The Transfiguration

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Archive for the ‘science and math’ Category

Prototype of the Day #2036

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Prototype of the Day #2036

I’ve been taking a machine learning course for the past few weeks. It’s just an online class, something I can work on at a leisurely pace, but it’s good to have something pushing me to keep learning.

This week’s assignment had me building a neural network – an algorithm to allow computers to learn and develop hypotheses about data, designed in a simplified fashion after how actual neurons connect and process information. This is how technologies like Google’s clever search suggestions and self-driving cars come from – the guided crunching of data, phenomena reduced to matrices, ground down and sifted until patterns emerge from the chaos. I’ve gotten the impression, somehow, that given enough time and information, a good neural network could work out any problem, be it structural engineering or musical composition. We’ll see, in time, if real artificial intelligence comes of this someday.

My own neural network here was asked to learn to understand handwritten numbers. From a sample of 5000 digits, it learned to read with an accuracy of about 95%; with the hundreds of thousands of samples available, it might become even better.

These pixelated swirls are a representation of the models the neural network keeps in mind when it hypothesizes what certain numbers looks like. Each swirl is meant to represent some different archetype of handwriting, a certain stroke or other pattern it can search for when it reads. This is still a bit of a black box to me, but I’m gradually getting better at understanding it myself – building my own mental models, I suppose.

Devising these artificial neural networks might give us some idea about what the brain is actually doing when it perceives something. Peering into brain activity via MRI or EEG lets us learn a few things, but the details of our thoughts remain a mystery; perhaps we might learn more about the brain by trying to reinvent it.

the black cap brotherhood

Written by Umbrella Man

April 20, 2014 at 2:01 am

Posted in pixels, science and math

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Apparatus of the Day #1571

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Apparatus of the Day #1571

This is the testing apparatus for one of the lab’s experiments, and today I played test-pilot for it. The study is in fear conditioning; electric shocks administered when specific images are displayed on the screen, and by various means my responses were measured for analysis. With two electrodes on my left hand and one on my right wrist, I sat here with my face in the harness and absorbed stimuli for about an hour.

At times it was an oddly disembodied experience: I kept my head on the chin rest so the eye tracker could measure my pupil dilation, and kept my hands perfectly still so as not to disturb the electrodes measuring skin conductance or applying shocks. Even my eyes were fixed on the center of the screen, watching tiny abstract color floes come and go. As I stared unblinking, all the photoreceptors in my retina grew tired of the monotony, and slowly the edges of the screen melted and faded into the darkness of the room. I felt very much like I was nothing but a brain sitting in an observation tank, subject to whatever tiny universe the researchers made to study how I tick.

When I saw an image that was associated with an electric shock, I noticed in myself some small reaction – subtle bracing for impact – and I wondered how much that was reflected in my eyes’ dilation. Even fMRI is only an indirect measurement of brain activity, and eye tracking is even far removed; even so, it’s remarkable how much it felt like that infrared camera was staring into my soul.

I’m feeling good about me

Written by Umbrella Man

January 10, 2013 at 12:44 am

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Constellation of the Day #1327

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Each of these spots, a colony in its own right, was founded by a single cell – individual colonists cast across the tiny agarose universe made for them. These cells plucked at bits of their sugary world and used it to remake themselves, leading to the island chains you see before you.

This is an idyllic little universe, full of food and devoid of threats, and it was a strange thing to hold it so easily in my hands. I suppose these cells will live out a few hundred generations, then face the world at large someday; I haven’t actually seen yet what we do with these plates when we’re done with them…

can you show me

Written by Umbrella Man

May 11, 2012 at 12:29 am

Ubiquity of the Day #1321

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My mind has been all crystals today, diffusion-limited aggregations of memories and languages and culture, self-similar skeins of fate, Turing patterns in everything from leopard spots to social circles – crystals grown in unquantifiable dimensions, but delicate and geometric nonetheless.

To clarify, a little, since this sounds like meaningless rambling: In biophysics we have recently given some attention to the patterns that naturally arise out chaotic systems. A few simple rules applied to proteins diffusing through an embryonic soup allow a growing animal to divide and subdivide into meaningful parts, grow a unique but functional neural anatomy, and – in the case of a leopard, for example – form patterns of fur that are like no other leopard, but still distinctly leopard in quality.

Another sort of pattern defines the way coral and snowflakes grow – gradual accumulations of particles building on a tiny nucleation point to develop into something complex and fractal.

These patterns are found in everything, from tectonic collisions to the flow of information through a single neuron, and I started to think how they could be applied to things without shape – to the paths that civilizations take as they develop, to human relationships and mindsets; if you were to map these things out, you might see the very same crystals forming.

I haven’t really settled these thoughts, but it is always amazing to reflect on how meaning can grow from chaos. Our universe was written well.

the grid

Written by Umbrella Man

May 5, 2012 at 1:20 am

Mind of the Day #1315

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It took a day’s worth of tinkering with my computer, but I may have finally made the tiniest step toward a future in deciphering the brain. These two digital wisps are slightly different interpretations of a sliver of a stranger’s mind – a visualization of data taken from a diffusion MRI scan. Supposedly these illustrate some of the long-distance tracts running through a person’s brain, from one realm of thought to another. I didn’t collect the data and I didn’t write any code involved here; I only managed to convince my computer to run some rather esoteric scripts.

But it was really exciting to see this finally appear on my screen, and with time perhaps I’ll learn enough about the language and math involved to glean something meaningful out of this information.

And with that, maybe I can contribute a little bit to understanding how you and I really work, and what we really are.

I can change

Written by Umbrella Man

April 29, 2012 at 4:39 am

Posted in pixels, science and math

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Wait of the Day #1313

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Producing competent cells – that is, cells that will accept a gene you’ve made for them – involves a lot of waiting around while the centrifuge spins your culture at thousands of gravities. It’s an exciting ride for Escherichia Coli, but leaves little work for the rest of us lab folk. The wait, then, very naturally becomes fertile ground for conversation to sprout. We talked with our instructor and with each other about veganism, the meat industry, prions, education and winemaking; the latter came up when my lab partner asked the instructor what he might have done differently if he could make a different decision ten years ago.

This was on an especially spin-heavy day, but we often use the smaller centrifuges for a minute or two at a time, in smaller groups. Like visits to the water cooler, these are lovely moments to exchange ideas large or small, and to connect a little to our labmates when we would otherwise be stuck working at our own benches.

So a short wait can be a good thing, indeed.

I wished it was warmer

Written by Umbrella Man

April 27, 2012 at 12:56 am

Posted in people, science and math

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Couple of the Day #1304

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I always like when scientists have fun naming their discoveries and creations, like the famous gene Sonic Hedgehog. Homer and Marge are promoters that work together to create thousands of copies of a given gene in PCR – the Polymerase Chain Reaction. Each binds to a certain genetic sequence and allows the production of a new strand of DNA; with both, you produce only the gene sequence you want. Homer is the more degenerate of the two – meaning that he’s more sloppy, binding to DNA with less specificity – which is entirely appropriate.

I learned today that my lab teacher keeps bees. Some of them escaped in a swarm last night, and he had to run through poison oak to capture them and bring them back home.

It’s been a good day.

construction of Kells

Written by Umbrella Man

April 17, 2012 at 10:10 pm

Posted in science and math

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