resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
`\pi` Day 2017 Art Posters - Star charts and extinct animals and plants
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.
Caelum non animum mutant qui trans mare currunt.
—Horace
This year: creatures that don't exist, but once did, in the skies.
And a poem Of Black Body.
This year's `\pi` day song is Exploration by Karminsky Experience Inc. Why? Because "you never know what you'll find on an exploration".
create myths and contribute!
Want to contribute to the mythology behind the constellations in the `\pi` in the sky? Many already have a story, but others still need one. Please submit your stories!
This year I wanted to something more than visuals. Space is vast, so let's fill it with words.
I asked my good friend and poet, Paolo Marcazzan, to collaborate. I described the idea for the art—a universe of stars based on `\pi` and the extinct creatures that live within it—and asked him to find the matching words.
And they could not have been more perfect.
Of Black Body
author's note
The poem situates the dark (black body, energy) as a place for contention and ongoing confrontation. Whether in the recesses of space or heart, the poem probes the territory of distance, absence, uncertainty and muteness. It considers the relational as default positioning of existence (earthly, universal), and that which remains unmet within that context.
Life in its dimension of cross-grained, often broken linearity is juxtaposed with a quote form Dante that references instead his vision of sidereal circularity as the benign force that moves all things in the universe. For the earthbound, the questions and concerns remain those of identity, passage, escape from transiency, and slow tempering of hope.
news + thoughts
Statistics vs Machine Learning
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.
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.
Happy 2018 `\pi` Day—Boonies, burbs and boutiques of `\pi`
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!
Intriguing and personal patterns of urban development for each city appear in the Boonies, Burbs and Boutiques series.
No color—just lines. Lines from Marrakesh, Prague, Istanbul, Nice and other destinations for the mind and the heart.
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)
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.
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.
Human Versus Machine
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
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.
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.
Snowflake simulation
Symmetric, beautiful and unique.Just in time for the season, I've simulated a snow-pile of snowflakes based on the Gravner-Griffeath model.
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.