Data Scientist
Jan Christian Refsgaard
Karma: 595
if I had to guess, then I would guess that 2⁄3 of the effects are none causal, and the other 1⁄3 are more or less fully causal, but that all of the effects sizes between 0.5-1 are exaggerated by a factor of 20-50% and the effects estimated below +0.5 IQ are exaggerated by much more.
But I think all of humanity is very confused about what IQ even is, especially outside the ranges of 70-130, so It’s hard to say if it is the outcome variable (IQ) or the additive assumption breaks down first, I imagine we could get super human IQ, and that after 1 generation of editing, we could close a lot of the causal gap. I also imagine there are big large edits with large effects, such as making brain cells smaller, like in birds, but that would require a lot of edits to get to work.
Statistical Challenges with Making Super IQ babies
This might help you https://github.com/MaksimIM/JaynesProbabilityTheory
But to be honest I did very few of the exercises, from chapter 4 and onward most of the stuff Jayne says are “over complicated” in the sense that he derives some fancy function, but that is actually just the poison likelihood or whatever, so as long as you can follow the math sufficiently to get a feel for what the text says, then you can enjoy that all of statistics is derivable from his axioms, but you don’t have to be able to derive it yourself, and if you ever want to do actual Bayesian statistics, then HMC is how you get a ‘real’ posterior, and all the math you need is simply an intuition for the geometry of the MCMC sampler so you can prevent it from diverging, and that has nothing to do with Jaynes and everything to do with the the leapfrogging part of the Hamiltonian and how that screws up the proposal part of the metropolis algorithm.
I am not aware of Savage much apart from both Bayesian and Frequentists not liking him. And I did not follow Jaynes math fully and there are some papers going back and forth on some of his assumptions, so the mathematical underpinnings may not be as strong as we would like.
I don’t know, Intuitively you should be able to ground the agent stuff in information theory, because the rules they put forwards are the same, Jaynes also has a chapter on decision theory where he makes the wonderful point that the utility function is way more arbitrary than a prior, so you might as well be Bayesian if you are into inventing ad hoc functions anyway.
Ahh, I know that is a first year course for most math students, but only math students take that class :), I have never read an analysis book :), I took the applied path and read 3 other bayesian books before this one, so I taught the math in this books were simultaneously very tedious and basic :)
If anyone relies on tags to find posts, and you feel this post is missing a tag, then “Tag suggestions” will be much appreciated
That surprising to me, I think you can read the book two ways, 1) you skim the math, enjoy the philosophy and take his word that the math says what he says it says 2) you try to understand the math, if you take 2) then you need to at least know the chain rule of integration and what a delta dirac function is, which seems like high level math concepts to me, full disclaimer I am a biochemist by training, so I have also read it without the prerequisite formal training. I think you are right that if you ignore chapter 2 and a few sections about partition functions and such then the math level for the other 80% is undergraduate level math
crap, you are right, this was one of the last things we changed before publishing because out previous example were to combative :(.
I will fix it later today.
E.T. Jaynes Probability Theory: The logic of Science I
I think this is a pedagogical Version of Andrew Gelmans shrinkage Triology
The most important paper also has a blog post, The very short version is if you z score the published effects, then then you can derive a prior for the 20.000+ effects from the Cochrane database. A Cauchy distribution fits very well. The Cauchy distribution has very fat tails, so you should regress small effects heavily towards the null and regress very large effects very little.
Here is a fun figure of the effects, Medline is published stuff, so no effects between −2 and 2 as they would be ‘insignificant’, In the Cochrane collaboration they also hunted down unpublished results.
Here you see the Cochrane prior In red, you can imagine drawing a lot of random point from the red and then “adding 1 sigma of random noise”, which “smears out” the effect creating the blue inflated effects we observe.
Notice this only works if you have standardized effects, if you observe that breast feeding makes you 4 time richer with sigma=2, then you have z=2 which is a tiny effect as you need 1.96 to reach significance at the 5% level in frequentest statistics, and you should thus regress it heavily towards the null, where if you observe that breast feeding makes you 1% richer with sigma=0.01% then this is a huge effect and it should be regressed towards the null very little
SR if you can only read one, if you do not expect to do fancy things then ROS may be better as it is very good and explains the basics better. The logic of Science should be your 5th book and is good goal to set, The logic of Science is probably the rationalist bible, much like the real bible everybody swears by it but nobody has read or understood it :)
Thanks for the reply, 3 seams very automatable, record all text before the image, if that’s 4 minuts then then put the image in after 4 min. But i totally get that stuff is more complicated than it initially seems, keep up the good work!
I agree tails are important, but for callibration few of your predictions should land in the tail, so imo you should focus on getting the trunk of the distribution right first, and the later learn to do overdispersed predictions, there is no closed form solution to callibration for a t distribution, but there is for a normal, so for pedagogical reasons I am biting the bullet and asuming the normal is correct :), part 10 in this series 3 years in the future may be some black magic of the posterior of your t predictions using HMC to approximate the 2d posterior of sigma and nu ;), and then you can complain “but what about skewed distributios” :P
The text to speech is phenomenal!, Only math and tables suck
Suggestions for future iterations:
allow filtering of the RSS by hacking the url, for example ?sources=LW,EA&quality=curated would give the curated posts from only EA and LW ignoring alignment forum
somehow allow us to convert our “read later” to an RSS :)
when there are figures in the post, then put them in the podcast “image” like SolenoidEntity does for the Astral Codex 10 podcast
put the text in the show notes so we can pause and look at tables
It would be nice if you wrote a short paragraph for each link, “requires download”, “questions are from 2011″, or you sorted the list somehow :)
Yes, You can change future by being smarter and future by being better calibrated, my rule assumes you don’t get smarter and therefore have to adjust only future .
If you actually get better at prediction you could argue you would need to update less than the RMSE estimate suggests :)
I agree with both points
If you are new to continuous predictions then you should focus on the 50% Interval as it gives you most information about your calibration, If you are skilled and use for example a t-distribution then you have for the trunk and for the tail, even then few predictions should land in the tails, so most data should provide more information about how to adjust , than how to adjust
Hot take: I think the focus 95% is an artifact of us focusing on p<0.05 in frequentest statistics.
Our ability to talk past each other is impressive :)
would have been an easier way to illustrate your point). I think this is actually the assumption you’re making. [Which is a horrible assumption, because if it were true, you would already be perfectly calibrated].
Yes this is almost the assumption I am making, the general point of this post is to assume that all your predictions follow a Normal distribution, with as “guessed” and with a that is different from what you guessed, and then use to get a point estimate for the counterfactual you should have used. And as you point out if (counterfactual) then the point estimate suggests you are well calibrated.
In the post counter factual is
Thanks!, I am planing on writing a few more in this vein, currently I have some rough drafts of:
30% Done, How to callibrate normal predictions
defence of my calibration scheme, and an explanation of how metaculus does.
10% Done, How to make overdispersed predictions
like this one for the logistic and t distribution.
70% Done, How to calibrate binary predictions
like this one + but gives a posterior over the callibration by doing an logistic regression with your predictions as “x” and outcome as “y”
I can’t promise they will be as good as this one, but if they are not terrible then I would like them to be turned into a sequence :), how do I do this?
One of us is wrong or confused, and since you are the genetisist it is probably me, in which case I should not have guessed how it works from statistical intuition but read more, I did not because I wanted to write my post before people forgot yours.
I assumed the spike and slap were across all SNPs, it sounds like it is per LD region, which is why you have multiple spikes?, I also assumed the slab part would shrink the original effect size, which was what I was mainly interested in. You are welcome to pm me to get my discord name or phone number if a quick call could give me the information to not misrepresent what you are doing
My main critique is that I think there is insufficient shrinkage, so it’s the shrinkage properties I am mostly interested in getting right :)