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outbreak + poetry

The 2020 π Day art celebrates the digits of π with piku (パイク) — poetry inspired by haiku. They serve as the form for The Outbreak Poems. On our 2022 Pi Day album "three one four: a number of notes", a piku accompanies each track.

The Outbreak Poems

Short emissions from piku actual during the coronavirus outbreak. Not just the pandemic, but also about other feelings. As they come.

Explore the collection by themes such as life, light, day, night, time, thought.

If you don't know how to feel about that, refer to my tree of emotional life.

The Outbreak Poems are piku.

A piku (`\pi`ku, パイク) is a poem whose line syllable count is based on the first three digits of `\pi`. Piku were created to celebrate the 2020 Pi Day.

I don't as much write piku as feel them, then filtered through a frosted window they come out as words.

Recently I've added comments to piku as I write them. Notes to (on) self.

latest outbreak poems

Wednesday, 19 May 2021

3 Your hours
1 will
4 last me my years.
403

3 Hole in heart
1 is
4 bigger than you
1 were.
402

3 From hand to
1 heart
4 in a flutter.
401

3 Come fly in
1 my
4 heart for a while.
400

3 Can't feel you
1 in
4 my hand, dying.
399

3 Need new words,
1 please,
4 for these feelings.
398

3 Mini dee
1 you
4 put you in me.
397
Mindy was a chickadee. And then she wasn't.

Read all past poems.

news + thoughts

Convolutional neural networks

Thu 17-08-2023

Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry. – Richard Feynman

Following up on our Neural network primer column, this month we explore a different kind of network architecture: a convolutional network.

The convolutional network replaces the hidden layer of a fully connected network (FCN) with one or more filters (a kind of neuron that looks at the input within a narrow window).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Convolutional neural networks. (read)

Even through convolutional networks have far fewer neurons that an FCN, they can perform substantially better for certain kinds of problems, such as sequence motif detection.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Convolutional neural networks. Nature Methods 20:.

Background reading

Derry, A., Krzywinski, M. & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

Neural network primer

Tue 10-01-2023

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Neural network primer. (read)

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 20:165–167.

Background reading

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Science Advances cover

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.

More details about the design.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Regression modeling of time-to-event data with censoring

Thu 17-08-2023

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).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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 19:1513–1515.

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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.


© 1999–2023 Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA