Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
In your hiding, you're alone. Kept your treasures with my bones.Coeur de Piratecrawl somewhere bettermore quotes

gravity: fun


EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 2017 Pi Day art imagines the digits of Pi as a star catalogue with constellations of extinct animals and plants. The work is featured in the article Pi in the Sky at the Scientific American SA Visual blog.

`\pi` Day 2016 Art Posters


Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2017 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` approximation day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circular `\pi` art

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.

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
All art posters are available for purchase.
I take custom requests.

This year's `\pi` day art collection celebrates not only the digit but also one of the fundamental forces in nature: gravity.

In February of 2016, for the first time, gravitational waves were detected at the Laser Interferometer Gravitational-Wave Observatory (LIGO).

The signal in the detector was sonified—a process by which any data can be encoded into sound to provide hints at patterns and structure that we might otherwise miss—and we finally heard what two black holes sound like. A buzz and chirp.

The art is featured in the Gravity of Pi article on the Scientific American SA Visual blog.

this year's theme music

All the art was processed while listening to Roses by Coeur de Pirate, a brilliant female French-Canadian songwriter, who sounds like a mix of Patricia Kaas and Lhasa. The lyrics Oublie-moi (Forget me) are fitting with this year's theme of gravity.

Mais laisse-moi tomber, laisse-nous tomber
Laisse la nuit trembler en moi
Laisse-moi tomber, laisse nous tomber
Cette fois

But let me fall, let us fall
Let the night tremble in me
Let me fall, let us fall
This time


Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
5 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
5 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
14 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
14 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
14 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
44 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
56 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
65 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
98 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
153 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
147 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
335 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
1,000 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
1,000 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
300 digits of `\pi`, `\phi` and `e`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
100 digits of `\pi`, `\phi` and `e`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
49 instances of 3 digits of `\pi`. (zoom, BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
49 instances of 3 digits of `\pi`. (zoom, BUY ARTWORK)
VIEW ALL

news + thoughts

Classification and regression trees

Fri 28-07-2017
Decision trees are a powerful but simple prediction method.

Decision trees classify data by splitting it along the predictor axes into partitions with homogeneous values of the dependent variable. Unlike logistic or linear regression, CART does not develop a prediction equation. Instead, data are predicted by a series of binary decisions based on the boundaries of the splits. Decision trees are very effective and the resulting rules are readily interpreted.

Trees can be built using different metrics that measure how well the splits divide up the data classes: Gini index, entropy or misclassification error.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Classification and decision trees. (read)

When the predictor variable is quantitative and not categorical, regression trees are used. Here, the data are still split but now the predictor variable is estimated by the average within the split boundaries. Tree growth can be controlled using the complexity parameter, a measure of the relative improvement of each new split.

Individual trees can be very sensitive to minor changes in the data and even better prediction can be achieved by exploiting this variability. Using ensemble methods, we can grow multiple trees from the same data.

Krzywinski, M. & Altman, N. (2017) Points of Significance: Classification and regression trees. Nature Methods 14:757–758.

Background reading

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

Altman, N. & Krzywinski, M. (2015) Points of Significance: Multiple Linear Regression Nature Methods 12:1103-1104.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Classifier evaluation. Nature Methods 13:603-604.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Model Selection and Overfitting. Nature Methods 13:703-704.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Regularization. Nature Methods 13:803-804.

...more about the Points of Significance column

Personal Oncogenomics Program 5 Year Anniversary Art

Wed 26-07-2017

The artwork was created in collaboration with my colleagues at the Genome Sciences Center to celebrate the 5 year anniversary of the Personalized Oncogenomics Program (POG).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. (left) Cases ordered chronologically by case number. (right) Cases grouped by diagnosis (tissue type) and then by similarity within group.

The Personal Oncogenomics Program (POG) is a collaborative research study including many BC Cancer Agency oncologists, pathologists and other clinicians along with Canada's Michael Smith Genome Sciences Centre with support from BC Cancer Foundation.

The aim of the program is to sequence, analyze and compare the genome of each patient's cancer—the entire DNA and RNA inside tumor cells— in order to understand what is enabling it to identify less toxic and more effective treatment options.

Principal component analysis

Thu 06-07-2017
PCA helps you interpret your data, but it will not always find the important patterns.

Principal component analysis (PCA) simplifies the complexity in high-dimensional data by reducing its number of dimensions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Principal component analysis. (read)

To retain trend and patterns in the reduced representation, PCA finds linear combinations of canonical dimensions that maximize the variance of the projection of the data.

PCA is helpful in visualizing high-dimensional data and scatter plots based on 2-dimensional PCA can reveal clusters.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Principal component analysis. Nature Methods 14:641–642.

Background reading

Altman, N. & Krzywinski, M. (2017) Points of Significance: Clustering. Nature Methods 14:545–546.

...more about the Points of Significance column

`k` index: a weightlighting and Crossfit performance measure

Wed 07-06-2017

Similar to the `h` index in publishing, the `k` index is a measure of fitness performance.

To achieve a `k` index for a movement you must perform `k` unbroken reps at `k`% 1RM.

The expected value for the `k` index is probably somewhere in the range of `k = 26` to `k=35`, with higher values progressively more difficult to achieve.

In my `k` index introduction article I provide detailed explanation, rep scheme table and WOD example.

Dark Matter of the English Language—the unwords

Wed 07-06-2017

I've applied the char-rnn recurrent neural network to generate new words, names of drugs and countries.

The effect is intriguing and facetious—yes, those are real words.

But these are not: necronology, abobionalism, gabdologist, and nonerify.

These places only exist in the mind: Conchar and Pobacia, Hzuuland, New Kain, Rabibus and Megee Islands, Sentip and Sitina, Sinistan and Urzenia.

And these are the imaginary afflictions of the imagination: ictophobia, myconomascophobia, and talmatomania.

And these, of the body: ophalosis, icabulosis, mediatopathy and bellotalgia.

Want to name your baby? Or someone else's baby? Try Ginavietta Xilly Anganelel or Ferandulde Hommanloco Kictortick.

When taking new therapeutics, never mix salivac and labromine. And don't forget that abadarone is best taken on an empty stomach.

And nothing increases the chance of getting that grant funded than proposing the study of a new –ome! We really need someone to looking into the femome and manome.

Dark Matter of the Genome—the nullomers

Wed 31-05-2017

An exploration of things that are missing in the human genome. The nullomers.

Julia Herold, Stefan Kurtz and Robert Giegerich. Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 9:167