Pi Day 2023 — Repeated Sequence — A modular synthesizer experience
On March 14th celebrate `\pi` Day. Hug `\pi`—find a way to do it.
For those who favour `\tau=2\pi` will have to postpone celebrations until July 26th. That's what you get for thinking that `\pi` is wrong. I sympathize with this position and have `\tau` day art too!
If you're not into details, you may opt to party on July 22nd, which is `\pi` approximation day (`\pi` ≈ 22/7). It's 20% more accurate that the official `\pi` day!
Finally, if you believe that `\pi = 3`, you should read why `\pi` is not equal to 3.
People find these numbers inconceivable — and I do too. Best thing to do is just relax and enjoy it. —Richard Feynman
Welcome to 2023 Pi Day: a celebration of `\pi` and mathematics, electronic music and cables. A lot of cables.
contents
This piece was created with a modular synthesizer system, which you can see in the video. Look for the closeups to meet some of the key modules in the patch, such as Vector Space and the Triple Sloths.
You've probably seen at least one synthesizer — most have a keyboard, which allow you to select a note, and they all have a bunch of knobs, which allow you to shape the sound giving you wide control over what a note will sound like. This latter process is broadly known as sound design.
If you were to open up such a synthesizer, you'd see a bunch of different circuits hooked up to the knobs, with each circuit having a specific role in the signal flow. This is a simplification, but it's good enough.
In a modular synthesizer, those individual circuits are broken up into modules that you purchase separately. Each module has its own function — everything from making a sound to filtering to mixing and more. It's probably best to call such a setup a modular system since it can veritably act as multiple synthesizers, each composed of a group of modules.
The modules themselves come in a wide variety of designs and sizes. Some modules are very narrow and some are very wide, though the height of the module is fixed within a given modular standards. For example, Eurorack modules are 5.25" in height (3U, 1U = 1.75") whereas the Buchla/Serge system uses 4U (7") and Moog modular synth modules are 8.75" tall. There are even some short 1.75" (1U) modules in the Eurorack world.
The Triple Sloth is chaos circuit module. It output is the solution to a system of differential equations, similar to the Lorentz System.
There are three sloths, called Torpor, Inertia and Apathy. These have periods of about 20 seconds (Torpor), 2 minutes (Apathy) and 20 minutes (Inertia). You can see the realtime output of the Inertia slot at this point in the video.
There's also a much slower sloth — Sloth DX — with a 20 hour period. This Sloth DX has capacitors that are so large that they stick out from the front of the module. As far as I know, this is the only module that exposes is internal components in this way.
This is a much longer version of the original 1 hour Repeated Sequence, which only went to the Feynman Point (769 digits).
In the 10 hour version we go to 10,000 digits. Up to the Feynman Point, this longer version is identical to the 1 hour version. After this point, though, it just keeps going — we let the modular patch play itself. During this time, we switch reels on the Morphagene to Esther and Anja giggling. There's mumbling too.
Starting at 8,000 digits, we ramp up the rack to a finale at 10,000 digits and then ramp down the rack for an outro. The last ~1,500 digits are read out at 4 digits per second in about 6 min 15 seconds.
If you'd like to learn the basics of modular synthesis, check out the Methods section.
Neural network primer
Nature is often hidden, sometimes overcome, seldom extinguished. —Francis Bacon
In the first of a series of columns about neural networks, we introduce them with an intuitive approach that draws from our discussion about logistic regression.
Simple neural networks are just a chain of linear regressions. And, although neural network models can get very complicated, their essence can be understood in terms of relatively basic principles.
We show how neural network components (neurons) can be arranged in the network and discuss the ideas of hidden layers. Using a simple data set we show how even a 3-neuron neural network can already model relatively complicated data patterns.
Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20.
Background reading
Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.
Cell Genomics cover
Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.
Designed in collaboration with with Carlos Urzua.
Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).
Browse my gallery of cover designs.
Science Advances cover
My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes.
More details about the design.
Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.
Browse my gallery of cover designs.
Regression modeling of time-to-event data with censoring
If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber
In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.
We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).
Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19.
Music video for Max Cooper's Ascent
My 5-dimensional animation sets the visual stage for Max Cooper's Ascent from the album Unspoken Words. I have previously collaborated with Max on telling a story about infinity for his Yearning for the Infinite album.
I provide a walkthrough the video, describe the animation system I created to generate the frames, and show you all the keyframes
The video recently premiered on YouTube.
Renders of the full scene are available as NFTs.
Gene Cultures exhibit — art at the MIT Museum
I am more than my genome and my genome is more than me.
The MIT Museum reopened at its new location on 2nd October 2022. The new Gene Cultures exhibit featured my visualization of the human genome, which walks through the size and organization of the genome and some of the important structures.
