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
Where am I supposed to go? Where was I supposed to know?Violet Indianaget lost in questionsmore quotes

english: fun


EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.


art + literature

daily quotation server archives

In the late 90’s I started (a good decade for starts) a daily quotation server project at www.quoteserver.ca. The domain is now defunct—some pages are partially viewable at the Way Back Machine.

Below is the list of quotes I had collected by the end of the life of the project. Most are about love—duh—and a few are jolly jests from funny trenches. You know, that place where mustard gas makes your eyes water.

The quotes weren’t scraped from quote archives—each is meaningful and hand-picked.

the quote archive

And now for full list of 1,600 other things worth reading. Such as everything Dorothy Parker has written and ... yes, even the Pinky and Brain quotes, which are a special kind of special.

Quote collections about love, heart, desire, life, death, god, mind, science.

Feeling lucky? Read 10 random quotes. Well, will you, punk?

Quotes about death

34
Little fly, thy summer’s play
My careless hand hath brushed away.
Am not I a fly like thee,
Or art not thou a man like me.
For I dance, and drink, and sing
Till some blind hand doth brush my wing.
If that is life, and strength, and breath
And the word of thought is death
Then am I a happy fly?
If I live, or if I die.
William Blake
45
Sleep is a death, O make me try
By sleeping, what it is to die,
And as gently lay my head
On my grave, as now my bed.
Sir Thomas Browne
Religio Medici, part II
48
I love thee with the love I seemed to lose
With my lost saints,—I love thee with the breath
Smiles, tears, of all my life!—and, if God choose,
I shall but love thee better after death.
Elizabeth Barrett Browning
Sonnets from the Portuguese
132
To-morrow, and to-morrow, and to-morrow,
Creeps in this petty pace from day to day
To the last syllable of recorded time,
And all our yesterdays have lighted fools
The way to dusty death.
Out, out, brief candle!
Life’s but a walking shadow, a poor player
That struts and frets his hour upon the stage
And then is heard no more: it is a tale
Told by an idiot, full of sound and fury,
Signifying nothing.
William Shakespeare
Macbeth, V. i. 19.
140
Half a league, half a league,
Half a league onward,
All in the valley of Death
Rode the six hundred.
Alfred Tennyson
Charge of the Light Brigade
154
Sleep—Death without dying—living, but not life.
Edwin Arnold
156
Death is sometimes a punishment, sometimes a gift;
To many it has come as a favor.
Seneca
157
The prince who kept the world in awe,
The judge whose dictate fix’d the law;
The rich, the poor, the great, the small,
Are levelled; death confounds ’em all.
Gay
158
Because I could not stop for Death,
He kindly stopped for me,
The carriage held but just ourselves
And Immortality.
Emily Dickinson
266
Life without a friend is like death without a witness.
299
Death comes with a crawl, or comes with a pounce,
And whether he’s slow or spry,
It isn’t the fact that you’re dead that counts,
But only, how did you die?
Edmund Vance Cooke
How Did You Die?
337
Windows NT crashed.
I am the Blue Screen of Death.
No one hears your screams.
A Haiku computer error message.
340
Three things are certain:
Death, taxes and lost data.
Guess which has occurred.
A Haiku computer error message.
417
Death is nature’s way of telling you to slow down.
431
Don’t be afraid of death so much as an inadequate life.
Bertolt Brecht
466
He is one of those people who would be enormously improved by death.
H.H. Munro
475
Those who fear death most are those who enjoy life least.
502
Marriage is the death of hope.
Woody Allen
524
At six o’clock we cleaned our cells,
At seven all was still,
But the sough and swing of a mighty wing
The prison seemed to fill,
For the Lord of Death with icy breath
Had entered in to kill.
Oscar Wilde
The Ballad of Reading Gaol
595
The smallest sprout shows there is really no death.
And if ever there was it led forward life, and does not
wait at the end to arrest it.
Walt Whitman
Song of Myself
645
I do not believe that any man fears to be dead, but
only the stroke of death.
Francis Bacon
An Essay on Death
712
All tragedies are finish’d by a death,
All comedies are ended by a marriage.
Lord Byron
Don Juan, c.iii, st. 9
729
Vivre est un maladie dont le sommeil nous soulage
toutes les 16 heures. C’est un pallatif. La mort
est le remede.
[Living is an illness to which sleep provides
relief every sixteen hours. It’s a palliative.
The remedy is death.]
Nicolas-Sebastien Chamfort
Maximes et Pensees, ch. 2
812
Death hath so many doors to let out life.
John Fletcher
The Custom of the Country, II.ii
885
Then, with no throbs of fiery pain,
No cold gradations of decay,
Death broke at once the vital chain,
And freed his soul the nearest way.
Samuel Johnson
Of Gray’s Odes
963
O death! I know it—’tis my famulus—
Thus turns to naught my fairest bliss!
That visions in abundance such as this
Must be disturbed by that dry prowler thus!
Johann Wolfgang von Goethe
Faust
1092
For the crown of our life as it closes
Is darkness, the fruit there of dust;
No thorns go as deep as the rose’s,
And love is more cruel than lust.
Time turns the old days to derision,
Our loves into corpses or wives;
And marriage and death and division
Make barren our lives.
Algernon Charles Swinburne
Dolores
1130
Though they go mad they shall be sane.
Though they sink through the sea, they shall rise again.
Though lovers be lost, love shall not,
And death shall have no dominion.
Dylan Thomas
1138
My life is light, waiting for the death wind,
Like a feather on the back of my hand.
T.S. Eliot
1141
Death be not proud, though some have called thee
Mighty and dreadful, for, thou art not so,
For, those, whom thou think’st, thou dost overthrow,
Die not, poor death, nor yet canst thou kill me.
John Donne
Holy Sonnets X
1142
Don’t strew me with roses after I’m dead.
When Death claims the light of my brow
No flowers of life will cheer me: instead
You may give me my roses now!
Thomas F. Healey
1194
Suffer me to take your hand.
Suffer me to cherish you
Till the dawn is in the sky.
Whether I be false or true,
Death comes in a day or two.
Edna St. Vincent Millay
Mariposa
1311
Show me a love was done and through,
Tell me a kiss escaped its debt!
Son, to your death you’ll pay your due—
Women and elephants never forget.
Dorothy Parker
Ballade of Unfortunate Mammals
1319
Oh, it is sure as it is sad
That any lad is every lad,
And what’s a girl, to dare impore
Her dear be hers forevermore?
Though he be tried and he be bold,
And swearing death should he be cold,
He’ll run the path the others went....
But you, my sweet, are different.
Dorothy Parker
Incurable
1446
In every parting there is an image of death.
George Eliot
1472
For the Angel of Death spread his wings on the blast,
And breathed in the face of the foe as he pass’d;
And the eyes of the sleepers wax’d deadly and chill,
And their hearts but once heaved, and for ever grew still!
Lord Byron
The Destruction of Sennacherib
1476
To die, to sleep—
To sleep, perchance to dream, ay there’s the rub,
For in that sleep of death what dreams may come
When we have shuffled off this mortal coil,
Must give us pause; there’s the respect
That makes calamity of so long life.
William Shakespeare
Hamlet
1485
The harder the conflict, the more glorious the triumph. What we obtain too cheap, we esteem too lightly; it is dearness only that gives everything its value. I love the man that can smile in trouble, that can gather strength from distress and grow brave by reflection. ’Tis the business of little minds to shrink; but he whose heart is firm, and whose conscience approves his conduct, will pursue his principles unto death.
Thomas Paine
1596
I do not want to believe that death is the gateway to another life. For me, it is a closed door. I do not say it is a step we must all take, but that it is a horrible and dirty adventure.
Albert Camus
1672
Life is short. But death is very, very long.
Henning Mankell
Quicksand
VIEW ALL

news + thoughts

Ensemble methods: Bagging and random forests

Mon 16-10-2017
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Ensemble methods: Bagging and random forests. (read)

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.

...more about the Points of Significance column

Classification and regression trees

Mon 16-10-2017
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Classification and decision trees. (read)

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.

...more about the Points of Significance column

Personal Oncogenomics Program 5 Year Anniversary Art

Wed 26-07-2017

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).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. (left) Cases ordered chronologically by case number. (right) Cases grouped by diagnosis (tissue type) and then by similarity within group.

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

Thu 06-07-2017
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Principal component analysis. (read)

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.

...more about the Points of Significance column

`k` index: a weightlighting and Crossfit performance measure

Wed 07-06-2017

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.