cricket, which we call the "escape paradigm." Using this operant associative learning test, we showed that crickets lacking neurogenesis exhibited delayed learning and reduced memory retention of the task when olfactory cues were used. Our results suggest that environmental cues are able to influence adult neurogenesis and that, in turn, newly generated neurons participate in olfactory integration, optimizing learning abilities of the animal, and thus its adaptation to its environment." M. Cayr, S. Scotto-Lomassese, J. Malaterre, C. Strambi and A. Strambi, "Understanding the Regulation and Function of Adult Neurogenesis: Contribution from an Insect Model, the House Cricket," Chemical Senses Advance Access, DOI 10.1093/chemse/bjm010, April 2, 2007. * Gould E, Reeves AJ, Graziano MS, Gross CG. (1999b). Neurogenesis in the neocortex of adult primates. Science. Oct 15;286(5439):548-52. PMID 10521353 * Ponti G, Peretto B, Bonfanti L (2008). "Genesis of neuronal and glial progenitors in the cerebellar cortex of peripuberal and adult rabbits". PLoS ONE 3 (6): e2366. PMID 18523645. * Rakic P. Neurogenesis in adult primate neocortex: an evaluation of the evidence. (2002). Nat Rev Neurosci. Jan;3(1):65-71. PMID 11823806 * Shankle, WR, Rafii, MS, Landing, BH, and Fallon, JH (1999) Approximate doubling of the numbers of neurons in the postnatal human cortex and in 35 specific cytoarchitectonic areas from birth to 72 months. Pediatric and Developmental Pathology 2:244-259. * Zhao M, Momma S, Delfani K, Carlen M, Cassidy RM, Johansson CB, Brismar H, Shupliakov O, Frisen J, Janson AM (2003). Evidence for neurogenesis in the adult mammalian substantia nigra. Proc Natl Acad Sci U S A. Jun 24;100(13):7925-30. PMID 12792021 -----Original Message----- From: comp-neuro-bounces@neuroinf.org [mailto:comp-neuro-bounces@neuroinf.org]On Behalf Of Garrison Cottrell Sent: Wednesday, September 03, 2008 8:30 AM To: Asim Roy Cc: CompNeuro List Subject: Re: [Comp-neuro] Discussion - Kuhn - and brief comments I hate to jump into this, but... Speaking as a true novice, I would like to point out that the neurogenesis that occurs on a daily basis is very specific to the dentate gyrus; if someone knows of "daily neurogenesis" elsewhere, I would like to hear about it. This is not the same as learning in an ANN - these new neurons have a specific function, which some of the best minds in our field are currently trying to figure out (see Aimone, J., Wiles, J., & Gage, F. (2006). Potential role for adult neurogenesis in the encoding of time in new memories. Nature Neuroscience, 9(6), 723-727. for one example). It is only if you don't have a good weight change rule (e.g., STDP) and/or you believe in localist encodings that you need neurogenesis to learn. (shields up! ;-)) g. On Sep 2, 2008, at 12:50 PM, Asim Roy wrote: Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" Jim Bower's response: And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Jim, would love to get some references for your statement:- "development probably recapitulating evolutionary history." This really is the kind of process in the brain that I am looking for. Just a few references would suffice. By the way, learning takes place during development too. Just ask anyone in cognitive science. Development is not disassociated from learning. And ANN never implied learning begins after development. That's a misconception. On the "blank slate" idea in ANN, just look at the phenomenon of adult neurogenesis. Our adult brains generate new cells in the thousands on a daily basis and they are part of the "blank slate" because they don't come with ready-made connections or anything. The process that you refer to as "development probably recapitulating evolutionary history" is called "learning" in ANN. It's that process that constructs networks out of these new cells and makes them operational. Asim Roy Arizona State University -----Original Message----- From: comp-neuro-bounces@neuroinf.org [ mailto:comp-neuro-bounces@neuroinf.org]On Behalf Of james bower Sent: Wednesday, August 27, 2008 9:05 AM To: CompNeuro List Subject: [Comp-neuro] Discussion - Kuhn - and brief comments A few brief comments -- given that school has started, and I now have to prepare to "influence" the latest next generation. First a BIG POINT: Klaus Stiefel: pre-paradigmatic " What he meant by that is a disagreement about the basic explainanda" No, Kuhn was focused on process to quote: "the early developmental stages of most sciences (are) characterized by continual competition between a number of distinct views of nature, each partially derived from, and all roughly compatible with, the dictates of scientific observation and method, (In pre-paradigmatic science) what differentiates these various schools (is) not one or another failure of method - they are all "scientific" - but what we shall come to call their incommensurable ways of seeing the world and practicing science within it" (pg 4 The Structure of Scientific Revolution.) If this discussion over the last two months doesn't make it clear that, as a field, we currently have "incommensurate ways of seeing the world and practicing science within it" I don't know what does. Kuhn goes on to say: "Men (sic) whose research is based on shared paradigms are committed to the same rules and standards for scientific practice." Again, this discussion makes it pretty clear to me that we have not yet reached that point. In fact, (and I would say reflecting this fact) the kind of discussion we have been having here seldom ever happens as we are content (and being pre-paradigmatic can get away with) agreeing to not discuss what we don't agree on, another characteristic of pre-paradigmatic science -- and the reason I don't mind starting these discussions. Bryan Bishop: "There's a few too many layers of folk psychology here," I agree, and have characterized all of biology as fundamentally folkloric in nature -- based on story telling, with few real definitions of anything. Something comp bio (neuro) will, I hope, eventually fix. And on to the approaches we don't agree on: Bryan Bishop: "I bet it becomes clear that trying to do "natural language processing" from statistical inferences doesn't get us as much hard science as the brain could provide." Of course, I agree -- and also agree that this field continues to be distorted by what is essential snake oil we sell to the Department of Defense about how studying the brain will help win wars. This rather self serving commitment to "neuro-morphic engineering" as it is now called, has been distorting our science for a while. In the last 8 years even more dramatically. Mario Negrello: "I'd say instead that some approaches gather more acolytes, and then overflow others in sheer voluminous quantity," Unfortunately, as just noted, very often related to who you are selling the science to (funders) and also, unfortunately, how 'easy' the methods are and therefore how many can jump on the bandwagon without much preparation (or even knowledge of the brain in this case) -- 20 years studying the realistic model of the Purkinje cell and counting. Bard Ermentrout: " I suspect that it would be too hard to adjust parameters for realistic models " Is hard bad? Or is the brain, in fact, hard? Igor Carron: "The groundwork of theory as you put it has, in nuclear technology, always been a way to acquire and use experimental findings." And this, in fact, is the value of theory -- not to capture 'truth' as many in comp neuro seem be believe, but to organize experimental studies -- the more the theory is removed from the actual structure of the brain - the more it exists by itself, disconnected from the ability to improve, or more importantly to refute it. Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Asim Roy: "Is there a way in computational neuroscience to verify any of these theories of learning? " Wrong question. Axel Hutt: " can (neuro)biology really treat a population of some thousand elements ? " We will need to figure out how - numerous groups are working on it. Anibalmastobiza: "cerebellum, usually considered as a center for motor processing and coordination just as it was for the basal ganglia that now we know that is also involve in cognition" While I appreciate the support, I have another question for cognitive neuroscientists, how come anything that lights up in a brain scan becomes a "cognitive center" seems weird to me. Jim ================================== Dr. James M. Bower Ph.D. Professor of Computational Neuroscience Research Imaging Center University of Texas Health Science Center - - San Antonio 8403 Floyd Curl Drive San Antonio Texas 78284-6240 Main Number: 210- 567-8100 Fax: 210 567-8152 Mobile: 210-382-0553 CONFIDENTIAL NOTICE: The contents of this email and any attachments to it may be privileged or contain privileged and confidential information. This information is only for the viewing or use of the intended recipient. If you have received this e-mail in error or are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of, or the taking of any action in reliance upon, any of the information contained in this e-mail, or any of the attachments to this e-mail, is strictly prohibited and that this e-mail and all of the attachments to this e-mail, if any, must be immediately returned to the sender or destroyed and, in either case, this e-mail and all attachments to this e-mail must be immediately deleted from your computer without making any copies hereof and any and all hard copies made must be destroyed. If you have received this e-mail in error, please notify the sender by e-mail immediately. _______________________________________________ Comp-neuro mailing list Comp-neuro@neuroinf.org http://www.neuroinf.org/mailman/listinfo/comp-neuro Gary Cottrell 858-534-6640 FAX: 858-534-7029 Computer Science and Engineering 0404 IF USING FED EX INCLUDE THE FOLLOWING LINE: CSE Building, Room 4130 University of California San Diego - 9500 Gilman Drive # 0404 La Jolla, Ca. 92093-0404 "Only connect!" -E.M. Forster "I am awaiting the day when people remember the fact that discovery does not work by deciding what you want and then discovering it." -David Mermin Email: gary@ucsd.edu Home page: http://www-cse.ucsd.edu/~gary/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080904/595a7e72/attachment.html From ASIM.ROY at asu.edu Thu Sep 4 22:02:17 2008 From: ASIM.ROY at asu.edu (Asim Roy) Date: Fri Sep 5 12:04:28 2008 Subject: [Comp-neuro] Development, Evolution and Learning (was) Discussion - Kuhn - and brief comments In-Reply-To: <6A80976B-6E85-4BC2-88B7-703C2BC08A8D@gmail.com> Message-ID: Perhaps Eugene can respond to some of the questions here. I am sure he understands and can relate to some of the ideas in artificial neural networks. And we of course learn all the time from new discoveries in biology and neuroscience. I believe the sense of the argument here is that learning is simply some "fine tuning" of some existing structures. Adult neurogenesis shows that new networks can be created and put into operation. And that's not some simple "fine tuning." And I believe there is plenty of evidence to show that there is remodeling and reconfiguration in the brain (new connections, synaptic adjustments). Perhaps someone can help out with some references. I don't have anything handy. Asim -----Original Message----- From: comp-neuro-bounces@neuroinf.org [mailto:comp-neuro-bounces@neuroinf.org]On Behalf Of Mario Negrello Sent: Thursday, September 04, 2008 2:17 AM To: CompNeuro List Subject: [Comp-neuro] Development,Evolution and Learning (was) Discussion - Kuhn - and brief comments Asim said: On the "blank slate" idea in ANN, just look at the phenomenon of adult neurogenesis. Our adult brains generate new cells in the thousands on a daily basis and they are part of the "blank slate" because they don't come with ready-made connections or anything. The process that you refer to as "development probably recapitulating evolutionary history" is called "learning" in ANN. It's that process that constructs networks out of these new cells and makes them operational. I guess that this varies with your level of analysis. Developmental recapitulation of evolutionary history is about major brain development, hubs and tracts and gross architecture, those features that are morphologically conspicuous in the brain. Learning is different, it's fine tuning, when an already functional brain develops further functionality by interacting with a complex environment. Moreover, as was pointed out by Cottrell, the new neurons you mention do not sprout anywhere, but presumably, noly where there is a reason or a function for them to do. One of the stories i know about new neurons being generated relates to communication behavior in fish. Fish that produce aggressive calls, grow new cells to make their calls more potent. This was solidly shown in: Dunlap, K.D., et al 2006. Social interaction and cortisol treatment increase cell addition and radial glia fiber density in the diencephalic periventricular zone of adult electric fish, Apteronotus leptorhynchus, Hormones & Behavior 50:10-17. So, between cell addition and brain development there is a considerable distance. I do not suppose that by explaining mechanisms of learning, we shall also understand the functional entailments of particular architectures. For instance, Eugene Izhikevich in a talk in 'Dynamical Systems in Neuroscience' at the NYU in June 2008 (if memory serves me right), showed the last output of his mega brain model. The model has the gross architecture of a human brain as seen through DTI (diffusion tensor imaging), and the microarchitecture derived from rats and cats. What surprised me in terms of the results, was that he claimed that frequencies measured from the model resembled those known from their correspodent areas of the brain. Alpha in V1, Theta in hippocampus, and others. I take that to mean that many functional capabilities of the brain will be effectively only learneable if the proper architecture is there. Else, if it were only learning, there would be little reason for a cat to be unable to learn the things a human does. Surely, one can draw analogies from evolution, through development, until learning. One can amalgamate all and say that they are all 'metastable adaptations', or something. But so far, the clear divisions that appear between the study of each, are fully justified: we need theories for each. For all, later. Learning needs its story as much as development. Gruss, M. -----Original Message----- From: comp-neuro-bounces@neuroinf.org [ mailto:comp-neuro-bounces@neuroinf.org]On Behalf Of james bower Sent: Wednesday, August 27, 2008 9:05 AM To: CompNeuro List Subject: [Comp-neuro] Discussion - Kuhn - and brief comments A few brief comments -- given that school has started, and I now have to prepare to "influence" the latest next generation. First a BIG POINT: Klaus Stiefel: pre-paradigmatic " What he meant by that is a disagreement about the basic explainanda" No, Kuhn was focused on process to quote: "the early developmental stages of most sciences (are) characterized by continual competition between a number of distinct views of nature, each partially derived from, and all roughly compatible with, the dictates of scientific observation and method, (In pre-paradigmatic science) what differentiates these various schools (is) not one or another failure of method - they are all "scientific" - but what we shall come to call their incommensurable ways of seeing the world and practicing science within it" (pg 4 The Structure of Scientific Revolution.) If this discussion over the last two months doesn't make it clear that, as a field, we currently have "incommensurate ways of seeing the world and practicing science within it" I don't know what does. Kuhn goes on to say: "Men (sic) whose research is based on shared paradigms are committed to the same rules and standards for scientific practice." Again, this discussion makes it pretty clear to me that we have not yet reached that point. In fact, (and I would say reflecting this fact) the kind of discussion we have been having here seldom ever happens as we are content (and being pre-paradigmatic can get away with) agreeing to not discuss what we don't agree on, another characteristic of pre-paradigmatic science -- and the reason I don't mind starting these discussions. Bryan Bishop: "There's a few too many layers of folk psychology here," I agree, and have characterized all of biology as fundamentally folkloric in nature -- based on story telling, with few real definitions of anything. Something comp bio (neuro) will, I hope, eventually fix. And on to the approaches we don't agree on: Bryan Bishop: "I bet it becomes clear that trying to do "natural language processing" from statistical inferences doesn't get us as much hard science as the brain could provide." Of course, I agree -- and also agree that this field continues to be distorted by what is essential snake oil we sell to the Department of Defense about how studying the brain will help win wars. This rather self serving commitment to "neuro-morphic engineering" as it is now called, has been distorting our science for a while. In the last 8 years even more dramatically. Mario Negrello: "I'd say instead that some approaches gather more acolytes, and then overflow others in sheer voluminous quantity," Unfortunately, as just noted, very often related to who you are selling the science to (funders) and also, unfortunately, how 'easy' the methods are and therefore how many can jump on the bandwagon without much preparation (or even knowledge of the brain in this case) -- 20 years studying the realistic model of the Purkinje cell and counting. Bard Ermentrout: " I suspect that it would be too hard to adjust parameters for realistic models " Is hard bad? Or is the brain, in fact, hard? Igor Carron: "The groundwork of theory as you put it has, in nuclear technology, always been a way to acquire and use experimental findings." And this, in fact, is the value of theory -- not to capture 'truth' as many in comp neuro seem be believe, but to organize experimental studies -- the more the theory is removed from the actual structure of the brain - the more it exists by itself, disconnected from the ability to improve, or more importantly to refute it. Asim Roy: "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -" And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history. Another reason why the mainstream ANN models make no sense. Asim Roy: "Is there a way in computational neuroscience to verify any of these theories of learning? " Wrong question. Axel Hutt: " can (neuro)biology really treat a population of some thousand elements ? " We will need to figure out how - numerous groups are working on it. Anibalmastobiza: "cerebellum, usually considered as a center for motor processing and coordination just as it was for the basal ganglia that now we know that is also involve in cognition" While I appreciate the support, I have another question for cognitive neuroscientists, how come anything that lights up in a brain scan becomes a "cognitive center" seems weird to me. Jim ================================== Dr. James M. Bower Ph.D. Professor of Computational Neuroscience Research Imaging Center University of Texas Health Science Center - - San Antonio 8403 Floyd Curl Drive San Antonio Texas 78284-6240 Main Number: 210- 567-8100 Fax: 210 567-8152 Mobile: 210-382-0553 CONFIDENTIAL NOTICE: The contents of this email and any attachments to it may be privileged or contain privileged and confidential information. This information is only for the viewing or use of the intended recipient. If you have received this e-mail in error or are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of, or the taking of any action in reliance upon, any of the information contained in this e-mail, or any of the attachments to this e-mail, is strictly prohibited and that this e-mail and all of the attachments to this e-mail, if any, must be immediately returned to the sender or destroyed and, in either case, this e-mail and all attachments to this e-mail must be immediately deleted from your computer without making any copies hereof and any and all hard copies made must be destroyed. If you have received this e-mail in error, please notify the sender by e-mail immediately. _______________________________________________ Comp-neuro mailing list Comp-neuro@neuroinf.org http://www.neuroinf.org/mailman/listinfo/comp-neuro -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080904/f426ee5d/attachment.html From carnevalet at sbcglobal.net Sun Sep 7 18:33:51 2008 From: carnevalet at sbcglobal.net (Ted Carnevale) Date: Mon Sep 8 09:50:20 2008 Subject: [Comp-neuro] NEURON course reminder: seats still available Message-ID: <48C4026F.809@sbcglobal.net> Registration is still open for "Using NEURON to Model Cells and Networks", the course that we will present on November 14, 2008, in Washington, DC as a satellite to the SFN meeting. For information about the course and an on-line registration form, see http://www.neuron.yale.edu/dc2008.html --Ted From mail at jan-peters.net Sat Sep 6 16:15:47 2008 From: mail at jan-peters.net (Jan Peters) Date: Mon Sep 8 09:51:24 2008 Subject: [Comp-neuro] CfP: Autonomous Robots - Special Issue on Robot Learning Message-ID: <907549EC-999B-4E8B-AA1B-5EC17FEA5473@jan-peters.net> Please be reminded of the Call for Papers for the Special Issue on Robot Learning of the Autonomous Robots journal! If you have questions, please contact us by email ASAP or talk to Jan Peters during IROS 2008! Best wishes, Jan Peters & Andrew Ng = = = ======================================================================== Call For Papers: Autonomous Robots - Special Issue on Robot Learning = = = ======================================================================== Quick Facts ========= Editors: Jan Peters, Max Planck Institute for Biological Cybernetics, Andrew Y. Ng, Stanford University Journal: Autonomous Robots Submission Deadline: November 8, 2008 Author Notification: March 1, 2009 Revised Manuscripts: June 1, 2009 Approximate Publication Date: 4th Quarter, 2009 Abstract ====== Creating autonomous robots that can learn to act in unpredictable environments has been a long standing goal of robotics, artificial intelligence, and the cognitive sciences. In contrast, current commercially available industrial and service robots mostly execute fixed tasks and exhibit little adaptability. To bridge this gap, machine learning offers a myriad set of methods some of which have already been applied with great success to robotics problems. Machine learning is also likely play an increasingly important role in robotics as we take robots out of research labs and factory floors, into the unstructured environments inhabited by humans and into other natural environments. To carry out increasingly difficult and diverse sets of tasks, future robots will need to make proper use of perceptual stimuli such as vision, lidar, proprioceptive sensing and tactile feedback, and translate these into appropriate motor commands. In order to close this complex loop from perception to action, machine learning will be needed in various stages such as scene understanding, sensory-based action generation, high-level plan generation, and torque level motor control. Among the important problems hidden in these steps are robotic perception, perceptuo-action coupling, imitation learning, movement decomposition, probabilistic planning, motor primitive learning, reinforcement learning, model learning, motor control, and many others. Driven by high-profile competitions such as RoboCup and the DARPA Challenges, as well as the growing number of robot learning research programs funded by governments around the world (e.g., FP7-ICT, the euCognition initiative, DARPA Legged Locomotion and LAGR programs), interest in robot learning has reached an unprecedented high point. The interest in machine learning and statistics within robotics has increased substantially; and, robot applications have also become important for motivating new algorithms and formalisms in the machine learning community. In this Autonomous Robots Special Issue on Robot Learning, we intend to outline recent successes in the application of domain-driven machine learning methods to robotics. Examples of topics of interest include, but are not limited to: ? learning models of robots, task or environments ? learning deep hierarchies or levels of representations from sensor & motor representations to task abstractions ? learning plans and control policies by imitation, apprenticeship and reinforcement learning ? finding low-dimensional embeddings of movement as implicit generative models ? integrating learning with control architectures ? methods for probabilistic inference from multi-modal sensory information (e.g., proprioceptive, tactile, vision) ? structured spatio-temporal representations designed for robot learning ? probabilistic inference in non-linear, non-Gaussian stochastic systems (e.g., for planning as well as for optimal or adaptive control) From several recent workshops, it has become apparent that there is a significant body of novel work on these topics. The special issue will only focus on high quality articles based on sound theoretical development as well as evaluations on real robot systems. Time Line ======== Submission Deadline: November 8, 2008 Author Notification: March 1, 2009 Revised Manuscripts: June 1, 2009 Approximate Publication Date: 4th Quarter, 2009 Editors ====== Inquiries on this special issue should be send to one of the editors listed below. Jan Peters (http://www.jan-peters.net/) Senior Research Scientist, Head of the Robot Learning Laboratory Department for Machine Learning and Empirical Inference, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany Andrew Y. Ng (http://ai.stanford.edu/~ang/) Assistant Professor Department of Computer Science, Stanford University, Palo Alto, USA From schwaber at mail.dbi.tju.edu Fri Sep 5 21:48:58 2008 From: schwaber at mail.dbi.tju.edu (James Schwaber) Date: Mon Sep 8 09:53:17 2008 Subject: [Comp-neuro] Discussion - Kuhn - and brief comments Message-ID: <48C18D2A.1050905@mail.dbi.tju.edu> This post provides a view of the disagreement about whether there is a comp-neuro paradigm. It argues that there is, but that in light of new data we can no longer believe the paradigm's core assertion, around which the field is organized, that a structural foundation underlying input-output electrophysiology is the fundamental unit for brain analysis. The comp-neuro paradigm is well-entrenched in this forum and in the homogeneous culture of communities that gather for the CNS meeting, CRCNS reviews, as NEURON-GENESIS users, etc. The paradigm formalizes the data and ideas developed in the classical era of neuroscience, extending into the early 80's. This era was dominated by experiments on tract-tracing/connectionism, neurophysiology and channels, and these were motivated by the ideas of that time as to 'how the brain works', as in the following 3 premises: (1) The neuron is the fundamental unit for analysis, a neuron's input-output membrane electrophysiology defines its function, and this arises from the detailed, precise structure of the neuron's somatic morphology, dendrite morphology and synapse-channel locations on same. (2) These specific neuronal structures are essentially structurally fixed, and are located in functionally specific connectional circuit architectures. (3) Neuronal structure and circuit architecture are the fingerprint of natural selection, the result of evolution's genetic program and thus it all "matters" - the brain is "Kolmogorov Complexity Complete" (KCC) - at a first approximation brain function (traits, behaviors, minds) arises from the naturally selected, structurally fixed, functionally specific structures as instinctive-ethological type outputs, approaching fixed action patterns. The comp-neuro paradigm has been immensely productive, arguably the most successful use of modeling within biology. However, equally arguably, progress has greatly slowed. Worse, its agenda now, at the limit, calls for 'KCC complete' type goals that are heroic if not completely out of bounds. Worst of all, the value in completing these goals appears questionable in light of more contemporary approaches such as systems biology, which for example shows that great 'biological variability (noise)' is expected, generates robust systems, and is normal among and within neurons. Even more important than the above difficulties within the comp-neuro paradigmatic structure itself is the fact that, from the early 80s on, neuroscience has undergone a technical revolution that has produced a wealth of new data and approaches, and these new data and ideas are not accounted for in the comp-neuro paradigm. For example: (1) Work in contemporary neuroscience emphasizes receptor complexity leading to combinatorially derived phenotype or function, including non-synaptic inputs and dominated by inputs not coupled to ion channels, without direct electrophysiological effects. By these mechanisms environmental experience is read and encoded. A neuron's receptor profile has downstream effects on signaling networks, gene networks and function. All these layers are interconnected by feedback, and each layer (signaling, genes, receptors, neurons etc.) is organized in networks that have nonlinear dynamics. The functional impact includes channel state, type, density, location but also has many dimensions beyond electrophysiology. If all this is true, then the first premise above is not. (2) Directly related to this is the known plasticity in modulators, networks and cellular physiology such that neurons are constantly changing, not in a structural steady state. This produces flexibility and variability in structural organization and in function. Similarly, at a higher level, the work of Mezernich and of Greenough and others on brain plasticity-remodeling comes to mind here, as well as the emerging literature on adult stem cells. If all this is true, then the second premise above is not. (3) The evidence from functional genomics and signaling systems likewise is not consistent with a structurally committed brain, but rather one using diverse strategies and ongoing remodeling, nor are recent epigenomic developments, suggesting rapid, current evolution of traits. The kind of genetic determinism inherent in the comp-neuro paradigm is na?ve. If all this is true, then the third premise is not. A new computational paradigm for neuroscience arguably not only has to account for these and other new data but also needs to develop a guiding concept of 'how brains work' that organizes the data, putting adaptive remodeling and fungible interactions of nonlinear dynamical networks in functional process in a central role. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080905/16e55863/attachment-0001.html From dchristi at med.cornell.edu Mon Sep 8 21:15:56 2008 From: dchristi at med.cornell.edu (David J. Christini) Date: Tue Sep 9 09:23:24 2008 Subject: [Comp-neuro] Announcement: PhD program in computational neuroscience - The Tri-Institutional Training Program in Computational Biology and Medicine Message-ID: Dear Colleagues, Please inform students interested in neuroscience PhD programs about the Tri-Institutional Training Program in Computational Biology and Medicine (CBM). CBM takes advantage of the outstanding educational and research resources of Cornell University in Ithaca, NY, the Weill Cornell Medical College in New York City, and the Sloan-Kettering Institute (the research arm of the Memorial Sloan-Kettering Cancer Center) to train computational biologists in the interdisciplinary approaches (quantitative and experimental) they need to solve the complex problems that characterize biology and medicine. This PhD program is recruiting highly qualified students from biological science and/or quantitative backgrounds. Neuroscience is one of CBM's main focus areas. Please contact cbm@triiprograms.org or visit www.triiprograms.org/cbm for more information. Thank you very much. Sincerely, David Christini Director, CBM Program From mail at jan-peters.net Tue Sep 9 11:04:13 2008 From: mail at jan-peters.net (Jan Peters) Date: Tue Sep 9 11:20:45 2008 Subject: [Comp-neuro] Junior Research Groups for Systems Neuroscience, Cognitive Neuroscience and Neurorobotics/Medical Robotics Message-ID: <63382CE4-A719-4C12-87E7-D8425EFCEA99@jan-peters.net> Junior Research Groups for Cognitive Neuroscience and Systems Neuroscience at the Werner Reichardt Centre for Integrative Neuroscience (CIN) The Werner Reichardt Centre for Integrative Neuroscience (CIN) is a newly established interdisciplinary institution at the Eberhard Karls University T?bingen funded by the German Excellence Initiative program. The CIN strives to deepen our understanding of how the brain generates function and how brain diseases impair functions. It will make use of newly acquired insights to help people with brain disorders and to launch new mind- and brain-inspired applications in many areas of engineering and computer science. Its scientific program is guided by the conviction that progress in the understanding of brain function can only be achieved with an integrative approach spanning multiple levels of organization and pooling the knowledge of researchers from many different fields. In order to strengthen the CINs' specific research aims, we are offering several junior group leader (JRG) positions (equivalent to Assistant Professorship) with tenure track options in the fields of ?Systems Neuroscience?, ?Cognitive Neuroscience?, ?Neurophilosophy? and ?Neurorobotics/Medical Robotics?. Submission deadline is Oct. 15th, 2008 (for Neurophilosophy Oct. 31st, 2008). Framework The intended duration of the position is for 5 years with evaluations by external experts at regular intervals. In case of positive evaluations after 3 years, the JRG will obtain a tenure track option, which may ultimately lead to a professorship at the University of T?bingen. Start-up funds as well as substantial funding for personnel and running costs will be available, but will depend on the qualification and prior experience of the applicant. Appointees will be full members and active participants in the CIN, which will also provide laboratory and/or office space. The JRG leader will be provided opportunities to contribute to research oriented training within the framework of the CIN Graduate Training Centre and the faculties involved in the CIN will provide opportunities for the German habilitation according to established rules, if desired. According to German law, severely disabled persons with equal occupational aptitude will be given preferred consideration. The University of T?bingen strives to promote equal opportunities in science and is committed to increasing the percentage of female scientists in teaching and research. Qualified female candidates are thus strongly encouraged to apply. Application Applicants should submit a curriculum vitae, pdf files of up to 5 key publications, statements of research achievements and future directions (not to exceed 3 pages) as well as the names and addresses of at least three referees. All documents should be submitted electronically to the Acting Director of the Werner Reichardt Centre for Integrative Neuroscience T?bingen, Prof. Dr. Peter Thier, at cin@uni-tuebingen.de. For further information on the CIN see: http://www.neuroscience-tuebingen.de/cin/. Submission deadline for all applications is Oct. 15th, for applications in the field of Neurophilosophy Oct. 31st. From harry.erwin at sunderland.ac.uk Tue Sep 9 13:16:07 2008 From: harry.erwin at sunderland.ac.uk (Harry Erwin) Date: Tue Sep 9 15:18:18 2008 Subject: [Comp-neuro] Calcium Spikes Concluded Message-ID: <044A905C-8F6B-4CE9-B96F-2FE3DE0A39BF@sunderland.ac.uk> My thanks to Andreas Schaefer for pointing me at Rhodes and Llinas (2005) "A model of thalamocortical relay cells", J Physio, 565.4: 765-781, which is an excellent study of the question. Their model appears to be good at describing what we also see in inferior colliculus rebound neurones, raising the question of why this single neurone type lends itself to two different functions. (IC rebound neurones seem to measure time intervals between sounds--we get remarkable duration hyperacuity in bats--on the order of 100 nanoseconds measured behaviourally by multiple labs. Jim Simmons has indicated about 10 nanoseconds , but that value is subject to argument.) Perhaps the two types of neurones aren't really different in what they do. -- Harry Erwin, PhD, Senior Lecturer of Computing, University of Sunderland. Computational neuroethologist: http://scat-he-g4.sunderland.ac.uk/~harryerw/phpwiki/index.php/AuditoryResearch From dglanzma at mail.nih.gov Tue Sep 9 18:00:10 2008 From: dglanzma at mail.nih.gov (Glanzman, Dennis (NIH/NIMH) [E]) Date: Tue Sep 9 18:19:07 2008 Subject: [Comp-neuro] Neuronal Variability and its Functional Significance Message-ID: <0EE5F9DA83318D47B16FB45A5CBA4A4A02C1887E@nihcesmlbx2.nih.gov> CALL FOR POSTERS 16th Annual Dynamical Neuroscience Satellite Symposium "Neuronal Variability and its Functional Significance" Preceding the 38th Annual Meeting of the Society for Neuroscience Thursday and Friday, November 13-14, 2008 The Capital Ballroom of the JW Marriott Hotel 1331 Pennsylvania Avenue Washington, DC The brain is restless. Physiological data recorded from the brain often have random-appearing components. Repeated stimuli evoke responses that are not identical from trial to trial. Not too long ago this variability was dismissed as noise and, through techniques such as signal averaging, removed from further consideration. More recent work has begun to examine the rich content of this variability and shed light on its functional consequences. Neural variability and noise has become an active field of research, generating a wealth of new knowledge and information. This symposium will assess the current status of four related areas: Characterizing Neuronal Variability; The Dynamics of Neural Ensembles; Neural Variability and Cognition; Neural Variability and Brain Disorders. Invited Speakers: Henry Abarbanel, Larry Abbott, Emery Brown, Richard Coppola Charles Gray, Terran Lane, Daeyeol Lee, Stephen Lisberger, Helen Mayberg Anna Roe, Nicholas Schiff, Charles Schroeder, Richard Stein and Akaysha Tang Keynote Address Presented by the inaugural recipient of the Swartz Prize for Theoretical and Computational Neuroscience Symposium Organizers: Mingzhou Ding, University of Florida Dennis Glanzman, NIMH/NIH For programmatic information, please contact: D. Glanzman National Institute of Mental Health 6001 Executive Boulevard, Rockville, MD 20857 Telephone: (301) 443-1576 Register for the meeting, and to submit a poster abstract (October 17 deadline for abstracts) here: http://neuro.dgimeetingsupport.com, or, contact: Nakia Wilson Telephone: (877) 772-9111 From nurban at cmu.edu Tue Sep 9 23:29:09 2008 From: nurban at cmu.edu (Nathan Urban) Date: Wed Sep 10 09:51:30 2008 Subject: [Comp-neuro] Postdoc positions in high dimensional data analysis for olfactory coding Message-ID: <48C6EAA5.6080802@cmu.edu> Two postdoctoral positions are available in the lab of Nathan Urban at Carnegie Mellon University to work as part of a DARPA-funded project (REALNOSE http://www.darpa.mil/dso/solicitations/baa07-21mod11.htm) on analysis of data from arrays of biologically-based chemical sensors. This position is part of a large multi-investigator project involving collaboration with biologists, engineers and computer scientists at several institutions. The ideal candidates would posses either 1) a Ph.D. in computer science, statistics or engineering and have experience with analyusis of high-dimensional data, including the use of supervised and unsupervised learning techniques such as nonparametric regression, clustering, and visualization. or 2) a Ph. D. in neuroscience, applied math or physics and have experience in developing spiking neuron and/or network simulations and have some familiarity with sensory systems. The positions offer an excellent training environment and excellent opportunities for collaboration with others in computational neuroscience, including those at Carnegie Mellon University and the University of Pittsburgh. Interested candidates should send a CV, statement of research experience and interests, and names and contact information for 3 references by e-mail to Dr. Nathan Urban, Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave. Pittsburgh PA 15213. e-mail nurban@cmu.edu. -- ____________________________________________ Nathan Urban, Ph.D. Associate Professor Department of Biological Sciences and Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave Pittsburgh PA 15213 ph. 412-268-5122 fax 412-268-8423 http://www.andrew.cmu.edu/user/nurban/Lab_pages/ From bard at math.pitt.edu Wed Sep 10 16:01:46 2008 From: bard at math.pitt.edu (G. Bard Ermentrout) Date: Wed Sep 10 17:00:13 2008 Subject: [Comp-neuro] postdoctoral position available Message-ID: Announcing a postdoc position at University of Pittsburgh Postdoctoral position available immediately for computational neuroscience. Topics of interest include but are not restricted to modeling spontaneous activity, waves, and synchronous oscillations in neuronal models and phase reseting curves in noisy and complex milieus. Applicants should have a good knowledge of basic concepts in nonlinear dynamics and a strong interest in applying this to neurobiological problems. Knowledge of neurosceince is useful but not necessary. The ability to write simulation code (either in MatLab, XPP, or C/C++) is also useful. This position is NSF funded for two years, and a competitive salary is available for qualified candidates. Pittsburgh is a medium-sized city with a relatively low cost of living and many of the amenities and cultural opportunities of a larger city. The Neuroscience community in Pittsburgh is large and very diverse with more than 100 faculty members affiliated with the Center for Neuroscience at the University of Pittsburgh ( CNUP ). Successful candidates would also have the opportunity to join the Center for the Neural Basis of Cognition ( CNBC ) which is a joint University of Pittsburgh/CMU center that involves 70 Faculty from the two Universities. Interested candidates should send (preferably via e-mail) their c.v. and the names and addresses of three references to Professor Bard Ermentrout, Department of Mathematics, University of Pittsburgh Pittsburgh, PA 15260 e-mail: bard+@pitt.edu For more information contact: Dr. Bard Ermentrout bard+@pitt.edu http://www.pitt.edu/~phase/ From dayalparhi at yahoo.com Thu Sep 11 06:31:51 2008 From: dayalparhi at yahoo.com (dayal parhi) Date: Thu Sep 11 09:07:10 2008 Subject: [Comp-neuro] Call for paper in International Journal In-Reply-To: <3774.147.197.165.232.1221032197.squirrel@castafiore.cde.ua.ac.be> Message-ID: <496077.57717.qm@web51801.mail.re2.yahoo.com> Dear Members, International Journal of Applied Artificial Intelligence in Engineering System publishes paper mainly on AI,Mechatronics, Nano Materials, MEMS, robotics. A special issue will come in December 2008. Dead line for submission of papers is 15th October 2008. Please visit the website for detail; "http://www.serialspublications.com/journals1.asp?jid=219&dtype=1&jtype=1" Best regards! Dr. Dayal R. Parhi Department of Mechanical Engineering National Institute of Technology Rourkela , Pin: 769008. Orissa , India Phone: ++916612464509 From vcu at cs.stir.ac.uk Thu Sep 11 10:35:12 2008 From: vcu at cs.stir.ac.uk (Dr. Vassilis Cutsuridis) Date: Thu Sep 11 12:00:08 2008 Subject: [Comp-neuro] Second CfP Neural Networks journal Special Issue on Cortical Microcircuits Message-ID: <002501c913e9$4eea5ea0$99e3e98f@Zeus> Second Call for Papers: Neural Networks Journal Special Issue on ======= Cortical Microcircuits ======== (formerly known as Neural models of Cortical microcircuits) Guest Editors: J.G. Taylor, T. Wennekers, B.P. Graham, I. Vida, V. Cutsuridis Special issue of the Elsevier Journal of Neural Networks http://helen.pion.ac.uk/microcircuits08 = SCOPE = To understand how perception, attention, action, learning and memory work, we need to gather data from multiple levels of complexity and from various brain states (normal and diseased) and integrate them at the brain-scale level. We need to identify the neuronal groups involved in these functions, their laminar distributions and their different types of neurons, draw detailed circuit diagrams, determine the forms of synaptic transmission and plasticity between different neurons and study the dynamics of the cortical microcircuits at the cellular and synaptic level that comprise these neuronal groups. Recent years have witnessed a dramatic accumulation of knowledge about the morphological, physiological and molecular characteristics, as well as the connectivity and synaptic properties of cortical neurons. Despite these advances, however, only limited insight was gained into the computational function of the neurons; in particular, the role of the various types of interneurons remains elusive. Mathematical and computational microcircuit models play an instrumental role in exploring microcircuit functions and facilitate the dissection the operations performed by diverse interneurons. The goal of the special issue is to provide a snapshot and a resum? of the current state-of-the-art of the ongoing research avenues concerning cortical microcircuits with particular emphasis on the functional roles of the various inhibitory interneurons in information processing within normal and diseased behavioural and cognitive states. The emphasis will be on computational models that are tightly grounded on experimental data. = SPECIFIC AIMS = - The interaction between the local micro circuit activity and global processing to achieve the desired overall processing functionality observed, say in perception and action, attention, learning and memory - Microcircuit architectures: networks of principal and inhibitory inter-neurons within and between lamina, columns, mini-columns, modules, areas and/or across areas in the brain and their functional roles in the network. -- Neo-cortex -- Hippocampus -- Sensory and Motor Systems - Cross-comparison of architectures from different brain areas - Identified computations performed by each type of neuron in a network - Identified modes of operation of a neuronal type and how they are related potentially to behaviour and cognition - What synaptic plasticity rules are used = SUBMISSIONS = New *extended* submission deadline: February 1st, 2009 Electronic submissions for the Neural Networks journal can be found under http://ees.elsevier.com/neunet/ Please indicate in your cover letter that your article is for the special issue "Cortical Microcircuits" Regards, Vassilis ---------------------------------------------------------------------------------- Dr. Vassilis Cutsuridis Department of Computing Science and Mathematics University of Stirling Stirling FK9 4LA SCOTLAND Tel: +44 1786 467422 Fax: +44 1786 464551 Email: vcu@cs.stir.ac.uk Web: http://www.cs.stir.ac.uk/~vcu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080911/446ecccc/attachment.html From I.Bojak at donders.ru.nl Thu Sep 11 20:35:20 2008 From: I.Bojak at donders.ru.nl (Ingo Bojak) Date: Fri Sep 12 09:59:09 2008 Subject: [Comp-neuro] PhD position in Computational Neuroscience (4 year contract), Radboud University Nijmegen Message-ID: <48C964E8.8040507@donders.ru.nl> Candidate profile The successful candidate has a strong background in physics and/or mathematics, is competent in applying numerical methods, and shows some grasp of, and great interest in, computational neuroscience. The main tasks of this research project involve theoretical calculations, computer simulations and experimental data analyses, using MATLAB. Specific methods and relevant background knowledge will be taught to the candidate ?on the job?, providing an excellent opportunity for an enthusiastic researcher to specialize in an exciting new field. Research topic Neuronal oscillations in the gamma frequency range (30-100 Hz) play a crucial role in information processing. Since gamma activity is effective in activating other neurons, the question arises which mechanism prohibits gamma activity to activate an ever-increasing number of neurons. Many focal epileptic seizures start with an increase of gamma activity with abnormal spreading. We will investigate the special role of inhibitory interneurons in the generation of a robust gamma rhythm. The hypothesis that some inhibitory regulation is disturbed in epileptic patients will be tested using mathematical analyses and extensive computer simulations of interactions between single neurons and populations of neurons. The results of these approaches will be compared to data in large databases at the Academic Hospital of the University Utrecht, obtained by subdural recordings in patients with normal task-related gamma activity and with epileptic seizures. The results of this project may allow pro-active recognition of starting epileptic activity. Research environment The Department of Biophysics of the Radboud University Nijmegen is part of the Centre for Neuroscience (http://www.ru.nl/dcn) within the Donders Institute for Brain, Cognition and Behaviour (http://www.ru.nl/donders/). The Donders Institute hosts many excellent researchers and owns advanced infrastructure and equipment, such as a PC-cluster for fast computer simulations. The offered PhD position is part of a large project in Computational Life Science, funded by the Dutch Science Foundation (NWO). The grant also includes 2 post-docs and another PhD student, and is a collaboration of several senior researchers at Radboud University and at the Mathematics Department of the University of Twente. Living in The Netherlands / Nijmegen The Netherlands are well-known as a liberal and modern European country with a unique and distinguished culture. It is one of most densely populated urban regions of the world, but the vibrant border city of Nijmegen (http://www.nijmegen.nl/) also offers access to the beautiful Dutch/German ?Lower Rhine? countryside. Salary Estimated gross salary: from about ?2050/month in the first year to ?2600/month in the last year (Dutch University Salaryscale 10), plus an 8% annual supplement and end-of-year bonus. For more information, please contact Prof. Dr. C. Gielen (S.Gielen@donders.ru.nl). From aonken at cs.tu-berlin.de Sat Sep 13 13:55:05 2008 From: aonken at cs.tu-berlin.de (Arno Onken) Date: Mon Sep 15 09:38:59 2008 Subject: [Comp-neuro] Call for Abstracts: NIPS Workshop 2008 Message-ID: <48CBAA19.9070808@cs.tu-berlin.de> You are invited to participate in the post-conference NIPS workshop "Statistical Analysis and Modeling of Response Dependencies in Neural Populations", taking place in Whistler, Canada, on December 12-13, 2008. It is well known that sensory and motor information is represented in the activity of large populations of neurons. Encoding and decoding is subject of active research. The two dominant theories of neural coding are rate and temporal coding. They are studied by considering the dependencies between responses of several neurons. In the typical theoretical framework, response dependencies are characterized by correlation coefficients and cross-correlograms. The main goal of this workshop is to challenge the dependency concepts that are typically applied and to disseminate more sophisticated concepts to a wider public. It will bring together experts from different fields and encourage exchange of insights between experimentalists and theoreticians. To participate in the workshop please submit an extended abstract as a two-page PDF attachment via email to aonken@cs.tu-berlin.de. The deadline for submission is October 15. The workshop chairs will select a couple of abstracts for oral presentation at the workshop. The other abstracts will be presented as posters on December 12. We are looking forward to seeing you in Whistler. Klaus Obermayer, Valentin Dragoi, Arno Onken, Steffen Gruenewaelder and Denise Berger (Workshop organizers) List of speakers (confirmed): * Wyeth Bair (University of Oxford) * Jeff Beck (University of Rochester) * Pietro Berkes (Brandeis University) * Valentin Dragoi (University of Texas, Workshop Chair) * Arnulf Graf (New York University) * Sonja Gr?n (RIKEN Brain Science Institute) * Rick Jenison (University of Wisconsin-Madison) * Dimitris Karlis (Athens University) * Stephen Lisberger (University of California, San Francisco) * Jakob Macke (Max Planck Institute for Biological Cybernetics) * Naoki Masuda (University of Tokyo) Workshop URL: http://ni.cs.tu-berlin.de/projects/nips2008/ From v.steuber at herts.ac.uk Mon Sep 15 12:49:09 2008 From: v.steuber at herts.ac.uk (Volker Steuber) Date: Mon Sep 15 13:32:21 2008 Subject: [Comp-neuro] PhD Studentship in Computational Neuroscience Message-ID: <48CE3DA5.1040804@herts.ac.uk> PhD Studentship in Computational Neuroscience Science and Technology Research Institute University of Hertfordshire UK Applications are invited for a 3 year PhD Studentship in Computational Neuroscience in the Science and Technology Research Institute at the University of Hertfordshire, UK. The studentship will cover a stipend of ?12,940 per year plus payment of the standard UK student fees. Candidates should be interested in information processing in biologically detailed models of neuronal networks. Our research involves close collaboration with experimentalists in Europe and the USA. More details can be found in these recent publications: Steuber, V., Mittmann, W., Hoebeek, F.E., Silver, R.A., De Zeeuw, C.I., Hausser, M. and De Schutter, E. (2007). Cerebellar LTD and pattern recognition by Purkinje cells. Neuron 54, 121-136. Gleeson, P., Steuber, V. and Silver, R.A. (2007). neuroConstruct: A tool for modeling networks of neurons in 3D space. Neuron 54, 219-35. Calcraft L., Adams R. and Davey N. (2007). Efficient Architectures for Sparsely-Connected High Capacity Associative Memory Models, Connection Science 6, 163-75. Applicants should have good computational and numerical skills and a good first degree in maths, computer science, physics, neuroscience or biology. Previous experience in neuroscience is not required but would be an advantage. The UH Science and Technology Research Institute has been rated as 4 (national excellence with evidence of international excellence) at the last UK university research assessment exercise. It is located in Hatfield in Hertfordshire, just north of London. For informal enquiries contact Dr Volker Steuber (v.steuber@herts.ac.uk ) or Dr Neil Davey (n.davey@herts.ac.uk ). Further information and an application form can be obtained from Mrs Lorraine Nicholls, Research Student Administrator, STRI, Faculty of Engineering and Information Sciences, University of Hertfordshire, College Lane, Hatfield, Herts, AL10 9AB. Tel: +44 1707 286083 Fax: +44 1707 284185 email: l.nicholls@herts.ac.uk. The short-listing process will begin on 1 October 2008. Dr Volker Steuber Senior Lecturer (Research) in Biocomputation Science and Technology Research Institute University of Hertfordshire Hatfield Herts AL10 9AB UK Tel +44 1707 284350 http://homepages.feis.herts.ac.uk/~comqvs/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080915/1ab45d2f/attachment.html From sabine.hauert at gmail.com Mon Sep 15 18:12:03 2008 From: sabine.hauert at gmail.com (Sabine Hauert) Date: Tue Sep 16 09:11:46 2008 Subject: [Comp-neuro] CFP: Special Session on Evolutionary Robotics - IEEE CEC 2009 Message-ID: <2d93ff9e0809150912w552c3a65ybeee7d0c4ba07fb3@mail.gmail.com> * Apologies for multiple postings * ================================================ CALL FOR PAPERS IEEE CEC 2009 - Special Session on "Evolutionary Robotics" Trondheim, Norway, 18th-21st of May, 2009 http://lis.epfl.ch/specialsessions/CEC09/ http://lis.epfl.ch/specialsessions/CEC09/CFP.pdf Paper submission deadline: 1st of November 2008 ================================================ ORGANISERS Patricia A. Vargas (University of Sussex) Sabine Hauert (EPFL-Lausanne) Dario Floreano (EPFL-Lausanne) Phil Husbands (University of Sussex) DESCRIPTION Evolutionary Robotics (ER) aims to apply evolutionary computation techniques, inspired by Darwin's principle of selective reproduction of the fittest, to automatically design the control and/or hardware of both real and simulated autonomous robots. Having an intrinsic interdisciplinary character, ER is being employed towards the development of many fields of research, among which we can highlight neuroscience, cognitive science, evolutionary biology and robotics. Hence the objective of this special session is to assemble a set of high-quality original contributions that reflect and advance the state-of-the-art in the area of Evolutionary Robotics, with an emphasis on the cross-fertilization between ER and the aforementioned research areas, ranging from theoretical analysis to real-life applications. Topics of interest include (but are are not restricted to): * Evolution of robots which display minimal cognitive behaviour, learning, memory, spatial cognition, adaptation or homeostasis. * Evolution of neural controllers for robots, aimed at giving an insight to neuroscientists or advancing control structures. * Evolution of communication, cooperation and competition, using robots as a research platform. * Co-evolution and the evolution of collective behaviour. * Evolution of morphology in close interaction with the environment, giving rise to self-reconfigurable, self-designing, self-healing and self-reproducing robots or humanoid and walking robots. * Evolution of robot systems aimed at real-world applications as in aerial robotics, space exploration, industry, search and rescue, robot companions, entertainment and games. * Evolution of controllers on board real robots or the real-time evolution of robot hardware. * Novel or improved algorithms for the evolution or robot systems. * The use of evolution for the artistic exploration of robot design. PAPER SUBMISSION Submissions should follow the guidance given on the IEEE CEC 2009 conference website: http://www.cec-2009.org/submission.shtml. When submitting, please select the special session on "Evolutionary Robotics". All submissions will be peer-reviewed with the same criteria used for other contributed papers. All accepted papers will be included in the published conference proceedings. POST CONFERENCE BOOK PUBLICATION Authors of the best selected paper from among those accepted for the "Evolutionary Robotics" session will be invited to submit an extended version for review for possible publication as a chapter in the forthcoming book "The Horizons of Evolutionary Robotics" edited by Patricia A. Vargas, Ezequiel Di Paolo, Inman Harvey and Phil Husbands (target publisher MIT Press). IMPORTANT DATES: Paper Submission:......................November 01, 2008 Notification of Acceptance:..........January 16, 2009 Camera-Ready Submission:........February 16, 2009 ------------------------------------------ Sabine Hauert Laboratory of Intelligent Systems EPFL, Switzerland http://lis.epfl.ch Phone: +4121 6937759 Email: sabine.hauert@epfl.ch ------------------------------------------ From vcu at cs.stir.ac.uk Mon Sep 15 15:44:53 2008 From: vcu at cs.stir.ac.uk (Dr. Vassilis Cutsuridis) Date: Tue Sep 16 09:11:50 2008 Subject: [Comp-neuro] 2nd CfP: Neural Networks - Special issue on Cortical microcircuits Message-ID: <000001c917c9$0e7936a0$99e3e98f@Zeus> Second Call for Papers on ======= Cortical Microcircuits ======== (formerly known as Neural models of Cortical microcircuits) Guest Editors: J.G. Taylor, T. Wennekers, B.P. Graham, I. Vida, V. Cutsuridis Special issue of the Elsevier Journal of Neural Networks http://helen.pion.ac.uk/microcircuits08 = SCOPE = To understand how perception, attention, action, learning and memory work, we need to gather data from multiple levels of complexity and from various brain states (normal and diseased) and integrate them at the brain-scale level. We need to identify the neuronal groups involved in these functions, their laminar distributions and their different types of neurons, draw detailed circuit diagrams, determine the forms of synaptic transmission and plasticity between different neurons and study the dynamics of the cortical microcircuits at the cellular and synaptic level that comprise these neuronal groups. Recent years have witnessed a dramatic accumulation of knowledge about the morphological, physiological and molecular characteristics, as well as the connectivity and synaptic properties of cortical neurons. Despite these advances, however, only limited insight was gained into the computational function of the neurons; in particular, the role of the various types of interneurons remains elusive. Mathematical and computational microcircuit models play an instrumental role in exploring microcircuit functions and facilitate the dissection the operations performed by diverse interneurons. The goal of the special issue is to provide a snapshot and a resum? of the current state-of-the-art of the ongoing research avenues concerning cortical microcircuits with particular emphasis on the functional roles of the various inhibitory interneurons in information processing within normal and diseased behavioural and cognitive states. The emphasis will be on computational models that are tightly grounded on experimental data. = SPECIFIC AIMS = - The interaction between the local micro circuit activity and global processing to achieve the desired overall processing functionality observed, say in perception and action, attention, learning and memory - Microcircuit architectures: networks of principal and inhibitory inter-neurons within and between lamina, columns, mini-columns, modules, areas and/or across areas in the brain and their functional roles in the network. -- Neo-cortex -- Hippocampus -- Sensory and Motor Systems - Cross-comparison of architectures from different brain areas - Identified computations performed by each type of neuron in a network - Identified modes of operation of a neuronal type and how they are related potentially to behaviour and cognition - What synaptic plasticity rules are used = SUBMISSIONS = Extended submission deadline: February 1st, 2009 Author notification: May 2, 2009 Revised manuscripts: July 1, 2009 Publication by journal: ~September/October, 2009 Electronic submissions for the Neural Networks journal can be found under http://ees.elsevier.com/neunet/ Please indicate in your cover letter that your article is for the special issue "Cortical Microcircuits" Regards, Vassilis ---------------------------------------------------------------------------------- Dr. Vassilis Cutsuridis Department of Computing Science and Mathematics University of Stirling Stirling FK9 4LA SCOTLAND Tel: +44 1786 467422 Fax: +44 1786 464551 Email: vcu@cs.stir.ac.uk Web: http://www.cs.stir.ac.uk/~vcu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080915/331a2964/attachment-0001.html From s.li.1 at bham.ac.uk Tue Sep 16 10:25:23 2008 From: s.li.1 at bham.ac.uk (Sheng Li) Date: Tue Sep 16 11:21:40 2008 Subject: [Comp-neuro] Research Fellow in Vision and NeuroImaging Message-ID: <468E635F877FE94BBEFFC0309BCA1954E75E61@psgfs4.adf.bham.ac.uk> Research Fellow in Vision and NeuroImaging A Post-doctoral Research Fellow position in Vision and NeuroImaging is available at the School of Psychology, University of Birmingham, UK. The work focuses on the neural basis of shape perception and learning combining behavioural paradigms, functional imaging and advanced computational methods for the analysis of multimodal imaging signals (fMRI-EEG). Research will be conducted within well-equipped labs that incorporate a range of bespoke equipment. The School of Psychology provides an excellent working environment with a pronounced research focus and international expertise in Vision Science, Behavioural Neuroscience and Cognitive Neuroscience. Facilities include an Imaging Centre with integrated equipment for the study of human brain and behaviour (3T scanner, EEG) as well as numerous virtual reality devices and eye trackers. Candidates should hold or expect to hold a Ph.D. in Experimental Psychology, Neuroscience, Computer Science, Engineering, Physics, Mathematics or a related field. Programming skills (e.g. Matlab, C, OpenGL) are necessary and experience with behavioural, imaging, signal processing methods and modelling is desirable. Further details on the project and informal enquiries can be addressed to Zoe Kourtzi: z.kourtzi@bham.ac.uk. Andrew Welchman : a.e.welchman@bham.ac.uk From wulfram.gerstner at epfl.ch Tue Sep 16 13:18:45 2008 From: wulfram.gerstner at epfl.ch (Wulfram Gerstner) Date: Tue Sep 16 13:56:09 2008 Subject: [Comp-neuro] 5 PhD and 4 PostDoc positions in reward-based learning (Switzerland) Message-ID: <48CF9615.60107@epfl.ch> Switzerland: 5 PhD and 4 PostDoc positions in reward-based learning The Swiss National Science Foundation funds a new collaborative project involving 3 groups at the EPFL (Wulfram Gerstner, Carmen Sandi, Michael Herzog) as well as groups in Berne (Walter Senn) and Lugano (Juergen Schmidhuber). We are particularly interested in biologically plausible models for learning and memory which explain animal and human behavior. The current project aims to extend the theory of reward-based learning in spiking neurons to networks, link it to formal policy gradient and TD methods, and apply it to perceptual learning, spatial navigation, and sequence learning. Applications should be submitted to the individual labs: Wulfram Gerstner http://lcn.epfl.ch Laboratory of Computational Neuroscience, EPFL Carmen Sandi http://lgc.epfl.ch Laboratory of Behavioral Genetics, EPFL Michael Herzog http://lpsy.epfl.ch/ Laboratory of Psychophysics, EPFL Juergen Schmidhuber http://www.idsia.ch/~juergen/sinergia2008.html IDSIA, Lugano Walter Senn (http://www.physio.unibe.ch/Positions/) Computational Neuroscience/Institute of Physiology, Berne PS: Switzerland is a good place for scientists. It is the origin of special relativity (1905) and the World Wide Web (1990), is associated with 105 Nobel laureates, and boasts the world's highest number of Nobel prizes per capita, the highest number of publications per capita, the highest number of patents per capita, the highest citation impact factor, the most cited single-author paper, etc. Switzerland also got the highest ranking in the list of happiest countries :-) From echicca at gmail.com Tue Sep 16 14:17:11 2008 From: echicca at gmail.com (elisabetta chicca) Date: Tue Sep 16 14:32:55 2008 Subject: [Comp-neuro] PhD position: Neuromorphic Attention Message-ID: <8dc520f30809160517w5d528edj5184be3e05c6cb5b@mail.gmail.com> The Institute of Neuroinformatics at UZH-ETH Zurich announces an opening for a PhD position. The mission of the Institute is to discover the key principles by which brains work and to implement these in artificial systems that interact intelligently with the real world. The aim of this project is to develop a real-time active vision system by interfacing neuromorphic VLSI selective attention chips to neuromorphic sensors and robotic actuators. The neuromorphic chips model the properties of biological systems down to the single neuron and synapse dynamics and use a digital asynchronous communication infrastructure. Requirements: Applicants should have * a strong interest in bio-inspired hardware engineering; * the ability to work independently; * good skills in programming C and Matlab; * basic knowledge of neural networks and machine vision; * fundamental notions of microelectronics and/or neuroscience. Contact: Giacomo Indiveri (giacomo@ini.phys.ethz.ch) See http://www.ini.uzh.ch/db/?id=12782&top=12782&showid=18525 for details. Elisabetta Chicca < chicca@ini.phys.ethz.ch> Institute of Neuroinformatics UNI - ETH Zurich -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080916/28a4b2c8/attachment.html From nips2008publicity at gmail.com Wed Sep 17 05:25:50 2008 From: nips2008publicity at gmail.com (Antonio Torralba) Date: Wed Sep 17 09:40:41 2008 Subject: [Comp-neuro] NIPS: Call for Demonstrations Reminder Message-ID: Reminder: The Call for Demos ends this Friday, Sept. 19. Please go here for detailed information: http://nips.cc/Conferences/2008/CallForDemos From tobias at nld.ds.mpg.de Wed Sep 17 15:36:08 2008 From: tobias at nld.ds.mpg.de (Tobias Niemann) Date: Wed Sep 17 17:23:20 2008 Subject: [Comp-neuro] Postdoctoral and PhD student positions in cellular neurophysics/neurophysiology In-Reply-To: <482D5437.6090809@nld.ds.mpg.de> References: <46F11EC5.4050208@nld.ds.mpg.de> <47DF9A94.8000309@nld.ds.mpg.de> <482D3F70.8030903@nld.ds.mpg.de> <482D5437.6090809@nld.ds.mpg.de> Message-ID: <48D107C8.2020700@nld.ds.mpg.de> The Bernstein Center for Computational Neuroscience G?ttingen invites applications for a Postdoctoral and PhD student positions in cellular neurophysics/neurophysiology The candidates?s research will experimentally analyze the dynamical properties of sodium channels in neocortical neurons in situ and model their role in the operation of cortical neurons and networks and will be part of an integrated international project of the Max Planck Institutes for Dynamics and Self-Organization (G?ttingen) and the Koret School of Veterinary Medicine of the Hebrew University of Jerusalem (Israel), supported by the German-Israeli Foundation for Scientific Research and Development. PhD students will work towards their doctorate either in G?ttingen University?s newly established Graduate School, GGNB or at the Hebrew University of Jerusalem. We are looking for young researchers with a background in biophysics, cellular electrophysiology, or cell biology and a keen interest in interdisciplinary research at the border of experimental and theoretical neuroscience. The ideal candidate will have the ability and desire to push the characterization of cortical sodium currents in intact cortical neurons to a new level of quantitative precision and to analyze their role in the operation of cortical neurons under physiologically realistic conditions. Prior experience with the biophysics of ion channels, with the electrophysiology of neurons, or with cellular imaging methods would be advantageous. Prior knowledge of Neurobiology is desirable but not required. G?ttingen is a center of neuroscience in Europe hosting numerous internationally recognized neuroscience research institutions, including three Max Planck Institutes, the European Neuroscience Institute, the German Primate Research Center, and G?ttingen University's Centers for Systems Neuroscience (ZNV) and for the Molecular Physiology of the Brain (CMPB). The BCCN integrates theoretical and experimental research groups from these institutions to foster interdisciplinary research in computational neuroscience specifically supporting close collaboration between theorists and experimental researchers. Please submit your application preferably in one single PDF-document, including cover letter, CV, list of publications, names of possible referees, relevant certificates until October 15, 2008, to: jobs@bccn-goettingen.de (Subject: NPhysNaCh) While e-mail is preferred, applications may also be submitted in hardcopy to the following address: Dr. Fred Wolf Subject: NPhysNaCh Bernstein Center for Computational Neuroscience (BCCN) G?ttingen Max-Planck-Institute for Dynamics and Self-Organization Bunsenstrasse 10 D - 37073 G?ttingen, Germany http://www.ds.mpg.de The MPIDS is an equal opportunity employer. From carnevalet at sbcglobal.net Fri Sep 19 05:05:31 2008 From: carnevalet at sbcglobal.net (Ted Carnevale) Date: Fri Sep 19 09:09:27 2008 Subject: [Comp-neuro] Parallel simulations with NEURON on multicore Macs and PCs Message-ID: <48D316FB.8000105@sbcglobal.net> By now, most NEURON users are aware that simulations can be sped up by running NEURON on workstation clusters and parallel supercomputers. But did you know that the next official release of NEURON (version 7) will offer multithreaded execution, so you can run parallel simulations on standalone multicore Macs or PCs? An alpha release of version 7 is already available at http://www.neuron.yale.edu To learn how to take advantage of this yourself, come to the NEURON course on Friday, Nov. 14, in Washington, DC. For the course description and online registration form, see http://www.neuron.yale.edu/dc2008.html You should act soon, because the registration deadline is Friday, October 17--just four weeks from now. In the meantime, you might want to check out the "Multithreaded simulation Q & A" on the NEURON Forum https://www.neuron.yale.edu/phpBB/viewtopic.php?f=31&t=1384 for a sense of the benefits of, and prerequisites for using, multithreaded simulations. From mnegrello at gmail.com Fri Sep 19 13:23:50 2008 From: mnegrello at gmail.com (Mario Negrello) Date: Fri Sep 19 18:56:32 2008 Subject: [Comp-neuro] Parallel simulations with NEURON on multicore Macs and PCs In-Reply-To: <48D316FB.8000105@sbcglobal.net> References: <48D316FB.8000105@sbcglobal.net> Message-ID: <35EC6AE5-D632-43C0-B541-BC12B9F6BBE6@gmail.com> Hi Ted, A little suggestion. For those of us which cannot participate, it would be cool if the sections were taped, then made available. Do you think it should be possible to record them? Best, M. On 19/set/08, at 05:05, Ted Carnevale wrote: > By now, most NEURON users are aware that simulations can be sped up > by running NEURON on workstation clusters and parallel supercomputers. > But did you know that the next official release of NEURON (version 7) > will offer multithreaded execution, so you can run parallel > simulations > on standalone multicore Macs or PCs? An alpha release of version 7 > is already available at http://www.neuron.yale.edu > > To learn how to take advantage of this yourself, come to the NEURON > course on Friday, Nov. 14, in Washington, DC. For the course > description and online registration form, see > http://www.neuron.yale.edu/dc2008.html > You should act soon, because the registration deadline is Friday, > October 17--just four weeks from now. > > In the meantime, you might want to check out the "Multithreaded > simulation Q & A" on the NEURON Forum > https://www.neuron.yale.edu/phpBB/viewtopic.php?f=31&t=1384 > for a sense of the benefits of, and prerequisites for using, > multithreaded simulations. > _______________________________________________ > Comp-neuro mailing list > Comp-neuro@neuroinf.org > http://www.neuroinf.org/mailman/listinfo/comp-neuro From luecke at fias.uni-frankfurt.de Fri Sep 19 13:21:30 2008 From: luecke at fias.uni-frankfurt.de (=?iso-8859-1?q?J=F6rg_L=FCcke?=) Date: Fri Sep 19 18:56:35 2008 Subject: [Comp-neuro] 3 PhD Positions for Research in Machine Learning and Computer Vision Message-ID: <200809191321.30972.luecke@fias.uni-frankfurt.de> PhD positions are available for research in the following areas: * non-linear component extraction * learning in visual object memories * visual object recognition In any of the projects above we are offering positions for qualified post-graduate students. Applicants should have a Master degree (or equivalent) in Physics, Mathematics, Computer Science, Electrical Engineering or Machine Learning. Strong analytical skills and programming experiences are required for all projects. An interest in computational and biological vision as well as in neuroscience is desirable. We are interested in applicants with experience in Machine Learning and/or Computer Vision as well as in applicants who graduated in other areas. Good communication skills in English are essential. The concrete PhD projects will be defined depending on the applicants' background knowledge and research interests. The offered positions are fully funded research positions with no or a limited amount of teaching activities. We offer competitive salaries in the range of the German BAT IIa level. Research is carried out within the German Bernstein Network for Computational Neuroscience (funded by the BMBF) and in collaboration with the Honda Research Institute Europe (HRI Europe). Successful applicants will work in international and interdisciplinary research groups at the Frankfurt Institute for Advanced Studies (FIAS), Goethe-Universit?t Frankfurt, Germany. Funding is planned to start in October 2008. The positions will be filled as soon as suitable candidates are found. For further information see: http://fias.uni-frankfurt.de/~luecke/OpenPositions/OpenPositions.html Application Procedure: The review of applications will begin immediately. Required application materials: * a complete scientific curriculum vitae * a copy of Master or Diploma certificate * a short statement of research interests and achievements * letters of reference (can also be provided at a later stage of the selection process) * if possible provide a proof of proficiency in English (e.g., TOEFL or similar) Please send electronic files and scanned-in versions of documents. Files should be compiled into a ZIP archive. Please direct your application to luecke@fias.uni-frankfurt.de, send a CC to julian.eggert@honda-ri.de, and use "Application for PhD Position" as subject. -- Dr. J?rg L?cke Frankfurt Institute for Advanced Studies (FIAS) Goethe-Universit?t Frankfurt Germany From eero at cns.nyu.edu Mon Sep 22 15:37:56 2008 From: eero at cns.nyu.edu (Eero Simoncelli) Date: Mon Sep 22 17:19:42 2008 Subject: [Comp-neuro] Doctoral studies in Vision at NYU Message-ID: New York University is home to a thriving interdisciplinary community of researchers in the visual sciences, spanning multiple departments. A listing of faculty, sorted by their primary departmental affiliation, is given below. Doctoral programs are flexible, allowing students to pursue research across departmental boundaries. Nevertheless, admissions are handled separately by each department, and students interested in pursuing graduate studies should submit an application to the program that best fits their goals and interests. Application deadlines vary per department, as indicated below. Center for Neural Science (CNS) (Deadline: 12 December) [http://www.cns.nyu.edu/doctoral/] * Michael Hawken (also in Psychology) - Neuronal mechanisms of visual perception. * Lynne Kiorpes (also in Psychology) - Development of visual function. * Tony Movshon (also in Psychology) - Vision and visual development. * Bijan Pesaran - Neuronal dynamics, visuo-motor control, and decision making. * John Rinzel (also in Mathematics) - Biophysical mechanisms and theory of neural computation. * Nava Rubin (also in Psychology) - Visual perception and the neural basis of vision. * Robert Shapley (also in Psychology and Biology) - Visual physiology and perception. * Eero Simoncelli (also in Mathematics and Psychology) - Computational vision. Psychology, Cognition & Perception program (Deadline: 18 December) [http://www.psych.nyu.edu/programs/cp/] * Marisa Carrasco (also in CNS) - Visual perception and attention. * David Heeger (also in CNS) - fMRI, computational neuroscience, vision, attention. * Michael Landy (also in CNS) - Computational approaches to vision. * Laurence Maloney (also in CNS) - Mathematical approaches to psychology and neuroscience. * Denis Pelli (also in CNS) - Object recognition. Computer Science (Deadline: 4 January) [http://www.cs.nyu.edu/web/Research/Areas/graphicsvisionui.html] * Chris Bregler - human motion modeling, computer vision, machine learning. * Rob Fergus - computer vision, machine learning, computer graphics. * Davi Geiger (also in CNS) - Computational vision and learning. * Yann LeCun - machine learning, hierarchical visual processing, robotics. Mathematics (Deadline: 18 December) [http://math.nyu.edu/degree/phd/] * David Cai - Nonlinear stochastic behavior in physical and biological systems. * David McLaughlin (also CNS) - Nonlinear wave equations, computational visual neuroscience. * Aaditya Rangan - computational neurobiology, numerical analysis. * Michael Shelley (also CNS) - Modeling and large-scale computation, computational visual neuroscience. Biology (Deadline: 12 December) [http://biology.as.nyu.edu/page/graduate.program] * Claude Desplan (also CNS) - Molecular/genetic basis for development, particularly color vision circuitry. * Daniel Tranchina (also Mathematics and CNS) - Information processing in the retina. Philsophy (Deadline: 4 January) [http://philosophy.fas.nyu.edu/page/graduate] * Ned Block (also psychology and CNS) - Foundations of consciousness. From clemoal at esf.org Tue Sep 23 11:40:48 2008 From: clemoal at esf.org (Corinne Wininger - Le Moal) Date: Tue Sep 23 12:26:21 2008 Subject: [Comp-neuro] Social Cognitive Neuroscience Conference, Italy, 27 February- 4 March 2009 Message-ID: CONFERENCE ANNOUNCEMENT ESF-JSPS Frontier Science Conference Series for Young Researchers SOCIAL COGNITIVE NEUROSCIENCE Hotel Villa del Mare, Acquafredda di Maratea, Italy 27 February- 4 March 2009 Chairs: Professor G?n R. Semin, Utrecht University, The Netherlands & Professor Shun-Ichi Amari, RIKEN Brain Science Institute, Japan Closing date for applications: 14 October 2008 Programme and application form accessible online from http://www.esf.org/conferences/09263 Applications will be accepted from young scholars and scientists, based in countries of ESF membership (http://www.esf.org/about-us/77-member-organisations.html) and Japan, who are doing outstanding and innovative work in their fields. To be eligible, young researchers must either have obtained a doctoral degree within 10 years prior to the conference or be scheduled to obtain a doctoral degree no later than 18 months after the conference. Selection will be based upon institutional affiliation of the participants. Participants are required to attend all sessions and programmes of the conference. Grants: All accepted participants will receive financial support to cover their registration fee, accommodation and meals during the conference. Travel expenses will be covered as much as possible, according to budget availability. For further information, please see http://www.esf.org/conferences/09263 or contact Ms. Jean Kelly (jkelly@esf.org) from ESF Research Conferences Unit. Kind regards, Corinne Wininger Communications Officer - ESF Conferences European Science Foundation - Communications Unit 1 quai Lezay-Marn?sia, BP 90015 67080 Strasbourg Cedex, France Phone: +33 (0)388 76 21 50 Fax: +33 (0)388 76 71 80 clemoal@esf.org www.esf.org/conferences -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080923/034dc4aa/attachment.html From wolfram.erlhagen at mct.uminho.pt Tue Sep 23 17:07:20 2008 From: wolfram.erlhagen at mct.uminho.pt (Wolfram Erlhagen) Date: Tue Sep 23 17:25:06 2008 Subject: [Comp-neuro] 5-YEAR RESEARCH POSITION in Theoretical Neuroscience Message-ID: <011601c91d8e$138d03e0$120f88c1@wolfram> 5-YEAR RESEARCH POSITION in THEORETICAL NEUROSCIENCE / COGNITIVE SCIENCE Mathematical Research Centre, University of Minho, Portugal Application Dead-line: September 30, 2008 --------------------------------------------------------------------------------------------------------- JOB SUMMARY The Centre of Mathematics at the University of Minho (Portugal, http://www.cmat.uminho.pt ) invites applications for a 5-year research position in "Mathematical and Computational Neuroscience/Cognitive Science". The position is part of a prestigious national program for research (http://alfa.fct.mctes.pt/apoios/contratacaodoutorados/index.phtml.en). JOB DESCRIPTION The research position is aimed at developing formal models based on mathematical, computational and information-theoretic principles for exploring the behavioural and cognitive significance of various aspects of nervous system. Research topics will be chosen to complement the individual interests and new ideas of the postdoctoral fellow, together with ongoing projects in the working group (see http://www.mct.uminho.pt/erlhagen) . The successful candidate would have (1) a deep interest in theoretical neuroscience and cognitive science; (2) a PhD in mathematics, applied mathematics, computer science, theoretical biology, statistics, physics, or a related area, (3) a demonstrated ability for independent research in the area, (4) an ability and affinity for communicating theoretical results clearly in cross-disciplinary collaborations. CONTRACT CONDITION The position can be filled immediately for duration of up to five years. The salary is highly competitive, in the order of 42.500 euros a year (before taxes), and includes social security and health insurance benefits. The position does not include teaching duties, but it is expected that the candidate contributes to the supervision and training of post-graduate students. HOW TO APPLY By email to c_math@math.uminho.pt (with a cc to wolfram.erlhagen@mct.uminho.pt ) with the following information: a.. a CV, including a brief research statement b.. 2-3 recent publications in electronic format c.. at least two letters of recommendation or references Deadline for the application is September 30, 2008 Informal enquiries can be directed to Prof. Wolfram Erlhagen, Dep. of Mathematics for S&T, University of Minho, Email: wolfram.erlhagen@mct.uminho.pt URL: www.mct.uminho.pt/erlhagen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080923/b04e31e1/attachment.html From giulio.sandini at iit.it Tue Sep 23 17:55:29 2008 From: giulio.sandini at iit.it (Giulio Sandini) Date: Tue Sep 23 18:21:51 2008 Subject: [Comp-neuro] PhD School at IIT - Italy Message-ID: <000d01c91d94$cd830190$688904b0$@sandini@iit.it> The Robotics, Brain and Cognitive Sciences (RBCS) Department of the Italian Institute of Technology (IIT) is offering fellowships in the area of HUMAN MOTOR LEARNING, BIOMECHANICS AND REHABILITATION ROBOTICS and BRAIN MACHINE INTERFACE. These fellowships are part of a multidisciplinary project aiming at 'reading' the brain to understand and extract motor signals which may be used to control an artificial limb. These two main streams of research will be developed jointly at RBCS department of IIT under the responsibility of Giulio Sandini and two groups of scientists coordinated by Thierry Pozzo (motor learning) Luciano Fadiga (Brain Machine Interface) and including: Lorenzo Masia, Stefano Panzeri, Alessandro Vato, Gytis Baranauskas, Davide Ricci and Franco Bertora, Marco Jacono. These projects address topics such as the design of microelectrode and microelectronics devices for chronic in-vivo recording, electrophysiological and brain signals recording, investigation of the coding/decoding issue, functional identification of brain motor/premotor areas, and direct connection to artificial actuators. More specifically the five research themes proposed are (short abstract and scientist in charge are included at the end of the message): Research Stream: Human Behavior, Perception and Biomechanics ? Theme 5.4: Psychophysical study of unimodal perception and multimodal integration ? Theme 5.5: Modular Control of Equilibrium and Movement ? Theme 5.6: Neural Correlates of Biological Motion Inference Research Stream: Brain Machine Interface ? Theme 5.7: Machinery for functional brain analysis ? Theme 5.8: The Neurophysiology of the Human Brain Interested applicants should refer to one of the following website to download instructions on how to apply and/or contact directly the scientists in charge (below) for more information regarding the individual research plans. http://www.liralab.it/iit2009phd.htm http://www.iit.it/phd_positions -------------------------------------------- RESEARCH TOPICS PROPOSED Research Stream : Human Behavior, Perception and Biomechanics Theme 5.4: Psychophysical study of unimodal perception and multimodal integration Tutor: Monica Gori N. Available positions: 1 In this project we will investigate the way in which unimodal sensory signals are integrated in order to obtain a robust multimodal perception of the world. As no single information-processing system can perceive optimally under all conditions, integration of multiple sources of sensory information makes perception more robust. Many recent studies have demonstrated the capacity of human observers to integrate information across various senses in a statistically optimal (sometimes termed ?Bayesian?) fashion, where greater weight is given to the sense carrying the more reliable information under any particular condition. Importantly, performance in the multimodal condition is always better than in either single modality. An aspect of the integration to be studied by our research group is to investigate at what age children start to integrate sensory signals, and if is this integration optimal. Another aspect to be studied is how dynamic information are integrated between different modalities, by studying the integration of visual and tactile integration of visual and tactile flow motion. One PhD student will be involved in psychophysical experiments of this research theme. The aim is to study and understand how our brain produces an integrated robust percept of the world. Backgrounds in experimental psychology, neuroscience and basic programming skills are required. For further details concerning the research project, please contact: monica.gori@iit.it Theme 5.5: Modular Control of Equilibrium and Movement Tutor: Prof. Thierry Pozzo N. available positions: 1 The program of research is based on previous results obtained during a paradigm that we developed to study both equilibrium and spatial components of a complex multijoint goal oriented task. When subjects reach targets positioned beyond arm length from the standing position, the central nervous system (CNS) has to specify the spatio-temporal characteristics of the arm movement while maintaining the whole body center of mass (CoM) within the supporting base (the feet). A number of interesting questions arise when considering together the control of equilibrium and arm trajectory formation : 1) Are the control laws governing arm movements, laid down largely using planar 2-joint tasks (and having little or no equilibrium constraints) applicable to multijoint reaching movements (requiring a high degree of equilibrium control and numerous DoF)? 2) How are equilibrium constraints integrated by the CNS during the formation of a specific end-point trajectory among a plethora of possible ones? 3) Is there a macroscopic representation (motor primitives) at spinal and/or supraspinal level of such components and can they be combined like building blocks to perform this task in different conditions? Within this field of research, one PhD student will study the interaction of these two components of the action by using experimental and computational approach and modelling. A simulator based on experimental results and optimization of iterative algorithms able to find the motor solution which, respecting the anatomical and task constraints, minimizes a given cost function, will be developed. We need therefore the contribute of one PhD students possessing basic competencies in robotic, control theory or computational neurosciences. For further details concerning the research project, please contact: thierry.pozzo@iit.it Theme 5.6: Neural Correlates of Biological Motion Inference Tutor: Prof. Thierry Pozzo N. available positions: 1 The spatiotemporal discontinuity of visual input (e.g., when a person suddenly disappears behind a wall) is a common experience for human beings. Non-human primate studies (Baker et al. 2001) demonstrated that cells in the superior temporal sulcus (STS) contribute to the perceptual capacity for object permanence and support the hypothesis that the motor representation of action performed by others can be internally generated in the observer's premotor cortex, even when a visual description of the action is lacking (Umilt? et al. 2001). Recent behavioral experiments (Pozzo et al. 2006, Saunier et al. 2008), suggest an implicit motor simulation during the complete occlusion of biological motion that compensates the lack of visual input. Little is known, however, about the neurophysiological basis of the biological motion permanence and of the capability to predict the outcome of others' actions. Within this field of research, one PhD student will be involved in the development of a high density EEG system which will enable to quantify, in humans, the involvement of action representation during the perception of biological motion. The aim is to develop a high temporal resolution EEG technique to better precise the functional roles played by the STS region and by the fronto-parietal network involved in the perception of biological motion. The student will be involved both in the recording techniques and in the online deocoding of neural signals, which will be perfomed with the aid advanced wavelet decomposition techniques to denoise the signal and information theoretic techniques to reveal the most informative components of the neural signal. The candidate should possess basic competencies in physicis, statistics, mathematics and computer science and will receive interdisciplinary training by a team composed of both experimental (Prof. Pozzo and Fadiga) and theoretical (Prof. Panzeri) neuroscientists. For further details concerning the research project, please contact: thierry.pozzo@iit.it Research Stream : Brain Machine Interface Theme 5.7: Machinery for functional brain analysis. Tutor: Prof. Franco Bertora N. of available positions: 1 There is at IIT an ongoing program to investigate the frontiers of functional MRI imaging. Any fMRI of the motor cortex has so far been performed on subjects confined in a supine/prone position in the limited volume of a traditional scanner. There are reasons to think that the analysis of subjects performing motor tasks in a more ?natural? environment could produce different and more meaningful results. A study is currently in progress for an open scanner, based on an innovative magnet design, allowing functional brain analysis of a human adult in a standing or sitting position. We are looking for one PhD student with background in physics, electronics, signal processing and MRI to participate in the design of the magnet and its related equipment and to explore and conceive novel imaging techniques (MRI sequences, data acquisition modalities and image reconstruction) to be included in the development of the scanner. For further details concerning the research project, please contact: franco.bertora@iit.it Theme 5.8: The Neurophysiology of the Human Brain Tutor: Dr. Elisa Molinari N. of available positions: 1 The Phd student will use brain mapping approaches based on functional magnetic resonance imaging to investigate the structural and functional organization of cortical and subcortical motor systems. Through this project we will better understand the functional correlates of motor planning/execution and the underlying motor circuits. Quantitative approaches to the anatomical definition of the cortical grey matter in healthy individuals are of specific interest. We are looking forward to one PhD student which should be competent in physics, computer science and basic neuroscience. For further details concerning the research project, please contact: elisa.molinari@iit.it --- Prof. Giulio Sandini Italian Institute of Technology Robotics, Brain and Cognitive Sciences Department Phone: +39 010 7178101 - Fax +39 010 720321 and LIRA-Lab, University of Genova Phone: +39 0103532779 - Fax: +39 010353.2948 http://www.liralab.it http://sandini.liralab.it From romain.brette at ens.fr Tue Sep 23 19:50:41 2008 From: romain.brette at ens.fr (Romain Brette) Date: Wed Sep 24 11:48:03 2008 Subject: [Comp-neuro] Brian 1.0: a pure Python neural simulator Message-ID: <48D92C71.90901@ens.fr> Brian 1.0: a pure Python neural simulator ------------------------------------- http://brian.di.ens.fr/ The 1.0 release of Brian is finally out! Brian is a new simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists. Brian is easy to learn and use, highly flexible and easily extensible. The Brian package itself and simulations using it are all written in the Python programming language, which is an easy, concise and highly developed language with many advanced features and development tools, excellent documentation and a large community of users providing support and extension packages. This makes Brian an excellent choice for teaching. Brian is being developed by Romain Brette (brette@di.ens.fr) and Dan Goodman (goodman@di.ens.fr). The web site (http://brian.di.ens.fr/) contains a few examples (click on Demo), installation instructions and the documentation. There is also a public forum where you can ask any questions: http://groups.google.fr/group/briansupport Romain Brette http://www.di.ens.fr/~brette/ From bazhenov at salk.edu Tue Sep 23 21:28:41 2008 From: bazhenov at salk.edu (Maxim Bazhenov) Date: Wed Sep 24 11:48:08 2008 Subject: [Comp-neuro] Postdoctoral position in computational neuroscience Message-ID: <48D94369.3040206@salk.edu> A full-time postdoctoral position in computational neuroscience is available immediately at the Institute for Integrative Genome Biology (http://www.genomics.ucr.edu/) and the Department of Cell Biology and Neuroscience at the University of California, Riverside. Research in our laboratory focuses on understanding cellular and network mechanisms underlying normal and paroxysmal oscillations in the brain and the role of neuronal oscillations and synchrony in information processing. Specific projects include: (1) Studying cellular and network mechanisms for normal (sleep, attentive states) and abnormal (epilepsy) oscillations in the thalamocortical system; (2) Studying role of oscillations and synchrony in olfactory coding ? this project is targeted to discover the general principles and the neural circuitry involved in the encoding of sensory information in the brain. More information about our research is available at http://www.snl.salk.edu/~bazhenov/ Successful candidate will join research team including computational neuroscience labs from UC Riverside, UC San Diego and Salk Institute, and will be responsible for designing network models based on experimental data, model analysis and may be involved in experimental testing of the model predictions. Qualified applicants are expected to have experience in computational neuroscience including conductance-based neural modeling. Programming experience with C/C++ and Matlab is very desirable. The UC Riverside campus is located in the heart of Riverside County within 1-hour drive from the cities of Los Angeles, San Diego and Irvine. The University of California offers excellent benefits. Salary is based on background and research experience. The initial appointment will be for 1 year with a possibility of extension up to 3-4 years. Applicants should send a brief statement of research interests, a CV and the names of three references electronically to Maxim Bazhenov at bazhenov@salk.edu or maksim.bazhenov@ucr.edu From wjma at cpu.bcm.edu Wed Sep 24 17:02:46 2008 From: wjma at cpu.bcm.edu (Wei Ji Ma) Date: Wed Sep 24 18:13:25 2008 Subject: [Comp-neuro] Postdoc in computational neuroscience Message-ID: <48071F74CBAD5B46973B3D2B90179BCB5D2F@stan.hou-ad.hnl.bcm.tmc.edu> Department of Neuroscience Baylor College of Medicine, Houston TX Postdoctoral Associate in Computational Neuroscience Applications are invited for a postdoctoral position (minimum 2 years) in the laboratory of Dr. Wei Ji Ma (http://neuro.bcm.edu/malab) in the Department of Neuroscience at Baylor College of Medicine, Houston, Texas. The long-range goal of our research is to understand the representation and processing of uncertainty in the human brain, both at the behavioral and at the neural level. The lab uses a combination of theoretical analysis, computational modeling, and theory-driven human experiments. Current areas of study include multisensory perception, decision-making, and visual search. The position provides an opportunity to take part in highly collaborative research programs within the Computational Psychiatry Unit (http://cpu.bcm.edu ) and the Department of Neuroscience as a whole. Applicants should have a Ph.D. in computational neuroscience, physics, mathematics, computer science, or a related field, and have a commitment to a research career in neuroscience. Programming experience with Matlab or C++ is very desirable. To apply, please send CV, statement of interest, and the names and contact information of two references to Wei Ji Ma at wjma@bcm.edu. Consideration of applications will begin immediately, and will end when the position is filled. Salary is competitive and will be commensurate with experience and qualifications. Baylor College of Medicine is an Equal-Opportunity, Affirmative-Action, and Equal-Access Employer. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080924/c776b436/attachment.html From dglanzma at mail.nih.gov Wed Sep 24 19:40:15 2008 From: dglanzma at mail.nih.gov (Glanzman, Dennis (NIH/NIMH) [E]) Date: Fri Sep 26 15:21:14 2008 Subject: [Comp-neuro] Dynamical Neurosceince: Agenda and Final Call for Posters Message-ID: <0EE5F9DA83318D47B16FB45A5CBA4A4A02C189B5@nihcesmlbx2.nih.gov> 16th Annual Dynamical Neuroscience Satellite Symposium "Neuronal Variability and Its Functional Significance" FINAL CALL FOR POSTERS Abstract Deadline October 17, 2008 Preceding the 38th Annual Meeting of the Society for Neuroscience Thursday and Friday, November 13-14, 2008 The Capital Ballroom of the JW Marriott Hotel 1331 Pennsylvania Ave. NW Washington, DC The brain is restless. Physiological data recorded from the brain often have random-appearing components. Repeated stimuli evoke responses that are not identical from trial to trial. Not too long ago this variability was dismissed as noise and, through techniques such as signal averaging, removed from further consideration. More recent work has begun to examine the rich content of this variability and shed light on its functional consequences. Neural variability and noise has become an active field of research, generating a wealth of new knowledge and information. This symposium will assess the current status of four related areas: Characterizing Neuronal Variability Larry Abbott, Columbia University, Contrasting Internal and External Sources of Variability Emery Brown, MIT & Harvard, How Well Do We Know What Single Neurons Do? Dynamics of Neuronal Ensembles Henry Abarbanel, UC San Diego, Dissecting and Modeling Neurobiological Networks: Dynamical Electrophysiology Anna Roe, Vanderbilt University, Beyond Correlated Noise: Evidence for Intra- and Inter-Areal Baseline Biases in Temporal Coincidence Neuronal Variability and Cognition Daeyeol Lee, Yale University School of Medicine, Order and Chaos in Decision Making Akaysha Tang, University of New Mexico, Top-Down Versus Bottom-up Processing in the Human Brain: Distinct Directional Influences Revealed by Integrating Second-Order Blind Identification and Granger Causality Charles Gray, Montana State University, Dynamics of Cortico-Cortical Interactions in the Macaque Charles Schroeder, Columbia University, Neuronal Oscillations as Instruments of Sensory Selection Stephen Lisberger, UC San Francisco, Variation, Signal, And Noise in the Neural Circuit for Smooth Pursuit Eye Movements Neuronal Variability and Brain Disorders Helen Mayberg, Emory University School of Medicine, Modulating Depression Circuits Using Deep Brain Stimulation Terran Lane, University of New Mexico, Population Variability and Bayesian Inference Richard Stein, University of Alberta, Canada, Coding of Sensory Information about Limb Position Richard Coppola, NIMH, Bethesda, MEG Dynamic Methods in Neuropsychiatric Research Nicholas Schiff, Weill Cornell Medical College, The role of the central thalamus in behavioral variability following severe brain injury: Circuit mechanisms and potential interventions Keynote Address Presented by the inaugural recipient of the Swartz Prize for Theoretical and Computational Neuroscience Organizers: Mingzhou Ding, University of Florida and Dennis Glanzman, NIMH/NIH For programmatic information, please contact: D. Glanzman National Institute of Mental Health 6001 Executive Boulevard, Rockville, MD 20857 Telephone: (301) 443-1576 Register for the meeting, and to submit a poster abstract (October 17 deadline for abstracts) here: http://neuro.dgimeetingsupport.com, or, contact: Nakia Wilson Telephone: (877) 772-9111 From I.Bojak at donders.ru.nl Fri Sep 26 10:03:20 2008 From: I.Bojak at donders.ru.nl (Ingo Bojak) Date: Fri Sep 26 15:21:17 2008 Subject: [Comp-neuro] Postdoc: Computational Neuroscience/Neuroimaging (1.5+3.5 years) Message-ID: <48DC9748.3040605@donders.ru.nl> Candidate profile In a multidisciplinary project we will investigate resting state and sleep with co-registered EEG/fMRI in a novel model-driven, computational analysis. Thus our ideal candidate for this post combines skills in neuroimaging, applied mathematics, and scientific programming with a background in sleep research, connectivity studies or mean field modeling. However, candidates with qualifications in relevant aspects and enthusiasm for broadening their existing scientific portfolio will also be considered. This project is a collaboration between experimentalists and theorists at the Donders Institute?s Centres for Cognitive Neuroimaging (DCCN) and Neuroscience (DCN). Hence it provides a unique opportunity to become part of an emerging group of neuroscientists comfortably crossing traditional faculty boundaries. Research topic How is the ubiquitous EEG ?alpha rhythm? of the unstimulated brain linked to the resting state ?default mode network? that has been identified with fMRI? What happens to the BOLD response as rest turns into sleep, in different stages that we know from their EEG patterns? The complementary nature of EEG and BOLD data requires innovative methods for synergistic data analysis. We will use a realistic mean field model for inverting co-registered EEG/fMRI data to the underlying cortical state through an iterative optimization of its biologically motivated parameters, including cortical connectivity. We will start out with the analysis of previously acquired resting-state data. During this pilot study we will seek extended funding, which will allow us to carry out the planned investigation of sleep stages with co-registered EEG/fMRI. Research environment The Neuro-Physiology and -Informatics group (http://neuroPI.org) at the DCN and the MR-methods for Cognitive Neuroscience group (http://tinyurl.com/4md98p) at the DCCN are part of the new Donders Institute for Brain, Cognition, and Behaviour (http://www.ru.nl/donders/). The offered position is part of a large project supported by the Donders Institute with a start-up grant. Living in The Netherlands / Nijmegen The Netherlands is well-known as a modern and very urbanized European country. However, the vibrant border city of Nijmegen (http://www.nijmegen.nl/) also offers access to the beautiful Dutch/German ?Lower Rhine? countryside. Salary The estimated gross salary will be between ? 3129/month and ? 4284/month, commensurate with experience, plus two yearly 8% supplements (vacation and end-of-year). The 1.5 years initial contract will be extended to up to 5 years, if sufficient external funds are acquired. A generous moving/bridging package is being provided. Contacts Send your applications with full CV, list of publications, and three referees to Ms. Stijns (Tildie.Stijns@donders.ru.nl). Submission deadline is the 31st of October. For more information about the position, contact Prof. R. K?tter (rk@donders.ru.nl), Prof. D. Norris (D.Norris@donders.ru.nl), or Dr. I. Bojak (I.Bojak@donders.ru.nl). From g.goodhill at uq.edu.au Fri Sep 26 12:11:45 2008 From: g.goodhill at uq.edu.au (Geoffrey Goodhill) Date: Fri Sep 26 15:21:20 2008 Subject: [Comp-neuro] Postdoc position in computational neuroscience Message-ID: A postdoc position is now available in the lab of Geoff Goodhill (http://cns.qbi.uq.edu.au) at the Queensland Brain Institute, University of Queensland, Brisbane, Australia. The position is funded by a 3-year HFSP grant entitled "Self-organized wiring of the cerebral cortex through thalamocortical growth cones: an integrated approach". Collaborators on the grant are Ole Paulsen (Oxford, UK), Tomomi Shimogori (Riken BSI, Japan), and Guillermina Lopez-Bendito (Alicante, Spain). The position will involve theoretical modelling of thalamocortical development, closely constrained by experimental data from all 4 labs. Applicants should have a background in mathematical modelling, ideally in a neuroscience context. To apply please send a CV, cover letter and contact information for at least 2 referees to Geoff Goodhill (g.goodhill@uq.edu.au). The Queensland Brain Institute (http://qbi.uq.edu.au) is part of the University of Queensland, one of the top 4 universities in Australia. The QBI is based in a new AU$63 million state-of-the-art facility and houses 24 Principal Investigators with research interests ranging from the molecular to cognitive level. It is one of the largest neuroscience institutes in the world dedicated to understanding the mechanisms underlying brain function and is funded by state, federal, university and philanthropic sources. Brisbane is a cosmopolitan city of 2 million people providing a vibrant cultural environment, a subtropical climate, and easy access to unspoilt beaches, rainforests, and the Great Barrier Reef. From oba at sys.i.kyoto-u.ac.jp Thu Sep 25 04:28:33 2008 From: oba at sys.i.kyoto-u.ac.jp (Shigeyuki Oba) Date: Fri Sep 26 15:41:56 2008 Subject: [Comp-neuro] Postdoctoral Positions - Visuo-Motor Network Simulation Message-ID: Postdoctoral Researchers and Scientific Programmers Brain and Neural Systems Team Integrated Life Simulation Project The goal of the Brain and Neural Systems Team of the Integrated Life Simulation Project is to understand how the brain achieves adaptive behaviors by re-creating the nervous system through integrating neurobiological data available at multiple-levels spanning from genes and molecules to neurons and behaviors. As the first step toward a whole-brain simulation of the human brain, the Visuo-Motor Network Group focuses on the network linking retinal input to eye-movement output, for which rich accumulation of neurobiological knowledge, experimental data, and computational models are available. The simulation model aims to reproduce natural eye-movement behaviors in a real visual environment by integrating the molecular mechanisms for synaptic plasticity, the cellular mechanisms for network development and adaptation, and the network mechanisms for attention and motivation. The research project is sponsored by the Next-Generation Supercomputer Project of the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT). The major goals in its first phase from FY2008 to 2010 are the following: 1) to set up a multi-scale neural simulation environment for linking dynamics at molecular, neuronal, and network levels; 2) to construct a model linking the retina, the superior colliculus, the oculomotor nuclei and the cerebellum to replicate spontaneous and visually evoked eye-movement behaviors. The simulation will be run on the next-generation super computer to boot up in 2011 with 10 peta-flops peak performance (http://www.nsc.riken.jp/project-eng.html). In the subsequent phase from FY2011, we will include the basal ganglia, the thalamus, and the cortical areas to achieve goal-directed visual search and human-like eye communication. We aim to understand the mechanisms of robust and flexible adaptation and to reveal the causes of eye-movement features found in disorders like schizophrenia, autism, and Parkinson's disease. Positions Available We have two postdoctoral researcher or scientific programmer positions starting October 2008. The candidate should have a strong computational background in areas including parallel programming, statistical machine learning, systems biology, image processing, and database management and have, or be willing to acquire, neurobiological knowledge to navigate the literature and databases. The research will be conducted at Kyoto University and other collaborating research institutes. Salary is commensurate with experience. The initial contract continues until March 2009 and is renewable yearly until March 2011. Candidates should send a CV, a list of publications and software projects, and a brief description of interests in science and computing by e-mail to bns08@sys.i.kyoto-u.ac.jp by October 10, 2008. The search will continue until the position is filled. Brain and Neural Systems Team: Shin Ishii, Kyoto University Kenji Doya, Okinawa Institute of Science and Technology --- Posted by Shigeyuki Oba, Kyoto University From nips2008publicity at gmail.com Fri Sep 26 06:24:07 2008 From: nips2008publicity at gmail.com (Antonio Torralba) Date: Fri Sep 26 15:42:02 2008 Subject: [Comp-neuro] NIPS Registration is now open Message-ID: Registration for NIPS 2008 is now open. You can register here: https://nips.cc/Register/ Go here to see the 2008 program highlights: http://nips.cc/Conferences/2008/Program/ Please note the following changes to NIPS in 2008: A new feature that is on the NIPS schedule this year is four Mini Symposia to be held in parallel during the afternoon of December 11, 2008 at the Hyatt Vancouver. The Mini Symposia will provide in depth explorations of current topics in a format that is less, formal than a plenary session but more structured than a workshop. Below are the topics and speakers for this year: Risi Kondor, Guy Lebanon and Jason Morton Gatsby Unit, UCL, Georgia Tech, Stanford University Algebraic and Combinatorial Methods in Machine Learning Bill Freeman and Bernhard Schoelkopf Massachusetts Institute of Technology, Max Planck Institute for Biological Cybernetics Computational Photography Gal Chechik, Christina Leslie, Quaid Morris, William Noble and Gunnar Raetsch Google, Memorial Sloan-Kettering Cancer Center, University of Toronto, University of Washington, Max Planck Society Machine Learning in Computational Biology Daniel Polani and Naftali Tishby University of Hertfordshire, Hebrew University Principled Theoretical Frameworks for the Perception-Action Cycle Attendence at the Mini-Symposia will be open to anyone who is registered for the main NIPS Conference or the NIPS Workshop in Whistler. *We've removed the cost of NIPS Items from Registration and are selling them as a la carte items: -Paper Programs -NIPS Coffee Mugs -NIPS T-Shirts *Refunds will not be given after November 14, 2008. *Payment is now done via Google Checkout. *Everyone will need to display their badge to participate in NIPS activities. We look forward to seeing you at NIPS 2008! From tobias at nld.ds.mpg.de Tue Sep 30 10:49:35 2008 From: tobias at nld.ds.mpg.de (Tobias Niemann) Date: Thu Oct 2 10:47:18 2008 Subject: [Comp-neuro] Full Professor for =?windows-1252?q?=93Sensory_Processing_in_the_?= =?windows-1252?q?Retina=94_=28W3=29?= In-Reply-To: <482D5437.6090809@nld.ds.mpg.de> References: <46F11EC5.4050208@nld.ds.mpg.de> <47DF9A94.8000309@nld.ds.mpg.de> <482D3F70.8030903@nld.ds.mpg.de> <482D5437.6090809@nld.ds.mpg.de> Message-ID: <48E1E81F.7080606@nld.ds.mpg.de> The University of G?ttingen Medical School invites applications for the position of a Full Professor for ?Sensory Processing in the Retina? (W3) We are looking for scientists with an established and internationally recognized, original track of research on the processing of visual information in the retina. The successful candidate will coordinate research at the Department of Ophthalmology and will actively participate in further strengthening the Neuroscience Focus of the G?ttingen Research Campus. Ideally, the candidate will bring expertise in physiological, morphological and/or genetic approaches to synaptic transmission in the retina. She/he is expected to closely interact with molecular, cellular, systems and computational neuroscientists within existing (e.g. http://www.cmpb.uni-goettingen.de/, http://www.bccn-goettingen.de/) and novel collaborative research activities such as a planned research center on the cellular mechanisms of sensory processing. The candidate?s teaching activities will contribute to graduate programs of the G?ttingen Graduate School of Neurosciences and Molecular Biosciences (http://www.uni-goettingen.de/en/56640.html) and the Master and PhD program Molecular Medicine (http://www.molmed-goettingen.de/inter/links.php?sp=en) (teaching language: English). G?ttingen is a center of neuroscience in Europe hosting numerous internationally recognized neuroscience research institutions, including the Centers for the Molecular Physiology of the Brain (CMPB) and for Systems Neuroscience (CSN), the European Neuroscience Institute and the Bernstein Center for Computational Neuroscience (BCCN) run jointly by the University of G?ttingen, three Max Planck Institutes and the German Primate Research Center. Qualifications required are the ?Habilitation? or an equivalent further qualification in research and university teaching; a sound teaching record is a further prerequisite. Experience with grant applications, research planning, as well as international research networking will be highly desirable. Appointments will be made by the Georg-August-Universit?t G?ttingen as a Public Law Foundation according to the Higher Education Law of Lower Saxony (Nieders?chsisches Hochschulgesetz Nds. GVBl. 2007, page 69). Further details will be provided on request. The position is open to German and foreign nationals. The University of G?ttingen is committed to employment equity and women are particularly encouraged to apply. Applicants with disabilities will be preferentially considered within the current legal regulations. Applications including a CV, a list of publications, reprints of the applicant?s five most significant publications, a description of achievements and future plans in teaching and research, as well as an overview of successful funding applications should reach the Faculty no later than 10th of October 2008 following announcement of the position. The Dean and Member of the Board of Directors for Research and Education of the University Medical School, Robert-Koch-Str. 42, D-37075 G?ttingen, Germany. Further general information for applicants and application forms are available on: http://www.universitaetsmedizin-goettingen.de/content/berufungen.html From ajmandell at charter.net Sat Sep 27 18:50:04 2008 From: ajmandell at charter.net (ajmandell) Date: Thu Oct 2 10:52:46 2008 Subject: [Comp-neuro] "Middle layer" coupled " neuron" program Message-ID: <595AE3CEE3B5448D933280ACF8D58ACD@shambala> To all, There's been some interest expressed in our coupled neuron, "MRM" map, some studies of which were published in Physica D in 1989. It might be fun for others to explore its behavior since most of its potential phenomenology has remained unexplored unreported) You can find it at www.cieloinstitute.org where you can use the coupled logistics button and find the zipped downloadable program and a data file. The data and graphics can be saved for analyses. . It runs on most common platforms. The published paper is also available at the site. The combined one and two dimensional dynamical system models the output of coupled neurons. The output of one modulates the parameter of the other. In its rather interesting two dimensional, quasi-symmetrical parameter space (illustrated in the paper ) moving along the diagonal generates most if not all known one dimensional dynamics. Off diagonal exploration yields all or most if not all known in two dimensions (Hopf, tangent, quasi-periodic, period adding etc bifurcations, Arnold's tongues in a dissipative system, etc. The output of the transitional parameter space between one and two dimensions is interesting and complex (and relatively unexplored). With some patience, it can be very rich. The hierarchical self similarity in some of the phase space objects is striking amd reminiscent of the "fractional scaling" reported in some brain data. The system is operated by four convenient parameter "handles" and programmed in very close to machine language so that things run relatively quickly. Cheers Arnold Arnold J. Mandell, M.D. Cielo Institute, Asheville, NC www.cieloinstitute.org ajmandell@charter.net Clinical Professor of Psychiatry and Human Behavior, Emory University, Adjunct Professor of Mathematical Sciences, FAU, Boca Raton, FL Founding Chairman and Professor Emeritus of Psychiatry (Neuroscience, Pharmacology, Mathematics) UCSD, La Jolla, CA MacArthur Prize Fellow Laureate in Theoretical Neuroscience Humboldt Prize Fellow Laureate in Dynamical Systems (Bremen University). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.neuroinf.org/pipermail/comp-neuro/attachments/20080927/793794f3/attachment.html