Tag Archives: statistics

Improving the accuracy of waist circumference measurement

Waistline needs to be measured for clothes size determination and health evaluation, but the instructions to do it are vague: keep the stomach neutral, neither sucked in nor bulged out, hold the measuring tape not too loosely nor too tight. A person’s waist expands and contracts with the breath, so at which point of the breath cycle should the measurement be taken? How much tension should the measuring tape have?

Averaging several measurements would be more accurate than a single vaguely defined one, both in the sense of replication across different measurers and in the sense of corresponding to the physical quantity of interest (health status, tightness of the clothes). One simple way is to average the measured perimeter of a maximally sucked-in gut and a maximally pushed-out gut.

A better measure, but quite difficult to take, is to average the waist circumference across the whole cycle of breathing in and out, for several cycles. A device to do this would be a loop of flexible measuring tape pulled into a roll by a spring, similarly to a construction measuring tape made of metal. The roll would contain electronics which continuously record how much tape is in the roll, therefore the length of the loop outside the roll. The length data could be averaged to obtain the average waistline.

A more modern method is to use two cameras pointed at the person from two sides at waist height, recording a 3D video of the waist over the breath cycle. The video could then be averaged on a computer to find the mean volume. Whole-body volume could be determined similarly – no need for Archimedes’ Eureka method of submerging the body in a bathtub with a volume scale on it. The volume and the weight determine the density of the body, which gives partial information about its fat percentage.

Identifying unmeasurable effort in contests

To distinguish unmeasurable effort from unmeasurable exogenous factors like talent or environmental interference in contests, assumptions are needed, even for partial identification when overall performance can be objectively measured (e.g., chess move quality evaluated by a computer). Combining one of the following assumptions with the additive separability of effort and the exogenous factors provides sign restrictions on coefficient estimates. Additive separability means that talent or the environment changes performance the same way at any effort level.

One such identifying assumption is that effort is greatest when it makes the most difference – against an equal opponent. By contrast, effort is lower against much better and much worse opponents.

A similar identifying assumption is that if there is personal conflict between some contest participants but not others, then effort is likely higher against a hated opponent than a neutral one.

The performance of a given contestant against an equal opponent compared to against an unequal one is a lower bound on how much effort affects performance. Similarly, the performance against a hated rival compared to against a neutral contestant is a lower bound on the effect of effort. The lower bound is not the total influence of effort, because even against an unequal neutral opponent, effort is still positive.

Computer vision training sets of photos are endogenous

In principle, every pixel could be independent of any other, so the set of possible photos is the number of pixels times the number of colours – billions at least. No training data set is large enough to cover these photo possibilities many times over, as required for statistical analysis, of which machine learning is a subfield. The problem is solved by restricting attention to a small subset of possible photos. In this case, there is a reasonable number of possible photos, which can be covered by a reasonably large training data set.

Useful photos on any topic usually contain just one main object, such as a face, with less than 100 secondary objects (furniture, clothes, equipment). There is a long right tail – some useful photos have dozens of the main object, like a group photo full of faces, but I do not know of a photo with a thousand distinguishable faces. Photos of mass events may have ten thousand people, but lack the resolution to make any face in these useful.

Only selected photos are worth analysing. Only photos sufficiently similar to these are worth putting in a computer vision training dataset. The sample selection occurs both on the input and the output side: few of the billions of pixel arrangements actually occur as photos to be classified by machine vision and most of the training photos are similar to those. There are thus fewer outputs to predict than would be generated from a uniform random distribution and more inputs close to those outputs than would occur if input data was uniform random. Both speed learning.

When photo resolution improves, more objects of interest may appear in photos without losing usefulness to blur. Then such photos become available in large numbers and are added to the datasets.

Moon phase and sleep correlation is not quite a sine wave

Casiraghi et al. (2021) in Science Advances (DOI: 10.1126/sciadv.abe0465) show that human sleep duration and onset depends on the phase of the moon. Their interpretation is that light availability during the night caused humans to adapt their sleep over evolutionary time. Casiraghi et al. fit a sine curve to both sleep duration and onset as functions of the day in the monthly lunar cycle, but their Figure 1 A, B for the full sample and the blue and orange curves for the rural groups in Figure 1 C, D show a statistically significant deviation from a sine function. Instead of same-sized symmetric peaks and troughs, sleep duration has two peaks with a small trough between, then a large sharp trough which falls more steeply than rises, then two peaks again. Sleep onset has a vertically reflected version of this pattern. These features are statistically significant, based on the confidence bands Casiraghi and coauthors have drawn in Figure 1.

The significant departure of sleep patterns from a sine wave calls into question the interpretation that light availability over evolutionary time caused these patterns. What fits the interpretation of Casiraghi et al. is that sleep duration is shortest right before full moon, but what does not fit is that the duration is longest right after full and new moons, but shorter during a waning crescent moon between these.

It would better summarise the data to use the first four terms of a Fourier series instead of just the first term. There seems little danger of overfitting, given N=69 and t>60.

A questionable choice of the authors is to plot the sleep duration and onset of only the 35 best-fitting participants in Figure 2. A more honest choice yielding the same number of plots would pick every other participant in the ranking from the best fit to the worst.

In the section Materials and Methods, Casiraghi et al. fitted both a 15-day and a 30-day cycle to test for the effect of the Moon’s gravitational pull on sleep. The 15-day component was weaker in urban communities than rural, but any effect of gravity should be the same in both. By contrast, the effect of moonlight should be weaker in urban communities, but the urban community data (Figure 1 C, D green curve) fits a simple sine curve better than rural. It seems strange that sleep in urban communities would correlate more strongly with the amount of moonlight, like Figure 1 shows.

Clinical trials of other drugs in other species to predict a drug’s effect in humans

Suppose we want to know whether a drug is safe or effective for humans, but do not have data on what it does in humans, only on its effects in mice, rats, rhesus macaques and chimpanzees. In general, we can predict the effect of the drug on humans better with the animal data than without it. Information on “nearby” realisations of a random variable (effect of the drug) helps predict the realisation we are interested in. The method should weight nearby observations more than observations further away when predicting. For example, if the drug has a positive effect in animals, then predicts a positive effect in humans, and the larger the effect in animals, the greater the predicted effect in humans.

A limitation of weighting is that it does not take into account the slope of the effect when moving from further observations to nearer. For example, a very large effect of the drug in mice and rats but a small effect in macaques and chimpanzees predicts the same effect in humans as a small effect in rodents and a large one in monkeys and apes, if the weighted average effect across animals is the same in both cases. However, intuitively, the first case should have a smaller predicted effect in humans than the second, because moving to animals more similar to humans, the effect becomes smaller in the first case but larger in the second. The idea is similar to a proportional integral-derivative (PID) controller in engineering.

The slope of the effect of the drug is extra information that increases the predictive power of the method if the assumption that the similarity of effects decreases in genetic distance holds. Of course, if this assumption fails in the data, then imposing it may result in bias.

Assumptions may be imposed on the method using constrained estimation. One constraint is the monotonicity of the effect in some measure of distance between observations. The method may allow for varying weights by adding interaction terms (e.g., the effect of the drug times genetic similarity). The interaction terms unfortunately require more data to estimate.

Extraneous information about the slope of the effect helps justify the constraints and reduces the need for adding interaction terms, thus decreases the data requirement. An example of such extra information is whether the effects of other drugs that have been tested in these animals as well as humans were monotone in genetic distance. Using information about these other drugs imposes the assumption that the slopes of the effects of different drugs are similar. The similarity of the slopes should intuitively depend on the chemical similarity of the drugs, with more distant drugs having more different profiles of effects across animals.

The similarity of species in terms of the effects drugs have on them need not correspond to genetic similarity or the closeness of any other observable characteristic of these organisms, although often these similarities are similar. The similarity of interest is how similar the effects of the drug are across these species. Estimating this similarity based on the similarity of other drugs across these animals may also be done by a weighted regression, perhaps with constraints or added interaction terms. More power for the estimation may be obtained from simultaneous estimation of the drug-effect-similarity of the species and the effect of the drug in humans. An analogy is demand and supply estimation in industrial organisation where observations about each side of the market give information about the other side. Another analogy is duality in mathematics, in this case between the drug-effect-similarity of the species and the given drug’s similarity of effects across these species.

The similarity of drugs in terms of their effects on each species need not correspond to chemical similarity, although it often does. The similarity of interest for the drugs is how similar their effects are in humans, and also in other species.

The inputs into the joint estimation of drug similarity, species similarity and the effect of the given drug in humans are the genetic similarity of the species, the chemical similarity of the drugs and the effects for all drug-species pairs that have been tested. In the matrix where the rows are the drugs and the columns the species, we are interested in filling in the cell in the row “drug of interest” and the column “human”. The values in all the other cells are informative about this cell. In other words, there is a benefit from filling in these other cells of the matrix.

Given the duality of drugs and species in the drug effect matrix, there is information to be gained from running clinical trials of chemically similar human-use-approved drugs in species in which the drug of interest has been tested but the chemically similar ones have not. The information is directly about the drug-effect-similarity of these species to humans, which indirectly helps predict the effect of the drug of interest in humans from the effects of it in other species. In summary, testing other drugs in other species is informative about what a given drug does in humans. Adapting methods from supply and demand estimation, or otherwise combining all the data in a principled theoretical framework, may increase the information gain from these other clinical trials.

Extending the reasoning, each (species, drug) pair has some unknown similarity to the (human, drug of interest) pair. A weighted method to predict the effect in the (human, drug of interest) pair may gain power from constraints that the similarity of different (species, drug) pairs increases in the genetic closeness of the species and the chemical closeness of the drugs.

Define Y_{sd} as the effect of drug d in species s. Define X_{si} as the observable characteristic (gene) i of species s. Define X_{dj} as the observable characteristic (chemical property) j of drug d. The simplest method is to regress Y_{sd} on all the X_{si} and X_{dj} and use the coefficients to predict the Y_{sd} of the (human, drug of interest) pair. If there are many characteristics i and j and few observations Y_{sd}, then variable selection or regularisation is needed. Constraints may be imposed, like X_{si}=X_i for all s and X_{dj}=X_j for all d.

Fused LASSO (least absolute shrinkage and selection operator), clustered LASSO and prior LASSO seem related to the above method.

Leader turnover due to organisation performance is underestimated

Berry and Fowler (2021) “Leadership or luck? Randomization inference for leader effects in politics, business, and sports” in Science Advances propose a method they call RIFLE for testing the null hypothesis that leaders have no effect on organisation performance. The method is robust to serial correlation in outcomes and leaders, but not to endogenous leader turnover, as Berry and Fowler honestly point out. The endogeneity is that the organisation’s performance influences the probability that the leader is replaced (economic growth causes voters to keep a politician in office, losing games causes a team to replace its coach).

To test whether such endogeneity is a significant problem for their results, Berry and Fowler regress the turnover probability on various measures of organisational performance. They find small effects, but this underestimates the endogeneity problem, because Berry and Fowler use linear regression, forcing the effect of performance on turnover to be monotone and linear.

If leader turnover is increased by both success (get a better job elsewhere if the organisation performs well, so quit voluntarily) and failure (fired for the organisation’s bad performance), then the relationship between turnover and performance is U-shaped. Average leaders keep their jobs, bad and good ones transition elsewhere. This is related to the Peter Principle that an employee is promoted to her or his level of incompetence. A linear regression finds a near-zero effect of performance on turnover in this case even if the true effect is large. How close the regression coefficient is to zero depends on how symmetric the effects of good and bad performance on leader transition are, not how large these effects are.

The problem for the RIFLE method of Berry and Fowler is that the small apparent effect of organisation performance on leader turnover from OLS regression misses the endogeneity in leader transitions. Such endogeneity biases RIFLE, as Berry and Fowler admit in their paper.

The endogeneity may explain why Berry and Fowler find stronger leader effects in sports (coaches in various US sports) than in business (CEOs) and politics (mayors, governors, heads of government). A sports coach may experience more asymmetry in the transition probabilities for good and bad performance than a politician. For example, if the teams fire coaches after bad performance much more frequently than poach coaches from well-performing competing teams, then the effect of performance on turnover is close to monotone: bad performance causes firing. OLS discovers this monotone effect. On the other hand, if politicians move with equal likelihood after exceptionally good and bad performance of the administrative units they lead, then linear regression finds no effect of performance on turnover. This misses the bias in RIFLE, which without the bias might show a large leader effect in politics also.

The unreasonably large effect of governors on crime (the governor effect explains 18-20% of the variation in both property and violent crime) and the difference between the zero effect of mayors on crime and the large effect of governors that Berry and Fowler find makes me suspect something is wrong with that particular analysis in their paper. In a checks-and-balances system, the governor should not have that large of influence on the state’s crime. A mayor works more closely with the local police, so would be expected to have more influence on crime.

Virulence of a disease may cause vaccines to be effective

My uninformed speculation: vaccines may be so effective against Covid-19 (90-95% vs flu vaccine 70%) for the same reason why Covid-19 is so infectious – it binds strongly to biochemicals in the organism. If high affinity to the angiotensin-converting enzyme 2 on the surfaces of lung cells is positively correlated with strong binding to antibodies and immune cells, then the immune system, once triggered, removes the viral particles faster for those respiratory viruses that infect cells more easily. Strong binding and the consequent intense immune triggering may also be the reason for the life-threatening immune overreaction (cytokine storm) to the novel coronavirus.
This hypothesis could be tested on a cross-sectional dataset of viral diseases using some measure of the infectiousness of a disease, the effectiveness of a vaccine against it and the frequency of immune overreaction to it.
Infectiousness may be measured by ID50: what number of microbes makes half the organisms exposed to this number sick. This measure depends on the state of the organisms studied. For example, if people’s immune system is weaker in the winter on average, then ID50 measured in the winter is lower than in the summer.
Vaccine effectiveness is typically measured in percent – what fraction of vaccinated people are protected, in the sense that they do not catch the disease in circumstances in which unvaccinated people catch it. This measure of may depend on what the exposure to the disease is. For example, if a large enough dose of the microbe makes everyone sick, vaccinated or no, then exposure to this dose shows zero effect of the vaccine. Similarly, if a small enough dose fails to infect anyone, then the vaccine effect seems zero, but at least the lack of infections among the unvaccinated shows that no information about vaccine efficacy can be obtained from this exposure test.
Immune overreaction needs to be confidently ascribable to the disease studied for it to be a relevant measure for testing the theory about the connection between virulence and vaccine efficacy.

Tissue sampling by piggybacking on vaccination or testing campaigns

Obtaining tissue samples from a large population of healthy individuals is useful for many research and testing applications. Establishing the distribution of genes, transcriptomes, cell distributions and morpologies in a normal population allows comparing clinical laboratory findings to reference values obtained from this baseline. The genetic composition of the population can be used to estimate historical migration patterns in paleoanthropology and selective pressures in evolutionary biology.

Gathering tissue samples from many people is expensive and time-consuming, unless it happens as a byproduct of existing programs. Collecting used vaccination needles or coronavirus nasal swabs that have a few cells attached allows anonymous tissue sampling of almost the entire population. A few cells per person are enough for many analyses in modern biology. Bulk collection of needles or swabs has built-in untraceability of biological material to an individual, which should alleviate privacy concerns and reduce the bureaucratic burden of ethics approvals.

If top people have families and hobbies, then success is not about productivity

Assume:

1 Productivity is continuous and weakly increasing in talent and effort.

2 The sum of efforts allocated to all activities is bounded, and this bound is similar across people.

3 Families and hobbies take some effort, thus less is left for work. (For this assumption to hold, it may be necessary to focus on families with children in which the partner is working in a different field. Otherwise, a stay-at-home partner may take care of the cooking and cleaning, freeing up time for the working spouse to allocate to work. A partner in the same field of work may provide a collaboration synergy. In both cases, the productivity of the top person in question may increase.)

4 The talent distribution is similar for people with and without families or hobbies. This assumption would be violated if for example talented people are much better at finding a partner and starting a family.

Under these assumptions, reasonably rational people would be more productive without families or hobbies. If success is mostly determined by productivity, then people without families should be more successful on average. In other words, most top people in any endeavour would not have families or hobbies that take time away from work.

In short, if responsibilities and distractions cause lower productivity, and productivity causes success, then success is negatively correlated with such distractions. Therefore, if successful people have families with a similar or greater frequency as the general population, then success is not driven by productivity.

One counterargument is that people first become successful and then start families. In order for this to explain the similar fractions of singles among top and bottom achievers, the rate of family formation after success must be much greater than among the unsuccessful, because catching up from a late start requires a higher rate of increase.

Another explanation is irrationality of a specific form – one which reduces the productivity of high effort significantly below that of medium effort. Then single people with lots of time for work would produce less through their high effort than those with families and hobbies via their medium effort. Productivity per hour naturally falls with increasing hours, but the issue here is total output (the hours times the per-hour productivity). An extra work hour has to contribute negatively to success to explain the lack of family-success correlation. One mechanism for a negative effect of hours on output is burnout of workaholics. For this explanation, people have to be irrational enough to keep working even when their total output falls as a result.

If the above explanations seem unlikely but the assumptions reasonable in a given field of human endeavour, then reaching the top and staying there is mostly not about productivity (talent and effort) in this field. For example, in academic research.

A related empirical test of whether success in a given field is caused by productivity is to check whether people from countries or groups that score highly on corruption indices disproportionately succeed in this field. Either conditional on entering the field or unconditionally. In academia, in fields where convincing others is more important than the objective correctness of one’s results, people from more nepotist cultures should have an advantage. The same applies to journals – the general interest ones care relatively more about a good story, the field journals more about correctness. Do people from more corrupt countries publish relatively more in general interest journals, given their total publications? Of course, conditional on their observable characteristics like the current country of employment.

Another related test for meritocracy in academia or the R&D industry is whether coauthored publications and patents are divided by the number of coauthors in their influence on salaries and promotions. If there is an established ranking of institutions or job titles, then do those at higher ranks have more quality-weighted coauthor-divided articles and patents? The quality-weighting is the difficult part, because usually there is no independent measure of quality (unaffected by the dependent variable, be it promotions, salary, publication venue).

Learning and evolution switch the sign of autocorrelations

Animals are more successful if they learn or evolve to predict locations of food, mates and predators. Prediction of anything relies on correlations over time in the environment. These correlations may be positive or negative. Learning is more difficult if the sign of the correlation switches over time, which occurs in nature due to resource depletion, learning and evolution.

If a herbivore eats a tasty patch of plants or a predator a nest full of eggs, then the next day that food is not there (negative correlation), but the next year at the same time it is probably there again (positive correlation) because the plants regrow from roots or seeds, and if the prey found the nesting spot attractive one year, then other members of the prey species will likely prefer it the next year as well. However, over many generations, if the plants in that location get eaten before dispersing seeds or the young in that nest before breeding, then the prey will either learn or evolve to avoid that location, or go extinct. This makes the autocorrelation negative again on sufficiently long timescales.

Positive correlation is the easiest to learn – just keep doing the same thing and achieve the same successful outcome. Negative correlation is harder, because the absence of success at one time predicts success from the same action at another time, and vice versa. Learning a changing correlation requires a multi-parameter mental model of the superimposed different-frequency oscillations of resource abundance.

There is a tradeoff between exploiting known short-period correlations and experimenting to learn longer-period correlations. There may always be a longer pattern to discover, but finite lifetimes make learning very low-frequency events not worthwhile.