Art is science in love.
— E.F. Weisslitz
In genomics, insights can hinge on a difference of one. One cellular mutation to go from healthy to diseased. One cell migration from tumor to metastasis. Even subtle differences in gene expression between healthy cells shapes their form and function.
In Data in New Dimensions, we’ve created an immersive data art experience celebrating the individuality and often underestimated influence of the single cell—captured by high-throughput single cell analysis.
Using the rich data from the very tools and instruments in this room, we’ve transformed data points back into cells and, informed by their differences, allowed those cells to once again rejoin the world of the viewer in the third dimension.
How do these canvases make you think about the difference of one in your work?
This piece contrasts two different blood cell states, diseased versus healthy, in such a way that the differences manifest as depth. Cells on the base plane (the closest to the wall) represent healthy control cells, while diseased cells ascend increasingly closer to the viewer based on how different they are from their healthy counterpart.
This piece paints a picture of the diversity of disease, showing how the cells of a tumor and its metastasis vary in expression patterns. These differences are manifested in the piece through each cell’s position in the third dimension. Cells from the primary tumor exist on the base layer (closest to the wall). Cells from the metastatic site project into the room based on the degree of difference from the nearest primary tumor cell in their cluster.
This piece explores the expression differences that help determine a healthy cell’s role within an organism. Each cluster corresponds to a different cell type along the renal tubule, with that cluster’s depth mapping to its position along the tubule. Blood enters the tubule through the cells on the base layer (closest to the wall) and is filtered by the cells in the successively ascending layers. The remaining waste exits past the cells in the layer nearest to the viewer.
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.
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.
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) 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.
Altman, N. & Krzywinski, M. (2017) Points of Significance: Clustering. Nature Methods 14:545–546.
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.
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.
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