Wednesday, September 12, 2012

The Embryology Of Spin

Yavchitz et al. looked at which factors correlated with the presence of "spin" in the reporting of medical randomized control trials. Spin is emphasizing the benefits of a treatment more than is appropriate on the basis of the data. They cooked up a multivariate regression with the explanatory variables of journal type, funding source, sample size, type of treatment (drug or other), results of the primary outcomes (all nonstatistically significant versus other), author of the press release, and the presence of “spin” in the abstract conclusion.

In their sample (N = 41), the only factor that correlated significantly with spin in the press release and news article was spin. Spin in the abstract conclusions of a study leads to a 5.6 (95% CI 2.8–11.1) times higher relative risk of there being spin in the press release and news reports. So, to the extent that we care about curbing vicious information cascades, it's essential for authors and editors to be conscientiousness about word choice and framing in the abstract. 

Tuesday, September 4, 2012

The Trade-Offs Of Publicizing Your Goals

In Ben Casnocha's reflections on writing his book The Start-Up Of You, he mentions this tidbit:
When you embark on a project that’s going to take awhile, you have to decide how much to publicize the fact – on your blog, to your friends — that you’ve started. ... When you publicly announce that you’re starting toward a goal, you can benefit from the self-fulfilling prophecy effect, you can collect feedback from your network, and be held accountable to lots of external people tracking your progress. On the flip side, when you announce a goal, you risk tricking your mind into believing you’ve already partially accomplished your it when in fact you’ve done nothing. Derek Sivers says: “Keep your goals to yourself.”) Plus, external accountability of the wrong kind can add unhealthy pressure.
This is a complicated and thus interesting trade-off. It involves an interaction between managing your own psychology and providing others the context they need to offer you help. The best-case scenario (not necessarily possible) would be for others to know what you are attempting to do without you knowing that they know. On the other hand, the worst-case scenario (much more plausible) is that you think others know when they don't.

In science, there are often norms against sharing too much of your project with outsiders, to prevent it from being "scooped". It strikes me now that these norms serve the dual purpose of preventing you from taking mental credit for something that you haven't yet done the grunt work to accomplish.

Anyway, I certainly don't have any general solutions to this trade-off, and it is something I worry about too.

I am probably slightly biased about the book because Ben is a friend, but I recommend it highly.

Thursday, August 30, 2012

In Praise Of The Obvious, Pt 2

Scott Aaronson explains the usefulness of the Church-Turing thesis in a way that makes intuitive sense to me, a newbie to TCS. Awesome! That kind of post is why I love subscribing to his blog. The commenter Keith apparently disagrees, saying,
It occurs to me that if you’re taking positions in arguments that I, a layman, could easily take, then you’re either wasting your time or indulging a hobby.
His attitude exemplifies why it's so important to relentlessly praise those who understand the minutia in a field yet take the time and status hit to point out the obvious. If the pressure to complicate is manifest in an academic's blog posts, just imagine what one would feel while writing an illustrious journal article. 

Tuesday, July 24, 2012

Book Review: Great Flicks By Dean Simonton

Attention conservation notice: Review and notes from a book discussing an academic topic that will likely only interest you insofar as it generalizes to other topics, unless you are both a huge stats and film nerd.

I'm fascinated by movie ratings and what they tell us about: 1) the best ways to use rigorous methods to study the quality of a subjective output, 2) how variable people's assessment of quality are, and 3) how people conceptualize their own opinion in the context of everyone else's. Dean Simonton is a giant in the psychology of creativity, and I loved his book Creativity in Science. So, as soon as I saw this one, I clicked "buy it now" on its Amazon page

My typical gripe against academic investigations of movie ratings is that they discount, a huge resource with millions of data points, segregated by age, gender, geographical location, on an incredibly rich array of movies. So, soon after buying the book, I searched in the Kindle app for "imdb" and found very few results. This predisposed me to disliking it. 

A few of my other gripes: 

1) It takes awhile to get used to Simonton's academic writing style. 

2) The book takes few risks stylistically. Each chapter feels like it could be its own separate article. Thus, he does not take full advantage of the long-form medium. 

3) When he discussed a few of the measures (such as the correlation between different award shows), I felt that there was some issues with his account of the causality. Surely there is some, non-negligible probability that people take the ratings of others' into account when they make their own judgments. He mentions this sometimes, but not enough for me, and ideally he'd come up with some creative way to try to get around it.

4) Finally, there are a few typos. I actually like seeing typos, because it makes me think that I am learning from a more niche source that others are less likely to appreciate, but YMMV.

By midway through the book, Simonton had won me back to a large extent. His analyses of his data were very well-done and he supplies tables so you can look at the regression coefficients yourself. And there are many good nuggets, such as: 

- the best predictors of higher ratings are awards for better stories (e.g., best screenplay and best director), as opposed to visual or musical awards
- having individuals on the production team who play multiple roles (such as writer, cinematographer, and editor all at once) makes the film more successful, presumably due to creative freedom 
- some amount of repeated collaboration over multiple films with the same individuals, but not too much, is optimal for winning awards (i.e., there is a trade-off between stimulation and stagnation) 
- higher box office returns are inversely correlated with success at awards shows
- the typical film is unprofitable; "about 80% of Hollywood's entire profit can be credited to just a little over 6% of the movies"  
- the curse of the superstar: "if a star is paid the expected increase in revenue associated with his or her performance in a movie then the movie will almost always lose money" (this is because revenue is so positively skewed) 
- divides movies into two types: those that are extremely successful commercially, and those that are extremely successful artistically (people often use the former to subsidize the latter) 
- negative critic reviews have a more detrimental impact than positive reviews have a boosting effect on box office returns
- on ratings, critics and consumers have similar tastes, although consumers' tastes are more difficult to predict, presumably because their proclivities are more diverse
- for a consumer, the most important factor for whether they will watch a movie is its genre (#2 is word of mouth) 
- dramas do worse in the box office, better at the awards shows; comedies are the reverse
- PG-13 movies make the most money; some romance, but no actual nudity, is best (and lots of action but no gore) 
- on average, sequels do far worse in ratings and awards than the original movies
- the greater the involvement of the author in an adapted movie, the less money it will make (they interfere more and might care more about "artistic integrity" than making money) 
- directors tend to peak in their late 30s; they have more success in their late 20s than their late 50s, on average
- divides directors into two types: conceptual (innovative and imaginative; think Welles) and experimental (technical and exacting; think Hitchcock)
- conceptual directors express ideas through visual imagery and emotions, often leave behind one defining film, and decline quickly
- experimental directors emphasize more realistic themes, slowly improve their methods, and their best films often occur towards (but almost never *at*) the end of their careers
- female actors make less money than their male counterpoints, and the best picture award correlates much better with best male actor than best female actor
- awards for scores are much better predictors of a film's quality than awards for songs

All in all, this book is far from perfect, but it is likely the best full-length treatment of quantitative movie ratings available. If you are interested in the topic, and occasionally find yourself doing things like browsing the rating histograms on imdb, then this is essential reading. 

Friday, July 20, 2012

Statistics Is Like Medicine, Not Software

Stats questions--even when they're pure cut-and-dried homework--require dialog. Medicine might be a better analogy than software: what competent doctor will prescribe a remedy immediately after hearing the patient's complaint? One of our problems is that the [Stack Exchange] mechanism is not ideally suited to the preliminary dialog that needs to go on.
That's from the ever erudite William Huber, in this chat about why the statistics Q&A site has problems that the software Q&A site does not. Some users argue that a high proportion of questions on the stats site should not be answered unless they are disambiguated further.

You might assume that "more answers are better," but answering an ill-posed question adds more noise to the internet. When searching to clarify an ambiguous term, somebody might find that question, read the answer, and end up even more confused. Recall that this is a field already stricken by diametric ideology and short-term incentives.

Here is my previous post on the wisdom of Huber

Sunday, July 8, 2012

The Psychosocial Costs Of Ambition

If I had accepted that leadership role, there would have been a lot of pressure on me to do something really exciting. I can sometimes do exciting things, but I can't do them on demand. My energy level waxes and wanes. My creativity is irregular. When I do have an idea, sometimes it catches on and other times people just stare at me and think "What's wrong with him?" 
To be ambitious is a commitment. It's saying "Take a chance on me, and I will continue being creative and exciting and dependable for the foreseeable future." It's promising people that you're never going to let them down. If you act ambitious, and then when push comes to shove you say "Nah, I don't need the aggravation", then you don't look ambitious and high-status, you look like a flake.
Scott's lucid explanation of the costs to ambition is a great example of hot and cold decision-making. We tend to overestimate the stability of our beliefs, so when we feel ambitious and full of energy (like, at the start of a project) we assume that this feeling will continue indefinitely.

Of course, this is unlikely. Most of us have daily circadian rhythms, some less-well understood medium-term fluctuations, and gradual decays in interest.

So, as Scott learned early in life, it is prudent to anticipate and explicitly correct for your likely decline in motivation towards a topic when you present yourself to the world. The insidious part of this is that if you want to obtain resources you need to actually complete a task (e.g., a job, a grant, collaborators), you will have to sell yourself. This is why trade-offs aren't fun; they're just real.

Friday, July 6, 2012

Is *Any* Human Activity Long-Run Sustainable?

Intensive rice agriculture began in the Yangtze basin about 8,000 years BP, a sustainable model for agriculture by any reasonable standard. The extensive water infrastructure network around Chengdu, China, has diverted part of the Min River through the Dujiangyan for both flood control and irrigation without restricting fish connectivity since 256 BC, while some forests in India have been actively managed by surrounding communities for even longer periods.
That's from a guardedly optimistic article by Matthews and Boltz. It's academic but contains most of the good aspects of scholarly writing (copious references, measured tone), without most of the others (argument to authority, unwillingness to point out the obvious). There are 2650 words so you should expect to read it in about 12 minutes. Assuming you are an average blog reader (well, above average if you're reading this one), I recommend it, unless you haven't stared at the Vostok ice core data recently, in which case you should do that for 15 seconds first. 

Wednesday, July 4, 2012

The Meaning Of The Mean

Bob Carpenter has a few enlightening thoughts on the distinctions between 1) the sample mean, 2) the expected value of a random variable, and 3) the mean of a distribution. I've long been confused by the difference between the mean and expected value, and his trichotomy helps alleviate my confusion. With that in mind, I changed the intro of the article mean, which had remained static since the dawn of time (2001, when the page was created).

Of the major subjects on Wikipedia, statistics seems to be the most convoluted. My two explanations for this are that 1) there are so many schools that disagree on fundamental interpretations (likelihood, non-parametric, empirical Bayesian, objective Bayesian, etc), and 2) many practitioners are so busy with applications that they don't have time to reconcile their disagreements.

Wednesday, June 20, 2012

When You Should Be Most Skeptical

One of the hardest things we can do as readers is disagree with the methods of authors we agree with ideologically. It makes us feel good to find authors who agree with us, but this is when we should be at our most skeptical. Searching the world for self-justification is not a worthwhile goal, it simply turns you into another short-sighted, argumentative know-it-all.
That's from Keely's scathing, analytical review of The Giver. I like the idea that we should be especially skeptical of the arguments of those we agree with, to counteract out natural tendency to the contrary.

Wednesday, June 13, 2012

When More Data Trumps Logic

A difficulty with the “more data is better” point of view is that it’s not clear how to determine what the tradeoffs are in practice: is the slope of the curve very shallow (more data helps more than better algorithms), or very steep (better algorithms help more than more data). To put it another way, it’s not obvious whether to focus on acquiring more data, or on improving your algorithms. Perhaps the correct moral to draw is that this is a key tradeoff to think about when deciding how to allocate effort. At least in the case of the AskMSR system, taking the more data idea seriously enabled the team to very quickly build a system that was competitive with other systems which had taken much longer to develop.
That's Michael Nielsen in an interesting post describing how machine learning question-and-answer systems work. I completely agree that identifying trade-offs is one of the most useful ways to decide how to proceed on a problem. That's why I think the general study of trade-offs, across fields, is underrated. 

Monday, May 28, 2012


In many American states it is legal to screen and select on the basis of sex, for non-medical reasons. In fact, a 2006 study (see below) found that 9% of [preimplanation genetic diagnosis] procedures carried out in [in-vitro fertilization] clinics in the U.S. were performed for this reason. Other reasons include screening for an embryo with the same immune type (“HLA type”) as a current child who is ill and requires a transplant of some sort. Screening for these “savior siblings” was done in 1% of PGD procedures. And 3% used it for a reason I personally find jarring – to specifically select embryos with a mutation causing a genetic condition. This is usually in cases where both parents have either deafness or dwarfism and they want their child to be similarly affected. This gets into the political movement objecting to society labelling conditions as “disabilities”. I can sympathise with that to some degree – more for some conditions than others – but I think, if it were my child, I would still rather he or she could hear.
That's Kevin Mitchell, discussing GATTACA, an entertaining sci-fi movie with a respectable 7.8 imdb rating. Spoiler alert, the premise of the movie is that at some point in the future there will be strong stratification of people into two classes, the "valids" and the "invalids", based on whether they had healthy traits selected for via preimplanation genetic diagnosis.

It seems to me highly unlikely (<0.01%) that a nightmare scenario of this sort would actually occur. One of the main reasons is because of the large plurality of values among parents, as seen above. A prevailing reason people have kids is to propagate a form of themselves into the future, and in many ways it defeats the purpose when you select against certain traits or even perform some sort of genetic engineering.

The other reason is something we know now better than we did 15 years ago, when GATTACA was released. And that is that DNA doesn't actually explain all that much of physiology and behavior--there are also strong epigenetic effects as well as stochastic effects of gene expression

Sunday, May 27, 2012

No Darkness But Ignorance

Here's Nancy Kanwisher's suggestion on how to improve the field of neuroimaging:
NIH sets up a web lottery, for real money, in which neuroscientists place bets on the replicability of any published neuroimaging paper. NIH further assembles a consortium of respected neuroimagers to attempt to replicate either a random subset of published studies, or perhaps any studies that a lot of people are betting on. Importantly, the purchased bets are made public immediately (the amount and number of bets, not the name of the bettors), so you get to see the whole neuroimaging community’s collective bet on which results are replicable and which are not. Now of course most studies will never be subjected to the NIH replication test. But because they MIGHT be, the votes of the community are real.... 
First and foremost, it would serve as a deterrent against publishing nonreplicable crap: If your colleagues may vote publicly against the replicability of your results, you might think twice before you publish them. Second, because the bets are public, you can get an immediate read of the opinion of the field on whether a given paper will replicate or not.
This is very similar to Robin Hanson's suggestion, and since I assume she came up with the idea independently, it bodes well for its success. Both Hanson and Kanwisher are motivated to promote an honest consensus on scientific questions.

When John Ioannidis came to give a talk at the NIH (which was interesting), I asked him (skip to 101:30) for his thoughts on this idea. He laughed and said that he has proposed something similar.

Could this actually happen? Over the next ten years, I'd guess almost certainly not in this precise form; first, gambling is illegal in the US, and second, the markets seem unlikely to scale all that well.

However, the randomized replication portion of the idea seems doable in the near term. This is actually now being done for psychology, which is a laudable effort. It seems to me that randomized replications are likely precursors to any prediction markets, so this is what interested parties should be pushing now.

One objection is that these systems might encourage scientists to undertake more iterative research, as opposed to game-changing research. I have two responses. First, given the current incentives in science (i.e., the primacy of sexy publications), this might actually be a useful countervailing force.

Second, it seems possible (and useful) to set up long-standing prediction markets for a field, such as, "will the FDA approve an anti-amyloid antibody drug to treat Alzheimer's disease in the next ten years?". This would allow scientists to point to the impact that their work had on major questions, quantified by (log) changes in the time series of that market after a publication. 

Saturday, May 26, 2012

Evaluating The Regret Heuristic, Part II

In a comment to my post on how our regrets change over time, Eric Schwitzgebel asks, 
But why adopt regret minimization as a goal at all? Regret seems distorted by hindsight bias, status quo bias, and sunk cost bias, at least.
I've written before that projecting your future views about your present actions can be a good way to make decisions. So, Eric's prompting is a good occasion to re-evaluate that.

Given perfect information, the theoretically best way to make decisions is to 1) calculate the costs and benefits of each possible outcome, 2) estimate how your choice affects the relative probability of those outcomes, 3) use the costs and benefits as inputs to some sort of valuation function, and 4) make the decision with the highest probabilistic value. 

Cost-benefit analysis is a common way to implement this, with, say, QALYs as the value measure. If you have perfect information, this is just math. 

But as Ben Casnocha says, if you don't have enough information, that framework can break down. In particular, even when #2 is pretty straightforward, #1 can still be very tricky. For example, although studying for the LSAT makes it much more likely that I will earn a JD, it's still hard to quantify the precise costs and benefits of entering that earning that degree. 

Here is where the regret heuristic can be useful. Instead of explicitly tallying each cost and benefit, it asks: in total, which would you regret more: studying or not studying? 

This is in fact a simplifying measure, but there remains oodles of freedom in how you perform the regret estimation. For example, you can:
Ultimately, I still think that the regret heuristic can be a useful one. But tread carefully, as there are many crucial micro-decisions to make; it's not magic. 

Friday, May 25, 2012

Age's Stealing Steps

Michael Wolff has written a gripping but narrative-heavy article about the troubles he has experienced in addressing his mother's worsening dementia. It is hard not to feel for him and his family. Still, I think there are two perspectives which his piece underemphasized:

1) Many debilitated but cognitively intact individuals do have a good quality of life. For example, in a recent survey of 62 seniors with an average of 2.4 daily living dependencies and fairly good cognitive well-being (≥ 17/30 on the MMSE), 87% reported that they had a quality of life somewhere in the fair to very good range. I consider this to be a testimony to the resiliency of the human psyche. Also, it makes me worry that people will read the article and think that LTC insurance is only useful for those with dementia, which Wolff implies, when that is far from the case.

2) Why is it that many of the doctors depicted his story seem so unhelpful? There's little doubt that fear of litigation plays a role. For example, in a Mar '12 study, over half of the 600+ palliative care physicians surveyed reported being accused of euthanasia or murder within the past five years. In many respects this is a legislative issue, and I wish his article had discussed that angle more.

Many pointers in this post go to the excellent blog GeriPal

Thursday, May 24, 2012

Should Revenge Have Bounds?

I recently finished Steven Pinker's book attempting to explain the decline of human-on-human violence over the last twenty thousand years. All in all, I recommend it. It has noteworthy psychology nuggets on nearly every page, explained with good data and lucid metaphors. I especially enjoyed how he built up many cute explanations of various phenomena--like the Freakonomics-popularized abortion theory of the crime rate decrease in the 1990s--only to soundly and evenly debunk them. My two major points of disagreement:

1) As Tyler Cowen argues, it is possible that although the mean number of causalities from interstate conflicts has been falling, the variance has been increasing. Aside from WWII, we can't easily observe this variance, though we can see signs of it in events like the Cuban Missile Crisis. Pinker employs per-capita log-scales for many of his charts and on these WWII does not seem quite as bad, but still it sticks out indelibly.

Wisely, Pinker does not project the decrease in violence indefinitely into the future, rather seeking to explain what we have observed so far, so his thesis is technically immune to this critique. Still, I imagine that there have been some not-easily observed historical aberrations which, if they had gone differently, would have meant that this book would never had been written. The winner's curse comes to mind.

2) As one reads about the incredible violence that occurs in US prisons, it is difficult not to wonder whether the benefits to decreasing violence always outweigh the costs. I have previously written about the protection vs freedom trade-off. The laudable decrease in person-to-person violence comes at the cost of constraining the actions of individuals by probabilistically putting them in prison. This is an imperfect process and has negative externalities in that it further exacerbates the burden of those locked up for non-violent crimes.

So, I would have liked to see more discussion about the violence in modern-day prisons and whether it is more apt to say that violence has been displaced rather than decreased. In a provocative article, Christopher Glazek argues that the US should be more like the UK and have slightly looser violent crime convictions which would make the conditions in prison slightly less awful. In most cases I would probably come down in favor of protecting innocent bystanders, but it is a conversation that needs to happen and that I wish Pinker had addressed. 

Sunday, April 29, 2012

A Brief History Of Bioinformatics, 1996-2011

That's from an interesting article by Christos Ouzounis. Here he discusses the "adolescence" period:
One factor in policymakers' high expectations might have been a certain lack of milestones: due to the field's dual nature, that of science and engineering, computational biology rarely has the “eureka” moment of a scientist's discovery and is grounded in the laborious yet inspired process of an engineer's invention. 
And there's this bit, too:
The notion of computing in biology, virtually a religious argument just 10 years ago, is now enthroned as the pillar of new biology.
So why has "bioinformatics" become less discussed? In part, because it has been so successful. 

Friday, April 13, 2012

Schelling Points And Bioinformatics

A lot of what think about when I do bioinformatics is how to set parameters non-arbitrarily. Basically I am looking for Schelling points: round, clear numbers that are easy to justify. The classic case is setting a p-value threshold to 0.05, which has been around for over eighty years and is still going strong, despite the haters. Other examples are setting e-value thresholds to 0.01 and setting Bayes factor thresholds of 10 as the first to indicate "strong" evidence. Like any threshold, these are arbitrary, but following the paradigm of statistics as rhetoric, their staying power make sense insofar as scientists need to be able to resort to standard procedures to settle debates. Anyway, I have no profound point here, I just think it's cool that a seemingly esoteric topic affects what I actually do on a day-to-day basis.

Is It Possible, In Principle, To Do Methodologically Sound Research?

In a paper published 31 years ago, Joseph McGrath argues (html, pdf) that the answer is no. Specifically, he claims that any research design faces two trade-offs: 1) being obtrusive vs unobstrusive (which maps to my terminology as acquiring info vs altering subject), and 2) being generalizable vs context-cognizant (which maps to my terminology as precision vs simplicity).

In his terminology, these trade-offs allow for the optimization of three distinct values (generalizability of samples to populations; precision in measuring variables; and context realism for the participants). Initially, I disagreed with this. To me, intuition suggests that there should be four points which maximize certain qualities when you are considering the intersection of two-trade offs: one in each corner of the 2-d space.

One way to get around this is if you claim that, in the context of this decision (study design), the trade-offs are not independent. For example, it might be very difficult for a design to be both highly generalizable and highly obstrusive.

Below I've drawn an example. Think of the dots as realizations of actually feasible study designs sampled from someone's mental generation process; i.e., they are probably not at the absolute extremes of the theoretical distribution, but with enough realizations, would come close.

I'm not sure that I agree with this exact distribution, and it would need some justification, but it seems like the only way to justify his three-pronged rather than four-pronged set-up.

Saturday, March 31, 2012

The Valiant Never Taste Death But Once

After reading this interesting excerpted article from Dick Teresi's book The Undead, which discusses the difficulties in defining death by a single, consistent set of criteria and the social qualms that stirs, I decided to check out the Amazon reviews. The associated ratings were (and still are) quite shockingly bad! They follow the classic "so bad it's good" distribution, with 5 5-star ratings, 1 3-star rating, and 33 1-star ratings. So, given that I am always up for a good controversy, I decided to read and review it myself. Ultimately I mostly side with the critics, giving it two stars. If you are interested in the subject matter, I'd suggest instead Kenneth Iserson's Death to Dust, which is a bit older but much more level-headed and thorough treatment of similar issues. 

Friday, March 30, 2012

What Makes Phrases Memorable

For 1000 movies, this study compared lines included on imdb's memorable quotes page to those that were not. People who hadn't seen the movies were able to pick the correct one 78% of the time, although, caveat lector, that's with only n = 68.

What features allow this above chance classification? The authors suggest 1) distinctiveness (i.e., a lower likelihood of coming from samples of standard English text), 2) generality (fewer personal pronouns, more present tense), and 3) complexity (words with more syllables and fewer coordinating conjunctions like "for" and "and").

Interestingly, their best support vector machine only correctly classified examples 64% of the time, so either the human data is somehow biased, or there are plenty more subtleties for machines to learn before they can best us humans in recognizing literary wit. 

Thursday, March 29, 2012

Indexing Wikipedia Article Submissions On Pubmed

I have complained before about few academics writing Wikipedia pages and instead writing reviews that few people will read. So, I feel compelled to admit that this is really cool:
We suggest a principal reason for this limited breadth and depth of coverage of topics in computational biology is one that affects a number of disciplines: reward. Authors in the biomedical sciences get academic reward for publishing papers in reputable journals that are indexed in PubMed and have associated digital object identifiers (DOIs).... 
Topic Pages are the version of record of a page to be posted to (the English version of) Wikipedia. In other words, PLoS Computational Biology publishes a version that is static, includes author attributions, and is indexed in PubMed. In addition, we intend to make the reviews and reviewer identities of Topic Pages available to our readership. Our hope is that the Wikipedia pages subsequently become living documents that will be updated and enhanced by the Wikipedia community...
I continue to be impressed by the innovation from the PLoS suite. 

Monday, March 26, 2012

Why Does Speed Variability Create Congestion?

Above are the results from one trial of an experiment designed to answer this question. Participants were randomly assigned to one of two groups, each with its own walking direction and color.

The authors defined "clusters" as groups of people walking in basically the same path, with some leeway. They then did simulations to determine the average lifetime of a cluster as a function of the group's variability in walking speed. As you can see, the greater the variability, the shorter the lifetime of the clusters.

N = the number of pedestrians in the simulation
This trend fits with their experimental results. Here's how the authors explain it:
[T]hose moving faster catch up with those walking slower, leaving an empty zone in front of the slow walkers ... [P]edestrians who are willing to walk faster than others make use of density gaps to overtake the slow walkers in front of them. By doing so, faster pedestrians move away from their lane, and meet the opposite flow head-on a few seconds later. This initial perturbation often triggers a complex sequence of avoidance maneuvers that results in the observed global instabilities. 
So here's a situation where more diversity, defined as inter-individual variability, leads to worse outcomes. Of course, as the authors mention, there are many other situations, such as collective decision making, where inter-individual variability is actually quite helpful.

Perhaps more diversity generally serves the function of pushing a group out of local optima. So you can think of diversity as shifting a group more towards the "explore" side of the exploration-exploitation trade-off. This would hurt in situations with a clearly defined goal, such as pedestrians walking in a circle as quickly as possible. But it might help in more complex situations.

Sunday, March 25, 2012

Comp Exams For Each Course

The solution I propose is comprehensive exams at the end of each course, much like Advanced Placement exams, that thoroughly and objectively distinguish students on merit alone. The emphasis in each classroom would then shift from fighting the teacher for high grades to cooperating with the teacher to learn the material necessary to perform on the exam.
That's from Andrew Knight, in an essay discussing problems that will not be new to anyone who is or has recently been in school; more here. This is exactly what I wanted during most of my science and math courses. The alternative is to place a greater emphasis on big standardized tests like the SAT, but there can be so much variability in results from just one day.

One question is whether such exams could be a part of classes that are less fact-based, such as history and english. There is actually a machine learning competition for automated essay grading going on right now. I don't pretend to know the answer to this question, but even if it is currently infeasible, that shouldn't stop the tests from being used in math, science, and foreign language classes. 

Saturday, February 25, 2012

Snub City At The Oscars

Of the Best Picture nominees, The Artist is currently the highest rated on imdb, at 8.4, though it will drop. A good comparison is Avatar, because both movies are technically adventurous, and they both have terrifyingly trite plots.

The main difference between Avatar and The Artist is that the latter is about the past, triggering nostalgia, whereas the former is about one possible version of the future, and is thus discomforting. This is why The Artist will win Best Picture and Avatar didn't come close. (No movie set in at any point in the future has ever won the award.)

But of course, the best movie of the past year is A Separation. The fact that it wasn't even nominated just showcases the Academy's striking anti-foreign film bias.


It is obviously very fun to hate on the Academy, and there are many good reasons to do so, but as imdb user Fish_Beauty reminds us, this year is highly unlikely to go down as the biggest black mark of all time. Here are the lowest rated Best Picture winners:

Around the World in Eighty Days (1956) 6.8/10 9,106 (which won over the amazing The Killing)
The Greatest Show on Earth (1952) 6.7/10 5,177 (which won over High Noon)
The Broadway Melody (1929) 6.4/10 2,459
Cavalcade (1933) 6.3/10 1,421
Cimarron (1931) 6.1/10 1,739 (which won over the best silent film ever, City Lights)

These are truly embarrassingly bad films.

Tuesday, February 21, 2012

Tuesday Statisticz: Pick Your Poison At Starbucks

Every healthy drink is the same, every unhealthy drink is unhealthy in its own way. That's my conclusion upon analyzing this data set containing nutrition info of Starbucks drinks from the data set aggregator Factual

It turns out that there's an inverse, non-linear relationship between the sodium and sugar content of a drink. Drinks with very little sodium tend to have lots of sugar. These are mainly things like lemonade and iced tea. (Of course, it's controversial whether salt is bad for you, but the prevailing evidence points to yes.) 

normalized to the number of calories, filtered for >50 calories only; code

Surely this is not a universal trade-off, but it seems to indicate that in order to survive as a popular drink, you have to offer consumers something that they'll enjoy. 

Monday, February 6, 2012

Inspiration To Be Better

There's always someone whose monster won't go to sleep, no matter what Molotov cocktail of drugs and poison the medical miracle-makers can concoct to throw at it. Good people, better than I, are doomed to such a fate. The thought of it just seems to drain all of the air out of the room. But it makes me want to be better. I know those people won't stop fighting until that final breath, and that's a lifetime's worth of inspiration for me. I will forever hesitate to take a simple moment in this life for granted, though it will probably take some getting used to, because I've never lived that way before. But, having thought about it, there's really no other way to live. It's all just too fleeting and too ephemeral to fail to take the time we do have here to try and be better. I'm going to be better to myself, more forgiving of my mistakes, better to those around me and to those close to me, because they deserve it. We all deserve it...
My friend Jon passed away a couple of days ago. Much of his writing, including the above, can be found here. I have many memories of our time together, and I cherish them. He will be missed. 

Friday, January 27, 2012

Trade-Offs In Evolvability

"[T]he main and broadly applicable effect of fluctuating selection on the evolution of gene regulatory networks that allow for a feedback loop is selection for specific system dynamics that confer an increased evolvability. Increased evolvability mainly results from evolution of system parameters controlling the feedback loop, into a nonlinear regime, where both phenotypic diversity and the amount of phenotypic shift caused by individual mutations are increased."
More here. To the extent that you expect your environment to change a lot (i.e., undergo "fluctuating selection"), you should prefer meta-level approaches which allow you to change your object-level strategy more quickly and less costly. To the extent that you expect your environment to remain constant, this ability and propensity to change will be a hindrance.

Saturday, January 21, 2012

A Separation

Finally it has come out in Bethesda! Spoiler alert, you can view it as a delectable set of plausible moral quandaries wrapped up in a family drama. You can also view it as a demonstration of how external stressors are what really kill relationships. My favorite line was, naturally, "what is wrong is wrong, no matter who said it or where it's written."


Completely unrelated, this is the funniest thing I've read so far this calendar year. Anything for science. 

Sunday, January 1, 2012

Seven Ideas From 2011

One Idea For Trepidation

1) U.S. Life Expectancies Stagnate: In more than 20% of counties, life expectancies for women declined between 1997 and 2007, driven largely by increased rates of smoking and high blood pressure. In some senses this is not unexpected, as the century-long gains in lifespan in developed nations have been more a story of asymptotically approaching the maximum human lifespan rather than pushing it back. And healthiness during one's lifespan is to some people the most important measure. Still, this is a major worry, and all of the other ideas on this list must be tainted by this one. (see here and here for more)

county-wide change in life expectancies over recent decades, left is males and right is females, green is positive and red is negative; doi:10.1371/journal.pmed.0050066 

Four Ideas For Optimism

2) Chip-Based Neuronal Nets: Memristors are circuit elements that can "remember" their resistance state even in the absence of curent. They open up a wealth of potential applications, including directly mimicking synaptic learning rules. The first implementation of the memristor is now slated for commercial release in less than two years. (see here, here, and here for more)

certain memristor architectures can store the topology of a maze in the state of its switches and thus allow all of the memristors to participate in the path calculation at once;

3) Altering DNA More Precisely. Zinc finger nucleases are proteins that can be engineered to target and cut a particular DNA sequence, thus allowing for manipulation of (human) genomes. This year a set of breakthroughs were announced which allow for researchers to query the specificity of ZFN's across the genome. This is crucial, because you really want to minimize any chance for error when you might accidentally mutate a tumor suppressor gene. The only clinical trial I know of with these is for HIV, which seems to have had some promising albeit highly preliminary results. (see herehere, and here for more)

a model of a zinc finger nuclease; doi:10.1186/1471-2164-12-83

4) Downloadable Sneakers. What will be the "killer app" of 3D printing that makes everybody want one as badly as they first wanted a personal computer? It's unclear, but the initial spread of the tech is already upon us, and the events of this year have me more convinced that it will prove similarly disruptive. (see here and here for more)

photo by photon

5) The End Of Drunk Driving. What if your smartphone could double as your chauffeur? Amazingly, we already have the basic autonomous driving capabilities. The most important reasons to care about this are a) the number of lives it could save and b) the amount of time it could free up. Yes, there are plenty of downsides, but they must be weighed at every step against these upsides. (see here, here, and here for more)

photo by jurvetson

Two Ideas To Think About

6) The Dimensions Of The DSM-5. To what extent will the dimensional approach to mental disorders make it into the next draft of the bible of psychiatry? This is not purely academic. Rating patients by the significance of their disorder would help eliminate arbitrary thresholds between the healthy and pathological. But if the switch is made too soon, before the levels can be validated, then it could turn into a bonanza of overmedication. (see here and here for more)

photo by ecstaticist

7) The Apogee Of The Corporation. As self-employment rises and technology advances, a smaller and smaller chunk of economic activity is being dictated by firms. Our very notions of the corporation and the employee seem to be on their way out, and perhaps they will be replaced by something that makes more sense for the society of tomorrow. (see here and here for more)

a network representation of strongly connected transnational corporations;  doi:10.1371/journal.pone.0025995; how long can or will they last?