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
Tango is a sad thought that is danced.Enrique Santos Discépolothink & dancemore quotes

understanding: FTW


In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017


data visualization + art

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
To view the art you'll need a pair of red-blue 3D glasses.
The data will stand out—and you will too.

BD Genomics stereoscopic art exhibit — AGBT 2017

Art is science in love.
— E.F. Weisslitz

BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Our art exhibit at AGBT 2017 asked new school questions in old school ways.
BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

the art of storytelling in science

BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Instead of 'explain, not merely show,' seek to 'narrate, not merely explain.' Krzywinski M & Cairo A (2013) Points of View: Storytelling. Nat. Methods 10:687.

Science cannot move forward without storytelling. While we learn about the world and its patterns through science, it is through stories that we can organize and sort through the observations and conclusions that drive the generation of scientific hypotheses.

With Alberto Cairo, I've written about the importance of storytelling as a tool to explain and narrate in Storytelling (2013) Nat. Methods 10:687. There we suggest that instead of "explain, not merely show," you should seek to "narrate, not merely explain."

Our account received support (Should scientists tell stories. (2013) Nat. Methods 10:1037) but not from all (Against storytelling of scientific results. (2013) Nat. Methods 10:1045).

A good science story must present facts and conclusions within a hierarchy—a bag of unsorted observations isn't likely to engage your readers. But while a story must always inform, it should also delight (as much as possible), and inspire. It should make the complexity of the problem accessible—or, at least, approachable—without simplifications that preclude insight into how concepts connect (they always do).

the story of making science stories

Just like science, explaining science is a process—one that can be more vexing than the science itself!

In science one tries to tell people, in such a way as to be understood by everyone, something that no one ever knew before. But in poetry, it’s the exact opposite.
—Paul Dirac, Mathematical Circles Adieu by H. Eves [quoted]

I have previously written about the process of taking a scientific statement (Creating Scientific American Graphic Science graphics) and turning it into a data visualization or, more broadly, visual story.

BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
December 2015. Composition of bacteria in household dust.
BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
June 2015. Relationship between genes and traits.
BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
September 2014. Similarity of human, Denisovan, chimp, bonobo, and gorilla genomes.

The process of the creation of one of these visual stories is itself a story. A story about how the genome is not a blueprint, a discovery of Hilbertonians, which are creatures that live on the Hilbert curve, how algorithms for protein folding can be used to generate art based on the digits of `\pi`, or how we can make human genome art by humans with genomes. I've also written about my design process in creating the cover for Genome Research and the cover of PNAS. As always, not everything works out all the time—read about the EMBO Journal covers that never made it.

BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover image accompanying our article on mouse vasculature development. Biology turns astrophysical. PNAS 1 May 2012; 109 (18)
BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover image accompanying Spark: A navigational paradigm for genomic data exploration. Genome Research 22 (11).
BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Pi Day 2014 poster | 132 paths with E=-23 of 64 digits of Pi, sorted by aspect ratio.

Here, I'd like to walk you through the process and sketches of creating a story based on the idea of differences in data and how the story can be used to understand the function of cells and disease.

the difference is in the differences

The visual story is a creative collaboration with Becton Dickinson and The Linus Group and its creation began with the concept of differences. The art was on display at AGBT 2017 conference and accompanies BD's launch of the Resolve platform and "Difference of One in Genomics".

Starting with the idea of the "difference of one", our goal was to create artistic representations of data sets generated using the BD Resolve platform, which generates single-cell transcriptomes, that captured a variety of differences that are relevant in genomics research.

The data art pieces were installed in a gallery style, with data visualization and artistic expression in equal parts.

The art itself is an old school take on virtual reality. Unlike modern VR, which isolates the participants from one another, we chose a low-tech route that not only brings the audience closer to the data but also to each other.

data in the art

The data were generated using the BD Resolve single-cell transcriptomics platform. For each of the three art pieces, we identified a data set that captured a variety of differences.

  1. disease onset—how does gene expression in tumor cells differ from normal cells?
  2. disease progression—as a tumor grows and spreads, how does expression change?
  3. background variation—how does gene expression change between normal cells that perform a different function?
BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

The real surprise and insight is in difference that ultimately advance our thinking (Data visualization: amgibuity as a fellow traveller. (2013) Nat. Methods 10:613-615).

Figuring out which differences are of this kind requires that instead of "What's new?" we ask "What's different?"

VIEW ALL

news + thoughts

Statistics vs Machine Learning

Tue 03-04-2018
We conclude our series on Machine Learning with a comparison of two approaches: classical statistical inference and machine learning. The boundary between them is subject to debate, but important generalizations can be made.

Inference creates a mathematical model of the datageneration process to formalize understanding or test a hypothesis about how the system behaves. Prediction aims at forecasting unobserved outcomes or future behavior. Typically we want to do both and know how biological processes work and what will happen next. Inference and ML are complementary in pointing us to biologically meaningful conclusions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Statistics vs machine learning. (read)

Statistics asks us to choose a model that incorporates our knowledge of the system, and ML requires us to choose a predictive algorithm by relying on its empirical capabilities. Justification for an inference model typically rests on whether we feel it adequately captures the essence of the system. The choice of pattern-learning algorithms often depends on measures of past performance in similar scenarios.

Bzdok, D., Krzywinski, M. & Altman, N. (2018) Points of Significance: Statistics vs machine learning. Nature Methods 15:233–234.

Background reading

Bzdok, D., Krzywinski, M. & Altman, N. (2017) Points of Significance: Machine learning: a primer. Nature Methods 14:1119–1120.

Bzdok, D., Krzywinski, M. & Altman, N. (2017) Points of Significance: Machine learning: supervised methods. Nature Methods 15:5–6.

...more about the Points of Significance column

Happy 2018 `\pi` Day—Boonies, burbs and boutiques of `\pi`

Wed 14-03-2018

Celebrate `\pi` Day (March 14th) and go to brand new places. Together with Jake Lever, this year we shrink the world and play with road maps.

Streets are seamlessly streets from across the world. Finally, a halva shop on the same block!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A great 10 km run loop between Istanbul, Copenhagen, San Francisco and Dublin. Stop off for halva, smørrebrød, espresso and a Guinness on the way. (details)

Intriguing and personal patterns of urban development for each city appear in the Boonies, Burbs and Boutiques series.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In the Boonies, Burbs and Boutiques of `\pi` we draw progressively denser patches using the digit sequence 159 to inform density. (details)

No color—just lines. Lines from Marrakesh, Prague, Istanbul, Nice and other destinations for the mind and the heart.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Roads from cities rearranged according to the digits of `\pi`. (details)

The art is featured in the Pi City on the Scientific American SA Visual blog.

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day and 2017 `\pi` Day.

Machine learning: supervised methods (SVM & kNN)

Thu 18-01-2018
Supervised learning algorithms extract general principles from observed examples guided by a specific prediction objective.

We examine two very common supervised machine learning methods: linear support vector machines (SVM) and k-nearest neighbors (kNN).

SVM is often less computationally demanding than kNN and is easier to interpret, but it can identify only a limited set of patterns. On the other hand, kNN can find very complex patterns, but its output is more challenging to interpret.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Machine learning: supervised methods (SVM & kNN). (read)

We illustrate SVM using a data set in which points fall into two categories, which are separated in SVM by a straight line "margin". SVM can be tuned using a parameter that influences the width and location of the margin, permitting points to fall within the margin or on the wrong side of the margin. We then show how kNN relaxes explicit boundary definitions, such as the straight line in SVM, and how kNN too can be tuned to create more robust classification.

Bzdok, D., Krzywinski, M. & Altman, N. (2018) Points of Significance: Machine learning: a primer. Nature Methods 15:5–6.

Background reading

Bzdok, D., Krzywinski, M. & Altman, N. (2017) Points of Significance: Machine learning: a primer. Nature Methods 14:1119–1120.

...more about the Points of Significance column

Human Versus Machine

Tue 16-01-2018
Balancing subjective design with objective optimization.

In a Nature graphics blog article, I present my process behind designing the stark black-and-white Nature 10 cover.

Nature 10, 18 December 2017

Machine learning: a primer

Thu 18-01-2018
Machine learning extracts patterns from data without explicit instructions.

In this primer, we focus on essential ML principles— a modeling strategy to let the data speak for themselves, to the extent possible.

The benefits of ML arise from its use of a large number of tuning parameters or weights, which control the algorithm’s complexity and are estimated from the data using numerical optimization. Often ML algorithms are motivated by heuristics such as models of interacting neurons or natural evolution—even if the underlying mechanism of the biological system being studied is substantially different. The utility of ML algorithms is typically assessed empirically by how well extracted patterns generalize to new observations.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Machine learning: a primer. (read)

We present a data scenario in which we fit to a model with 5 predictors using polynomials and show what to expect from ML when noise and sample size vary. We also demonstrate the consequences of excluding an important predictor or including a spurious one.

Bzdok, D., Krzywinski, M. & Altman, N. (2017) Points of Significance: Machine learning: a primer. Nature Methods 14:1119–1120.

...more about the Points of Significance column

Snowflake simulation

Tue 16-01-2018
Symmetric, beautiful and unique.

Just in time for the season, I've simulated a snow-pile of snowflakes based on the Gravner-Griffeath model.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A few of the beautiful snowflakes generated by the Gravner-Griffeath model. (explore)

The work is described as a wintertime tale in In Silico Flurries: Computing a world of snow and co-authored with Jake Lever in the Scientific American SA Blog.

Gravner, J. & Griffeath, D. (2007) Modeling Snow Crystal Growth II: A mesoscopic lattice map with plausible dynamics.