Random stuff

i. Your Care Home in 120 Seconds. Some quotes:

“In order to get an overall estimate of mental power, psychologists have chosen a series of tasks to represent some of the basic elements of problem solving. The selection is based on looking at the sorts of problems people have to solve in everyday life, with particular attention to learning at school and then taking up occupations with varying intellectual demands. Those tasks vary somewhat, though they have a core in common.

Most tests include Vocabulary, examples: either asking for the definition of words of increasing rarity; or the names of pictured objects or activities; or the synonyms or antonyms of words.

Most tests include Reasoning, examples: either determining which pattern best completes the missing cell in a matrix (like Raven’s Matrices); or putting in the word which completes a sequence; or finding the odd word out in a series.

Most tests include visualization of shapes, examples: determining the correspondence between a 3-D figure and alternative 2-D figures; determining the pattern of holes that would result from a sequence of folds and a punch through folded paper; determining which combinations of shapes are needed to fill a larger shape.

Most tests include episodic memory, examples: number of idea units recalled across two or three stories; number of words recalled from across 1 to 4 trials of a repeated word list; number of words recalled when presented with a stimulus term in a paired-associate learning task.

Most tests include a rather simple set of basic tasks called Processing Skills. They are rather humdrum activities, like checking for errors, applying simple codes, and checking for similarities or differences in word strings or line patterns. They may seem low grade, but they are necessary when we try to organise ourselves to carry out planned activities. They tend to decline with age, leading to patchy, unreliable performance, and a tendency to muddled and even harmful errors. […]

A brain scan, for all its apparent precision, is not a direct measure of actual performance. Currently, scans are not as accurate in predicting behaviour as is a simple test of behaviour. This is a simple but crucial point: so long as you are willing to conduct actual tests, you can get a good understanding of a person’s capacities even on a very brief examination of their performance. […] There are several tests which have the benefit of being quick to administer and powerful in their predictions.[..] All these tests are good at picking up illness related cognitive changes, as in diabetes. (Intelligence testing is rarely criticized when used in medical settings). Delayed memory and working memory are both affected during diabetic crises. Digit Symbol is reduced during hypoglycaemia, as are Digits Backwards. Digit Symbol is very good at showing general cognitive changes from age 70 to 76. Again, although this is a limited time period in the elderly, the decline in speed is a notable feature. […]

The most robust and consistent predictor of cognitive change within old age, even after control for all the other variables, was the presence of the APOE e4 allele. APOE e4 carriers showed over half a standard deviation more general cognitive decline compared to noncarriers, with particularly pronounced decline in their Speed and numerically smaller, but still significant, declines in their verbal memory.

It is rare to have a big effect from one gene. Few people carry it, and it is not good to have.

ii. What are common mistakes junior data scientists make?

Apparently the OP had second thoughts about this query so s/he deleted the question and marked the thread nsfw (??? …nothing remotely nsfw in that thread…). Fortunately the replies are all still there, there are quite a few good responses in the thread. I added some examples below:

“I think underestimating the domain/business side of things and focusing too much on tools and methodology. As a fairly new data scientist myself, I found myself humbled during this one project where I had I spent a lot of time tweaking parameters and making sure the numbers worked just right. After going into a meeting about it became clear pretty quickly that my little micro-optimizations were hardly important, and instead there were X Y Z big picture considerations I was missing in my analysis.”


  • Forgetting to check how actionable the model (or features) are. It doesn’t matter if you have amazing model for cancer prediction, if it’s based on features from tests performed as part of the post-mortem. Similarly, predicting account fraud after the money has been transferred is not going to be very useful.

  • Emphasis on lack of understanding of the business/domain.

  • Lack of communication and presentation of the impact. If improving your model (which is a quarter of the overall pipeline) by 10% in reducing customer churn is worth just ~100K a year, then it may not be worth putting into production in a large company.

  • Underestimating how hard it is to productionize models. This includes acting on the models outputs, it’s not just “run model, get score out per sample”.

  • Forgetting about model and feature decay over time, concept drift.

  • Underestimating the amount of time for data cleaning.

  • Thinking that data cleaning errors will be complicated.

  • Thinking that data cleaning will be simple to automate.

  • Thinking that automation is always better than heuristics from domain experts.

  • Focusing on modelling at the expense of [everything] else”

“unhealthy attachments to tools. It really doesn’t matter if you use R, Python, SAS or Excel, did you solve the problem?”

“Starting with actual modelling way too soon: you’ll end up with a model that’s really good at answering the wrong question.
First, make sure that you’re trying to answer the right question, with the right considerations. This is typically not what the client initially told you. It’s (mainly) a data scientist’s job to help the client with formulating the right question.”

iii. Some random wikipedia links: Ottoman–Habsburg wars. Planetshine. Anticipation (genetics). Cloze test. Loop quantum gravity. Implicature. Starfish Prime. Stall (fluid dynamics). White Australia policy. Apostatic selection. Deimatic behaviour. Anti-predator adaptation. Lefschetz fixed-point theorem. Hairy ball theorem. Macedonia naming dispute. Holevo’s theorem. Holmström’s theorem. Sparse matrix. Binary search algorithm. Battle of the Bismarck Sea.

iv. 5-HTTLPR: A Pointed Review. This one is hard to quote, you should read all of it. I did however decide to add a few quotes from the post, as well as a few quotes from the comments:

“…what bothers me isn’t just that people said 5-HTTLPR mattered and it didn’t. It’s that we built whole imaginary edifices, whole castles in the air on top of this idea of 5-HTTLPR mattering. We “figured out” how 5-HTTLPR exerted its effects, what parts of the brain it was active in, what sorts of things it interacted with, how its effects were enhanced or suppressed by the effects of other imaginary depression genes. This isn’t just an explorer coming back from the Orient and claiming there are unicorns there. It’s the explorer describing the life cycle of unicorns, what unicorns eat, all the different subspecies of unicorn, which cuts of unicorn meat are tastiest, and a blow-by-blow account of a wrestling match between unicorns and Bigfoot.

This is why I start worrying when people talk about how maybe the replication crisis is overblown because sometimes experiments will go differently in different contexts. The problem isn’t just that sometimes an effect exists in a cold room but not in a hot room. The problem is more like “you can get an entire field with hundreds of studies analyzing the behavior of something that doesn’t exist”. There is no amount of context-sensitivity that can help this. […] The problem is that the studies came out positive when they shouldn’t have. This was a perfectly fine thing to study before we understood genetics well, but the whole point of studying is that, once you have done 450 studies on something, you should end up with more knowledge than you started with. In this case we ended up with less. […] I think we should take a second to remember that yes, this is really bad. That this is a rare case where methodological improvements allowed a conclusive test of a popular hypothesis, and it failed badly. How many other cases like this are there, where there’s no geneticist with a 600,000 person sample size to check if it’s true or not? How many of our scientific edifices are built on air? How many useless products are out there under the guise of good science? We still don’t know.”

A few more quotes from the comment section of the post:

“most things that are obviously advantageous or deleterious in a major way aren’t gonna hover at 10%/50%/70% allele frequency.

Population variance where they claim some gene found in > [non trivial]% of the population does something big… I’ll mostly tend to roll to disbelieve.

But if someone claims a family/village with a load of weirdly depressed people (or almost any other disorder affecting anything related to the human condition in any horrifying way you can imagine) are depressed because of a genetic quirk… believable but still make sure they’ve confirmed it segregates with the condition or they’ve got decent backing.

And a large fraction of people have some kind of rare disorder […]. Long tail. Lots of disorders so quite a lot of people with something odd.

It’s not that single variants can’t have a big effect. It’s that really big effects either win and spread to everyone or lose and end up carried by a tiny minority of families where it hasn’t had time to die out yet.

Very few variants with big effect sizes are going to be half way through that process at any given time.

Exceptions are

1: mutations that confer resistance to some disease as a tradeoff for something else […] 2: Genes that confer a big advantage against something that’s only a very recent issue.”

“I think the summary could be something like:
A single gene determining 50% of the variance in any complex trait is inherently atypical, because variance depends on the population plus environment and the selection for such a gene would be strong, rapidly reducing that variance.
However, if the environment has recently changed or is highly variable, or there is a trade-off against adverse effects it is more likely.
Furthermore – if the test population is specifically engineered to target an observed trait following an apparently Mendelian inheritance pattern – such as a family group or a small genetically isolated population plus controls – 50% of the variance could easily be due to a single gene.”

v. Less research is needed.

“The most over-used and under-analyzed statement in the academic vocabulary is surely “more research is needed”. These four words, occasionally justified when they appear as the last sentence in a Masters dissertation, are as often to be found as the coda for a mega-trial that consumed the lion’s share of a national research budget, or that of a Cochrane review which began with dozens or even hundreds of primary studies and progressively excluded most of them on the grounds that they were “methodologically flawed”. Yet however large the trial or however comprehensive the review, the answer always seems to lie just around the next empirical corner.

With due respect to all those who have used “more research is needed” to sum up months or years of their own work on a topic, this ultimate academic cliché is usually an indicator that serious scholarly thinking on the topic has ceased. It is almost never the only logical conclusion that can be drawn from a set of negative, ambiguous, incomplete or contradictory data.” […]

“Here is a quote from a typical genome-wide association study:

“Genome-wide association (GWA) studies on coronary artery disease (CAD) have been very successful, identifying a total of 32 susceptibility loci so far. Although these loci have provided valuable insights into the etiology of CAD, their cumulative effect explains surprisingly little of the total CAD heritability.”  [1]

The authors conclude that not only is more research needed into the genomic loci putatively linked to coronary artery disease, but that – precisely because the model they developed was so weak – further sets of variables (“genetic, epigenetic, transcriptomic, proteomic, metabolic and intermediate outcome variables”) should be added to it. By adding in more and more sets of variables, the authors suggest, we will progressively and substantially reduce the uncertainty about the multiple and complex gene-environment interactions that lead to coronary artery disease. […] We predict tomorrow’s weather, more or less accurately, by measuring dynamic trends in today’s air temperature, wind speed, humidity, barometric pressure and a host of other meteorological variables. But when we try to predict what the weather will be next month, the accuracy of our prediction falls to little better than random. Perhaps we should spend huge sums of money on a more sophisticated weather-prediction model, incorporating the tides on the seas of Mars and the flutter of butterflies’ wings? Of course we shouldn’t. Not only would such a hyper-inclusive model fail to improve the accuracy of our predictive modeling, there are good statistical and operational reasons why it could well make it less accurate.”

vi. Why software projects take longer than you think – a statistical model.

Anyone who built software for a while knows that estimating how long something is going to take is hard. It’s hard to come up with an unbiased estimate of how long something will take, when fundamentally the work in itself is about solving something. One pet theory I’ve had for a really long time, is that some of this is really just a statistical artifact.

Let’s say you estimate a project to take 1 week. Let’s say there are three equally likely outcomes: either it takes 1/2 week, or 1 week, or 2 weeks. The median outcome is actually the same as the estimate: 1 week, but the mean (aka average, aka expected value) is 7/6 = 1.17 weeks. The estimate is actually calibrated (unbiased) for the median (which is 1), but not for the the mean.

A reasonable model for the “blowup factor” (actual time divided by estimated time) would be something like a log-normal distribution. If the estimate is one week, then let’s model the real outcome as a random variable distributed according to the log-normal distribution around one week. This has the property that the median of the distribution is exactly one week, but the mean is much larger […] Intuitively the reason the mean is so large is that tasks that complete faster than estimated have no way to compensate for the tasks that take much longer than estimated. We’re bounded by 0, but unbounded in the other direction.”

I like this way to conceptually frame the problem, and I definitely do not think it only applies to software development.

“I filed this in my brain under “curious toy models” for a long time, occasionally thinking that it’s a neat illustration of a real world phenomenon I’ve observed. But surfing around on the interwebs one day, I encountered an interesting dataset of project estimation and actual times. Fantastic! […] The median blowup factor turns out to be exactly 1x for this dataset, whereas the mean blowup factor is 1.81x. Again, this confirms the hunch that developers estimate the median well, but the mean ends up being much higher. […]

If my model is right (a big if) then here’s what we can learn:

  • People estimate the median completion time well, but not the mean.
  • The mean turns out to be substantially worse than the median, due to the distribution being skewed (log-normally).
  • When you add up the estimates for n tasks, things get even worse.
  • Tasks with the most uncertainty (rather the biggest size) can often dominate the mean time it takes to complete all tasks.”

vii. Attraction inequality and the dating economy.

“…the relentless focus on inequality among politicians is usually quite narrow: they tend to consider inequality only in monetary terms, and to treat “inequality” as basically synonymous with “income inequality.” There are so many other types of inequality that get air time less often or not at all: inequality of talent, height, number of friends, longevity, inner peace, health, charm, gumption, intelligence, and fortitude. And finally, there is a type of inequality that everyone thinks about occasionally and that young single people obsess over almost constantly: inequality of sexual attractiveness. […] One of the useful tools that economists use to study inequality is the Gini coefficient. This is simply a number between zero and one that is meant to represent the degree of income inequality in any given nation or group. An egalitarian group in which each individual has the same income would have a Gini coefficient of zero, while an unequal group in which one individual had all the income and the rest had none would have a Gini coefficient close to one. […] Some enterprising data nerds have taken on the challenge of estimating Gini coefficients for the dating “economy.” […] The Gini coefficient for [heterosexual] men collectively is determined by [-ll-] women’s collective preferences, and vice versa. If women all find every man equally attractive, the male dating economy will have a Gini coefficient of zero. If men all find the same one woman attractive and consider all other women unattractive, the female dating economy will have a Gini coefficient close to one.”

“A data scientist representing the popular dating app “Hinge” reported on the Gini coefficients he had found in his company’s abundant data, treating “likes” as the equivalent of income. He reported that heterosexual females faced a Gini coefficient of 0.324, while heterosexual males faced a much higher Gini coefficient of 0.542. So neither sex has complete equality: in both cases, there are some “wealthy” people with access to more romantic experiences and some “poor” who have access to few or none. But while the situation for women is something like an economy with some poor, some middle class, and some millionaires, the situation for men is closer to a world with a small number of super-billionaires surrounded by huge masses who possess almost nothing. According to the Hinge analyst:

On a list of 149 countries’ Gini indices provided by the CIA World Factbook, this would place the female dating economy as 75th most unequal (average—think Western Europe) and the male dating economy as the 8th most unequal (kleptocracy, apartheid, perpetual civil war—think South Africa).”

Btw., I’m reasonably certain “Western Europe” as most people think of it is not average in terms of Gini, and that half-way down the list should rather be represented by some other region or country type, like, say Mongolia or Bulgaria. A brief look at Gini lists seemed to support this impression.

Quartz reported on this finding, and also cited another article about an experiment with Tinder that claimed that that “the bottom 80% of men (in terms of attractiveness) are competing for the bottom 22% of women and the top 78% of women are competing for the top 20% of men.” These studies examined “likes” and “swipes” on Hinge and Tinder, respectively, which are required if there is to be any contact (via messages) between prospective matches. […] Yet another study, run by OkCupid on their huge datasets, found that women rate 80 percent of men as “worse-looking than medium,” and that this 80 percent “below-average” block received replies to messages only about 30 percent of the time or less. By contrast, men rate women as worse-looking than medium only about 50 percent of the time, and this 50 percent below-average block received message replies closer to 40 percent of the time or higher.

If these findings are to be believed, the great majority of women are only willing to communicate romantically with a small minority of men while most men are willing to communicate romantically with most women. […] It seems hard to avoid a basic conclusion: that the majority of women find the majority of men unattractive and not worth engaging with romantically, while the reverse is not true. Stated in another way, it seems that men collectively create a “dating economy” for women with relatively low inequality, while women collectively create a “dating economy” for men with very high inequality.”

I think the author goes a bit off the rails later in the post, but the data is interesting. It’s however important keeping in mind in contexts like these that sexual selection pressures apply at multiple levels, not just one, and that partner preferences can be non-trivial to model satisfactorily; for example as many women have learned the hard way, males may have very different standards for whom to a) ‘engage with romantically’ and b) ‘consider a long-term partner’.

viii. Flipping the Metabolic Switch: Understanding and Applying Health Benefits of Fasting.

“Intermittent fasting (IF) is a term used to describe a variety of eating patterns in which no or few calories are consumed for time periods that can range from 12 hours to several days, on a recurring basis. Here we focus on the physiological responses of major organ systems, including the musculoskeletal system, to the onset of the metabolic switch – the point of negative energy balance at which liver glycogen stores are depleted and fatty acids are mobilized (typically beyond 12 hours after cessation of food intake). Emerging findings suggest the metabolic switch from glucose to fatty acid-derived ketones represents an evolutionarily conserved trigger point that shifts metabolism from lipid/cholesterol synthesis and fat storage to mobilization of fat through fatty acid oxidation and fatty-acid derived ketones, which serve to preserve muscle mass and function. Thus, IF regimens that induce the metabolic switch have the potential to improve body composition in overweight individuals. […] many experts have suggested IF regimens may have potential in the treatment of obesity and related metabolic conditions, including metabolic syndrome and type 2 diabetes.()”

“In most studies, IF regimens have been shown to reduce overall fat mass and visceral fat both of which have been linked to increased diabetes risk.() IF regimens ranging in duration from 8 to 24 weeks have consistently been found to decrease insulin resistance.(, , , , , , , , , ) In line with this, many, but not all,() large-scale observational studies have also shown a reduced risk of diabetes in participants following an IF eating pattern.”

“…we suggest that future randomized controlled IF trials should use biomarkers of the metabolic switch (e.g., plasma ketone levels) as a measure of compliance and the magnitude of negative energy balance during the fasting period. It is critical for this switch to occur in order to shift metabolism from lipidogenesis (fat storage) to fat mobilization for energy through fatty acid β-oxidation. […] As the health benefits and therapeutic efficacies of IF in different disease conditions emerge from RCTs, it is important to understand the current barriers to widespread use of IF by the medical and nutrition community and to develop strategies for broad implementation. One argument against IF is that, despite the plethora of animal data, some human studies have failed to show such significant benefits of IF over CR [Calorie Restriction].() Adherence to fasting interventions has been variable, some short-term studies have reported over 90% adherence,() whereas in a one year ADMF study the dropout rate was 38% vs 29% in the standard caloric restriction group.()”

ix. Self-repairing cells: How single cells heal membrane ruptures and restore lost structures.

June 2, 2019 - Posted by | Astronomy, Biology, Data, Diabetes, Economics, Evolutionary biology, Genetics, Geography, History, Mathematics, Medicine, Physics, Psychology, Statistics, Wikipedia

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