Blue Brain: researching the way the brain encodes information

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Blue Brain: researching the way the brain encodes information

Postby Dimebag » Sat Jun 17, 2017 2:14 pm

https://blog.frontiersin.org/2017/06/12/blue-brain-team-discovers-a-multi-dimensional-universe-in-brain-networks/
http://bluebrain.epfl.ch/page-56882-en.html
Using mathematics in a novel way in neuroscience, the Blue Brain Project shows that the brain operates on many dimensions, not just the three dimensions that we are accustomed to.

For most people, it is a stretch of the imagination to understand the world in four dimensions but a new study has discovered structures in the brain with up to eleven dimensions – ground-breaking work that is beginning to reveal the brain’s deepest architectural secrets.

Using algebraic topology in a way that it has never been used before in neuroscience, a team from the Blue Brain Project has uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.

The research, published today in Frontiers in Computational Neuroscience, shows that these structures arise when a group of neurons forms a clique: each neuron connects to every other neuron in the group in a very specific way that generates a precise geometric object. The more neurons there are in a clique, the higher the dimension of the geometric object.
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PR neuroscience news topology blue brain project markramTopology in neuroscience: The image attempts to illustrate something that can not be imaged – a universe of multi-dimensional structures and spaces. On the left is a digital copy of a part of the neocortex, the most evolved part of the brain. On the right are shapes of different sizes and geometries in an attempt to represent structures ranging from 1D to 7D and beyond. The “black-hole” in the middle is used to symbolise a complex x of multi-dimensional spaces, or cavities. Courtesy of the Blue Brain Project
“We found a world that we had never imagined,” says neuroscientist Henry Markram, director of Blue Brain Project and professor at the EPFL in Lausanne, Switzerland, “there are tens of millions of these objects even in a small speck of the brain, up through seven dimensions. In some networks, we even found structures with up to eleven dimensions.”

Markram suggests this may explain why it has been so hard to understand the brain. “The mathematics usually applied to study networks cannot detect the high-dimensional structures and spaces that we now see clearly.”

If 4D worlds stretch our imagination, worlds with 5, 6 or more dimensions are too complex for most of us to comprehend. This is where algebraic topology comes in: a branch of mathematics that can describe systems with any number of dimensions. The mathematicians who brought algebraic topology to the study of brain networks in the Blue Brain Project were Kathryn Hess from EPFL and Ran Levi from Aberdeen University.

“Algebraic topology is like a telescope and microscope at the same time. It can zoom into networks to find hidden structures – the trees in the forest – and see the empty spaces – the clearings – all at the same time,” explains Hess.

In 2015, Blue Brain published the first digital copy of a piece of the neocortex – the most evolved part of the brain and the seat of our sensations, actions, and consciousness. In this latest research, using algebraic topology, multiple tests were performed on the virtual brain tissue to show that the multi-dimensional brain structures discovered could never be produced by chance. Experiments were then performed on real brain tissue in the Blue Brain’s wet lab in Lausanne confirming that the earlier discoveries in the virtual tissue are biologically relevant and also suggesting that the brain constantly rewires during development to build a network with as many high-dimensional structures as possible.

When the researchers presented the virtual brain tissue with a stimulus, cliques of progressively higher dimensions assembled momentarily to enclose high-dimensional holes, that the researchers refer to as cavities. “The appearance of high-dimensional cavities when the brain is processing information means that the neurons in the network react to stimuli in an extremely organized manner,” says Levi. “It is as if the brain reacts to a stimulus by building then razing a tower of multi-dimensional blocks, starting with rods (1D), then planks (2D), then cubes (3D), and then more complex geometries with 4D, 5D, etc. The progression of activity through the brain resembles a multi-dimensional sandcastle that materializes out of the sand and then disintegrates.”

The big question these researchers are asking now is whether the intricacy of tasks we can perform depends on the complexity of the multi-dimensional “sandcastles” the brain can build. Neuroscience has also been struggling to find where the brain stores its memories. “They may be ‘hiding’ in high-dimensional cavities,” Markram speculates.

Read the full paper: http://journal.frontiersin.org/article/ ... 8/abstract

Citation: Reimann MW, Nolte M, Scolamiero M, Turner K, Perin R, Chindemi G, Dłotko P, Levi R, Hess K and Markram H (2017) Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function. Front. Comput. Neurosci. 11:48. doi: 10.3389/fncom.2017.00048

This research was funded by: ETH Domain for the Blue Brain Project (BBP) and the Laboratory of Neural Microcircuitry (LNMC); The Blue Brain Project’s IBM BlueGene/Q system, BlueBrain IV, funded by ETH Board and hosted at the Swiss National Supercomputing Center (CSCS); NCCR Synapsy grant of the Swiss National Science Foundation; GUDHI project, supported by an Advanced Investigator Grant of the European Research Council and hosted by INRIA.

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Re: Blue Brain: researching the way the brain encodes information

Postby bobbo_the_Pragmatist » Sat Jun 17, 2017 8:27 pm

You do know that Math doesn't "prove" anything in the real world? All the formulas have to be confirmed as to results by measurement or observation. Its ironic given the very formal definition of "proof" is reserved for mathematics. But Math is a proof that may or may not be true....because Math is a logical system based on a set of assumptions.

"What Works." So much more interesting than multiple dimensions proposed on mathematical modelling.
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Re: Blue Brain: researching the way the brain encodes information

Postby Dimebag » Sat Jun 17, 2017 10:50 pm

bobbo_the_Pragmatist wrote:You do know that Math doesn't "prove" anything in the real world? All the formulas have to be confirmed as to results by measurement or observation. Its ironic given the very formal definition of "proof" is reserved for mathematics. But Math is a proof that may or may not be true....because Math is a logical system based on a set of assumptions.

"What Works." So much more interesting than multiple dimensions proposed on mathematical modelling.

I have drawn no conclusions from the research, however I find it highly interesting, albeit a little over my head. Suffice to say I will be watching this space along with the connectome project for new developments. But it is no real surprise that we find something we weren't aware of previously, we know little to nothing about how memory is encoded in the brain, nor how information is represented.

BTW, here is the original journal report, if anyone is interested in looking deeper: http://journal.frontiersin.org/article/10.3389/fncom.2017.00048/full

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Re: Blue Brain: researching the way the brain encodes information

Postby Nikki Nyx » Sun Jun 18, 2017 3:47 am

My BS detector went off at "eleven dimensions," so I took an hour to do some research. There are a number of serious issues with this so-called study.

1. The journal in which it was published, Frontiers in Computational Neuroscience, is wholly owned by Frontiers Media, which was founded by Henry Markram...who's also the founding director of Blue Brain.

2. Markram was ousted from the multimillion dollar Human Brain Project, sponsored by the EU, following a petition by 815 European neuroscientists that included allegations of fund mismanagement, an overly-narrow focus to the detriment of the broader scope of the Project, and poor governance.

3. Markram's work at Blue Brain has been excoriated by his peers as being bad science. One common complaint was that Markram studied neurons in vitro, and that says nothing about what neurons do in vivo. Another frequent comment was that Markram was indulging in pseudo-science. This rant, while filled with profanity, presents the issues rationally and in non-technical language. And it's funny.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
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Re: Blue Brain: researching the way the brain encodes information

Postby Matthew Ellard » Sun Jun 18, 2017 4:24 am

LunaNik wrote: BS detector went off at "eleven dimensions,".
I agree. Even stranger, the 11 dimensions are a concept from String M-theory in physics, which has yet to be locked down. It seems to me they are using "11 dimensions" as a buzz phrase, like wooists use "quantum mechanics".

https://en.wikipedia.org/wiki/String_theory
"One notable feature of string theories is that these theories require extra dimensions of spacetime for their mathematical consistency. In bosonic string theory, spacetime is 26-dimensional, while in superstring theory it is 10-dimensional, and in M-theory it is 11-dimensional.

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Re: Blue Brain: researching the way the brain encodes information

Postby Nikki Nyx » Sun Jun 18, 2017 4:43 am

Matthew Ellard wrote:
LunaNik wrote: BS detector went off at "eleven dimensions,".
I agree. Even stranger, the 11 dimensions are a concept from String M-theory in physics, which has yet to be locked down. It seems to me they are using "11 dimensions" as a buzz phrase, like wooists use "quantum mechanics".

https://en.wikipedia.org/wiki/String_theory
"One notable feature of string theories is that these theories require extra dimensions of spacetime for their mathematical consistency. In bosonic string theory, spacetime is 26-dimensional, while in superstring theory it is 10-dimensional, and in M-theory it is 11-dimensional.

Well, that explains why my BS detector went off. I thought I'd read "eleven dimensions" somewhere, and I should've guessed it was as aspect of physics, since that's where all my WikiLoops end up at one point or another.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
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Re: Blue Brain: researching the way the brain encodes information

Postby TJrandom » Sun Jun 18, 2017 5:59 am

And not even an April 1st publication date. :twisted:

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Re: Blue Brain: researching the way the brain encodes information

Postby Gord » Sun Jun 18, 2017 6:47 am

Dimebag wrote:
Using mathematics in a novel way in neuroscience, the Blue Brain Project shows that the brain operates on many dimensions, not just the three dimensions that we are accustomed to.

To sum up, "Using mathematics wrong, the Blue Brain Project says stupid stuff it can't support in a peer-reviewed journal so we're putting it here instead".
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Re: Blue Brain: researching the way the brain encodes information

Postby Gord » Sun Jun 18, 2017 7:07 am

LunaNik wrote:This rant, while filled with profanity, presents the issues rationally and in non-technical language. And it's funny.

If you like funny rants about mathematics (in this case, statistics), I recommend this one: A simple mathematical model of congressional geriatric penis pumps

It explains the underlying meaning of a phrase someone spoke while being interviewed by Samantha Bee:

...Ilyse Hogue proclaims authoritatively:

“Statistics show that probably some our members of congress have a vested interested in having penis pumps covered by Medicare!”

Ilya’s wording is vague, and intentionally so. Statistically, a lot of things are “probably” true, and many details are contained in the word “probably”. In this post we present a simple statistical model to clarify what Ilya means.

:heh: I love smart people.
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Re: Blue Brain: researching the way the brain encodes information

Postby bobbo_the_Pragmatist » Sun Jun 18, 2017 10:09 am

Gord wrote:
LunaNik wrote: Statistically, a lot of things are “probably” true, and many details are contained in the word “probably”.

Without reading the links yet, I wonder if a better word/concept for probably would be "could"? Probably true has a positive predictive element to it that I don't think is meant? Probably true: more likely than not, aka: 51%? Could be true could mean any percentage at all including zero as zero is not acceptable to science in most cases.
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Re: Blue Brain: researching the way the brain encodes information

Postby Gord » Sun Jun 18, 2017 10:26 am

bobbo_the_Pragmatist wrote:
Gord wrote:
LunaNik wrote: Statistically, a lot of things are “probably” true, and many details are contained in the word “probably”.

Without reading the links yet, I wonder if a better word/concept for probably would be "could"? Probably true has a positive predictive element to it that I don't think is meant? Probably true: more likely than not, aka: 51%? Could be true could mean any percentage at all including zero as zero is not acceptable to science in most cases.

LunaNik didn't say that, I did.

But the word "probably" is exactly the word they mean to use, as they explain.
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Re: Blue Brain: researching the way the brain encodes information

Postby bobbo_the_Pragmatist » Sun Jun 18, 2017 10:29 am

Gord wrote: But the word "probably" is exactly the word they mean to use, as they explain.

That could be true.
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Re: Blue Brain: researching the way the brain encodes information

Postby Gord » Sun Jun 18, 2017 10:48 am

...just read the damn article. :facepalm:
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Re: Blue Brain: researching the way the brain encodes information

Postby bobbo_the_Pragmatist » Sun Jun 18, 2017 10:55 am

Now who refuses the joke?
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Re: Blue Brain: researching the way the brain encodes information

Postby Gord » Sun Jun 18, 2017 11:00 am

I said I love smart people, not smartass people.


...I also said :facepalm:
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Re: Blue Brain: researching the way the brain encodes information

Postby Dimebag » Sun Jun 18, 2017 12:44 pm

After reading about some of the criticisms of the project, it does seem to have had quite a bit of controversy, which is probably no surprise considering what they are trying to achieve and given the huge budgets involved. Whether this Markram guy is legit or not, I am more concerned with what the projects aim to achieve, And what potential findings they might uncover.

To say the projects are totally without merit is a bit unfair, however, given the budget of such a huge project involving hundreds of scientists across the globe, I would agree they need to set clear and reasonable goals. The idea of a collaborative joint effort of researchers being able to contribute to a simulation of the human brain seems almost set up for great problems. Almost like a Wikipedia of the brain.

Nevertheless, the projects have been running for some time now, they claim to be able to simulate an entire brain by 2023, I think that's a bit optimistic, especially considering the fact that we don't truly know everything there is to know about the brain. What emerges might be like the brain of someone in a vegetative state, which will be about as interesting to simulate as a pile of rocks.

Who knows, at least they are trying new things.

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Re: Blue Brain: researching the way the brain encodes information

Postby Nikki Nyx » Sun Jun 18, 2017 4:41 pm

Dimebag wrote:To say the projects are totally without merit is a bit unfair, however, given the budget of such a huge project involving hundreds of scientists across the globe, I would agree they need to set clear and reasonable goals.
The project, as its goal is defined, is without merit. You can make a model of the human brain on your computer, but without clearcut meaningful data on the interrelationships, your simulation will simply be a static model. Markram seems to believe he can linearly "level up" from his working simulation of one cubic millimeter of a mouse's brain—which is based on data garnered from mouse neurons in vitro—to a working simulation of the human brain in its entirety. Clearly, that's not a remotely feasible goal.

It's like saying you can make a working model of our solar system, then use that data to make a working simulation of the entire universe. Think of what your universe model would be missing if you did this: singularities, nebulae, pulsars, GRBs, etc.

Meanwhile, the money and resources he's wasting could be used to accomplish useful research with realistic goals. Markram's model, as the ranter to whom I linked pointed out, is about as useful as a Cargo Cult airplane knocked together from scraps.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
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Re: Blue Brain: researching the way the brain encodes information

Postby Nikki Nyx » Sun Jun 18, 2017 5:06 pm

Gord wrote:If you like funny rants about mathematics (in this case, statistics), I recommend this one: A simple mathematical model of congressional geriatric penis pumps

It explains the underlying meaning of a phrase someone spoke while being interviewed by Samantha Bee:

...Ilyse Hogue proclaims authoritatively:

“Statistics show that probably some our members of congress have a vested interested in having penis pumps covered by Medicare!”

Ilya’s wording is vague, and intentionally so. Statistically, a lot of things are “probably” true, and many details are contained in the word “probably”. In this post we present a simple statistical model to clarify what Ilya means.

:heh: I love smart people.

That was funny. The first comment made it even more so.
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein

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Re: Blue Brain: researching the way the brain encodes information

Postby Gord » Tue Jun 20, 2017 6:04 am

LunaNik wrote:...Markram seems to believe he can linearly "level up" from his working simulation of one cubic millimeter of a mouse's brain—which is based on data garnered from mouse neurons in vitro—to a working simulation of the human brain in its entirety.....

And don't forget: https://mathbabe.org/2015/10/20/guest-p ... n-project/

...Of course he never published anything showing that these simulations lead to any understanding of brain function whatsoever....

What working simulation of one cubic millimetre of a mouse's brain?
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Re: Blue Brain: researching the way the brain encodes information

Postby Nikki Nyx » Tue Jun 20, 2017 3:40 pm

Gord wrote:
LunaNik wrote:...Markram seems to believe he can linearly "level up" from his working simulation of one cubic millimeter of a mouse's brain—which is based on data garnered from mouse neurons in vitro—to a working simulation of the human brain in its entirety.....

And don't forget: https://mathbabe.org/2015/10/20/guest-p ... n-project/

...Of course he never published anything showing that these simulations lead to any understanding of brain function whatsoever....

What working simulation of one cubic millimetre of a mouse's brain?

I think I may have misspoken, Gord. I believe I meant to write "structural simulation," rather than "working simulation." That makes a difference, doesn't it? Good grief. Not "working" in the sense of computational functioning. Rather, he garnered date from mouse neurons in vitro, then made a structural simulation based on that, expecting his model to work like it would in vivo. Thanks for catching that!
What are the facts? Again and again and again-what are the facts? Shun wishful thinking, ignore divine revelation, forget what “the stars foretell,” avoid opinion, care not what the neighbors think, never mind the unguessable “verdict of history”--what are the facts, and to how many decimal places? You pilot always into an unknown future; facts are your single clue. Get the facts!
—Lazarus Long, from Time Enough for Love, by Robert A. Heinlein


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