neuralreckoning

neuralreckoning, 6 days ago to random

OK, let's try something new. I'm not well connected because I'm bad at in person networking, and this is compounded by my decision to stop flying to conferences. So, can I use mastodon to find potential experimental colleagues who would like to work together?

Ideally for me, this would be people in Europe so I can visit by train, but it's not essential. I have some ideas for interesting projects and grant applications, and I'd love to develop those into concrete projects in close participation with experimental colleagues.

One of the main themes I'm interested in is how we can relate various neural mechanisms (e.g. inhibition, recurrence, nonlinear responses) to functions, using computational modelling to ask 'what if' questions that couldn't be answered by experiments alone.

I'm also interested in thinking about how we can use "information bottleneck" ideas to think more clearly about what computations networks of neurons are doing, going the next step beyond representing information to computing / discarding information.

A big question I'd like to answer is to find out how different brain regions work together in such a flexible and scalable way.

A technique I'm very excited about at the moment is using modern ML algorithms to train spiking neural networks at cognitively challenging tasks, making them directly comparable to both psychophysical and electrophysiological data.

Part of that could involve building in new mechanisms, like dendritic structure or neuromodulators into those networks and allowing the trained networks to make use of them in the best way possible.

I'd also love to build jointly motivated experimental and theoretical/synthetic datasets to test models against.

If any of that sounds interesting to you, take a look at some of my recent papers and get in touch. I'd love to hear from you.

http://neural-reckoning.org/publications.html

neuralreckoning, 11 days ago to random

In Marseille, giving a talk in 45m arguing that modelling is essential if we want to understand neural function, and presenting some of our recent research. You can also join by zoom:

https://conect-int.github.io/talk/2024-05-17-int-conect-seminar-by-dan-goodman/

neuralreckoning, 15 days ago to random

I love markdown, particularly @mystmarkdown, but... it's not clear to me that the specification will end up much simpler than LaTeX in the end, and has the downside of less tooling and less standardisation. There's so many flavours of markdown now that it's hard to find correct information. Thoughts? Maybe something @rowan and @choldgraf would be interested in weighing in on.

neuralreckoning, 17 days ago to random

Sometimes I regret staying up until 2am, but not tonight. Saw the northern lights visible by eye in London. Never thought that would be possible. Didn't quite look as good by eye as this 6s exposure, but was still amazing. Fun atmosphere on parliament hill too.

neuralreckoning, 20 days ago to random

UX peeve. Lamps that you have to tap repeatedly to adjust brightness so that if you want it to get less bright you have to cycle through more bright first. Bring back clunky analogue switches. Touch interface is bad for everything except a phone.

neuralreckoning, 20 days ago to science

Thought about hypothesis testing as an approach to doing science. Not sure if new, would be interested if it's already been discussed. Basically, hypothesis testing is inefficient because you can only get 1 bit of information per experiment at most.

In practice, much less on average. If the hypothesis is not rejected you get close to 0 bits, and if it is rejected it's not even 1 bit because there's a chance the experiment is wrong.

One way to think about this is error signals. In machine learning we do much better if we can have a gradient than just a correct/false signal. How do you design science to maximise the information content of the error signal?

In modelling I think you can partly do that by conducting detailed parameters sweeps and model comparisons. More generally, I think you want to maximise the gain in "understanding" the model behaviour, in some sense.

This is very different to using a model to fit existing data (0 bits per study) or make a prediction (at most 1 bit per model+experiment). I think it might be more compatible with thinking of modelling as conceptual play.

I feel like both experimentalists and modellers do this when given the freedom to do so, but when they impose a particular philosophy of hypothesis testing on each other (grant and publication review), this gets lost.

Incidentally this is also exactly the problem with our traditional publication system that only gives you 1 bit of information about a paper (that it was accepted), rather than giving a richer, open system of peer feedback.

#science #philosophy

neuralreckoning, 27 days ago to random

Three grant rejections in one week. Sigh.

neuralreckoning, 27 days ago to random

Now seems hard to deny that the main risk for universities is the actions of those at the very top. Not just in the USA btw. So how do we address this and reclaim our universities?

neuralreckoning, 29 days ago to science

Suppose you were a funder wanting to design a system to fund science projects that were bottom up rather than top down. How would you do it?

I think you'd want to restrict it to non-faculty to start with, and have some sort of consensus-building rather than competitive approach. Like, maybe you could have an initial round where people proposed ideas, followed by a second round where people indicated who they'd be willing to work with and which aspects of their ideas they'd be willing to drop or modify in order to build consensus. Possibly you might need multiple rounds like this until you iterated on a solution that worked.

Would there by problematic hidden power dynamics in an approach like that? I guess so, there always are. But maybe still better than top down approach?

And is there any chance of finding a funder who would be willing to experiment with such an idea? Or any existing examples of experiments like that? Or more generally, examples of funders taking a non-competitive approach?

#AcademicChatter #Science

neuralreckoning, 1 month ago to academia

So oral exam at end of PhD. Good idea or just a tradition that doesn't make any sense any more? What are the good things about them? If we didn't do them, how else could we get those good things? #academia #academicchatter

neuralreckoning, 1 month ago to random

Thread viewer for Mastodon. If you're looking for an easier way to navigate deep threads with many contributions, check out "mastodon thread viewer" (early beta for the moment).

https://thesamovar.github.io/masto-thread-view/

The way it works is you bookmark one of the view types on that page, and then when you're viewing a post from a mastodon thread in your browser, simply click your bookmark and it will open a new tab with the page you're currently viewing rendered as a thread (either tree or table view).

It's early days so there may be bugs, etc., but I think it's already useful. Please give feedback on bugs/feature requests either here or via issues at https://github.com/thesamovar/masto-thread-view.

neuralreckoning, 1 month ago to random

So what would it take to publish a paper here on mastodon and do public peer review? Just an agreement to use a few hashtags like #Paper, and in replies things like #PeerReview, #Accept, #Revise, #Reject? Some automatically generated web and pdf output summarising the thread? Submission to something like Zenodo to give a DOI? Linking user accounts to orcid to verify identity? Only real problem I see is that even with markdown and LaTeX, Mastodon posts are not well suited for longer posts with multiple figures etc. Maybe fine for short results though?

neuralreckoning, 1 month ago to random

Early prototype of Mastodon thread viewer:

https://thesamovar.github.io/masto-thread-view/test.html

Just paste the URL of the thread into the box at the top and hit the "linear thread view" button below and it will give you a view of the thread with hierarchical replies sorted by how many engagements they got (reposts + favourites + replies).

It's very early days so it doesn't yet show any images, the design is not ideal, not optimised for mobile, etc. But I already find this useful for getting a feel of big threads.

My aim here is to give people a better way to navigate overwhelmingly large threads and to allow for a sort of archive of interesting threads. If we want to make Mastodon into a viable option for having scientific debates (e.g. alternative to peer review), we need some way to make them more accessible to outsiders and to surface the most interesting and relevant content.

So I'm particularly interested in hearing suggestions for features or other ideas on how to display threads in the context of long lasting discussions with some permanence to them.

At the moment it's just a very simple idea, but I have other ideas for how to display threads that are a bit wackier and I'll add these as extra buttons as and when I work on this. I'm also going to see how feasible it is to make this into a bookmarklet so you can just hit the 'render thread' bookmark in your browser and open a tab with this. Should be straightforward.

If you're interested, please feel free to post suggestions and issues either here or on github: https://github.com/thesamovar/masto-thread-view

May be of interest to @NicoleCRust @jonny

neuralreckoning, 1 month ago to random

My university will hire a couple of undergrads to help turn my neuroscience course https://neuro4ml.github.io/ into an interactive textbook along the lines of @neuromatch academy https://compneuro.neuromatch.io. I'd like to try a little more though.

I'd like to write some extensions to JupyterBook so that I don't have to maintain separate slides but have everything integrated into one structure, including video recordings, so that you can be watching like a lecture, pause and you're already at the code you can run, etc.

Anyone seen anything like this done before? Any tips? Any thoughts on how to do it? Features it should have? Be ambitious! In my head I'm calling this "textbook of the future" just to give you an idea of how grandiose you should be. 😉 Cc @choldgraf @rowancockett

neuralreckoning, 1 month ago to random

#SilentSunday 2

neuralreckoning, 1 month ago to random

#SilentSunday although not entirely silent because there's a woodpecker up there somewhere but couldn't spot it.

neuralreckoning, 1 month ago to random

So I'm convinced that bureaucratic solutions to our problems are not really solutions, they're just creating bigger problems down the line. But, how do I convince people of that when they've thought of such a bureaucratic solution and I don't have an alternative better solution? As an example, the CREDIT system of writing detailed tables of who did what in a paper. This adds more work and stress into our lives, and puts more power in the hands of the data owners and surveillance companies (RELX etc), but how else do we stop all the biases that this system is trying to address? I feel like there's a comprehensive world view that gives a better way, but that's such a hard sell when people - understandably - feel like small tweaks to the current system are more likely to work. I'd like to say that if a solution will make things worse, start by not doing it. But that's all to easy to see as an argument for keeping things as they are, which is not acceptable. I'm interested in how other people fighting for change who don't believe in bureaucratic solutions approach this issue.

neuralreckoning, 1 month ago to random

So what would happen if someone just started fake signing documents they didn't actually want to sign? Presumably this wouldn't actually work in letting them later claim they didn't sign it? I'm thinking about someone slightly illegibly scribbling "signed under duress". Illegible enough not to be obvious but legible enough to be obvious on a close look.

Just asking a question btw, not suggesting that I or anyone else should do this, obviously.

neuralreckoning, 1 month ago to random

Someone is proposing to delete the @briansimulator wikipedia article because the software is "not notable". Please do join the discussion if you are a wiki editor and feel that it is notable.

https://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Brian_(software)

neuralreckoning, 1 month ago to random

Beautiful evening walk on Hampstead Heath.

Tree silhouette and bird against orange and purple dusk sky
Old fallen tree in dusk light
Tree silhouette against yellow sunset

neuralreckoning, 1 month ago to random

If you're considering a life in academia it's worth watching this video and deciding if it's worth it to you or not. All of this is true.

https://www.youtube.com/watch?v=LKiBlGDfRU8

For me the answer is yes, despite all the problems, for two reasons.

Firstly, I'm lucky enough that I do have considerable freedom to work on the things that I'm interested in. If I was more interested in success or if I was on a 'soft money' position and forced to chase constant grants, I don't know if that would be true. But, such luck is rare.

Secondly, as a socialist I would feel very uncomfortable spending my creative energy on most of the non-academic things I'm qualified for: advertising and surveillance (i.e. tech companies), finance, or startups (making venture capitalists even richer). I could imagine academia getting bad enough that I'd make that choice, but for me it's not there yet. I completely understand that it is that bad for others and I mean no criticism of them.

In a way I suppose this is a sort of defence of academia, but it's a half hearted one at best. I think it's absolutely tragic and depressing that academia has become like this. Doing research should be one of the most joyful and creative things anyone could do with their lives.

neuralreckoning, 1 month ago to random

Fellowship opportunity for ECRs <4y post-PhD. Engineering. 5 year funding. Significant advantage given to people from "underrepresented groups" (see below). Internal deadline of May 6. Comp neuro has done well recently in our dept. Email me if interested.

https://raeng.org.uk/research-fellowships

"The Academy has identified the following groups that are currently clearly significantly underrepresented in UK engineering research:
• Women
• Black people, including those with any mixed ethnicity with Black ethnic background(s)
• Disabled people"

The application process is that candidates need to apply initially to our department, who will select up to 2 applicants to submit to the university as a whole, who select up to 4 applicants (at least 2 from underrepresented groups) for the national competition.

This is an engineering post so it can't be pure neuroscience, but we've had good success recently getting engineering fellowships for @marcusghosh (multimodal processing in the brain with possible applications) and @danakarca (spatially distributed spiking neural networks).

neuralreckoning, 1 month ago to random

Is anyone else feeling uncomfortable about the increasing punching down aspect to science sleuthing? Someone posted a list of all suspected undeclared uses of ChatGPT referenced on pubpeer and it felt like the majority were just researchers at less rich universities who clearly didn't speak English very well using it to translate.

neuralreckoning, 1 month ago to random

Advice to designers of bureaucratic forms. If you don't want to waste you and your colleagues' time reading LLM-generated bullshit, don't have a minimum word count. (And apologies to the people whose job is read these things but who didn't design them.)

neuralreckoning, 2 months ago to random

What if the reason that publishers are unwilling to make review processes public is that if we knew what the average peer review process looked like, we might not think it was such a sacred and essential part of science?