Creating new words is fun. It exercises the mind and adds a playful dimension to prosaic speech, without succumbing to bombast associated with deployment of arcane (and often lengthy) words.
When one's own neologisms are heard in use by other people, it also exercises the ego.
1a circularly arranged visualization created using Circos
2any circular visualization with concentric tracks, and especially those using lines or curves connecting points on the circumferenceusage of circos plot: "Genome visualization without Circos is like a fish with a bicycle." origin of circos plot: Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645
1having desirable qualities, often emphasizing visual qualities, so overly maximized as to be disfunctional or unuseable
2perfectly secure, but practically unusable, by virtue of physical and electronic isolation
3anything that is only great on paperusage of compure: "The IT department built us a compure network. Unfortunately, nobody can log on." usage of compure: "The apartment was compure—easy on the eyes but we couldn't figure out how to open the cupboards." usage of compure: "Beautiful and dumb, she was truly compure." origin of compure: computer + pure
1a statement which is not strictly inconversible, but due to cultural or social constraints and customs, is practically so because uttering its converse would invite disgraceusage of culturally inconversible: "Politicians habitually employ cultural inconversibles to position themselves safely in the eyes of the public." example of culturally inconversible: "Men and women should be treated equally." see also: inconversible
1suspenders, discreetly worn under clothing, designed to hold up adult incontinence briefs or any other pads, guards and absorbency products
2suspenders worn under clothingusage of dependers: "Bob's dependers ensured him with not only peace of mind but also a snug and comfortable fit." origin of dependers: Depend + suspenders
1spam reformatted to the style of the poet ee cummings
2a specific instance of spammingsusage of ee spammings: "ee spammings extract a useful dimension from unsolicited communication." example of ee spammings: "please reply / me back i have / something to tell / you (inmportant)" origin of ee spammings: spam + ee cummings see also: spammings
1characterized by existential angst, in particular to a small degree
2slightly miffed at the apparent lack of purpose of life and direction of the expanding universeusage of existangsty: "That cosmology video made me existangsty." origin of existangsty: existential + angst
1an occasion, time or day of celebration associated with specific rituals and/or dress, whose origins have been forgotten, with time but usually purposefully, because they harken to a time that was unprosperous, calamitous or embarrassing.
2an unfortunate event whose memory is purposefully perceived as positive to avoid embarrassment or conflictusage of fezday: "They celebrated fezday, like it was a good thing." usage of fezday: "Nobody could remember the origins of fezday, but everyone always had a good time." usage of fezday: "You couldn't tell the celebrants they looked ridiculous at the risk of incuring their wrath, which always seemed close to the surface." usage of fezday: "Let's have a fezday with this." origin of fezday: fez + day. Based on the legendary account of a long-fought battle which ended in a humiliating defeat, made visibly worse by the victor demanding that the losing side wear a fez each year in shame. Many years passed. Over time the losing side's embarrassment and resentment grew. The fez embodied their humiliation and loss, both intolerable. Eventually, the original reason for the fez was struck from historical record. The day was turned into a celebration of independence and identity. The fez became a national symbol and was widely worn.
1a creature that lives on 3 adjacent orders of the Hilbert curve.
2a creature of one of the 14 classes of Hilbertonians: alien, voyager, crossfit, breaker, spider, sentinel, dasher, creeper, poser, screamer, chopper, veggie, fez and peep.usage of hilbertonian: "I think this Hilbertonian is a creeper." example of hilbertonian: "Classification of Hilbertonians." origin of hilbertonian: from Hilbert curve
1a matrix of hive plots presenting multiple independent visual signatures of a networkusage of hive panel: "The hive panels of these two networks helped me see minor differences in structure I would have normally missed." see also: hive plot, ratio hive
1a network visualization method which assigns and positions nodes on linear axes using rules based on structural properties of the network
2periodic parallel axis plot in which the axes are arranged radially, like in a radar plotusage of hive plot: "Hive plots create rational network visualizations that can be easily interpreted and compared." see also: hive panel, ratio hive
1typically refering to a statement, something whose converse is illogical or senseless, thereby diluting the substance and information content of the original.
2anything whose converse is senseless, either by definition or logicusage of inconversible: "He concealed the lack of substance in his delivery by long inconversible statements" example of inconversible: "I like to have fun." origin of inconversible: in- (non) and conversible see also: culturally inconversible
1The collection of annotations, such as user comments, literature citations and functional and structural interpretations, of an omome.usage of metaomome: "Many centers lack the computational resources to study the entire omome and, instead, focus on metaomomics — the study of its annotations, a more tractable challenge." example of metaomome: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of metaomome: meta + omeome see also: omeomics, omome
1terrific, but for unknown or mysterious reasons
2strangely wonderfulusage of mystific: "Waiter, this meal is mystific. Can you give me a hint?" origin of mystific: mysterious + terrific
1a belief system in which it is taken on faith that God does not exist.usage of naytheism: "My position of naytheism is unassailable by the theists because it uses the same modes of reasoning." origin of naytheism: nay + theism see also: naytheist
1a person who takes it on faith that God doesn't exist.usage of naytheist: "As a naytheist, I count on my faith to support my views." origin of naytheist: nay + theism see also: naytheism
1typically to a yes or no question, a response suggesting that both answers hold equal merit in such balance that deciding is difficult and potentially impossible; distinguished from maybe in that nes does not require the speaker to ever reach a decision, nor communicate their intention to do so.usage of nes: "When John asked me on a date, I said 'nes'." origin of nes: no + yes; counterparts in other languages may exist, such as noui in French (non/oui), jain in German (ja/nein), and niak in Polish (nie/tak) — notice that the order of the words can vary in different languages to create the more appealing combination
1fear elicited by direct chemical or electrical stimulation of the brain, without an external fearsome stimulususage of neuroterror: "After the development of aerosolized fear-causing neuromodulators, the courts had a difficult time in determining whether their use was captured by the laws governing the classical definition of terror." see also: neuroterrorism
1use of neuroterror for coersion or controlusage of neuroterrorism: "It was unclear whether last month's incident was an act of neuroterror or simply spontaneous mass panic." see also: neuroterror
1replace something with a newer thingusage of newgrade: "I had to newgrade my phone—they sure don't make things like they used to!" usage of newgrade: "This phone oldgrade is definitely a downgrade." origin of newgrade: Provides the equivalent of downgrade and upgrade, but relative to age and not function or quality. see also: oldgrade
1without direction or intentusage of noward: "Your focus is pointing noward." origin of noward: As an analogy to forward, onward and backward, noward is the directional equivalent of the positional nowhere. Words relating to movement with a specific destination in mind would use nowhere (i.e. no place), those hinged on direction would use noward (i.e. no direction).
1the guilty's garbage canusage of nonposter: "Looking at the contents of your nonposter, I see that you are not engaged in environmental causes." origin of nonposter: non + composter
1replace something with an older thingusage of oldgrade: "I've oldgraded my car—I love classics." usage of oldgrade: "I decided to upgrade and oldgraded my espresso machine." origin of oldgrade: Provides the equivalent of downgrade and upgrade, but relative to age and not function or quality. see also: newgrade
1The collective set of all omics, such as genomics, proteomics, exomics, metabolomics, etc.example of omome: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of omome: omics + -ome see also: metaomeome, omeomics, omicsophy
1synonym for omicsophyexample of omeomics: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of omeomics: omics + -sophy see also: metaomeome, omicsophy
1The study of the collection of omics, the broad fields whose name ends in the omics suffix (commonly found in the biological sciences), such as genomics, proteomics, exomics, metabolomics, etc.example of omicsophy: "Ome, the Sound of the Scientific Universe Expanding in the NYT" origin of omicsophy: omics + -sophy see also: metaomeome, omeomics, omome
1a sleepover, but without sleep, ideally ending in a prekfast.usage of over: "After last night's over, I was exhausted but happy the next day." see also: prekfast
1liquid unit of measure, equivalent to a pinch
2spontaneous urination from a small, typically obnoxious, dog, amidst excitement
3in general, a small amount of any liquid uncontrollably producedexample of piddle: "This Yorkshire pudding recipe calls for a piddle of drippings." origin of piddle: off-label use of piddle
1a method in computer security to authenticate a remote host with a server without the use of any open portsusage of port knocking: "My server cannot be detected by a port scan, but I can still login because I use port knocking." origin of port knocking: Krzywinski, M. Port Knocking: Network authentication across closed ports. SysAdmin Magazine (2003) 12:12-17
1a small meal ordered after dessert, consumed during examination and settling of the billusage of postpetizer: "The desert was delicious but we are still peckish — could you bring us a postpetizer with the bill please?" see also: prepetizer
1offer praise in anticipation of success
2offer contratulations before success is achievedusage of pregratulate: "On my first day of college my parents pregratulated me on my graduation." origin of pregratulate: pre + contratulate see also: prenopsis
1a light snack, before breakfast, typically prepared and presented by one's sleep partner and consumed in bedusage of prekfast: "She was thoughtful to bring me a prekfast after our over." origin of prekfast: pre + breakfast see also: over
1a summary, such as of a book, program or event, formed purely on expectation, bias and hope, formulated before the object or event is experiencedusage of prenopsis: "Looking at the book's cover in the store, I quickly formulated a prenopsis which proved suprisingly accurate."
1a small meal, typically delivered quickly, ordered after the arrival, but before reading, of the menu, intended to quench the initial hunger until the arrival of the appetizerusage of prepetizer: "We are starving — could you bring us a prepetizer while we look at the menu?" origin of prepetizer: pre + appetizer similar to: amuse-bouche see also: postpetizer
1a person or thing possessing rare or special qualities or traits, thereby potentially embodying the fifth essenceusage of quinty: "This dessert is so divine, as to be almost quinty." origin of quinty: diminutive of quintessential, in a more relaxed use
1a hive plot used to visualize ratio quantities between three or more axes, employing stacked ribbons to show the cumulative distribution of values
2periodic stacked bar plot in which the axes are arranged radially, like in a radar plotusage of ratio hive: "Ratio hives can be used to illustrate differences in composition or structure of various object." see also: hive panel, hive plot
1short form of ee spammings
2unsolicited communication reformatted, with poetic license, into a more palatable formsee also: ee spammings
1to raise an individual's life energy so far beyond previous highest level as to give the impression of life for the first time
2to animate, energize, or stimulate an entity to a new level of liveliness.
3(figurative) to breate life into, for the first timeusage of suscitate: "Looks like meeting Mary really suscitated John. I've never seen him this alive." origin of suscitate: resuscitate, except without re-, implying that the entity has never lived
1without a sense of proprietyusage of unappropriate: "Nobody was certain whether to be affended—she appeared entirely unappropriate." origin of unappropriate: Immoral is to inappropriate as amoral is to unappropriate.
It is important to understand both what a classification metric expresses and what it hides.
We examine various metrics use to assess the performance of a classifier. We show that a single metric is insufficient to capture performance—for any metric, a variety of scenarios yield the same value.
We also discuss ROC and AUC curves and how their interpretation changes based on class balance.
Altman, N. & Krzywinski, M. (2016) Points of Significance: Classifier evaluation. Nature Methods 13:603-604.
Today is the day and it's hardly an approximation. In fact, `22/7` is 20% more accurate of a representation of `\pi` than `3.14`!
Time to celebrate, graphically. This year I do so with perfect packing of circles that embody the approximation.
By warping the circle by 8% along one axis, we can create a shape whose ratio of circumference to diameter, taken as twice the average radius, is 22/7.
Regression can be used on categorical responses to estimate probabilities and to classify.
The next column in our series on regression deals with how to classify categorical data.
We show how linear regression can be used for classification and demonstrate that it can be unreliable in the presence of outliers. Using a logistic regression, which fits a linear model to the log odds ratio, improves robustness.
Logistic regression is solved numerically and in most cases, the maximum-likelihood estimates are unique and optimal. However, when the classes are perfectly separable, the numerical approach fails because there is an infinite number of solutions.
Altman, N. & Krzywinski, M. (2016) Points of Significance: Logistic regression. Nature Methods 13:541-542.
Altman, N. & Krzywinski, M. (2016) Points of Significance: Regression diagnostics? Nature Methods 13:385-386.
Altman, N. & Krzywinski, M. (2015) Points of Significance: Multiple Linear Regression Nature Methods 12:1103-1104.
Altman, N. & Krzywinski, M. (2015) Points of significance: Simple Linear Regression Nature Methods 12:999-1000.
Genomic instability is one of the defining characteristics of cancer and within a tumor, which is an ever-evolving population of cells, there are many genomes. Mutations accumulate and propagate to create subpopulations and these groups of cells, called clones, may respond differently to treatment.
It is now possible to sequence individual cells within a tumor to create a profile of genomes. This profile changes with time, both in the kinds of mutation that are found and in their proportion in the overall population.
Clone evolution diagrams visualize these data. These diagrams can be qualitative, showing only trends, or quantitative, showing temporal and population changes to scale. In this Molecular Cell forum article I provide guidelines for drawing these diagrams, focusing with how to use color and navigational elements, such as grids, to clarify the relationships between clones.
Krzywinski, M. (2016) Visualizing Clonal Evolution in Cancer. Mol Cell 62:652-656.