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# Edinburgh, Bayes-250

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Slides of my talk at Bayes-250 in Edinburgh, Sept. 6, 2011

Slides of my talk at Bayes-250 in Edinburgh, Sept. 6, 2011

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• 1. ABC Methods for Bayesian Model Choice ABC Methods for Bayesian Model Choice Christian P. Robert Universit´ Paris-Dauphine, IuF, & CREST e http://www.ceremade.dauphine.fr/~xian Bayes-250, Edinburgh, September 6, 2011
• 2. ABC Methods for Bayesian Model Choice Approximate Bayesian computationApproximate Bayesian computation Approximate Bayesian computation ABC for model choice Gibbs random ﬁelds Generic ABC model choice
• 3. ABC Methods for Bayesian Model Choice Approximate Bayesian computationRegular Bayesian computation issues When faced with a non-standard posterior distribution π(θ|y) ∝ π(θ)L(θ|y) the standard solution is to use simulation (Monte Carlo) to produce a sample θ1 , . . . , θ T from π(θ|y) (or approximately by Markov chain Monte Carlo methods) [Robert & Casella, 2004]
• 4. ABC Methods for Bayesian Model Choice Approximate Bayesian computationUntractable likelihoods Cases when the likelihood function f (y|θ) is unavailable and when the completion step f (y|θ) = f (y, z|θ) dz Z is impossible or too costly because of the dimension of z c MCMC cannot be implemented!
• 5. ABC Methods for Bayesian Model Choice Approximate Bayesian computationUntractable likelihoods c MCMC cannot be implemented!
• 6. ABC Methods for Bayesian Model Choice Approximate Bayesian computationThe ABC method Bayesian setting: target is π(θ)f (x|θ)
• 7. ABC Methods for Bayesian Model Choice Approximate Bayesian computationThe ABC method Bayesian setting: target is π(θ)f (x|θ) When likelihood f (x|θ) not in closed form, likelihood-free rejection technique:
• 8. ABC Methods for Bayesian Model Choice Approximate Bayesian computationThe ABC method Bayesian setting: target is π(θ)f (x|θ) When likelihood f (x|θ) not in closed form, likelihood-free rejection technique: ABC algorithm For an observation y ∼ f (y|θ), under the prior π(θ), keep jointly simulating θ ∼ π(θ) , z ∼ f (z|θ ) , until the auxiliary variable z is equal to the observed value, z = y. [Tavar´ et al., 1997] e
• 9. ABC Methods for Bayesian Model Choice Approximate Bayesian computationA as approximative When y is a continuous random variable, equality z = y is replaced with a tolerance condition, (y, z) ≤ where is a distance
• 10. ABC Methods for Bayesian Model Choice Approximate Bayesian computationA as approximative When y is a continuous random variable, equality z = y is replaced with a tolerance condition, (y, z) ≤ where is a distance Output distributed from π(θ) Pθ { (y, z) < } ∝ π(θ| (y, z) < )
• 11. ABC Methods for Bayesian Model Choice Approximate Bayesian computationABC algorithm Algorithm 1 Likelihood-free rejection sampler for i = 1 to N do repeat generate θ from the prior distribution π(·) generate z from the likelihood f (·|θ ) until ρ{η(z), η(y)} ≤ set θi = θ end for where η(y) deﬁnes a (maybe in-suﬃcient) statistic
• 12. ABC Methods for Bayesian Model Choice Approximate Bayesian computationOutput The likelihood-free algorithm samples from the marginal in z of: π(θ)f (z|θ)IA ,y (z) π (θ, z|y) = , A ,y ×Θ π(θ)f (z|θ)dzdθ where A ,y = {z ∈ D|ρ(η(z), η(y)) < }.
• 13. ABC Methods for Bayesian Model Choice Approximate Bayesian computationOutput The likelihood-free algorithm samples from the marginal in z of: π(θ)f (z|θ)IA ,y (z) π (θ, z|y) = , A ,y ×Θ π(θ)f (z|θ)dzdθ where A ,y = {z ∈ D|ρ(η(z), η(y)) < }. The idea behind ABC is that the summary statistics coupled with a small tolerance should provide a good approximation of the posterior distribution: π (θ|y) = π (θ, z|y)dz ≈ π(θ|y) .
• 14. ABC Methods for Bayesian Model Choice Approximate Bayesian computationMA example Consider the MA(q) model q xt = t+ ϑi t−i i=1 Simple prior: uniform prior over the identiﬁability zone, e.g. triangle for MA(2)
• 15. ABC Methods for Bayesian Model Choice Approximate Bayesian computationMA example (2) ABC algorithm thus made of 1. picking a new value (ϑ1 , ϑ2 ) in the triangle 2. generating an iid sequence ( t )−q<t≤T 3. producing a simulated series (xt )1≤t≤T
• 16. ABC Methods for Bayesian Model Choice Approximate Bayesian computationMA example (2) ABC algorithm thus made of 1. picking a new value (ϑ1 , ϑ2 ) in the triangle 2. generating an iid sequence ( t )−q<t≤T 3. producing a simulated series (xt )1≤t≤T Distance: basic distance between the series T ρ((xt )1≤t≤T , (xt )1≤t≤T ) = (xt − xt )2 t=1 or between summary statistics like the ﬁrst q autocorrelations T τj = xt xt−j t=j+1
• 17. ABC Methods for Bayesian Model Choice Approximate Bayesian computationComparison of distance impact Evaluation of the tolerance on the ABC sample against both distances ( = 100%, 10%, 1%, 0.1%) for an MA(2) model
• 18. ABC Methods for Bayesian Model Choice Approximate Bayesian computationComparison of distance impact 4 1.5 3 1.0 2 0.5 1 0.0 0 0.0 0.2 0.4 0.6 0.8 −2.0 −1.0 0.0 0.5 1.0 1.5 θ1 θ2 Evaluation of the tolerance on the ABC sample against both distances ( = 100%, 10%, 1%, 0.1%) for an MA(2) model
• 19. ABC Methods for Bayesian Model Choice Approximate Bayesian computationComparison of distance impact 4 1.5 3 1.0 2 0.5 1 0.0 0 0.0 0.2 0.4 0.6 0.8 −2.0 −1.0 0.0 0.5 1.0 1.5 θ1 θ2 Evaluation of the tolerance on the ABC sample against both distances ( = 100%, 10%, 1%, 0.1%) for an MA(2) model
• 20. ABC Methods for Bayesian Model Choice ABC for model choiceABC for model choice Approximate Bayesian computation ABC for model choice Gibbs random ﬁelds Generic ABC model choice
• 21. ABC Methods for Bayesian Model Choice ABC for model choiceBayesian model choice Principle Several models M1 , M2 , . . . are considered simultaneously for dataset y and model index M central to inference. Use of a prior π(M = m), plus a prior distribution on the parameter conditional on the value m of the model index, πm (θ m ) Goal is to derive the posterior distribution of M, a challenging computational target when models are complex.
• 22. ABC Methods for Bayesian Model Choice ABC for model choiceGeneric ABC for model choice Algorithm 2 Likelihood-free model choice sampler (ABC-MC) for t = 1 to T do repeat Generate m from the prior π(M = m) Generate θ m from the prior πm (θ m ) Generate z from the model fm (z|θ m ) until ρ{η(z), η(y)} < Set m(t) = m and θ (t) = θ m end for [Toni, Welch, Strelkowa, Ipsen & Stumpf, 2009]
• 23. ABC Methods for Bayesian Model Choice ABC for model choiceABC estimates Posterior probability π(M = m|y) approximated by the frequency of acceptances from model m T 1 Im(t) =m . T t=1 Early issues with implementation: should tolerances be the same for all models? should summary statistics vary across models? incl. their dimension? should the distance measure ρ vary across models?
• 24. ABC Methods for Bayesian Model Choice ABC for model choiceABC estimates Posterior probability π(M = m|y) approximated by the frequency of acceptances from model m T 1 Im(t) =m . T t=1 Early issues with implementation: then needs to become part of the model Varying statistics incompatible with Bayesian model choice proper ρ then part of the model Extension to a weighted polychotomous logistic regression estimate of π(M = m|y), with non-parametric kernel weights [Cornuet et al., DIYABC, 2009]
• 25. ABC Methods for Bayesian Model Choice ABC for model choiceThe great ABC controversy On-going controvery in phylogeographic genetics about the validity of using ABC for testing Against: Templeton, 2008, 2009, 2010a, 2010b, 2010c, &tc argues that nested hypotheses cannot have higher probabilities than nesting hypotheses (!)
• 26. ABC Methods for Bayesian Model Choice ABC for model choiceThe great ABC controversy On-going controvery in phylogeographic genetics about the validity of using ABC for testing Replies: Fagundes et al., 2008, Against: Templeton, 2008, Beaumont et al., 2010, Berger et 2009, 2010a, 2010b, 2010c, &tc al., 2010, Csill`ry et al., 2010 e argues that nested hypotheses point out that the criticisms are cannot have higher probabilities addressed at [Bayesian] than nesting hypotheses (!) model-based inference and have nothing to do with ABC...
• 27. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsPotts model Potts model c∈C Vc (y) is of the form Vc (y) = θS(y) = θ δyl =yi c∈C l∼i where l∼i denotes a neighbourhood structure
• 28. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsPotts model Potts model c∈C Vc (y) is of the form Vc (y) = θS(y) = θ δyl =yi c∈C l∼i where l∼i denotes a neighbourhood structure In most realistic settings, summation Zθ = exp{θ T S(x)} x∈X involves too many terms to be manageable and numerical approximations cannot always be trusted [Cucala et al., 2009]
• 29. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsNeighbourhood relations Setup Choice to be made between M neighbourhood relations m i∼i (0 ≤ m ≤ M − 1) with Sm (x) = I{xi =xi } m i∼i driven by the posterior probabilities of the models.
• 30. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsModel index Computational target: P(M = m|x) ∝ fm (x|θm )πm (θm ) dθm π(M = m) Θm
• 31. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsModel index Computational target: P(M = m|x) ∝ fm (x|θm )πm (θm ) dθm π(M = m) Θm If S(x) suﬃcient statistic for the joint parameters (M, θ0 , . . . , θM −1 ), P(M = m|x) = P(M = m|S(x)) .
• 32. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsSuﬃcient statistics in Gibbs random ﬁelds
• 33. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsSuﬃcient statistics in Gibbs random ﬁelds Each model m has its own suﬃcient statistic Sm (·) and S(·) = (S0 (·), . . . , SM −1 (·)) is also (model-)suﬃcient.
• 34. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsSuﬃcient statistics in Gibbs random ﬁelds Each model m has its own suﬃcient statistic Sm (·) and S(·) = (S0 (·), . . . , SM −1 (·)) is also (model-)suﬃcient. Explanation: For Gibbs random ﬁelds, 1 2 x|M = m ∼ fm (x|θm ) = fm (x|S(x))fm (S(x)|θm ) 1 = f 2 (S(x)|θm ) n(S(x)) m where n(S(x)) = {˜ ∈ X : S(˜ ) = S(x)} x x c S(x) is therefore also suﬃcient for the joint parameters
• 35. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsToy example iid Bernoulli model versus two-state ﬁrst-order Markov chain, i.e. n f0 (x|θ0 ) = exp θ0 I{xi =1} {1 + exp(θ0 )}n , i=1 versus n 1 f1 (x|θ1 ) = exp θ1 I{xi =xi−1 } {1 + exp(θ1 )}n−1 , 2 i=2 with priors θ0 ∼ U(−5, 5) and θ1 ∼ U(0, 6) (inspired by “phase transition” boundaries).
• 36. ABC Methods for Bayesian Model Choice Gibbs random ﬁeldsToy example (2) ^ BF01 −5 0 5 −40 −20 BF01 0 10 ^ BF01 −10 −5 0 5 10 −40 −20 BF01 0 10 (left) Comparison of the true BF m0 /m1 (x0 ) with BF m0 /m1 (x0 ) (in logs) over 2, 000 simulations and 4.106 proposals from the prior. (right) Same when using tolerance corresponding to the 1% quantile on the distances.
• 37. ABC Methods for Bayesian Model Choice Generic ABC model choiceBack to suﬃciency ‘Suﬃcient statistics for individual models are unlikely to be very informative for the model probability. This is already well known and understood by the ABC-user community.’ [Scott Sisson, Jan. 31, 2011, ’Og]
• 38. ABC Methods for Bayesian Model Choice Generic ABC model choiceBack to suﬃciency ‘Suﬃcient statistics for individual models are unlikely to be very informative for the model probability. This is already well known and understood by the ABC-user community.’ [Scott Sisson, Jan. 31, 2011, ’Og] If η1 (x) suﬃcient statistic for model m = 1 and parameter θ1 and η2 (x) suﬃcient statistic for model m = 2 and parameter θ2 , (η1 (x), η2 (x)) is not always suﬃcient for (m, θm )
• 39. ABC Methods for Bayesian Model Choice Generic ABC model choiceBack to suﬃciency ‘Suﬃcient statistics for individual models are unlikely to be very informative for the model probability. This is already well known and understood by the ABC-user community.’ [Scott Sisson, Jan. 31, 2011, ’Og] If η1 (x) suﬃcient statistic for model m = 1 and parameter θ1 and η2 (x) suﬃcient statistic for model m = 2 and parameter θ2 , (η1 (x), η2 (x)) is not always suﬃcient for (m, θm ) c Potential loss of information at the testing level
• 40. ABC Methods for Bayesian Model Choice Generic ABC model choiceLimiting behaviour of B12 (T → ∞) ABC approximation T t=1 Imt =1 Iρ{η(zt ),η(y)}≤ B12 (y) = T , t=1 Imt =2 Iρ{η(zt ),η(y)}≤ where the (mt , z t )’s are simulated from the (joint) prior
• 41. ABC Methods for Bayesian Model Choice Generic ABC model choiceLimiting behaviour of B12 (T → ∞) ABC approximation T t=1 Imt =1 Iρ{η(zt ),η(y)}≤ B12 (y) = T , t=1 Imt =2 Iρ{η(zt ),η(y)}≤ where the (mt , z t )’s are simulated from the (joint) prior As T go to inﬁnity, limit Iρ{η(z),η(y)}≤ π1 (θ 1 )f1 (z|θ 1 ) dz dθ 1 B12 (y) = Iρ{η(z),η(y)}≤ π2 (θ 2 )f2 (z|θ 2 ) dz dθ 2 η Iρ{η,η(y)}≤ π1 (θ 1 )f1 (η|θ 1 ) dη dθ 1 = η , Iρ{η,η(y)}≤ π2 (θ 2 )f2 (η|θ 2 ) dη dθ 2 η η where f1 (η|θ 1 ) and f2 (η|θ 2 ) distributions of η(z)
• 42. ABC Methods for Bayesian Model Choice Generic ABC model choiceLimiting behaviour of B12 ( → 0) When goes to zero, η η π1 (θ 1 )f1 (η(y)|θ 1 ) dθ 1 B12 (y) = η π2 (θ 2 )f2 (η(y)|θ 2 ) dθ 2
• 43. ABC Methods for Bayesian Model Choice Generic ABC model choiceLimiting behaviour of B12 ( → 0) When goes to zero, η η π1 (θ 1 )f1 (η(y)|θ 1 ) dθ 1 B12 (y) = η π2 (θ 2 )f2 (η(y)|θ 2 ) dθ 2 Bayes factor based on the sole observation of η(y)
• 44. ABC Methods for Bayesian Model Choice Generic ABC model choiceLimiting behaviour of B12 (under suﬃciency) If η(y) suﬃcient statistic in both models, fi (y|θ i ) = gi (y)fiη (η(y)|θ i ) Thus η Θ1 π(θ 1 )g1 (y)f1 (η(y)|θ 1 ) dθ 1 B12 (y) = η Θ2 π(θ 2 )g2 (y)f2 (η(y)|θ 2 ) dθ 2 η g1 (y) π1 (θ 1 )f1 (η(y)|θ 1 ) dθ 1 g1 (y) η = η = B (y) . g2 (y) π2 (θ 2 )f2 (η(y)|θ 2 ) dθ 2 g2 (y) 12 [Didelot, Everitt, Johansen & Lawson, 2011]
• 45. ABC Methods for Bayesian Model Choice Generic ABC model choiceLimiting behaviour of B12 (under suﬃciency) If η(y) suﬃcient statistic in both models, fi (y|θ i ) = gi (y)fiη (η(y)|θ i ) Thus η Θ1 π(θ 1 )g1 (y)f1 (η(y)|θ 1 ) dθ 1 B12 (y) = η Θ2 π(θ 2 )g2 (y)f2 (η(y)|θ 2 ) dθ 2 η g1 (y) π1 (θ 1 )f1 (η(y)|θ 1 ) dθ 1 g1 (y) η = η = B (y) . g2 (y) π2 (θ 2 )f2 (η(y)|θ 2 ) dθ 2 g2 (y) 12 [Didelot, Everitt, Johansen & Lawson, 2011] c No discrepancy only when cross-model suﬃciency
• 46. ABC Methods for Bayesian Model Choice Generic ABC model choicePoisson/geometric example Sample x = (x1 , . . . , xn ) from either a Poisson P(λ) or from a geometric G(p) Sum n S= xi = η(x) i=1 suﬃcient statistic for either model but not simultaneously Discrepancy ratio g1 (x) S!n−S / i xi ! = g2 (x) 1 n+S−1 S
• 47. ABC Methods for Bayesian Model Choice Generic ABC model choicePoisson/geometric discrepancy η Range of B12 (x) versus B12 (x): The values produced have nothing in common.
• 48. ABC Methods for Bayesian Model Choice Generic ABC model choiceFormal recovery Creating an encompassing exponential family T T f (x|θ1 , θ2 , α1 , α2 ) ∝ exp{θ1 η1 (x) + θ1 η1 (x) + α1 t1 (x) + α2 t2 (x)} leads to a suﬃcient statistic (η1 (x), η2 (x), t1 (x), t2 (x)) [Didelot, Everitt, Johansen & Lawson, 2011]
• 49. ABC Methods for Bayesian Model Choice Generic ABC model choiceFormal recovery Creating an encompassing exponential family T T f (x|θ1 , θ2 , α1 , α2 ) ∝ exp{θ1 η1 (x) + θ1 η1 (x) + α1 t1 (x) + α2 t2 (x)} leads to a suﬃcient statistic (η1 (x), η2 (x), t1 (x), t2 (x)) [Didelot, Everitt, Johansen & Lawson, 2011] In the Poisson/geometric case, if i xi ! is added to S, no discrepancy
• 50. ABC Methods for Bayesian Model Choice Generic ABC model choiceFormal recovery Creating an encompassing exponential family T T f (x|θ1 , θ2 , α1 , α2 ) ∝ exp{θ1 η1 (x) + θ1 η1 (x) + α1 t1 (x) + α2 t2 (x)} leads to a suﬃcient statistic (η1 (x), η2 (x), t1 (x), t2 (x)) [Didelot, Everitt, Johansen & Lawson, 2011] Only applies in genuine suﬃciency settings... c Inability to evaluate loss brought by summary statistics
• 51. ABC Methods for Bayesian Model Choice Generic ABC model choiceThe Pitman–Koopman lemma Eﬃcient suﬃciency is not such a common occurrence: Lemma A necessary and suﬃcient condition for the existence of a suﬃcient statistic with ﬁxed dimension whatever the sample size is that the sampling distribution belongs to an exponential family. [Pitman, 1933; Koopman, 1933]
• 52. ABC Methods for Bayesian Model Choice Generic ABC model choiceThe Pitman–Koopman lemma Eﬃcient suﬃciency is not such a common occurrence: Lemma A necessary and suﬃcient condition for the existence of a suﬃcient statistic with ﬁxed dimension whatever the sample size is that the sampling distribution belongs to an exponential family. [Pitman, 1933; Koopman, 1933] Provision of ﬁxed support (consider U(0, θ) counterexample)
• 53. ABC Methods for Bayesian Model Choice Generic ABC model choiceMeaning of the ABC-Bayes factor ‘This is also why focus on model discrimination typically (...) proceeds by (...) accepting that the Bayes Factor that one obtains is only derived from the summary statistics and may in no way correspond to that of the full model.’ [Scott Sisson, Jan. 31, 2011, ’Og]
• 54. ABC Methods for Bayesian Model Choice Generic ABC model choiceMeaning of the ABC-Bayes factor ‘This is also why focus on model discrimination typically (...) proceeds by (...) accepting that the Bayes Factor that one obtains is only derived from the summary statistics and may in no way correspond to that of the full model.’ [Scott Sisson, Jan. 31, 2011, ’Og] In the Poisson/geometric case, if E[yi ] = θ0 > 0, η (θ0 + 1)2 −θ0 lim B12 (y) = e n→∞ θ0
• 55. ABC Methods for Bayesian Model Choice Generic ABC model choiceMA example 0.7 0.6 0.6 0.6 0.6 0.5 0.5 0.5 0.5 0.4 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.2 0.2 0.2 0.2 0.1 0.1 0.1 0.1 0.0 0.0 0.0 0.0 1 2 1 2 1 2 1 2 Evolution [against ] of ABC Bayes factor, in terms of frequencies of visits to models MA(1) (left) and MA(2) (right) when equal to 10, 1, .1, .01% quantiles on insuﬃcient autocovariance distances. Sample of 50 points from a MA(2) with θ1 = 0.6, θ2 = 0.2. True Bayes factor equal to 17.71.
• 56. ABC Methods for Bayesian Model Choice Generic ABC model choiceMA example 0.8 0.6 0.6 0.6 0.6 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 1 2 1 2 1 2 1 2 Evolution [against ] of ABC Bayes factor, in terms of frequencies of visits to models MA(1) (left) and MA(2) (right) when equal to 10, 1, .1, .01% quantiles on insuﬃcient autocovariance distances. Sample of 50 points from a MA(1) model with θ1 = 0.6. True Bayes factor B21 equal to .004.
• 57. ABC Methods for Bayesian Model Choice Generic ABC model choiceFurther comments ‘There should be the possibility that for the same model, but diﬀerent (non-minimal) [summary] statistics (so ∗ diﬀerent η’s: η1 and η1 ) the ratio of evidences may no longer be equal to one.’ [Michael Stumpf, Jan. 28, 2011, ’Og] Using diﬀerent summary statistics [on diﬀerent models] may indicate the loss of information brought by each set but agreement does not lead to trustworthy approximations.
• 58. ABC Methods for Bayesian Model Choice Generic ABC model choiceA population genetics evaluation Population genetics example with 3 populations 2 scenari 15 individuals 5 loci single mutation parameter
• 59. ABC Methods for Bayesian Model Choice Generic ABC model choiceA population genetics evaluation Population genetics example with 3 populations 2 scenari 15 individuals 5 loci single mutation parameter 24 summary statistics 2 million ABC proposal importance [tree] sampling alternative
• 60. ABC Methods for Bayesian Model Choice Generic ABC model choiceStability of importance sampling 1.0 1.0 1.0 1.0 1.0 q q 0.8 0.8 0.8 0.8 0.8 0.6 0.6 0.6 0.6 0.6 q 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0
• 61. ABC Methods for Bayesian Model Choice Generic ABC model choiceComparison with ABC Use of 24 summary statistics and DIY-ABC logistic correction 1.0 qq qq qq qq qqq qq q q qq q q qq q q q q q q q q q q qq q q qq q q q qq qq qq q q q q qq q q q q q q q q q q q qq q q q qq q q 0.8 q q q q q q q q q q q q qq q q q q q q q qq q q q q q qqq q q qq q ABC direct and logistic q q qq q q q q q q q 0.6 q q q qq q q qq q q q q q q q q q q q q q q q q q q q q q q q q q qq qq q q qq 0.4 qq q q q q q q q q q q q q q q q q q 0.2 q qq q q q q q q q q q q 0.0 qq 0.0 0.2 0.4 0.6 0.8 1.0 importance sampling
• 62. ABC Methods for Bayesian Model Choice Generic ABC model choiceComparison with ABC Use of 15 summary statistics and DIY-ABC logistic correction 6 4 q q q q q q q qq 2 q q q q qq ABC direct q q q qq q qq q q q q qq qq q qq q q q q q qq q q q q q qq q q qq q qq q q qq q q q qqq q q q q q q q q 0 qq qq q q q q qq qq q q qq q q q q q q q q −2 −4 −4 −2 0 2 4 6 importance sampling
• 63. ABC Methods for Bayesian Model Choice Generic ABC model choiceComparison with ABC Use of 15 summary statistics and DIY-ABC logistic correction qq 6 q q q q q q q q q q q 4 q qq q qq qq q q q q q q q q q q qq q q q q q q q ABC direct and logistic q q q q q q q qq q q q q q q q qq q 2 q q q q q qq q qq q q q qq qq q qq qq q q q qq q q qq qq qq q q qqqq qq q q q qqqqq qq q q q qq q q q q qq q qq q q qqq q q qqqqq q q qq q q qq q q q qq 0 qq qqq q q qq q qqq q q q q q q q q q q q q q q q q q q q q qq q q −2 q q q q q −4 q q q −4 −2 0 2 4 6 importance sampling
• 64. ABC Methods for Bayesian Model Choice Generic ABC model choiceComparison with ABC Use of 15 summary statistics and DIY-ABC logistic correction q 2 q q 1 q q q q q q q q q q log−ratio q q q q q qq q q q qqq q q q q q q q qq q q q q q qq qq q qq q q qqqqqq q q qqqq qq qq q qq qq q qq q qq qq q q q qq q qq q q qqq q 0 q q q q qq q q q qq q q q q q q qq q qq q qq qq q qq qqq qq qq q q q q qq q qqqq q q q q q q q q qq qqq q qq qq q q qq q q q q qq q q qq q q q q q q q q qq qqqq q q q q q q q q q −1 q q q q −2 q 0 20 40 60 80 100 index
• 65. ABC Methods for Bayesian Model Choice Generic ABC model choiceA second population genetics experiment three populations, two divergent 100 gen. ago two scenarios [third pop. recent admixture between ﬁrst two pop. / diverging from pop. 1 5 gen. ago] In scenario 1, admixture rate 0.7 from pop. 1 100 datasets with 100 diploid individuals per population, 50 independent microsatellite loci. Eﬀective population size of 1000 and mutation rates of 0.0005. 6 parameters: admixture rate (U [0.1, 0.9]), three eﬀective population sizes (U [200, 2000]), the time of admixture/second divergence (U [1, 10]) and time of ﬁrst divergence (U [50, 500]).
• 66. ABC Methods for Bayesian Model Choice Generic ABC model choiceResults IS algorithm performed with 100 coalescent trees per particle and 50,000 particles [12 calendar days using 376 processors] Using ten times as many loci and seven times as many individuals degrades the conﬁdence in the importance sampling approximation because of an increased variability in the likelihood. 1.0 q qq q qq q q qqqq qq q q qq q q q q qq qq q q qq q q q q q 0.8 q Importance Sampling estimates of q P(M=1|y) with 1,000 particles q q 0.6 0.4 0.2 0.0 0.0 0.2 0.4 0.6 0.8 1.0 Importance Sampling estimates of
• 67. ABC Methods for Bayesian Model Choice Generic ABC model choiceResults Blurs potential divergence between ABC and genuine posterior probabilities because both are overwhelmingly close to one, due to the high information content of the data. 1.0 q q qqq q qqqq q q qqqqq q qqq qq qq qq qq qq q q q qq qqq Importance Sampling estimates of P(M=1|y) with 50,000 particles q q qq q q q qq q q q q q 0.8 q q q q 0.6 0.4 0.2 0.0 0.0 0.2 0.4 0.6 0.8 1.0 ABC estimates of P(M=1|y)
• 68. ABC Methods for Bayesian Model Choice Generic ABC model choiceThe only safe cases??? Besides speciﬁc models like Gibbs random ﬁelds, using distances over the data itself escapes the discrepancy... [Toni & Stumpf, 2010;Sousa et al., 2009]
• 69. ABC Methods for Bayesian Model Choice Generic ABC model choiceThe only safe cases??? Besides speciﬁc models like Gibbs random ﬁelds, using distances over the data itself escapes the discrepancy... [Toni & Stumpf, 2010;Sousa et al., 2009] ...and so does the use of more informal model ﬁtting measures [Ratmann, Andrieu, Richardson and Wiujf, 2009]