resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
art + science
Bloomberg Businessweek Design Conference — San Francisco, 2013
science ♥ design
Together with Alberto Cairo, I presented at the Bloomberg Businessweek Design Conference (highlights) on the topic of design and communication in the sciences.
Alberto, as the journalist, motivated why communication should include access to detail through an engaging narrative. He made the distinction between the specialist (heavy on detail) and the communicator (focus on narrative) and emphasized that the distinction is artificial, though often played out (watch video).
I, as the scientist, underscored the importance of clear communication between scientists. As the specialists, they are often very poor communicators. Pick up any science journal and you'll quickly discover that scientists either aren't good at telling stories or are discouraged to do so by the medium. The consequence is the same: papers read like a wall of text. TL;DR anyone? The quality of visual communication in general ranges from muddled to abysmal (watch video).
We need more leaders in the field, such as Nature Publishing Group, to reward and emphasize good visual communication (e.g. Nature Cancer Review 2013 Figure Calendar).
Our presentations concluded with a 15 minute moderated discussion with Sam Grobart, senior Businesssweek writer. Everyone got a little cheeky. Good fun.
presentation video
Watch: my presentation, conversation with Alberto Cairo, moderated by Sam Grobart. (Bloomberg TV), Albert Cairo's presentation.
presentation slides
This was a lightning 7 minute talk. I did more planning about what to say than I usually do, given that there was virtually no opportunity for any kind of backtracking, and include a running narrative below each slide.
download presentation
My slides are available as PDF, keynote (zipped) or Quicktime. The format is 16:9 HD.
Bloomberg Businessweek Design Issue
On 28 Jan 2013, Bloomberg Businessweek Design Issue will capture the ideas from the conference and the personalities that generated them.
During the conference, each talk was captured in a series of sketches by Tom Wujec: my talk sketch and moderated discussion sketch.
news + thoughts
Classification and regression trees
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.
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.
Personal Oncogenomics Program 5 Year Anniversary Art
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).
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
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.
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.
`k` index: a weightlighting and Crossfit performance measure
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
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.