Talk:Computational neuroscience

Lehession (talk) 02:46, 14 January 2015 (UTC)

refactoring

Ok. I can't edit this page if my edits get undone. I am a leading expert in the field, and as opposed to the person undoing my edits not anonymous. The text does not properly represent the mainstream views of the field. The other editor may know the trappenberg book (as they say, it has 400 cites"). I know all the major text books (and many others, e.g. Dayan and Abbott are far more popular). And I organized the leading conference in the area and thus know the spectrum of what people work on. My version before the undo was far better than what we have now. but I have no interest in participating in an edit war. Best. Konrad Kording — Preceding unsigned comment added by Koerding (talk • contribs) 19:47, 26 January 2020 (UTC)

I will soon call for colleagues fora refactoring of the page as a portal, please contact me if intersted Meduz (talk) 10:26, 4 May 2008 (UTC)

The page urgently needs to be refactored. It is quite embarrassing as it stands. E.g. The data vs theory part needs to make its way into the major topics section. — Preceding unsigned comment added by Koerding (talk • contribs) 13:51, 4 July 2019 (UTC)

definition

It is not the case that ML, etc is not part of comp neuro, there are literally 1000s of papers bridging between the two. Maybe that criticism should be edited back in as something related to disagreements in the field. — Preceding unsigned comment added by Koerding (talk • contribs) 18:43, 15 April 2019 (UTC)

Just to add some concrete names: DiCarlo, Yamins, Kording, Kriegeskorte, Richards, Naud are all doing connectionist computational neuroscience. They are funded by e.g. CRCNS which explicitly highlights that the field views this as computational neuroscience.

Theoretical neuroscience is near universally seen as part of computational neuroscience. Theoretical neuroscience deals with theory. Neural data science deals with data. Both fall under the computational neuroscience umbrella. The old discussion on this page already discusses that. — Preceding unsigned comment added by Koerding (talk • contribs) 13:00, 4 July 2019 (UTC)

And the definition on the nature webpage: https://www.nature.com/subjects/computational-neuroscience and crcns.org (https://www.cnsorg.org/computational-neuroscience)

Computational

I thought "computational" was meant in the sense of "looking for computations in the brain" and not "using computers to model the brain". the last option is certainly something of little future since the field is studying the interactions of multiples agents at different levels (synapses, neurons, assemblies, areas, ...). Meduz (talk) 09:01, 8 January 2008 (UTC)

I've fixed some problems with the entry and I'll soon add content to all of the subsections. Also can someone fix the "categories page"? I don't know how to do it. thx --sluox

Computational neuroscience is more of a general descriptor of a branch of science that uses computational and mathematical methods for examine the processes of the brain, whereas neuro cybernetics is more specifically about designing interfaces. I believe neurocybernetics should be combined with Brain-computer interface instead.

Semiconscious 19:22, 22 Jun 2005 (UTC)

Another possible definition is along the lines of the division between a theoretical physicist and an experimental physicist. Thus the term 'computational neuroscience' becomes 'theoretical neuroscience'. The justification for this? Simply that the computer is merely a tool which allows for the testing of neuroscientific hypotheses, the models are derived theoretically from both consideration of the data gathered by the 'experimental neuroscientists' and from the insight (mathematical or otherwise) into the nature of neural computation provided by the 'computational neuroscientists'.

In addition, the field is also populated by systems engineers and electronics engineers.

There is a reference to a work by Shlens, et al., for which there is no full citation.

I agree that the definition of computational neuroscience is too narrow. Computational neuroscience in my opinion is far more than using computers to build toy models of neurons. Sure, that is part of it, but only a part. More generally I would say that computational neuroscience is a paradigm in neuroscience that views the brain as an information processing machine (a computer if you will). Often people studying this paradigm use models (both computational AND mathematical) encompassing many levels of description (eg, low level sub cellular, cellular, network or even abstract: for example probabilistic models or temporal difference learning etc...). Also I would say that one can be a computational neuroscientist and be an experimentalist (which is probably pretty much what a 'systems' neuroscientist is). To say that computational neuroscience is just about building twitchy Hodgin Huxley models of cells is a huge misunderstanding of the field as a scientific movement.

neuroinformatics

I think this article should not be merged with neuroinformatics, as computational neuroscience deals with computational models for various levels of neuroscience and is hence more theoretical, on the other hand neuroinformatics deals with software applications and projects used to build these, and is hence more practical. Computational models are not always necessarily made using a neuroinformatics tool. 82.6.110.89 07:50, 16 May 2007 (UTC)

Please contribute to the whole brain emulation article

Especially the Current research section. It needs sources discussing mapping and simulation of animal brains such as C. elegans. Mange01 (talk) 21:39, 2 April 2009 (UTC)

Merger proposal

Agreement reached with the author of Dynamical neuroscience.

I suggest we import whatever is possible from Dynamical Neuroscience and make it a redirect. The new article at Dynamical Neuroscience is tendentious, and the fundamentals behind it are just false. Many unsupported claims and personal opinions such as "With the explosion of technology and communication in the last couple of decades, the nomenclature of the brain fields has gotten somewhat tangled. The following context-sensitive definitions will hopefully help clarify what dynamical neuroscience is." make it an unacceptable article and moreover, dynamical neuroscience is, from what the author seems to say, nothing else than computational neuroscience with non-linear equations. Since all biological systems are non-linear and especially the brain and since computational neuroscience have been non-linear since their creation, I don't see the point of inventing a subdiscipline in a Wikipedia article. Furthermore, the author could not provide satisfying references showing that Dynamical neuroscience is a generally accepted term in the field of computational neuroscience. All the references use "theoritical neuroscience" or "dynamical systems in neuroscience" rather than "dynamical neuroscience". Googling the term gives very few results beside the own author's attempt at promoting this term. A discussion occured here and here and many people reported issues with the article. I thus suggest essentially a deletion with some merging of stuff that could be useful in the Computational Neuroscience page (there won't be much) Jean-Francois Gariepy (talk) 02:26, 6 August 2010 (UTC). I've made my case in the Dynamical Neuroscience discussion section. Xurtio (talk) 03:12, 6 August 2010 (UTC) Well then if dynamical neuroscience is referenced in 5 places in the free world, I think it does deserve a deletion/merge. In the event that people would not adopt my view, I suggest you rewrite the article in the style of Neurophysics, which is much more conservative and doesn't try to encompass the whole history of computational neuroscience as a pre-cursor to the subfield. There isn't much to say about dynamical neuroscience other than it's a subdiscipline of theoritical neuroscience interested in the use of non-linearity to model brain functions. I would thus expect a 5-lines page, which could really fit as a chapter of Computational neuroscience. What I would certainly do is remove the current references and put an emphasis on those you provided - the course link and the laboratory link, since these are really the only references advocating for the presence of this page. I maintain my comment on the personal views expressed in the article - they are unacceptable. You also say that you are "learning about the dynamical approach to neuroscience and started writing this article to learn about it.". This is not acceptable, as a Wikipedia editor you should have knowledge and build the encyclopedia with it, not build the encyclopedia while you invent the knowledge. I personaly think the field of dynamical neuroscience does not respect the notability standards. Again, not all the references you provide, even in your reply, use the term dynamical neuroscience. "Dynamical Cognitive Science" and "Dynamical Psychology" are different terms and cannot justify the existence of the page. To say that 1 course or 1 laboratory in the whole world uses this terminology to put an emphasis on their interest in dynamical systems is one thing, but we're still far from an actual subdiscipline with its own definition. All these tips are just in case people vote for maintaining the article. I personaly maintain my merger proposal and I'm waiting for the input of other people in the community Jean-Francois Gariepy (talk) 03:43, 6 August 2010 (UTC) I agree that personal opinions should be removed. I'm also waiting for more input from others. Xurtio (talk) 03:51, 6 August 2010 (UTC) I have to say though that this is a silly suggestion of yours: only use the references that use the word "Dynamical neuroscience" Are you serious? Look at the kind of work they do... it's the same work that's done by the people in the other references (namely Dynamical Systems in the Neurosciences). If you don't like the name, that's understandable. If you want it merged, that's understandable. But you're really going too far when you start suggesting that the same subject be torn apart by how it's labeled.... ? No? Xurtio (talk) 04:12, 6 August 2010 (UTC) I'd be the first to use arguments such as those you present in a discussion where I would express my personal opinion about things and about, for example, how the division between psychology and biology is not justified since both sciences study the brain at the end. But Wikipedia is not a place to fight about personal opinions, and you have to do just like me : forget your personal opinions and try to respect the fields as they are and not as you wish they were. If someone says he uses dynamical systems to model the brain, that'a a technique that's a particular procedure used by a particular researcher. If that researcher does not say on his website or whatever text he publishes that he is studying dynamical neuroscience, it just adds to my view that there shouldn't be a Wikipedia article about it. I personaly use extracellular electrodes to study the brain. That is not a good reason to create a Wikipedia article about "Extracellular neuroscience". If I would want to include knowledge about this specific technique to Wikipedia, I would probably have to create a technical article about how extracellular amplifier work. In the end, I would suggest a merge of my article to a sentence in the Amplifier article just to mention that amplifiers are also used in electrophysiological recordings. It is the job of the encyclopedist to regroup and classify knowledge to present its general structure to humanity. An encyclopedia is not a place to discuss about how things should be in an utopic world and how interdiscplinary we should all be and how in the end all sciences study the special arrengements of the same physical atoms. An encyclopedia just reports how knowledge is organized and thought by experts in the field, when there is a field. Jean-Francois Gariepy (talk) 04:23, 6 August 2010 ( My original article was based strictly of physiological approaches (i.e. Dynamical Systems in the Neurosciences inspired it). I actually have research experience there. The addition of sections beyond that were due to criticism from others (specifically at physicsforums.com in the medical sciences section) that I thought were fair, claiming that neuroscience was more than just neurons now. Anyway, I'm still awaiting more input from others. And of course, I'm not going to camp my watch-list and undo any changes brought about by community scrutiny. Xurtio (talk) 05:17, 6 August 2010 (UTC) Here is a supplementary argument that I presented on the other page : I just consulted the Encyclopedia of Neuroscience edited by Binder et al., a more than 4000 pages collective work that seeks to index all concepts and words used in the field of neuroscience and give a short explanation about it. It is a very specialized encyclopedia that contains explanation for many subdisciplines of theoritical neurosciences, and was written by hundreds of leading experts in the field. Just a couple of concepts that are indexed, to give you an idea of the level of specialization, it goes from : actinopterygian, mammals, vertebrates to the across-fiber pattern code hypothesis, the actin-associating protein kinase, or balance laws. There is no mention of dynamical neuroscience, not even as an indexed substitute word. It would be weird if a general encyclopedia like Wikipedia seeked to be more specialized than a specialized encyclopedia made for people in the field. They do mention dynamical systems as a concept used in engineering which is relevant to modelisation in computational neuroscience, but clearly they don't mention Dynamical neuroscience, and they tend to be very bold in defining substitue words. Jean-Francois Gariepy (talk) 05:18, 6 August 2010 (UTC) Here's some authors besides me explaining the motivation for the dynamical approach (using the term dynamical neuroscience): http://www3.interscience.wiley.com/cgi-bin/fulltext/119114969/HTMLSTART Explicitly: "In this section, we pose some practical questions about time and suggest that neuroscience might be close to a turning point, wherein an understanding of the dynamics at one level (e.g., small networks of neurons) may be used to determine knowledge about another level (e.g., cognition). This is a recurring theme in mind-brain studies. Undoubtedly it was a central thrust in the Project's attempt to develop a working neural model of psychological processes. Perhaps some principles in dynamical neuroscience, which were not evident in Freud's day, are now available to synthesize a better bridging model." Please also notice that Computational Neuroscience introduces itself as interdisciplinary as well. Xurtio (talk) 05:48, 6 August 2010 (UTC) Philosophy and Mathematics professors use the term too, calling it a 'perspective': http://books.google.com/books?hl=en&lr=&id=D7tq8BI_9tEC&oi=fnd&pg=PA187&ots=Cz1fwScgtO&sig=1UkzlwwXx9PWpwW4hkLqDvcT9Us#v=onepage&q=%22dynamical%20neuroscience%22&f=false Xurtio (talk) 06:04, 6 August 2010 (UTC) Oppose merger for now, leave the possibility open for the future. I share some of Jean-Francois' concerns (albeit not the bitey tone), and I support the idea of editing this page further to make it more WP:NPOV and WP:NOR compliant, but I would rather wait a bit and see how the page looks after some further work. Depending on how that goes, a merge might be appropriate at that point. --Tryptofish (talk) 15:02, 6 August 2010 (UTC) any specific input on NPOV and NOR would be appreciated. That goes for Jean too, it's difficult to make sense of destructive input. We could, for instance, rename the page neurodynamics as our own wiki, neural oscillation calls it, so that our local neuroscientists don't instantly reject it out of unfamiliarity. I didn't think dynamical neuroscience was such an unfamiliar term. Xurtio (talk) 15:58, 6 August 2010 (UTC) The major problem with NPOV is how you seem to take from all areas of computational neuroscience to justify how dynamical neuroscience are important, when actually most people quoted do not consider themselves as part of the field of "dynamical neuroscience" and have never been referred to as dynamical neuroscientists. Of course the easy way out is to stop calling it dynamical neuroscience and call it Dynamical Systems in Neuroscience. The use of the term "draw" in many instances contributes to the very disturbed view that emerges of what dynamical neuroscience really is. I would definetly remove "drawing largely on nonlinear dynamics and neurobiology" and "Information theory draws on thermodynamics in the development of infodynamics which" and clearly state in a very simple sentence how dynamical system approaches were applied to neuroscience. Other sentences cause problems such as "With the explosion of technology and communication in the last couple of decades," (the whole nomenclature part should be removed. If you can't state what a field is in a single simple sentence, it is not a field. The history part in itself is an issue. What I read there is not the history of dynamical neuroscience, it is the history of computational neuroscience. A clear line should be drawn defining what Dynamical neuroscience are in the introduction and then we could talk about the historical part after that. "The motivation for a dynamical approach to neuroscience stems from an interest in the physical complexity of neuron behavior. As an example, consider the coupled interaction b" this is the kind of sentence you'll see in a discussion of a primary research article, not in an encyclopedia. "See the Morris Lecar paper[12] for a in-depth understanding of the model." you can't talk to the reader like that. Also why would we introduce the equations modeling single neurons, these are already introduced in many other pages in Wikipedia; it is not their place especially if dynamical neuroscience is the study of large networks of these single neurons. A simple reference should be given stating that the huge networks that are modelised use single neurons models as a basis. "One of the predominant themes in classical neurobiology is the concept of a digital component to neurons. This concept was quickly absorbed by computer scientists where it evolved into the simple weighting function for coupled artificial neural networks." Neurobiology is not classical, it's an on-going very active field. Digital component of neurons are a predominant theme in classical neurobiology ? Where does that come from ? "Neurobiologists call the critical voltage at which neurons fire a threshold. The dynamical criticism of this digital concept is that neurons don't truly exhibit all-or-none firing and should instead be thought of as resonators." This is so wrong. The output of a neuron IS digital, but neurobiologists never stated that this was the only aspect of neuronal communications. Very complex dendritic operations were identified by neurobiologist, networks properties were shown to exist. You can't write an article where everything that happened before Dynamical neuroscience was so wrong and now we're so right because we have a dynamical approach. In the 19th century, authors specialised in the brain and biomechanics were already describing potential mathematical approaches to describe complex motor or cognitive processes, read the introduction of "La machine animale" by Étienne-Jules Marey if you don't believe me. They had already invented all the concepts of emergences from complex systems applied to biology, they just did not have the computers to do it. "The global dynamics of a network of neurons depend on at least the first three of four attributes:" what is the reference stating these four attributes ? "In dynamical neuroscience, certain types of attractor networks are being associated with certain brain functions" This part should be removed and you should just point to scholarpedia in a simple sentence. You can't link those attractors to brain functions like that without providing any reference and any context on how they were used. "Biological neural networks (BNNs) are the actual chunk of brain matter in which real couple" Please don't use chunk. "Beyond neurons" This section should be removed. It is duplicate low-quality content of other Wikipedia pages. That was my specific input for now. Jean-Francois Gariepy (talk) 16:50, 6 August 2010 (UTC) Thank you for your input. Izhikivech's argument is that the output is actually 'not' digital. I referenced that paragraph with a citation; I can actually quote the author there if it will make it clearer, instead of paraphrasing, but this is an important aspect of the dynamical perspective; that excitability is a matter of resonance. See (Izhikivech, 2007) section: "where is the threshold?" Where he starts with "Here we challenge the classical view of a threshold." I will seriously consider your other comments, but I have to let my hippocampus grind on it before I go tearing the guts up. I realize that my whole research paper approach is wrong, now. Thank you for that insight. I will try to adapt to the encyclopedia mentality. Xurtio (talk) 17:50, 6 August 2010 (UTC) Anyways the idea that other things than treshold can occur including for instance inhibitory modulation of axon branches or pre synaptic boutons, or feedback from spikes reaching dendrite is as old as neuroscience and I doubt it justifies the creation of a new field in 2007. Even if it would, the article would not be the right place to discuss about it. 173.177.146.156 (talk) 18:18, 6 August 2010 (UTC) That's not the justification. It's an example of the justification. The justification is that nonlinear sciences in general are a difficult and complex mathematical topic and cannot be covered in depth in the course of a biological degree. Just like most branches, it's a result of technocracy. Dynamical neuroscience (or whatever you want to call it, that's not the point, we should hear more opinions on the title) is the application of this deep mathematical topic to experimentally observable variables in neuroscience. Being a nonlinear scientist isn't enough: you also have to be able to take the terms in the mathematica context: bifuraction, oscillations, limit cycle, stable point, unstable focus, etc. and point to what phenomena (and terms) they represent in the neuroscience context. In other words, "dynamical neuroscience" is an approach that formally integrates many (but not all!) seemingly unconnected observed phenomena into one mathematical framework via bifurcation, a qualitative change in behavior that can be mathematically represent a neuron acting in several different regimes, that previously would have required several different models. Xurtio (talk) 19:44, 6 August 2010 (UTC) Possible Solution I've just discovered something. The last link I posted above referenced Cosmelli (2007) who talks about "neurodynamics". From our "neural oscillations" wiki: "The study of neural oscillations belongs to the field of “neurodynamics”, an area of research in the cognitive sciences that places a strong focus upon the dynamic character of neural activity in describing brain function. The term neurodynamics dates back before the 1940s,[4] and is an offshoot of neuro-cybernetics using differential equations to describe neural activity patterns. Research in neurodynamics involves the interdisciplinary areas of contemporary theoretical neurobiology, nonlinear dynamics, complex adaptive systems and statistical physics. Neurodynamics is often contrasted with the popular computational and modular approaches of cognitive neuroscience, and with the implicit or explicit representationalism in cognitive science." Notice how our own wiki author calls it a field. So: "Dynamical Systems in Neuroscience", "Dynamical Neuroscience", and "neurodynamics" all seem to be the same thing to me and they seem to meet notability requirements when you include the more popular term, "neurodynamics". Xurtio (talk) 06:19, 6 August 2010 (UTC) Ok, but you should choose a title and a subject for that article. Because right now what I see in this article is a description of computational neuroscience with higher number of computers. Evolving technology does increase the amount of computations we can make every year, but that does not, in my view, justify the creation of a new terminology for a field that is using the same old equations on a greater scale. And some of the references you bring here are just beside the track; in the article you write about single neuron modelisation and in the references they mention how cognitive processes could be modeled in huge networks. From reading the article right now, I don't see anything stating that cognitive neuroscience is the main focus that distinguishes dynamical neuroscience from other approaches. I don't have anything against the author you cite or against people identifying themselves to that approache, I'm saying the current article has nothing to do with what you describe. The first 2-3 sentences of wiki article about an approach needs to state clearly for everybody what the field studies and how it relates to other fields. "A dynamical system can be represented with a geometric map that describes the trajectories of variables in the phase space. Such systems can experience bifurcation (a qualitative change in behavior) as a function of the bifurcation parameter and often exhibit chaos. Dynamical systems generally require the tools of nonlinear analysis to investigate." is not an understandable definition of the field. I'll adopt Tryptofish's stance; make some major modifications, remove the stuff that actually does not belong to this subfield and if the article is of acceptable quality I won't oppose to remove the merge. Jean-Francois Gariepy (talk) 16:10, 6 August 2010 (UTC) I agree. I think this is the state of the discipline though, too, that makes it difficult to define. It seems to have originated from cognitive neurosciences... but it seems many physicists and neurobiologists are actually doing the physiological data simulation (not paying much mind to the cognitive aspect of it) and then collaborating with the cognitive scientists. If you look at Eugene Izhikivech's CV, you may see what I mean (for instance, his book "Dynamical Systems in Neuroscience" is all physiological... but he attended a Dynamical Neuroscience meeting that consists of cognitive scientists and psychologists. I don't know what the cognitive scientists do with it, cause I'm on the physiological end. I will have to spend some time researching that. Chaos theory is also an important topic here that hasn't been brought up. Actually, chaos theory may well be the main course because it accounts for apparent stochastics in a classical regime. Bifurcation allows for systems to transfer from chaos, to oscillatory, to steady state, chaos being the most rich in terms of dynamics. I do somewhat reluctantly appreciate your scrutiny Jean, thank you. Xurtio (talk) 16:31, 6 August 2010 (UTC) SFN Symposiums I'd like to point out that for the past 17 years the SFN meeting has had a satellite called Dynamical Neuroscience -- the 18th is coming up. The attendance is quite substantial. Looie496 (talk) 19:13, 6 August 2010 (UTC) Of course I already mentioned it in the first paragraph of my merger proposal. The SfN uses this term to designate a certain approach using dynamical systems in neuroscience. This has nothing to do with what is described currently in your article. It should be stated clearly what this "field" (I wouldn't call it a field, I would specify it's a method, an approach, etc...) is and it shouldn't encompass things such as single neuron models. If it does, then Hodgkin was a dynamical neuroscientist ? And then if it does, why do we even have a page on computational neuroscience since everyone is a dynamical neuroscientist. 173.177.146.156 (talk) 19:24, 6 August 2010 (UTC) Sorry, I'm having trouble integrating all the discussion. To me the two terms are quite distinct: computational neuroscience is the interface between neuroscience and computer science; dynamical neuroscience is the interface between neuroscience and mathematical physics. Looie496 (talk) 19:35, 6 August 2010 (UTC) Yes, Looie, that is the point I was trying to make with the nomenclature section that I deleted now for Jean. Izhikivech, Dahlem, and Cowan all make important points about this, and these are all the sections Jean wants removed. 137.229.76.13 (talk) 19:40, 6 August 2010 (UTC) If that would be your actual point you could easily explain it in a very simple manner, 1 sentence, like Looie496 just did. We don't need a whole paragraph. I want the paragraph removed because it's essentially discussion-style and because it doesn't state clearly as Looie496 just did how dynamical neurosciene are defined. Jean, I'd like to point out another fallacy in your argument: "If it does, then Hodgkin was a dynamical neuroscientist". Consider Einstein for instance, and Planck, who were canonical in the formation of quantum physics. They weren't, however, quantum physicists. In fact, Einstein didn't care much for quantum physics, despite being a founder. There's many more examples like this. A field develops as a collective conscious, even if members of that collective aren't part of the field. The problem here is that the said collective consciousness has not developed to a point where you can easily bring text references showing that these are distinct things beside 3 guys, and when I go read those references I realize that they are more talking about the "use of dynamical systems as a tool in neuroscience" rather than Dynamical neuroscience, which seems like a good term to make it short but fails so much at notability that when I google it I end up on your own forum posts about it. The case you quote is very interesting; because it is a very well-known case and the history of the development of quantum physics has been well described and primary and secondary works are available. For dynamical neuroscience, you are trying to push the collective consciousness through encyclopedia editing, and that is one of the greatest problem with Wikipedia, it is that people can actually invent a new science and define it like they want, including whole chunks of other sciences in their new term without worrying about it. You are minimizing again, "only 3 guys"... yeah, 3 guys, five (plus the philosophy/mathematics paper) other examples in the US alone that use the term, and a symposium called "Dynamical Neuroscience" that encompasses pretty much everything I've discussed, from single neurons to cognitive approaches. Oh yeah, also a page here on wikipedia that talks about the same thing, only calls it "neurodynamics" for which there's a whole slough of the same information (nonlinear dynamics in neurons). I would also direct you, once again, to neural oscillation (a subject of 'dynamical neuroscience') to help clear up your confusion. I do foresee a possible merge with that article, but 'dynamical neuroscience' would be the parent. Xurtio (talk) 19:55, 6 August 2010 (UTC) Ok this dicussion has reached a level of bad faith that I can't handle. I'm deleting it from my watchlist and never coming back. You are telling me that neural oscillations identified, theorized and known for over a century and a half are a subject of a sub discipline invented in 1992. Do what you want with this article I think I'm losing too much of my time here. Wikipedia is worse today than it was yesterday. Jean-Francois Gariepy (talk) 20:47, 6 August 2010 (UTC) Forgot to mention, you can do whatever you want with the merger template, including deleting it. For what it's worth, I think Xurtio's comments have been in good faith. And I will delete the merger templates. --Tryptofish (talk) 21:00, 6 August 2010 (UTC) X: Another fallacious argument, really. Solid state matter has been studied for centuries, but it was only when technology was sufficient that Solid State Physics came about and we gained a deeper understanding of the mechanisms behind what we previously called matter. I'm really starting to feel like you're reaching. As with all the other branches of physics... all their subjects were studied for eons as "natural philosophy" before enough people moved into particular aspects of the field. Xurtio (talk) 04:30, 7 August 2010 (UTC) Although we have reached an agreement and this discussion is over, for the record, the sentence you just wrote there would probably be considered insulting by more than 95% of neurobiologists. You're talking about physiologists who discovered the mechanisms underlying oscillatory mechanisms whether it's in the spinal cord for motor control or on EEG recordings and you're saying that before the arrival of physics and computers they were "philosophers" ? Haha. Jean-Francois Gariepy (talk) 17:40, 7 August 2010 (UTC) Sorry to come back, I said I wouldn't, but still I cannot believe we have a neuroscience article in Wikipedia saying that : "Neurons are a namesake of neuroscience, despite only being a star cell on a stage of many important players. At times, it seems their role is overemphasized. After all, nature wasn't at a loss for communication before neurons evolved." ... So although I don't want to spend my personal time fighting for a merge, if anyone wants to take the matter in hand I'll support. Jean-Francois Gariepy (talk) 03:42, 7 August 2010 (UTC) You keep going back and forth. I don't know how much of your comments are legitimate or if you're just bitter in general. Either way, you're not communicating very effectively and you're certainly not being helpful. Try to remove the pathos and implore some logos so we can understand you. You're not the lonely hero, here to save the day. We all want to adhere to standards, but your animosity, tone, and general brute-force method aren't being effective. I've already said a title change doesn't bother me, but you're really the only one criticizing, and you're criticizing EVERYTHING with brute-force tactics, and any reasonable complaints you may have are getting washed away in a sea of boiling pathos and fallacy that comes up with it. It's not coherent or productive. Please regroup and try again. I'm not working on the article any time soon, because you've fired me up too and now I'm confused and I have to regroup my thoughts and do some more research before I write the article. Be patient and wait until I make changes. Xurtio (talk) 04:18, 7 August 2010 (UTC) I have no problem being clearer. When I attack articles, I try to invoke Wikipedia rules and everything, but since you seem to be interested in a clearer stance I'll take it : You wrote an article about a subject you don't know very much about, and that's a fundamental problem. That's why there are so many false declarations in the article that I don't even want to correct them because 1) it would be too long 2) my name would be associated with a poorly written article and I would be listed as a contributor. And that's why you have to make it up as we discuss and you have to go read again everytime I ask a question. I come to the same conclusion that apeiron reached at the physicsforum, he has more than 1400 posts there and discussed about it with you until he couldn't continue, just like me. He gave up and said : "You think you know what you are talking about? Fine." and that's pretty much all I can do too since not much people are participating in the merge vote and the ones who do seem to believe that the article can actually improve, or maybe they just don't want to be too rude with you since you are a new contributor and they plan on merging in 2 months. I guess only time will tell us, but right now I do not want to get in a fight and I already spent too much time explaining to you the fact that hollistic approaches, mathematical modeling and non-linearity in computational neurosciences have not been around since 2007, they've been around for as long as we've had models, so I should really stop answering you. The least would be to put up a sign on top of the article saying the content is false and being improved, or at least work on it on the talk page and leave the page blank for now, because we are misleading readers right now. They are being misled in terms of clarity, in terms of historical description and in terms of terminology. As I said, I won't do it myself because it frustrates me too much to have spent that much time for so few improvements. As far as the legitimity of my comments and my bitterness goes, please Wikipedia:Assume good faith. Do you think I would have spent half a day of my time just to be a troll ? I'm actually worried by this article and by the inaction of the community toward it. Jean-Francois Gariepy (talk) 04:44, 7 August 2010 (UTC) If you are sure that something is false, but the tags up, please! You're unwillingness to do so only makes me think that you, a professional, are unsure of yourself. Apeiron and me continued our conversation in PM. He was mostly angry because he thought I meant a) reductionism, not b) reducitonism. In his e-mail, he also said "I wrote about dynamical vs. computationalism, so I feel I know something about the topic" and suggested Friston as an author to me. Like you, he seemed to go back and forth about whether it was it's own discipline or not. No I don't think you're trolling, I think you saw something you didn't like, and you got up on a high-horse and started charging blindly and ingnorantly after that point. I think you're intentions were originally in the right place. DISCUSSION PARTICIPANTS BESIDES JEAN: if you are taking my side only to be nice, stop right now. I won't run away if you take his side. Xurtio (talk) 05:03, 7 August 2010 (UTC) Article Deleted I guess if there's even the slightest chance, I don't want to mislead people. I'll come back and write this article in about five years if somebody who knows what they're talking about doesn't first. In the meantime, I'm going to contribute to my field (that you don't believe in) by doing the Morris-Lecar Model as that's the specific research I do. I would enjoy your criticism there, as well. Xurtio (talk) 05:12, 7 August 2010 (UTC) Of course I'm happy the article is deleted in its current state but I'll be available if you want to work on it on a talk page or something to provide comments. I'd like to specify that I never said I do not believe in your field, I said that the way it was presented was 1) redundant with other pages in Wikipedia 2) not clear 3) historically false. I provided numerous specific comments by putting emphasis on what was false, and it was essentially because of the pseudo-revolutionary tone where all neurobiologists were wrong and thought the neurons were simple after which dynamical neuroscience came and showed us how complex they were. I hope you won't be discouraged by this experience, I think you work well and you seem to take critics seriously. Jean-Francois Gariepy (talk) 13:30, 7 August 2010 (UTC) I see that a lot has happened since I logged out last night. If I understand correctly from the deletion edit summary, it was Xurtio who requested the deletion, and I guess that's your business. In response to a comment a little higher up, no, I do not make a practice of being nice to editors if I feel that they are incorrect on the merits, and there is absolutely no justification for implying otherwise. I call them like I see them. As I've previously told Jean-Francois, I appreciate very much your work expanding our previously weak coverage of neuroscience history. As I've previously told Xurtio, I welcome your bringing of your area of expertise to this project. And I'm going to tell both of you right now that it does no one any good to personalize differences of opinion about content. There was no need for the bitterness that accompanied the recent discussion here. If either of you wants to contact me on my talk to discuss this any further, I will welcome that, but I'm otherwise walking away from this page now. --Tryptofish (talk) 16:07, 7 August 2010 (UTC) Scraps The article is is on my user page: User:Xurtio/Dynamical_neuroscience If anyone wants to rip some stuff out of it to put in Computational neuroscience. But please let me know what you use on the discussion page there so that there's no overlap if I ever come back to this project. Xurtio (talk) 18:36, 7 August 2010 (UTC)

Theoretical neuroscience is not Computational neuroscience

... but computational neuroscience is a branch of theoretical neuroscience. The hierarchy I've always understood was that Theoretical neuroscience was just that. A theoretical approach to neuroscience. Theoretical neuroscience, however, encompasses two subjects: mathematical and computational modeling. I've seen this differentiation made in a class syllabus , but also see:

https://redwood.berkeley.edu/bruno/papers/TN-review.pdf

"There tend to be two camps in the field of computational neuroscience, and they are probably best exemplified by how they use the term ‘‘computation.’’ In one, mathematical models are constructed primarily to describe or characterize existing data, and computation is used mainly as a means to simulate or analyze the data, in rather the same way as computational chemistry or computational fluid dynamics. In the other camp, computation is applied in a more theoretical manner, as a metaphor for what the brain is actually doing."

And see my talk page for a discussion by someone who studies the same subject I do ("neurodynamics" is a popular name in Google Scholar that explicitly describes the field, though I've never heard it before. I've heard "dynamical neuroscience" but you can see the problems that caused above. Anyway, it conforms to that mathematical branch of theoretical neuroscience. I'm a grad student, so a PhD that studies the mathematical approaches would have the highest value input, imo.

I think there should be a general Theoretical neuroscience page that differentiates mathematical from computational methods. Xurtio (talk) 06:07, 14 August 2010 (UTC)

I basically agree with the conclusion but would like to adjust the explanation a bit. "Computational neuroscience" actually comprises two quite distinct things: (1) the study of how neurons compute, (2) the use of computers to study the nervous system. The first is a branch of theoretical neuroscience, the second is not necessarily. Looie496 (talk) 19:01, 14 August 2010 (UTC)

what you've said here, I agree with; but in the context of theoretical neuroscience, the (2) is necessarily theoretical. But more than that... what about theoretical neuroscience methods that don't require a computer? Are they suddenly not "theoretical neuroscience" despite being theoretical and neuroscience? Xurtio (talk) 03:35, 16 August 2010 (UTC)

Is #2 above like when a neuroscientist uses a computer to analyze an EEG or MRI, or maybe when they use one to get spectra of neuron spikes from a rat brain probe? Those are definitely not "computational neuroscience" by any definition I'd ever hear - those are clinical and/or experimental. Let's not get too beyond mainstream here. Anyway, when it comes to mathematical models and optimization of algorithms, theoretical and computational neuroscience are identical, and I don't think they are anywhere near the academic segregation of, say, how theoretical vs. computational physics/mathematics are split. SamuelRiv (talk) 20:02, 18 August 2010 (UTC)

Consider for instance, the Hodgkins-Huxley model that were nonlinear differential equation models of neurons before computers were around. Theoretical analysis of dynamical systems requires a lot of mathematical background and despite being nonlinear, there were practical methods conceived for finding out properties of the system (Strogatz, "Nonlinear Dynamics and Chaos" is the modern text on the subject). Even though no solutions were found. (2) refers to this very same analysis, only nowadays you have the luxury of using a computer instead of paper and pencil. It's a matter of convenience. Computational theory, on the other hand, is literally based on the computational properties of neurons. Steroetypically speaking, and over-generalizing, the one (2) is a physicist/mathematical biology approach, the other (1) is a computer science/electrical engineer approach. AI is generally pursued by (1), not (2). (2) is generally a reductionist method that's more useful to physiology and medical applications, (1) is more the study of information flow regardless of the physics. These are generalizations of course( i.e Karl Friston, who utilizes the concepts of thermodynamics to make a holistic model of the brain- "Free Energy Principle of the Brain"). Jack Cowan (mentioned as a forefather in "Theoretical Neuroscience" is one of the people who made the distinction clear:

• http://www.scilogs.eu/en/blog/gray-matters/2010-06-16/mathematical-and-computational-neuroscience.

One of the major differences seems to be that (1) makes interpretations from cognitive psychology data, (2) uses experimental data from the the physics of the neurons alone.

As an alternative, we could at least break up the article Computational neuroscience into two sections (within the same page): mathematical methods and computational methods. That's how the canonical textbook, "Theoretical Neuroscience" is broken up, and it appears to be the same subject matter.

Xurtio (talk) 05:10, 19 August 2010 (UTC)

Another option (or a first step) is to create a short section in the Neuroscience article, summarizing these issues, but leave this article as it is. The section might be entitled "Mathematical models" (which I prefer) or "Theoretical and computational neuroscience".

If the mathematical models section becomes large, a separate article on Mathematical models in neuroscience can be created.

Can you give an example of a mathematical model that is not used in computational neuroscience, perhaps because it is too simple or idealized? Generally, in various computer simulation and numerical computation application areas, you tend to use more accurate and advanced models than in analytical math. However, most mathematical models can be used both in numerical computing and mathematical analysis, so it is really hard do draw a firm line between them. It is normally easier to differentiate mathematical models from simulation tools and simulation results.Mange01 (talk) 08:58, 19 August 2010 (UTC)

Your last sentence is actually my point. Computational models that have nothing to do with mathematics are the "computational approach" while mathematics models, even if they use computers, are the "mathematical approach". As Looie said, the problem is what "computation" means. 1) computer as a tool, 2) computational theory. When you're a (1) doing mathematical biology, think you're a (2) when you talk about "computational neuroscience". Originally, it would have meant the same thing as "computational physics", i.e., (1), computation is a tool to study your mathematical models. Unfortunately, (2) uses the same name, and then Abbot put the (1) and (2) in a book together called, "Theoretical Neuroscience", and some scientists ARE both (1) and (2).z

As for Mathematical models in neuroscience we currently have Biological neuron models, but it just gives the specific models, it doesn't talk about the field in general. You're other suggestion hough, to add a section explaining the difference is a good idea. And possibly my above explanation (with valid citations/research) could be a section in the Computational neuroscience article. Thanks for your input. Xurtio (talk) 01:48, 20 August 2010 (UTC)

Distinguishing a field that uses the computer as a "tool" versus using it as an intrinsic mode of study is like calling a carpenter who uses a power drill a "machinist". Everybody uses computers to investigate every mathematical model and every iota of quantitative data. The difference comes when the model and the computer simulation are intrinsically linked. For example, some mathematical models only produce useful results when integrated and relaxed over an enormous number of points (ie Lattice QCD), so deriving and manipulating those equations would still be a computational methodology. There is just no such thing, in current research, as a mathematical investigation without using a computer, or a computational investigation without using mathematics. But as in physics, there are lines at which the methodologies can be separated into different fields - my contention is that this separation does not yet exist in theoretical neuroscience without, as in using ANNs to analyze handwriting, ceasing to be neuroscience. SamuelRiv (talk) 06:16, 21 August 2010 (UTC)

By your analogy, I think you're missing the point. We're talking about a theory called "computational theory" that encompasses a philosophical ideology about how neurons work (see the first sentence of this wiki article) vs. a computational tool (for ANY theoretical approach). For the carpenter, it's as if we were saying pythagoras theorem and the power drill are the same thing to make the analogy proper. Carpenters use math, too. But, I mean, so does everybody. We can all count to 100. But a mathematical model is different than a computational model that uses math. And of course, to confuse the issue, they're not mutually exclusive, either.

I mean, isn't that why the distinction is made in Dayan's book? https://redwood.berkeley.edu/bruno/papers/TN-review.pdf Xurtio (talk) 07:58, 21 August 2010 (UTC)

Okay then, you are suggesting that comp. neuro. encompasses the philosophy that the tool is analogous to the real-life mechanism. This seems to be primarily suggesting that the computational neuroscience is about connectionism - that a ANN model reflects the reality of how neurons actually physically arrange, as opposed to being an analogy of how the computation can work. In this way, my previous statement that such a philosophy in exclusion to other approaches then "ceases to be neuroscience", as function/result supersedes the physical model (such as a biologically-motivated H-H circuit network).

At my undergrad,incidentally, the respective courses were called "Computational Intelligence" for ANNs and "Computational Neuroscience" for H-H etc, each with various degrees of exclusion (one CN prof worked with ANNs in robotics, while the other CN prof eschewed ANNs, and the CI prof hated biology). SamuelRiv (talk) 17:38, 22 September 2011 (UTC)

The dayan article is great and appears to be misunderstood. Within theoretical neuroscience there is a theory section (using math) and a computational section (use simulations). But Comp neuro contains data analysis parts that do not fall into theoretical neuroscience. — Preceding unsigned comment added by Koerding (talk • contribs) 13:03, 4 July 2019 (UTC)

Cruft

I have a strong urge to de-cruftify this article, which has become essentially a link page. Any objections to doing that? Looie496 (talk) 15:14, 7 September 2011 (UTC)

Okay, I've just done a thorough housecleaning. There may still be a little bit of cruft left, but I think I got rid of most of it. Looie496 (talk) 16:43, 21 September 2011 (UTC)

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