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Indian Statistical Institute admission tests Bayesian Inference: practice questions

Indian Statistical Institute admission tests (BStat, MStat, JRF in Statistics) · India · Indian Statistical Institute

Original practice questions written to the published syllabus · not past papers
10worked here, free
58written to this exam in this subject
11syllabus units

What this subject covers

Inference through prior and posterior: conjugate analysis, prior choice, credible intervals, Bayes factors and decision theory, hierarchical models, and computation by Markov-chain Monte Carlo, with agricultural uses in variety trials, genomic prediction and small-area estimation.

In the exams: Not an explicit unit in AICE-JRF Ag Stat; PhD course in most programmes; GATE ST Bayes' theorem (light); UPSC ISS decision theory (present)

Where the 58 questions fall

How our questions for Indian Statistical Institute admission tests spread across the units of Bayesian Inference. Difficulty: 18 easy, 31 medium, 9 hard.

Posterior summaries and credible intervals7
Convergence diagnostics7
Posterior predictive checks and model comparison (DIC, WAIC)7
Bayes' theorem for parameters: prior, likelihood and posterior6
Non-informative and weakly informative priors6
Markov chain Monte Carlo: Gibbs sampling and Metropolis-Hastings6
Bayesian hypothesis testing and Bayes factors5
Hierarchical (multilevel) models4
Empirical Bayes4
Conjugate families3
Decision theory: loss functions and Bayes risk3

10 practice questions, worked

Choose an answer, then open the working. Each explanation says why the right answer is right and why the others are not.

1 · Conjugate families · medium

Counts are Poisson(λ) with a gamma prior on λ. What is the posterior predictive distribution of a new count?

  1. Poisson with the posterior mean
  2. Negative binomial
  3. Beta-binomial
  4. Gamma
Answer and working

B. Negative binomial

Mixing a Poisson over a gamma distribution for its mean gives a negative binomial; the extra variance reflects uncertainty about λ. Beta-binomial is the predictive for binomial data with a beta prior.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

2 · Non-informative and weakly informative priors · easy

A uniform prior is placed on a germination probability p. Which statement is correct?

  1. It is improper, because p has no upper bound
  2. It is Jeffreys' prior for the binomial model
  3. It is not uniform on the log-odds scale
  4. It is uniform on every transformation of p
Answer and working

C. It is not uniform on the log-odds scale

Flatness depends on the parameterisation; transforming p changes the density by the Jacobian. The uniform on (0, 1) is proper, and Jeffreys' prior is beta(1/2, 1/2), not uniform.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

3 · Decision theory: loss functions and Bayes risk · medium

Before a further season of variety trials, an analyst computes the expected value of sample information (EVSI). How is it used?

  1. Reject the variety if EVSI is below zero
  2. Use EVSI as the prior mean for yield
  3. Release the variety if EVSI is positive
  4. Run them only if EVSI exceeds their cost
Answer and working

D. Run them only if EVSI exceeds their cost

EVSI is the expected improvement in the decision's value from the extra data; it is never negative. Comparing it with the trial cost decides whether the information is worth buying.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

4 · Convergence diagnostics · easy

What does the Gelman-Rubin R̂ compare?

  1. Between-chain and within-chain variance
  2. Autocorrelation at lags 1 and 2
  3. Prior and posterior variance
  4. Early and late halves of one chain's mean
Answer and working

A. Between-chain and within-chain variance

R̂ near 1 means the chains, started from dispersed values, agree. Comparing early and late segments of one chain is Geweke's diagnostic.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

5 · Convergence diagnostics · medium

Why are several chains started from dispersed values instead of one long chain?

  1. A single chain cannot have a stationary distribution
  2. Disagreement between chains exposes problems
  3. Dispersed starts remove the need for burn-in
  4. Several chains always converge faster than one
Answer and working

B. Disagreement between chains exposes problems

If chains from different regions have not mixed, their summaries differ, which R̂ and trace plots expose; one chain stuck in one mode can look perfectly stable.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

6 · Convergence diagnostics · medium

What does Geweke's diagnostic test?

  1. Independence of the prior and the likelihood
  2. Normality of the posterior distribution
  3. Equality of means in an early and a late segment of one chain
  4. Equality of variances between several chains
Answer and working

C. Equality of means in an early and a late segment of one chain

Geweke compares the mean of, say, the first 10% and the last 50% of a chain with a z-score adjusted for autocorrelation; a large |z| suggests the chain had not settled.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

7 · Convergence diagnostics · medium

An HMC sampler reports many divergent transitions. What should be done?

  1. Increase the burn-in and keep the model unchanged
  2. Investigate and reparameterise, since parts of the posterior are not explored reliably
  3. Thin the chain to remove the divergent draws
  4. Ignore them if R̂ is below 1.1
Answer and working

B. Investigate and reparameterise, since parts of the posterior are not explored reliably

Divergences indicate regions of high curvature where the sampler fails, which biases estimates; reparameterisation or a smaller step size is needed. R̂ may still look fine.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

8 · Posterior predictive checks and model comparison (DIC, WAIC) · medium

A model has log pointwise predictive density lppd = −120 and p_WAIC = 6. What is WAIC on the deviance scale?

  1. 252
  2. 240
  3. 126
  4. 228
Answer and working

A. 252

WAIC = −2(lppd − p_WAIC) = −2(−126) = 252. Omitting the penalty gives 240; adding it with the wrong sign gives 228.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

9 · Posterior predictive checks and model comparison (DIC, WAIC) · hard

In what situation can DIC be unreliable, even giving a negative effective number of parameters p_D?

  1. When the posterior is strongly non-normal or multimodal, as in mixtures
  2. When the posterior mean equals the posterior mode
  3. When the prior is conjugate
  4. When the model has only one parameter
Answer and working

A. When the posterior is strongly non-normal or multimodal, as in mixtures

p_D = D̄ − D(θ̄) depends on the deviance at the posterior mean, which can be a poor point for skewed or multimodal posteriors; WAIC and PSIS-LOO avoid this.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

10 · Empirical Bayes · medium

When the number of groups is large, how do empirical Bayes and full hierarchical Bayes estimates of group means compare?

  1. They diverge, because empirical Bayes ignores the data
  2. Full Bayes always shrinks less than empirical Bayes
  3. They are close, because hyperparameter uncertainty is small
  4. Empirical Bayes estimates equal the raw group means
Answer and working

C. They are close, because hyperparameter uncertainty is small

With many groups the hyperparameters are well estimated, so plugging them in loses little. The two differ most with few groups.

Further reading: Gelman et al., Bayesian Data Analysis; Berger, Statistical Decision Theory and Bayesian Analysis; Robert, The Bayesian Choice

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Bayesian InferenceThe full study manual, free Indian Statistical Institute admission testsFormat, sections and how it has changed

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