Archive for bias

no country for old biases

Posted in Books, Kids, Statistics with tags , , , , , on March 20, 2018 by xi'an

Following a X validated question, I read a 1994 paper by Phil Dawid on the selection paradoxes in Bayesian statistics, which first sounded like another version of the stopping rule paradox. And upon reading, less so. As described above, the issue stands with drawing inference on the index and value, (i⁰,μ⁰), of the largest mean of a sample of Normal rvs. What I find surprising in Phil’s presentation is that the Bayesian analysis does not sound that Bayesian. If given the whole sample, a Bayesian approach should produce a posterior distribution on (i⁰,μ⁰), rather than follow estimation steps, from estimating i⁰ to estimating the associated mean. And if needed, estimators should come from the definition of a particular loss function. When, instead, given the largest point in the sample, and only that point, its distribution changes, so I am fairly bemused by the statement that no adjustment is needed.

The prior modelling is also rather surprising in that the priors on the means should be joint rather than a product of independent Normals, since these means are compared and hence comparable. For instance a hierarchical prior seems more appropriate, with location and scale to be estimated from the whole data. Creating a connection between the means… A relevant objection to the use of independent improper priors is that the maximum mean μ⁰ then does not have a well-defined measure. However, I do not think a criticism of some priors versus other is a relevant attack on this “paradox”.

about paradoxes

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , on December 5, 2017 by xi'an

An email I received earlier today about statistical paradoxes:

I am a PhD student in biostatistics, and an avid reader of your work. I recently came across this blog post, where you review a text on statistical paradoxes, and I was struck by this section:

“For instance, the author considers the MLE being biased to be a paradox (p.117), while omitting the much more substantial “paradox” of the non-existence of unbiased estimators of most parameters—which simply means unbiasedness is irrelevant. Or the other even more puzzling “paradox” that the secondary MLE derived from the likelihood associated with the distribution of a primary MLE may differ from the primary. (My favourite!)”

I found this section provocative, but I am unclear on the nature of these “paradoxes”. I reviewed my stat inference notes and came across the classic example that there is no unbiased estimator for 1/p w.r.t. a binomial distribution, but I believe you are getting at a much more general result. If it’s not too much trouble, I would sincerely appreciate it if you could point me in the direction of a reference or provide a bit more detail for these two “paradoxes”.

The text is Chang’s Paradoxes in Scientific Inference, which I indeed reviewed negatively. To answer about the bias “paradox”, it is indeed a neglected fact that, while the average of any transform of a sample obviously is an unbiased estimator of its mean (!), the converse does not hold, namely, an arbitrary transform of the model parameter θ is not necessarily enjoying an unbiased estimator. In Lehmann and Casella, Chapter 2, Section 4, this issue is (just slightly) discussed. But essentially, transforms that lead to unbiased estimators are mostly the polynomial transforms of the mean parameters… (This also somewhat connects to a recent X validated question as to why MLEs are not always unbiased. Although the simplest explanation is that the transform of the MLE is the MLE of the transform!) In exponential families, I would deem the range of transforms with unbiased estimators closely related to the collection of functions that allow for inverse Laplace transforms, although I cannot quote a specific result on this hunch.

The other “paradox” is that, if h(X) is the MLE of the model parameter θ for the observable X, the distribution of h(X) has a density different from the density of X and, hence, its maximisation in the parameter θ may differ. An example (my favourite!) is the MLE of ||a||² based on x N(a,I) which is ||x||², a poor estimate, and which (strongly) differs from the MLE of ||a||² based on ||x||², which is close to (1-p/||x||²)²||x||² and (nearly) admissible [as discussed in the Bayesian Choice].

adaptive exchange

Posted in Books, Statistics, University life with tags , , , , , , , , , , on October 27, 2016 by xi'an

In the March 2016 issue of JASA that currently sits on my desk, there is a paper by Liang, Jim, Song and Liu on the adaptive exchange algorithm, which aims at handling posteriors for sampling distributions with intractable normalising constants. The concept behind the algorithm is the exchange principle initiated by Jesper Møller and co-authors in 2006, where an auxiliary pseudo-observation is simulated for the missing constants to vanish in a Metropolis-Hastings ratio. (The name exchangeable was introduced in a subsequent paper by Iain Murray, Zoubin Ghahramani and David MacKay, also in 2006.)

 The crux of the method is to run an iteration as [where y denotes the observation]

  1. Proposing a new value θ’ of the parameter from a proposal q(θ’|θ);
  2. Generate a pseudo-observation z~ƒ(z|θ’);
  3. Accept with probability


which has the appeal to cancel all normalising constants. And the repeal of requiring an exact simulation from the very distribution with the missing constant, ƒ(.|θ). Which means that in practice a finite number of MCMC steps will be used and will bias the outcome. The algorithm is unusual in that it replaces the exact proposal q(θ’|θ) with an unbiased random version q(θ’|θ)ƒ(z|θ’), z being just an augmentation of the proposal. (The current JASA paper by Liang et al. seems to confuse augment and argument, see p.378.)

To avoid the difficulty in simulating from ƒ(.|θ), the authors draw pseudo-observations from sampling distributions with a finite number m of parameter values under the [unrealistic] assumption (A⁰) that this collection of values provides an almost complete cover of the posterior support. One of the tricks stands with an auxiliary [time-heterogeneous] chain of pseudo-observations generated by single Metropolis steps from one of these m fixed targets. These pseudo-observations are then used in the main (or target) chain to define the above exchange probability. The auxiliary chain is Markov but time-heterogeneous since the probabilities of accepting a move are evolving with time according to a simulated annealing schedule. Which produces a convergent estimate of the m normalising constants. The main chain is not Markov in that it depends on the whole history of the auxiliary chain [see Step 5, p.380]. Even jointly the collection of both chains is not Markov. The paper prefers to consider the process as an adaptive Markov chain. I did not check the rather intricate in details, so cannot judge of the validity of the overall algorithm; I simply note that one condition (A², p.383) is incredibly strong in that it assumes the Markov transition kernel to be Doeblin uniformly on any compact set of the calibration parameters. However, the major difficulty with this approach seems to be in its delicate calibration. From providing a reference set of m parameter values scanning the posterior support to picking transition kernels on both the parameter and the sample spaces, to properly cooling the annealing schedule [always a fun part!], there seems to be [from my armchair expert’s perspective, of course!] a wide range of opportunities for missing the target or running into zero acceptance problems. Both examples analysed in the paper, the auto-logistic and the auto-normal models, are actually of limited complexity in that they depend on a few parameters, 2 and 4 resp., and enjoy sufficient statistics, of dimensions 2 and 4 as well. Hence simulating (pseudo-)realisations of those sufficient statistics should be less challenging than the original approach replicating an entire vector of thousands of dimensions.

automatic variational ABC

Posted in pictures, Statistics with tags , , , , , , , , , , on July 8, 2016 by xi'an

Amster11“Stochastic Variational inference is an appealing alternative to the inefficient sampling approaches commonly used in ABC.”

Moreno et al. [including Ted Meeds and Max Welling] recently arXived a paper merging variational inference and ABC. The argument for turning variational is computational speedup. The traditional (in variational inference) divergence decomposition of the log-marginal likelihood is replaced by an ABC version, parameterised in terms of intrinsic generators (i.e., generators that do not depend on cyber-parameters, like the U(0,1) or the N(0,1) generators). Or simulation code in the authors’ terms. Which leads to the automatic aspect of the approach. In the paper the derivation of the gradient is indeed automated.

“One issue is that even assuming that the ABC likelihood is an unbiased estimator of the true likelihood (which it is not), taking the log introduces a bias, so that we now have a biased estimate of the lower bound and thus biased gradients.”

I wonder how much of an issue this is, since we consider the variational lower bound. To be optimised in terms of the parameters of the variational posterior. Indeed, the endpoint of the analysis is to provide an optimal variational approximation, which remains an approximation whether or not the likelihood estimator is unbiased. A more “severe” limitation may be in the inversion constraint, since it seems to eliminate Beta or Gamma distributions. (Even though calling qbeta(runif(1),a,b) definitely is achievable… And not rejected by a Kolmogorov-Smirnov test.)

Incidentally, I discovered through the paper the existence of the Kumaraswamy distribution, which main appeal seems to be the ability to produce a closed-form quantile function, while bearing some resemblance with the Beta distribution. (Another arXival by Baltasar Trancón y Widemann studies some connections between those, but does not tell how to select the parameters to optimise the similarity.)

the penalty method

Posted in Statistics, University life with tags , , , , , , , , , , on July 7, 2016 by xi'an

“In this paper we will make conceptually simple generalization of Metropolis algorithm, by adjusting the acceptance ratio formula so that the transition probabilities are unaffected by the fluctuations in the estimate of [the acceptance ratio]…”

Last Friday, in Paris-Dauphine, my PhD student Changye Wu showed me a paper of Ceperley and Dewing entitled the penalty method for random walks with uncertain energies. Of which I was unaware of (and which alas pre-dated a recent advance made by Changye).  Despite its physics connections, the paper is actually about estimating a Metropolis-Hastings acceptance ratio and correcting the Metropolis-Hastings move for this estimation. While there is no generic solution to this problem, assuming that the logarithm of the acceptance ratio estimate is Gaussian around the true log acceptance ratio (and hence unbiased) leads to a log-normal correction for the acceptance probability.

“Unfortunately there is a serious complication: the variance needed in the noise penalty is also unknown.”

Even when the Gaussian assumption is acceptable, there is a further issue with this approach, namely that it also depends on an unknown variance term. And replacing it with an estimate induces further bias. So it may be that this method has not met with many followers because of those two penalising factors. Despite precluding the pseudo-marginal approach of Mark Beaumont (2003) by a few years, with the later estimating separately numerator and denominator in the Metropolis-Hastings acceptance ratio. And hence being applicable in a much wider collection of cases. Although I wonder if some generic approaches like path sampling or the exchange algorithm could be applied on a generic basis… [I just realised the title could be confusing in relation with the current football competition!]

stopping rule impact

Posted in Books, R, Statistics, University life with tags , , , on May 9, 2014 by xi'an

shravanHere is a question from my friend Shravan Vasishth about the consequences of using a stopping rule:

Psycholinguists and psychologists often adopt the following type of data-gathering procedure: The experimenter gathers n data points, then checks for significance (p<0.05 or not). If it’s not significant, he gets more data (n more data points). Since time and money are limited, he might decide to stop anyway at sample size, say, some multiple of n.  One can play with different scenarios here. A typical n might be 10 or 15.

This approach would give us a distribution of t-values and p-values under repeated sampling. Theoretically, under the standard assumptions of frequentist methods, we expect a Type I error to be 0.05. This is the case in standard analyses (I also track the t-statistic, in order to compare it with my stopping rule code below).

Here’s a simulation showing what happens. I wanted to ask you whether this simulation makes sense. I assume here that the experimenter gathers 10 data points, then checks for significance (p<0.05 or not). If it’s not significant, he gets more data (10 more data points). Since time and money are limited, he might decide to stop anyway at sample size 60. This gives us p-values under repeated sampling. Theoretically, under the standard assumptions of frequentist methods, we expect a Type I error to be 0.05. This is the case in standard analyses:
n<-10 # sample size
nsim<-1000 # number of simulations
stddev<-1 # standard dev
mn<-0 ## mean

for(i in 1:nsim){

## Type I error rate: about 5% as theory says:

But the situation quickly deteriorates as soon as adopt the strategy I outlined above:

## how many subjects can I run?

for(i in 1:nsim){
## at the outset we have no significant result:
## null hyp is going to be true,
## so any rejection is a mistake.
## take sample:
 while(!significant & length(x)<upper_bound){
  ## if not significant:
  ## get more data:
  ## otherwise stop:
  } else {significant<-TRUE}}
## will be either significant or not:

Now let’s compare the distribution of the t-statistic in the standard case vs with the above stopping rule. We get fatter tails with the above stopping rule, as shown by the histogram below.

Is this a correct way to think about the stopping rule problem?


To which I replied the following:

By adopting a stopping rule on a random iid sequence, you favour values in the sequence that agree with your stopping condition, hence modify the distribution of the outcome. To take an extreme example, if you draw N(0,1) variates until the empirical average is between -2 and 2, the average thus produced cannot remain N(0,1/n) but have a different distribution.

The t-test statistic you build from your experiment is no longer distributed as a uniform variate because of the stopping rule: the sample(x1,…,x10m) (with random size 10m [resulting from increases in the sample size by adding 10 more observations at a time] is distributed from

\prod_{i=1}^{10m} \phi(x_i) \times \prod_{j=1}^{m-1} \mathbb{I}_{t(x_1,\ldots,x_{10j})>.05} \times \mathbb{I}_{t(x_1,\ldots,x_{10m})<.05}

if 10m<60 [assuming the maximal acceptable sample size is 60] and from

\prod_{i=1}^{60} \phi(x_i) \times \prod_{j=1}^{5} \mathbb{I}_{t(x_1,\ldots,x_{10j})>.05}

otherwise. The histogram at the top of this post is the empirical distribution of the average of those observations, clearly far from a normal distribution.

bounded target support [#2]

Posted in Books, Kids, Statistics, University life with tags , , , , , on July 8, 2013 by xi'an

In a sort of echo from an earlier post, I received this emailed question from Gabriel:

I am contacting you in connection with my internship and your book «Le choix bayésien» where I cannot find an answer to my question. Given a constrained parameter space and an unconstrained Markov chain, is it correct to subsample the chain in order to keep only those points that satisfy the constraint?

To which I replied that this would induce a bias in the outcome, even though this is a marginally valid argument (if  the Markov chain is in its stationary regime, picking one value at random from those satisfying the constraint is akin to accept-reject). The unbiased approach is to resort to Metropolis-Hastings steps in Gabriel’s Gibbs sampler to check whether or not each proposed move stays within the constrained space. If not, one need to replicate the current value of the chain…

Update: Following comments by Ajay and David, I withdraw the term “bias”. The method works as a low key accept-reject but can be very inefficient, to the extent of having no visit to the constrained set. (However, in the event of a practically/numerically disconnected support with a huge gap between the connected components, it may also be more efficient than a low energy Metropolis-Hastings algorithm. Mileage may vary!)