Archive for the ‘Teaching’ Category

Late homework


My Bayesian Case Studies students had to hand in their final report last week; as I expected, some handed it in after the deadline.

I know several colleagues whose official position is that if the report is handed in late, the student fails the course. This is fine if the report is very late, but it seems a bit drastic for a small delay (e.g. a few minutes!). The problem of course is to define very and small in the previous sentence. And even if you decide that the course is failed for students who are more than (say) 24 hours late, it seems a bit unfair to have such a big difference between being 23 hours 59 minutes late and 24 hours 1 minute…

This time, I am using a continuous decreasing function as penalty: I told the students that

“Your report should be sent by e-mail by 2 April 2013 at noon. In case of a late submission, your grade will be multiplied by exp(-0.001 ⋅ t³ /86400³ ) where t is the number of seconds between the deadline and your submission.”

This basically means that they can be 2 days late for free. If a student has a legitimate reason for being late, they will usually manage to fit in that window, so they do not need to explain their lateness. Being 4 days late knocks off 6% of the grade; being a week late knocks off 30%. A student more than 8.8 days late loses 50% of their grade, meaning the course is necessarily failed, even if the report is perfect.

In this case, the last student to hand in his work was about 3.5 days late, meaning the mark will be multiplied by 0.953.

I quite like this system, although I think it was a bit too generous with this exact implementation. I cannot claim to have invented it; I read about it somewhere else, with a different penalty function, but cannot find where.

Edit: Thanks to Mahendra for the original post: here, on the Messy Matters blog.

Bayesian model choice for the Poisson model


Following Arthur Charpentier‘s example, I am going to try to post occasionally on material covered during my courses, in the hope that it might be useful to my students, but also to others.

In the second practical of the Bayesian Case Studies course, we looked at Bayesian model choice and basic Monte Carlo methods, looking at data about the number of oral questions asked by French deputies (Members of Parliament). We wanted to know whether male and female deputies behave differently in this matter. If we model the number of questions Y_i asked by a deputy by a Poisson random variable and denote Z_i their gender (1 for men, 2 for women), we thus need to choose between the following two models. (See the course website for the question sheet and other material; the slides are below.)

Slides2 from Robin Ryder

Model 1: Y_i\sim Poisson(\lambda); \quad \lambda \sim \Gamma(a,b)

Model 2: Y_i|Z_i=k\sim Poisson(\lambda_k); \quad \lambda_1\sim \Gamma(a,b); \quad \lambda_2\sim \Gamma(a,b)

First download the data and set some variables:

 > deputes=read.csv2('')
 > attach(deputes)#Q1
 > summary(questions_orales)
 > hist(questions_orales,breaks=(0:6-.5))
 > (n=length(questions_orales))
 > (nh=sum(sexe=="H"))
 > (nf=sum(sexe=="F"))
 > (qtot=sum(questions_orales))
 > (qh=sum(questions_orales[sexe=="H"]))
 > (qf=sum(questions_orales[sexe=="F"]))

Since the Gamma prior is a conjugate prior for the Poisson model, we get a Gamma distribution as our posterior. Using a \Gamma(2,2) as prior, here is a comparison of the prior and the posteriors for the two models (in the bottom plot, \lambda_1 is in black and \lambda_2 in red.


Two observations here: First, the posterior is much more peaked than the prior, which is expected since the number of data points is large. Second, in model 2, it seems that there may be a difference between men and women, with women asking slightly less questions in Parliament.To verify this, we compute a Bayes factor to compare the two models. In this case, the Bayes factor is available in closed form, but an initial computation does not work because n is too large:

> BF_analytical=function(a,b,y1,n1,y2,n2){
+   m1=b^a/gamma(a)*gamma(a+y1+y2)/(b+n1+n2)^(a+y1+y2)
+   m2=b^(2*a)/gamma(a)^2*gamma(a+y1)/(b+n1)^(a+y1)*gamma(a+y2)/(b+n2)^(a+y2)
+   return(m2/m1)
+ }
> BF_analytical(2,2,qh,nh,qf,nf)
[1] NaN
Warning messages:
1: In BF_analytical(2, 2, qh, nh, qf, nf) :
  value out of range in 'gammafn'
2: In BF_analytical(2, 2, qh, nh, qf, nf) :
  value out of range in 'gammafn'

However, we are able to compute the Bayes factor analytically by using the log-scale instead.

> BF_analytical2=function(a,b,y1,n1,y2,n2){
+   m1=a*log(b)-lgamma(a)+lgamma(a+y1+y2)-(a+y1+y2)*log(b+n1+n2)
+   m2=2*a*log(b)-2*lgamma(a)+lgamma(a+y1)-(a+y1)*log(b+n1)+lgamma(a+y2)-(a+y2)*log(b+n2)
+   return(exp(m2-m1))
+ }
> BF_analytical2(2,2,qh,nh,qf,nf)
[1] 0.1875569
> log10(BF_analytical2(2,2,qh,nh,qf,nf))
[1] -0.726867

Using Jeffrey’s scale of evidence, this corresponds to “substantial” evidence in favour of model 1 (i.e. no difference between men and women).

Even if we had not been able to calculate the Bayes factor exactly, we could have approximated it using Monte Carlo. We first create two functions to calculate the likelihood under model 1 and model 2, and start with vanilla Monte Carlo.

> lkd.model1=function(y,n,lambda){  return(exp(-n*lambda+y*log(lambda))) }
> lkd.model2=function(y1,n1,y2,n2,lambda1,lambda2){  return(exp(-n1*lambda1+y1*log(lambda1)-n2*lambda2+y2*log(lambda2))) }

> BF_MC=function(a,b,y1,n1,y2,n2,M){
 +  lambda1=rgamma(M,a,b)
 +  m1=cumsum(lkd.model1(y1+y2,n1+n2,lambda1))/(1:M)
 + lambda2.1=rgamma(M,a,b)
 + lambda2.2=rgamma(M,a,b)
 +  m2=cumsum(lkd.model2(y1,n1,y2,n2,lambda2.1,lambda2.2))/(1:M)
 +  return(m2/m1)
 + }

> M=100000
> BF_MC(2,2,qh,nh,qf,nf,M)[M]
[1] 0.1776931
> plot(100:M,BF_MC(2,2,qh,nh,qf,nf,M)[100:M], type="l")

The last line creates a plot of how our Monte Carlo estimate of the Bayes factor changes as the number of iterations M increases. It is useful to check convergence.vanilla

Here, it is clear that the method converges after a few tens of thousands iterations. Our estimate for M=10^5 is close to the true value (two decimal places precision). Next, we try the harmonic mean method:

> BF_HM=function(a,b,y1,n1,y2,n2,M){
+   lambda1=rgamma(M,a+y1+y2,b+n1+n2)
+   m1=(1:M)/(cumsum(1/lkd.model1(y1+y2,n1+n2,lambda1)))
 +  lambda2.1=rgamma(M,a+y1,b+n1)
 +  lambda2.2=rgamma(M,a+y2,b+n2)
 +  m2=(1:M)/cumsum(1/lkd.model2(y1,n1,y2,n2,lambda2.1,lambda2.2))
+   return(m2/m1)  
+ }

> BF_HM(2,2,qh,nh,qf,nf,M)[M]
[1] 0.2451013
> plot(100:M,BF_HM(2,2,qh,nh,qf,nf,M)[100:M], type="l")

We observe that this does not appear to converge. It is known that in general, the harmonic mean method is unreliable.

We finally move on to importance sampling. In importance sampling, we want to estimate E[h(X)] where X\sim f by using simulations from an alternate density g. This will be most efficient when g is close to $h\times f$. In this case, we therefore need g to be similar to the posterior distribution, so we take a normal density with mean and variance the same as the posterior distribution:

> BF_IS=function(a,b,y1,n1,y2,n2,M){
+  mean1=(a+y1+y2)/(b+n1+n2)
+  mean2.1=(a+y1)/(b+n1)
+  mean2.2=(a+y2)/(b+n2)

+  sigma1=sqrt((a+y1+y2)/(b+n1+n2)^2)
+  sigma2.1=sqrt((a+y1)/(b+n1)^2)
+  sigma2.2=sqrt((a+y2)/(b+n2)^2)

+  lambda1=rnorm(M,mean1,sigma1)
+  m1=cumsum( lkd.model1(y1+y2,n1+n2,lambda1) * dgamma(lambda1,a, b) / dnorm(lambda1,mean1,sigma1))/(1:M)

+  lambda2.1=rnorm(M,mean2.1, sigma2.1)
+  lambda2.2=rnorm(M,mean2.2, sigma2.2)
+  m2=cumsum( lkd.model2(y1,n1,y2,n2,lambda2.1,lambda2.2) * dgamma(lambda2.1,a, b) * dgamma(lambda2.2,a,b) / 
+    (dnorm(lambda2.1,mean2.1,sigma2.1)*dnorm(lambda2.2,mean2.2,sigma2.2))) / (1:M)

+  return(m2/m1)
+ }

> BF_IS(2,2,qh,nh,qf,nf,M)[M]
[1] 0.1875875
> plot(100:M,BF_IS(2,2,qh,nh,qf,nf,M)[100:M], type="l")

ISThis method converges. Note that the y-scale is much tighter than for vanilla Monte Carlo: convergence is in fact much faster, and we get a more precise estimate than by using vanilla Monte Carlo. This is more obvious if we look at both methods on the same graph.

> plot(100:M,BF_MC(2,2,qh,nh,qf,nf,M)[100:M], type="l") 
> lines(100:M,BF_IS(2,2,qh,nh,qf,nf,M)[100:M], col="red")

It is much more visible now that importance sampling is a clear winner.

With this computation of the Bayes factor, we choose model 1: a single parameter can be used to model the behaviour of men and women.