resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
writing
Writing
Poetry
Inked Sadness is a collection of poems written in that difficult time between being no longer young, but not yet old.
Expressions and Conversations of Love are short heart-breakers.
Scripts
Proverbial Man considers how our names and expectations limit our perceptions and freedoms. No answers are offered. I don't think I finished this.
The Surrogate echoes my own fears of fleeing from Poland in the early 80s. Or at least the fears I retroactively erected, to add drama. Count on the Polish for drama.
Narrative
Thirty Reasons should be enough to decide a place isn't worth returning to.
NeverEnder — Epic Space Poem
By my friend and colleague Emanuele Raffaele Ettore Libertini, the NeverEnder is a voyage through space and words.
news + thoughts
Ensemble methods: Bagging and random forests
Many heads are better than one.We introduce two common ensemble methods: bagging and random forests. Both of these methods repeat a statistical analysis on a bootstrap sample to improve the accuracy of the predictor. Our column shows these methods as applied to Classification and Regression Trees.
For example, we can sample the space of values more finely when using bagging with regression trees because each sample has potentially different boundaries at which the tree splits.
Random forests generate a large number of trees by not only generating bootstrap samples but also randomly choosing which predictor variables are considered at each split in the tree.
Krzywinski, M. & Altman, N. (2017) Points of Significance: Ensemble methods: bagging and random forests. Nature Methods 14:933–934.
Background reading
Krzywinski, M. & Altman, N. (2017) Points of Significance: Classification and regression trees. Nature Methods 14:757–758.
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.