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Visions of Type

1 · Typography and bird songs

If you live in a city, birds are essentially the only wildlife that you meet during your day.

Depending on where you live, you might come several species without even trying. In Vancouver, on a 10 minute walk around my house, I have a good chance to see rock doves (pigeons), crows, mallars, wigeons, hooded mergansers (if I'm lucky), common starlings, house sparrows (sigh), house finches, song sparrows, red-winged black birds, white-crowned sparrows, bushtits, black-capped chickadees, northern flickers, great blue herons, and the mother-of-all-honkers: Canada geese.

Birds and letters are everywhere—art of nature and man.

Letter forms, on the other hand, are the art that is also everywhere. Every typeface is an artistic expression.

Regardless where you live, sadly, you are likely to come across mutants like Comic Sans, Arial and Times New Roman — odious creatures from the shallows. Try to find Gotham, Gill Sans, Frutiger, or Garamond.

2 · The Spectrogram

Bird songs can be visualized with a spectrogram — a visualization of the frequency components (vertical axis) in the call as a function of time (horizontal axis).

For example, below is a crop of a recording of the American goldfinch, who eats a potato chip in about 0.5 seconds. And when in flight, he has it with dip.


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The spectrogram of the American goldfinch, who eats a potato chip in about 0.5 seconds. (Macaulay Library asset 94457)

The full recording from the Cornell Lab Macaulay Library is shown below.

Spectrograms give us detailed insight into the fine structure of a vocalization. For example, the black-capped chicadee's “fee-bee” (or cheeseburger) actually has a very short pause (about 50 ms) in the “bee”, making it more of a “be-e”. Below is a recording of this call.

One of my favourite bird sounds is the “sawing machine” of the marsh wren. They often hide in tall reeds around ponds and lakes, making them hard to spot — by eye, but not by ear!

3 · Learning bird songs

Mnemonics of bird songs help you remember the call and recognize the bird. It's so much easier to think "Quick, three beers!" — the call of the Olive-sided flycatcher — rather than "Chirp, chirp, chirp."

The mnemonic captures the cadence and repetition scheme of the song. For example, if you listen to the white-throated sparrow you can't help but think that this little guy is trying to tell us something.

4 · The mnemonics

French Zonotrichia albicollis: Baisse ta jupe, Philomène, Philomène, Philomène. How differently we hear!
—Madelaine Lemieux (via Twitter)

Potato chip!
American Goldfinch (Spinus tristis)

Here here. Come right here, dear.
Baltimore Oriole (Icterus galbula)

Who cooks for you?
Barred Owl (Strix varia)

Here sweetie.
Black-capped Chickadee (Poecile atricapillus)

Trees, trees, murmuring trees.
Black-throated Green Warbler (Setophaga virens)

Drink your tea.
Eastern Towhee (Pipilo erythrophthalmus)

Are you awake? Me too.
Great Horned Owl (Bubo virginianus)

Qu'est-ce qu-il dit?
Great Kiskadee (Pitangus sulphuratus)

Fire fire. Where where? Here here! See it, see it.
Indigo Bunting (Passerina cyanea)

Clear. Wick, wick, wick.
Northern Flicker (Colaptes auratus)

Quick, three beers!
Olive-sided Flycatcher (Contopus cooperi)

Where are you? Here I am.
Red-eyed Vireo (Vireo olivaceus)

Chubby chubby cheeks. Chubby cheeks.
Ruby-crowned Kinglet (Regulus calendula)

See me, pretty, pretty me.
White-crowned Sparrow (Zonotrichia leucophrys)

Dear sweet Canada Canada Canada.
White-throated Sparrow (Zonotrichia albicollis)

5 · The posters

buy artwork Song of the Northern Flicker (Colaptes auratus) by Martin Krzywinski
CLEAR. WICK, WICK, WICK | Song of the Northern Flicker. (buy artwork / see all my art)

If you love birds and typography, these posters are for you. The mnemonic for the bird's song is presented on a background that proportionally presents the bird's plumage colors.

5.1 · Poster sets

Some posters create natural sets.

5.2 · Individual posters

And if you explore the posters, you just might find the bird too.


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
POTATO CHIP! | Song of the American Goldfinch (Spinus tristis) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
HERE HERE. COME RIGHT HERE, DEAR. | Song of the Baltimore Oriole (Icterus galbula) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
WHO COOKS FOR YOU? | Song of the Barred Owl (Strix varia) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
HERE SWEETIE. | Song of the Black-capped Chickadee (Poecile atricapillus) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
TREES, TREES, MURMURING TREES. | Song of the Black-throated Green Warbler (Setophaga virens) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
DRINK YOUR TEA. | Song of the Eastern Towhee (Pipilo erythrophthalmus) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
ARE YOU AWAKE? ME TOO. | Song of the Great Horned Owl (Bubo virginianus) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
QU'EST-CE QU-IL DIT? | Song of the Great Kiskadee (Pitangus sulphuratus) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
FIRE FIRE. WHERE WHERE? HERE HERE! SEE IT, SEE IT. | Song of the Indigo Bunting (Passerina cyanea) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
CLEAR. WICK, WICK, WICK. | Song of the Northern Flicker (Colaptes auratus) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
QUICK, THREE BEERS! | Song of the Olive-sided Flycatcher (Contopus cooperi) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
WHERE ARE YOU? HERE I AM. | Song of the Red-eyed Vireo (Vireo olivaceus) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
CHUBBY CHUBBY CHEEKS. CHUBBY CHEEKS. | Song of the Ruby-crowned Kinglet (Regulus calendula) (BUY ARTWORK)

Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
SEE ME, PRETTY, PRETTY ME. | Song of the White-crowned Sparrow (Zonotrichia leucophrys) (BUY ARTWORK)


Typographical posters of bird songs
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
DEAR SWEET CANADA CANADA CANADA. | Song of the White-throated Sparrow (Zonotrichia albicollis) (BUY ARTWORK)
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.


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