Inference-first 0.3.0: likelihoods as programs, optimizer mode, Pareto posterior, prior-owned encodings (#20)

* 0.3.0: inference-first — likelihoods as programs, optimizer mode, Pareto posterior, prior-owned encodings

Closes the three caveats left by the 0.2.0 refactor, completing the
"implementation of fugue for running evolutionary algorithms as Bayesian
inference" identity:

Fix A — likelihoods as programs (inference/likelihood.rs):
- GenomeLikelihood<G>: observation program p(data|g) with observes, factors,
  and latent nuisance parameters jointly inferred with the genome.
- tempered_observe helper; FactorFitness adapter (black-box mode = explicit
  Gibbs/generalized-Bayes posterior); NoLikelihood; MemoizedFitness
  (exact-key shared cache).
- EvolutionModel<P, L> generalization; new(prior, fitness) still works via
  FactorFitness; from_likelihood accepts any observation program.
- GaussianRegression with NoiseSpec::Infer: observation noise as a latent
  site, posterior read off particle traces (test recovers sigma=0.3).

Fix B1 — optimizer mode: EvolutionSMC::anneal continues the tempering
ladder past beta=1 (fugue primitives only: incremental reweight, normalize,
resample, rejuvenate, optional crossover sweep), concentrating on optima
with uncertainty attached. Head-to-head example vs SimpleGA.

Fix B2 — multi-objective as inference (inference/pareto.rs):
ParetoScalarization puts the scalarization weight inside the model
(uniform-simplex stick-breaking), so the posterior marginal traces the
Pareto front; particle_weights locates each particle on it. Analytic
biobjective validation (Pareto set [0,2], x*(w) = 2(1-w)).

Fix C — prior-owned encodings: GenomePrior::trace_of (grammar prior
overrides with the exact inverse of its generative walk; pinned by
inversion + hand-computed PCFG score tests); score/to_weighted_trace work
for grammar trees; EvolutionChain::init_from warm-starts from any genome.

Fix B3 — identity: `classic` feature gates the EC toolkit
(MultiObjectiveFitness moved to core fitness::multi_objective); std,ppl
builds inference standalone; std,parallel,checkpoint,classic builds classic
fugue-free; README/description lead with the inference identity.

All 9 suites green in default config; both minimal configs check clean;
clippy/fmt clean; wasm unchanged.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HmWLBR9Zq6hPG5o7URDuNJ

* Fix refactor-induced broken intra-doc links (rustdoc now warning-free)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HmWLBR9Zq6hPG5o7URDuNJ

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

Author: alexnodeland

CHANGELOG.md

@@ -7,6 +7,70 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.3.0] - 2026-07-28
+
+**Inference-first.** fugue-evo's identity is now "an implementation of fugue
+for running evolutionary algorithms as Bayesian inference"; the classic EC
+toolkit is a standalone, feature-gated companion. This release closes the
+three caveats left by 0.2.0: black-box-only fitness, the classic layer's
+monopoly on optimization/multi-objective, and the tree-encoding seam.
+
+### Added
+
+- **Likelihoods as programs** (`inference::likelihood`): the new
+  `GenomeLikelihood<G>` trait — an observation program `p(data|x)` that may
+  contain per-datum `observe` statements, `factor`s, and **latent nuisance
+  parameters jointly inferred with the genome**. `tempered_observe` helper;
+  `FactorFitness` adapter keeps the classical black-box mode as an explicit
+  Gibbs / generalized-Bayes posterior; `NoLikelihood` for prior-only runs.
+  `GaussianRegression` (`inference::grammar`) demonstrates the payoff: the
+  observation noise is a latent site (`NoiseSpec::Infer`), and its posterior
+  is read off the particle traces — pinned by
+  `test_symreg_infers_noise_jointly` (recovers a true sigma of 0.3).
+- **Optimizer mode** (`EvolutionSMC::anneal`): continue the tempering ladder
+  past beta = 1 toward `beta_max` (incremental reweight + resample +
+  pi_beta-invariant rejuvenation + optional crossover sweeps, all fugue
+  primitives), concentrating the population on the optima — a principled,
+  uncertainty-carrying single-objective optimizer. Pinned by
+  `test_anneal_concentrates_on_optimum`; head-to-head with SimpleGA in
+  `examples/optimize_by_inference.rs`.
+- **Multi-objective as inference** (`inference::pareto`):
+  `ParetoScalarization` puts the scalarization weight *inside the model*
+  (uniform-simplex stick-breaking Beta sites), so the joint posterior's
+  marginal traces the Pareto front and `particle_weights` reads each
+  particle's front position off its trace. Pinned analytically by
+  `test_pareto_posterior_traces_the_front` (biobjective with Pareto set
+  [0,2]: mass on the set, both ends covered, particles near their weight's
+  scalarized optimum x* = 2(1-w)).
+- **Prior-owned encodings** (`GenomePrior::trace_of`): encode a genome under
+  *the prior's* address scheme (default: the canonical `TraceGenome`
+  encoding; `ArithmeticGrammarPrior` overrides with the exact inverse of its
+  generative walk — pinned by `test_trace_of_inverts_generative_run` and a
+  hand-computed PCFG score). `EvolutionModel::score`/`to_weighted_trace` now
+  work for grammar trees, and the new `EvolutionChain::init_from(genome)`
+  warm-starts a chain from any in-support genome — including a classic GA/GP
+  result.
+- **`MemoizedFitness`**: exact-key (bincode) shared-cache fitness wrapper,
+  removing repeated evaluations under replay-heavy inference.
+
+### Changed (breaking)
+
+- `EvolutionModel<P, F>` is now `EvolutionModel<P, L: GenomeLikelihood>`.
+  `EvolutionModel::new(prior, fitness)` still works (it now returns
+  `EvolutionModel<P, FactorFitness<F>>`); explicit type annotations need the
+  `FactorFitness` wrapper. `from_likelihood(prior, likelihood)` accepts any
+  observation program. `fitness_value`/`log_weight`/`to_weighted_trace` are
+  specific to the `FactorFitness` mode (EV-52 unchanged and green).
+- **`classic` feature (default on)**: `algorithms`, `operators`,
+  `population`, `hyperparameter`, `interactive`, `checkpoint`,
+  `diagnostics`, `termination` are now gated. `--no-default-features
+  --features std,ppl` builds the inference layer with no classic EC code;
+  `--features std,parallel,checkpoint,classic` builds classic with no fugue.
+  `MultiObjectiveFitness`/`ClosureMultiObjective` moved to the core
+  `fitness::multi_objective` (re-exported from `algorithms::nsga2`).
+- Crate description and README lead with the inference identity.
+
+
 ## [0.2.0] - 2026-07-28
 
 **"Evolutionary algorithms as probabilistic programs"** — the two-layer

CLAUDE.md

@@ -44,7 +44,10 @@ fugue-evo is a **two-layer** evolutionary-computation library:
 
 - `EvolutionaryGenome` (src/genome/traits.rs): the classic, fugue-free genome trait (decode/dimension/generate/distance).
 - `TraceGenome` (src/genome/trace_genome.rs, `ppl`): extension trait adding `to_trace`/`from_trace`/`trace_prefix` — the boundary into the inference layer. `Permutation` uses a Lehmer-code (rank) encoding so single-site MH moves stay valid.
-- `GenomePrior` (src/inference/prior.rs): a prior as a program — `fn model(&self) -> fugue::Model<G>` returning the decoded genome. Built-ins: `UniformBoxPrior`, `GaussianPrior`, `BitStringPrior`, `PermutationPrior`, `ArithmeticGrammarPrior`.
+- `GenomePrior` (src/inference/prior.rs): a prior as a program — `fn model(&self) -> fugue::Model<G>` returning the decoded genome, plus `trace_of` (encode a genome under the prior's address scheme; grammar prior overrides it). Built-ins: `UniformBoxPrior`, `GaussianPrior`, `BitStringPrior`, `PermutationPrior`, `ArithmeticGrammarPrior`.
+- `GenomeLikelihood` (src/inference/likelihood.rs): an observation program `p(data|g)` — observes, factors, latent nuisance sites (jointly inferred). `FactorFitness` is the black-box Gibbs-posterior adapter; `MemoizedFitness` caches expensive evaluations.
+- Optimizer mode: `EvolutionSMC::anneal` tempers past beta=1. Multi-objective: `ParetoScalarization` (src/inference/pareto.rs) — scalarization weight as a latent site; posterior traces the Pareto front.
+- Feature matrix: `classic` gates the EC toolkit; `ppl` gates inference; each builds without the other (`std,ppl` and `std,parallel,checkpoint,classic` are both CI-relevant configs).
 
 Built-in genome types: `RealVector`, `BitString`, `Permutation`, `TreeGenome`
 

Cargo.lock

@@ -12,10 +12,10 @@ lto = true
 
 [package]
 name = "fugue-evo"
-version = "0.2.0"
+version = "0.3.0"
 edition = "2021"
 authors = ["Alex Nodeland"]
-description = "Evolutionary computation for Rust: classical EC algorithms plus evolutionary inference - evolutionary algorithms as probabilistic programs (tempered SMC in trace space, built on fugue-ppl)"
+description = "An implementation of fugue for running evolutionary algorithms as Bayesian inference: priors and likelihoods as probabilistic programs, tempered SMC in trace space, annealed optimization, Pareto posteriors - plus a standalone classical EC toolkit"
 license = "MIT"
 repository = "https://github.com/alexnodeland/fugue-evo"
 documentation = "https://docs.rs/fugue-evo"
@@ -24,10 +24,16 @@ keywords = ["genetic-algorithm", "evolution", "optimization", "bayesian", "ppl"]
 categories = ["algorithms", "science"]
 
 [features]
-default = ["std", "parallel", "checkpoint", "ppl"]
+default = ["std", "parallel", "checkpoint", "ppl", "classic"]
 std = []
 parallel = ["rayon"]
 checkpoint = []  # File-based checkpointing (requires std)
+# Classic EC layer: algorithms, operators, population machinery, checkpointing,
+# hyperparameter tuning, interactive GA, diagnostics, termination. Off => only
+# the core (error/fitness/genome) and, with `ppl`, the inference layer compile.
+# `checkpoint` and `parallel` only affect classic code paths, so they are inert
+# without `classic`.
+classic = []
 # Probabilistic-programming bridge: the TraceGenome extension trait and the
 # fugue-native inference layer. Off => the classic EC layer compiles with no
 # fugue-ppl dependency at all.
@@ -88,10 +94,38 @@ criterion = "0.5"
 approx = "0.5"
 tempfile = "3.10"
 
-# Examples requiring parallel feature
+# Examples gated on the features they exercise
 [[example]]
 name = "island_model"
-required-features = ["parallel"]
+required-features = ["parallel", "classic"]
+
+[[example]]
+name = "sphere_optimization"
+required-features = ["classic"]
+
+[[example]]
+name = "rastrigin_benchmark"
+required-features = ["classic"]
+
+[[example]]
+name = "cma_es_example"
+required-features = ["classic"]
+
+[[example]]
+name = "hyperparameter_learning"
+required-features = ["classic"]
+
+[[example]]
+name = "symbolic_regression"
+required-features = ["classic"]
+
+[[example]]
+name = "checkpointing"
+required-features = ["classic", "checkpoint"]
+
+[[example]]
+name = "interactive_evolution"
+required-features = ["classic"]
 
 [[example]]
 name = "bayesian_evolution"
@@ -100,3 +134,7 @@ required-features = ["ppl"]
 [[example]]
 name = "symbolic_regression_inference"
 required-features = ["ppl"]
+
+[[example]]
+name = "optimize_by_inference"
+required-features = ["ppl", "classic"]

Cargo.toml

@@ -4,7 +4,7 @@
 
 # Fugue Evo
 
-**Two layers: classical evolutionary algorithms (standalone), and evolutionary inference — evolutionary algorithms *as* probabilistic programs (tempered SMC in trace space, built on [Fugue](https://github.com/alexnodeland/fugue))**
+**An implementation of [Fugue](https://github.com/alexnodeland/fugue) for running evolutionary algorithms as Bayesian inference — priors and likelihoods as probabilistic programs, tempered SMC in trace space — plus a standalone classical EC toolkit**
 
 *Populations hunting real landscapes, live in your browser: every figure in the docs at [evo.fugue.run](https://evo.fugue.run) runs the actual crate, compiled to WASM.*
 
@@ -16,10 +16,14 @@
 
 </div>
 
-An evolutionary-computation library for Rust with an architectural split that keeps both halves honest:
+fugue-evo runs evolution as inference. The prior over genomes is a user-written fugue `Model<G>` (a `GenomePrior`); the data enter through a `GenomeLikelihood` — an *observation program* that may contain per-datum `observe` statements, latent nuisance parameters (e.g. an unknown noise scale, jointly inferred with the genome), or a black-box `factor(β·f(x))` (the classical Gibbs-posterior mode). The target `π_β(x) ∝ p(x)·p(data|x)^β` **is a fugue program**, and every sampler is fugue's own inference machinery:
 
-- **Classic EC (no fugue dependency).** SimpleGA, CMA-ES, NSGA-II, Island Model, Evolution Strategy, EDA/UMDA, SteadyState, all operators, checkpointing, and the WASM surface. Build with `--no-default-features --features std,parallel,checkpoint` and there is no probabilistic-programming dependency at all.
-- **Evolutionary inference (`ppl` feature, on by default): evolutionary algorithms *as* probabilistic programs.** The prior over genomes is a user-written fugue `Model<G>` (a `GenomePrior`), fitness enters as `factor(β·f(x))`, so the Boltzmann posterior `π_β(x) ∝ p(x)·exp(β·f(x))` **is a fugue program** — and every sampler is fugue's own inference machinery: `EvolutionChain` (typed single-site MH), `EvolutionSMC` (adaptive tempered SMC with a population-coupled crossover kernel and an unbiased log-evidence estimate), and `ArithmeticGrammarPrior` (genetic programming over a probabilistic grammar, where subtree mutation and crossover are generic trace moves). See `examples/symbolic_regression_inference.rs` — symbolic regression as exact Bayesian inference.
+- **`EvolutionChain`** — typed single-site MH (every site kind moves: reals, bits, permutation ranks, tree structure with automatic reversible-jump corrections), warm-startable from any genome via `init_from`.
+- **`EvolutionSMC`** — adaptive tempered SMC with a population-coupled crossover kernel, decode-replay genome recovery, and an unbiased **log-evidence** estimate for Bayesian model comparison. `EvolutionSMC::anneal` keeps tempering past β = 1 for **optimizer mode** — a principled single-objective optimizer with uncertainty attached.
+- **`ArithmeticGrammarPrior`** — genetic programming over a probabilistic grammar: subtree mutation and crossover are generic trace moves. `examples/symbolic_regression_inference.rs` does symbolic regression as exact Bayesian inference.
+- **`ParetoScalarization`** — multi-objective optimization as inference: the scalarization weight is a latent model site, so the posterior marginal *traces the Pareto front* and each particle knows where on the front it lives.
+
+The **classic EC toolkit** (`classic` feature, on by default) — SimpleGA, CMA-ES, NSGA-II, Island Model, ES, EDA/UMDA, operators, checkpointing, the WASM surface — remains fully standalone: build with `--no-default-features --features std,parallel,checkpoint,classic` and there is no probabilistic-programming dependency at all. Conversely, `--features std,ppl` builds the inference layer with no classic EC code. CMA-ES and NSGA-II are deliberately *not* reframed as inference (CMA-ES is not a posterior sampler); they serve as baselines.
 
 ## Features
 

README.md

@@ -17,8 +17,8 @@ publish = false
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
-# Core library without parallel/checkpoint features
-fugue-evo = { path = "../..", default-features = false, features = ["std"] }
+# Classic EC layer without parallel/checkpoint/ppl features
+fugue-evo = { path = "../..", default-features = false, features = ["std", "classic"] }
 
 # WASM bindings
 wasm-bindgen = "0.2"

crates/fugue-evo-wasm/Cargo.toml

@@ -0,0 +1,73 @@
+//! Optimizer mode: annealed inference vs a classic GA on the same problem.
+//!
+//! `EvolutionSMC::anneal` keeps tempering past the posterior (β = 1) toward
+//! `β_max`, so the particle population concentrates on the optima — a
+//! principled, uncertainty-aware single-objective optimizer built entirely
+//! from inference machinery. This example runs it head-to-head with the
+//! classic `SimpleGA` on the sphere benchmark and prints what each layer
+//! gives you.
+//!
+//! Run with: `cargo run --example optimize_by_inference`
+
+use fugue_evo::prelude::*;
+use rand::rngs::StdRng;
+use rand::SeedableRng;
+
+const DIM: usize = 4;
+
+fn main() -> Result<(), Box<dyn std::error::Error>> {
+    println!("=== Single-objective optimization: annealed inference vs classic GA ===\n");
+    let mut rng = StdRng::seed_from_u64(20260728);
+
+    // Sphere: f(x) = -Σx², optimum 0 at the origin.
+    let fitness = Sphere::new(DIM);
+    let bounds = MultiBounds::symmetric(5.12, DIM);
+
+    // ---------------- Classic GA ----------------
+    let ga_result = SimpleGABuilder::real_valued()
+        .population_size(100)
+        .bounds(bounds.clone())
+        .fitness(Sphere::new(DIM))
+        .max_generations(200)
+        .build()?
+        .run(&mut rng)?;
+    println!("-- SimpleGA (classic layer) --");
+    println!(
+        "  best fitness: {:.6}   (~{} fitness evaluations)",
+        ga_result.best_fitness,
+        100 * 200
+    );
+
+    // ---------------- Annealed inference ----------------
+    let model = EvolutionModel::new(UniformBoxPrior::new(bounds), fitness.clone());
+    let annealed = EvolutionSMC::anneal(
+        &mut rng,
+        &model,
+        EvoSmcConfig {
+            num_particles: 300,
+            rejuvenation_steps: 4,
+            crossover: Some(CrossoverConfig::default()),
+            ..Default::default()
+        },
+        500.0, // β_max: how hard to anneal
+        15,    // annealing rungs past β = 1
+    );
+    let model_fn = model.smc_model();
+    let (best, best_f) = annealed.best(&fitness, &model_fn).unwrap();
+    println!("\n-- EvolutionSMC::anneal (inference layer) --");
+    println!("  best fitness: {:.6}", best_f);
+    println!("  best genome:  {:?}", best.genes());
+    println!(
+        "  population spread at β=500: {:.4} (posterior-style uncertainty, not a point)",
+        (0..DIM)
+            .map(|i| annealed.weighted_variance(i))
+            .sum::<f64>()
+            .sqrt()
+    );
+    println!(
+        "  log evidence (β ≤ 1 ladder): {:.3} — a model score no GA can report",
+        annealed.log_evidence
+    );
+
+    Ok(())
+}

examples/optimize_by_inference.rs

@@ -60,14 +60,13 @@ impl Fitness for SymRegFit {
     }
 }
 
-fn run_inference(
-    rng: &mut StdRng,
-    fitness: &SymRegFit,
-    n_functions: usize,
-) -> (
-    EvolutionPosterior<TreeGenome<ArithmeticTerminal, ArithmeticFunction>>,
-    EvolutionModel<ArithmeticGrammarPrior, SymRegFit>,
-) {
+type SymRegTree = TreeGenome<ArithmeticTerminal, ArithmeticFunction>;
+type SymRegResult = (
+    EvolutionPosterior<SymRegTree>,
+    EvolutionModel<ArithmeticGrammarPrior, FactorFitness<SymRegFit>>,
+);
+
+fn run_inference(rng: &mut StdRng, fitness: &SymRegFit, n_functions: usize) -> SymRegResult {
     let prior = ArithmeticGrammarPrior {
         terminal_prob: 0.35,
         max_depth: 5,