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ABC-MCMC and ABC-sequential Monte Carlo — Examples
1 · Prerequisites
- ABC-MCMC and ABC-sequential Monte Carlo
- Absolute and Conditional Convergence; Rearrangement; Products
- Approximate Bayesian computation and summary-based inference
- Bayesian models, priors, and posterior laws
- Binary Operations, Monoids, Groups and Subgroups
- Compactness in Metric Spaces
- Complete Metrizability, Čech-Completeness, and Baire Category
- Completeness, Completion, and Uniform Continuity
- Conditional Distributions and Regular Conditional Probability
- Conditional Expectation
- Construction of the Natural Numbers
- Construction of the Real Numbers via Cauchy Sequences
- Construction of the Real Numbers via Dedekind Cuts
- Continuity, IVT, EVT, and Uniform Continuity
- Cosets, Index and Lagrange's Theorem
- Countability and Uncountability
- Countability Axioms and Cardinal Functions
- Discrete Time Martingales
- Divisibility, Euclidean Domains, Principal Ideal Domains and Unique Factorisation
- Domination and Likelihood Ratios
- Estimators and Randomized Procedures
- Feynman–Kac targets and sequential particle filters
- Finite Counting, Factorials and Binomial Coefficients
- Foundations of the Real Numbers for Analysis
- General-state Markov kernels, invariance, and reversibility
- Ideals, Quotient Rings and the Isomorphism Theorems for Rings
- Infinite Product Measures and Kolmogorov Extension
- Limits of Real Functions
- limsup, liminf, and Subsequential Limits
- Loss, Risk and Decision Theory
- Markov Kernels and Markov Chains
- Measurable Functions and Simple Approximation
- Measures and Their Basic Properties
- Metric Spaces
- Metropolis–Hastings kernels
- Monotone Functions, Discontinuities, and Continuity Sets
- Monotone Sequences, Bolzano-Weierstrass, and Cauchy Completeness
- Normal Subgroups and Quotient Groups
- Order, Zorn's Lemma, and the Axiom of Choice
- Outer Measure and the Caratheodory Extension Theorem
- Polynomial Rings, the Division Algorithm and Roots
- Power Series and Real-Analytic Functions
- Probability Spaces Random Variables and Expectation
- Product Measures and the Fubini Tonelli Theorems
- Properties of the Integral and the Working FTC
- Recurrence Transience and Hitting Times for Markov Chains
- Relations, Functions, and Quotients
- Rings, Subrings, Integral Domains and Fields
- Roots, Rational Powers, and Classical Inequalities
- Separation Axioms: the Hierarchy
- Sequences and Limits
- Sequences and Series of Functions; Uniform Convergence
- Series: Convergence and the Nonnegative Tests
- Sigma Algebras and Borel Sets
- Signed and Complex Measures Hahn and Jordan
- Simple Field Extensions and the Construction of the Complex Numbers
- Standard-Borel Real Codings and Determining Classes
- Stationary Markov Chains and Ergodic Limits
- Statistical Experiments, Models and Identifiability
- Subspaces, Products, and Quotients
- Suprema and Infima
- The Cantor Set, Baire Category, and Measure Zero in ℝ
- The Derivative and the Mean Value Theorems
- The Exponential Function
- The Lebesgue Integral and the Convergence Theorems
- The Logarithm and General Powers
- The Lᵖ Spaces Holder Minkowski and Riesz Fischer
- The Radon Nikodym Theorem and Lebesgue Decomposition
- The Riemann Integral: Definition and Integrability
- The Topology of Euclidean Space
- The ZFC Axioms and the Basic Set Constructions
- Topological Spaces and Continuity
- Topology of ℝ
- Triangularisation, Generalised Eigenspaces and Jordan Canonical Form
- Vector Spaces, Linear Subspaces, Span and Direct Sums
2 · Summary
These finite and continuous examples calculate the augmented stationary target, show how a positive tolerance and a summary can differ from the exact-data posterior, derive an ABC-SMC mixture weight by hand, and exhibit vanishing acceptance and finite-particle collapse. Each calculation checks only its stated model and does not establish general accuracy or convergence.
3 · Logical flowchart
4 · Definitions, theorems and proofs
None yet.
5 · Examples, counterexamples and false statements
ABC acceptance probability vanishes with the tolerance
Example
Let the parameter space be the singleton with its unit prior and let the simulator return , independently of the parameter. Use the independence proposal , meaning that each proposal draws the singleton parameter and a fresh uniform datum. Take , observation , and absolute distance. For , the tolerance event is ; for it contains the full simulator support . For positive tolerance use the explicit Metropolis–Hastings density representatives constructed below; acceptance at individual starting states can depend on this choice.
Verification
Given: A uniform simulator on , the stated summary and observation, and a tolerance .
[F1] Augmented ABC tolerance target: the prior-predictive tolerance-event probability is , and the indicator target is defined only when .
[F2] ABC Metropolis–Hastings on simulator-augmented states: a proposed augmented state is simulated and retained only according to the fixed-tolerance Metropolis–Hastings accepted-flow rule.
[F3] Metropolis–Hastings kernel: the generic procedure accepts with the density of the common symmetric part of the forward and transposed proposal flows relative to the forward flow and otherwise makes a self-transition. The procedure chooses measurable representatives and with everywhere, and uses when and when .
For , the tolerance interval has length , so the singleton prior gives ; for it covers all of , so .
Fix and write for the tolerance indicator of the datum in the augmented state . Relative to , the forward and transposed flows have densities and . Choose and when , and otherwise. These are measurable, sum to one everywhere, and multiplying them by the density of recovers the two flow densities; hence they are valid representatives for [F3].
At every admissible current state , , so these representatives give , and thus . Consequently the acceptance probability is , equal to for and to for . At , and [F1] assigns no target. The pointwise acceptance calculation uses the specified representatives, rather than arbitrary modifications on flow-null sets.
A positive-tolerance ABC-MH stationary law can differ from the exact-data posterior
Example
Let have the uniform prior and let . The simulator probabilities are Take summary , , observed summary , distance , and positive tolerance . Thus the accepted data set is . Use the independence simulator proposal , where is the prior-simulator law.
Verification
Given: The finite prior, simulator, summary, tolerance, and independence proposal specified in the Example.
[F1] Augmented ABC tolerance target: the augmented target is when .
[F2] The augmented ABC target has the tolerance posterior as its parameter marginal: the parameter marginal of the augmented target is the tolerance-conditioned ABC law.
[F3] ABC Metropolis–Hastings on simulator-augmented states: ABC-MH applies the general Metropolis–Hastings accepted-flow construction to this target and the simulator-based proposal, keeping rejected proposals as self-transitions.
[F4] ABC Metropolis–Hastings preserves its augmented tolerance target: the resulting kernel is reversible with respect to and leaves invariant this fixed-tolerance target.
[F5] Metropolis–Hastings kernel: the general accepted-flow procedure uses the common part of the forward and transposed proposal flows and retains rejected proposals as self-transitions.
The accepted prior-simulator masses are , , , and , while has mass outside the tolerance; hence .
Dividing those four accepted masses by gives augmented masses and, by [F2], parameter marginal .
Given exact data , the prior-weighted likelihood masses are at and at , so the exact posterior is , different from because the tolerance summary merges with .
For accepted current and proposed states, the forward flow is , symmetric under swap, so [F5] accepts; for proposal the transposed flow is zero and the proposal is rejected. Thus for accepted , and integration gives , verifying stationarity consistently with [F4].
A finite ABC-SMC tolerance schedule and its mixture weights
Example
Let have the uniform prior and . The simulator has and , while , , and . Take , , and . Let and . At stage every simulated datum meets the tolerance. Condition on the possible stage-0 population with weights . At stage use a perturbation kernel with and , and set the same row from so is fully specified.
Verification
Given: The model, tolerances, previous weighted population, and perturbation kernel specified in the Example.
[F1] Augmented ABC tolerance target: the tolerance target has unnormalized measure and normalizer .
[F2] Sequential ABC importance-resampling with tolerance populations: the proposal mixture is the weighted mixture of perturbation kernels, and the incremental weight is the tolerance indicator times .
[F3] Sequential ABC Radon–Nikodym weights target each tolerance law: under the mixture support condition, the conditional expected unnormalized weighted proposal law is , whose total mass is . Dividing this measure by gives the current normalized tolerance target; this does not assert unbiasedness of a self-normalized finite-particle estimate.
At , all simulated summaries are accepted, so ; at , acceptance probabilities are and at the two parameter values, giving and target parameter masses .
For the previous population , and , so it dominates the uniform prior and the RN ratios are and .
A proposal matches tolerance with probability ; its expected weight contributions at are and , totaling . Their ratio is , the population target marginal by [F3]; these are normalized expected unnormalized weights, not a realized self-normalized finite-particle estimate.
Finite ABC-SMC particles can miss target support despite a valid mixture weight
Example
Let have the uniform prior and . The simulator has and , while , , and . Take , , , and . Let the previous two-particle population be with equal weights and use the stage-1 kernel , , with the same row from . The proposal mixture has full prior support, and its Radon–Nikodym weights are finite.
Verification
Given: The stage-1 prior, simulator, tolerance event, proposal mixture, and particle count specified in the Example.
[F1] Sequential ABC importance-resampling with tolerance populations: a candidate receives weight , and a zero-total-weight population is reported as degenerate.
[F2] Sequential ABC Radon–Nikodym weights target each tolerance law: the theorem does not claim that a finite self-normalized particle population represents all positive target mass.
The proposal masses are and , so the uniform prior is dominated and the finite RN weights are and . Tolerance acceptance is certain at and has probability at , so and the unnormalized target mass at is , giving normalized mass .
Each proposal has parameter with probability , independently conditional on the previous population, so both have parameter with probability ; on this event both weights equal and the normalized empirical measure assigns zero mass to .
Step 1.1 gives true target mass at , whereas the positive-probability event in step 2.1 has no empirical mass there; any resampled offspring also stay at . This illustrates the finite-particle caveat in [F2] despite valid support and weights.
Sources
- Jarno Lintusaari, Michael U. Gutmann, Ritabrata Dutta, Samuel Kaski, and Jukka Corander, Fundamentals and Recent Developments in Approximate Bayesian Computation, §§4–5
- Benjamin M. Turner and Thomas Van Zandt, A tutorial on approximate Bayesian computation, §3.1
- Jarno Lintusaari, Michael U. Gutmann, Ritabrata Dutta, Samuel Kaski, and Jukka Corander, Fundamentals and Recent Developments in Approximate Bayesian Computation, §5
- Jarno Lintusaari, Michael U. Gutmann, Ritabrata Dutta, Samuel Kaski, and Jukka Corander, Fundamentals and Recent Developments in Approximate Bayesian Computation, §5.2 and Appendix, Algorithm 4
- Benjamin M. Turner and Thomas Van Zandt, A tutorial on approximate Bayesian computation, §3.2
- Osvaldo A. Martin, Ravin Kumar, and Junpeng Lao, Bayesian Modeling and Computation in Python, Chapter 8
- Jarno Lintusaari, Michael U. Gutmann, Ritabrata Dutta, Samuel Kaski, and Jukka Corander, Fundamentals and Recent Developments in Approximate Bayesian Computation, §5.2