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visualization + math

The 2022 π Day art is a music album composed by Greg Coles for solo piano. It tells stories from the very beginning (314…) to the very (known) end of π (…264) as well as math (Wallis Product) and math jokes (Feynman Point), repetition (nn) and zeroes (null).

# $\pi$ Day 2014 Art Posters

2021 $\pi$ reminds us that good things grow for those who wait.' edition.
2019 $\pi$ has hundreds of digits, hundreds of languages and a special kids' edition.
2018 $\pi$ day stitches street maps into new destinations.
2017 $\pi$ day imagines the sky in a new way.

2016 $\pi$ approximation day wonders what would happen if about right was right.
2016 $\pi$ day sees digits really fall for each other.
2015 $\pi$ day maps transcendentally.
2014 $\pi$ approx day spirals into roughness.

2014 $\pi$ day hypnotizes you into looking.
2014 $\pi$ day
2013 $\pi$ day is where it started
Circular $\pi$ art and other distractions

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.

Most of the art is available for purchase as framed prints and, yes, even pillows. Sleep's never been more important — I take custom requests.

For the 2014 $\pi$ day, two styles of posters are available: folded paths and frequency circles.

The folded paths show $\pi$ on a path that maximizes adjacent prime digits and were created using a protein-folding algorithm.

The frequency circles colourfully depict the ratio of digits in groupings of 3 or 6. Oh, look, there's the Feynman Point!

### get simulation code

Download the HP lattice simulation binary. You'll need one of the three 2D methods — I used $rem2dm$, which does local and pull moves. If you'd like to learn more about the algorithm, read the publication.

A replica exchange Monte Carlo algorithm for protein folding in the HP model. Chris Thachuk, Alena Shmygelska and Holger H Hoos, BMC Bioinformatics 2007, 8:342 (17 Sep 2007).

### run simulation

When you run the 64-digit simulation, you're likely to find a path with $E=-23$, which is the lowest energy I've been able to sample. On my Intel Xeon E5540 (2.53 GHz) it takes anywhere from 1-30 seconds to find a $E=-23$ path (there are many possible paths at this energy), depending on the random seed. Here's the output of a typical run of the 64-digit folding simulation

$> rem2dm -seq=hppphphphhhpphphhhppphpphhphhhphphppppphppphpphhhpphphpphpppphph -maxT=220 -numLocalSteps=500 -eng=100 -maxRunTime=60 -traceFile=pi.64 -minT=160 -expID=pi.64 -numReps=10 REMC-HP2D-M Begin Simulation 0.01: Current Best Solution: -8 0.01: Current Best Solution: -10 0.01: Current Best Solution: -13 0.02: Current Best Solution: -15 0.03: Current Best Solution: -16 0.03: Current Best Solution: -17 0.04: Current Best Solution: -18 0.04: Current Best Solution: -19 0.16: Current Best Solution: -20 0.27: Current Best Solution: -21 0.69: Current Best Solution: -22 36.23: Current Best Solution: -23 Real time: 120 ggslrrsrllssrrlrrllsrrlrrlslslrrsrlssrrsllrslrrlrsllsrsrrlsrssrs p--h--p | | h--h h--p--p--p | | p--p h H h--p--p | | | | | p--h h--h--p p p--p | | | p--p--h h--p p--p p | | | | | h--h h h--p--h h--p | | | p--h h h--p--H h--p | | | | p--p p p--h--h | | p p--h--p | | p--p--h h | | p--p End Simulation$

If you want to apply this to different number (e.g. φ or e ), you'll need to replace the digits with either $p$ or $h$. Remember, the simulation will try to group the $h$'s together. You can download 1,000,000 of π , φ and e .

The best path I could find for 768 digits is one with $E=-223$. In 1000s of simulations this solution came up only once. I also saw one path at $E=-222$. After that, there were many solutions at each of the less optimal energy levels.

If you manage to find a better one, let me know right away!

## common problems

### segmental fault

If you obtain a segmentation fault,

$> ./rem2dlm REMC-HP2D-LM Begin Simulation Real time: 0 Segmentation fault$

don't panic just yet. The folding binaries don't do a lot of error checking, so you have to get the input parameters correct.

For example, if you do not include the $-eng$ parameter, the code will segfault.

Try one of the batch files above (64 digit batch file, 768 digit batch file) or the following simple job

$> bin/rem2dm -seq=hhpppphhhhpppphh -maxRunTime=5 -eng 10 REMC-HP2D-M Begin Simulation 3.13877e-17: Current Best Solution: -2 5.49284e-17: Current Best Solution: -3 1.0201e-16: Current Best Solution: -4 1.33398e-16: Current Best Solution: -5 Real time: 5 ggrllslsssrllsls p--p--p | | h h--p | | H h | H h | | p--h h | | p--p--p$

If this segfaults, then you'll need to recompile the code (see below).

### compile code (optional—only if binaries don't work)

Precompiled binaries are available for download directly: rem2dm, rem2dlm, rem2dpm, rem3dm, rem3dlm, rem3dpm.

If these don't work on your system, you need to recompile them. Download the the protein folding code and see INSTALL.txt for compilation instructions.

news + thoughts

# Cell Genomics cover

Mon 16-01-2023

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.

Our Cell Genomics cover depicts parent-of-origin assignment as a circuit (volume 3, issue 1, 11 January 2023). (more)

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.

A catalogue of my journal and magazine cover designs. (more)

Thu 05-01-2023

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.

My Science Advances cover that encodes sequence onto hypercubes (volume 9, issue 1, 6 January 2023). (more)

Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9

Browse my gallery of cover designs.

A catalogue of my journal and magazine cover designs. (more)

# Regression modeling of time-to-event data with censoring

Mon 21-11-2022

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).

Nature Methods Points of Significance column: Regression modeling of time-to-event data with censoring. (read)

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

Tue 25-10-2022

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

Frame 4897 from the music video of Max Cooper's Asent.

The video recently premiered on YouTube.

Renders of the full scene are available as NFTs.

# Gene Cultures exhibit — art at the MIT Museum

Tue 25-10-2022

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.

My art at the MIT Museum Gene Cultures exhibit tells shows the scale and structure of the human genome. Pay no attention to the pink chicken.

# Annals of Oncology cover

Wed 14-09-2022

My cover design on the 1 September 2022 Annals of Oncology issue shows 570 individual cases of difficult-to-treat cancers. Each case shows the number and type of actionable genomic alterations that were detected and the length of therapies that resulted from the analysis.

An organic arrangement of 570 individual cases of difficult-to-treat cancers showing genomic changes and therapies. Apperas on Annals of Oncology cover (volume 33, issue 9, 1 September 2022).

Pleasance E et al. Whole-genome and transcriptome analysis enhances precision cancer treatment options (2022) Annals of Oncology 33:939–949.

My Annals of Oncology 570 cancer cohort cover (volume 33, issue 9, 1 September 2022). (more)

Browse my gallery of cover designs.

A catalogue of my journal and magazine cover designs. (more)