Add Topic Model

Add a topic model to topica

Port a new topic-modeling algorithm into topica as a faithful, fast, conventional, and validated addition. The deliverable is a merged PR: a Rust-core model with Python bindings, validated against its reference implementation, with the README and docs updated.

This is a long, multi-phase task. Run the phases in order. Each builds on the last; do not skip the validation phases — faithfulness to the reference is the whole point of a port.

Two dual-review gates bracket the implementation. A fixed pair of reviewers — Reviewer A (faithful / full parity, Codex) and Reviewer B (adversarial, Gemini), with a Claude subagent as the per-slot fallback — reviews the work twice: once after the plan is approved and before any code (Gate A, below after Phase 2), and once after implementation and before opening the PR (Gate B, Phase 5). The roles and their backing models stay fixed across both gates; do not swap who is faithful-parity and who is adversarial. See references/evaluation-agents.md for the mechanism, prompts, and synthesis rule.

Orient first (read these once)

• CONTRIBUTING-MODELS.md — the deep implementer's playbook for the Rust/PyO3 mechanics (the Estimator trait, the binding, the conformance checks, the add-a-model checklist). This skill orchestrates the process; that file is the how-to for Phase 3. Read it before implementing.
• CLAUDE.md — build/test commands, layout, conventions, branching. Authoritative.
• docs/contributing/conventions.md and tests/test_naming_conventions.py — the enforced cross-model naming/API contract. New models must pass that test.
• references/conventions.md (in this skill) — the distilled rules you will apply constantly: the fitted-model surface, naming + alias philosophy, the determinism guarantee, build/test gates.

Then pick a short kebab name for the model and its canonical class name early; it threads through every phase.

Phase 1 — Ground it in the literature

Goal: a written spec you can implement and check against, before any code.

1. Identify the algorithm and read its source paper(s). Capture, in a scratch note (/private/tmp/<model>-spec.md): the generative model, the inference method (collapsed Gibbs / variational EM / VAE / optimal transport / …), every hyperparameter and its default, and what outputs define a correct fit (topic-word, doc-topic, and any model-specific diagnostics, e.g. a covariate effect, a change-point, a keyword rate).
2. Decide where it sits in topica's family (count-based Gibbs, logistic-normal variational, embedding-based, …) — this determines which existing core file it most resembles. The core is split across two crates (a Cargo workspace):
   • topica-core/src/ holds the logistic-normal structural cluster and shared numerics — ctm.rs (CTM/STM/SAGE), spectral.rs, cvb0.rs, estimator.rs, linalg.rs, and the variational/ kernels (L-BFGS, the Laplace E-step, the Σ/Γ M-step). This crate is dependency-light so downstream Rust (e.g. faSTM) can vendor it; touch it only for the structural-variational family.
   • src/ holds every other model (keyatm.rs, etm.rs, dmr.rs, hdp.rs, prodlda.rs, the Gibbs/embedding/VAE models, …) plus the shared sampler.rs, optimize.rs, coherence.rs. topica re-exports topica-core, so topica::ctm::* still resolves. Most new models land here. Reuse the closest shared machinery rather than re-deriving it.
3. Fix the public name now: the canonical topica name follows our conventions, with aliases for the reference package's spelling. See references/conventions.md.

Phase 2 — Reference implementation and gold standard

Goal: a frozen set of reference outputs the topica port must reproduce.

Read references/reference-and-gold-standard.md for the full procedure. In short:

1. Find the reference implementation (the paper's repo, an R/Python/C++ package).
2. Check the license before reading or porting its code. Permissive (MIT/BSD/ Apache) — read freely to match algorithmic detail. Copyleft (GPL/AGPL) or unclear — do NOT copy code; implement from the paper and treat the reference as a black box. Record the license and your decision in the spec note.
3. Install and run it on a small, fixed-seed synthetic corpus. Capture a gold-standard result set (topic-word, doc-topic, diagnostics, settings, seed) to a parity fixture. This is the target the port must match.
4. Add a check under parity/ that re-runs the reference when its tool is present and skips cleanly when it is not (mirror the existing parity/ scripts).

Gate A — dual review of the plan (before any code)

Goal: catch a faithfulness or completeness problem in the design before you spend a multi-phase implementation on it.

Once the Phase-1/2 spec is written and you (with the user) have approved the plan — which core file, which estimator, the defaults, the public surface — hand it to the two fixed reviewers before writing model code:

1. Reviewer A (faithful / full parity — Codex) via the codex skill. It reads the spec, the paper, and the reference code (where the license allows) and judges whether this plan reproduces the method faithfully and completely.
2. Reviewer B (adversarial — Gemini) via the antigravity skill. It attacks the plan: the single most likely way this design yields a plausible-but-wrong model, and what to test early to catch it.

If the codex CLI or Antigravity is unavailable, run that slot as a Claude subagent (Agent tool, model opus) — same role, do not swap. Then synthesize both reports into one findings list, resolve blockers with the user, and only then proceed to Phase 3. Use the exact prompts and synthesis rule in references/evaluation-agents.md (§Gate A, §Reviewer A/B prompts, §Synthesis).

Phase 3 — Implement: Rust core + Python bindings

Goal: a working model that builds, passes the conventions test, and is deterministic.

Follow references/conventions.md closely. In short:

0. Scaffold the touchpoints first. Run just new-model <ModelName> (or python scripts/new_model.py --name <ModelName>) to generate src/<model>.rs, src/python/<model>.rs, and tests/test_<model>.py from templates, each stamped with a SCAFFOLD(<ModelName>) marker, plus a printed checklist of the wiring steps. It wires nothing in (an un-finished model stays inert), and tests/test_scaffold_guard.py fails once the model is registered if any SCAFFOLD marker survives — so you can't ship a half-filled placeholder. Fill in the templates below; the steps that follow are that checklist in prose.
1. Implement src/<model>.rs with the fit/inference loop. Preserve topica's bit-for-bit determinism: a fixed seed (and thread count, for samplers) must reproduce exactly; parallel reductions must sum in a fixed (document) order.
2. Wire the PyO3 binding in src/python/ (a directory module, not a single file): add src/python/<model>.rs with the pyclass and bring it in via use super::* (the established per-model recipe — see nmf_lsa.rs), and register it in src/python/mod.rs. Keep python/topica/_topica.pyi in sync with the binding signature. Expose the standard surface every model has: fit(docs, …), then topic_word, doc_topic, top_words(n), save/load.
3. Apply the naming contract: canonical argument names, reference-package aliases where helpful, iters for the iteration count, seed=, no deprecation cycles.
4. Build and gate after every change. The just runner wraps the release rebuild and the VIRTUAL_ENV/.venv-dev handshake:

   just build          # maturin develop --release --features python
   just test           # cargo test (core + feature-gated) + pytest
   

   The raw commands still work if just is unavailable:

   VIRTUAL_ENV="$PWD/.venv-dev" .venv-dev/bin/maturin develop --release --features python
   cargo test --workspace --lib                                   # add --features embeddings,umap,tsne for an embedding model
   VIRTUAL_ENV="$PWD/.venv-dev" .venv-dev/bin/python -m pytest tests/ -q
   

   Add a Rust unit test and a tests/test_<model>.py. The new model must pass tests/test_naming_conventions.py.

Do this implementation work on a short-lived branch off main (see CLAUDE.md branching). Use uv for any Python env/package work.

Phase 4 — Benchmark against the reference

Goal: an unbiased measurement of fidelity and speed — the empirical substrate the Gate-B reviewers judge against.

Measure the finished model against the Phase-2 gold standard and the live reference: topic-aligned parity (cosine / Jaccard / doc-topic correlation with the noise floor), model-specific diagnostics, determinism, and fit speed across corpus sizes. Do this in an isolated git worktree with its own venv — either inline or via a Claude benchmark subagent that did NOT write the model (independence matters). Use the rubric in references/evaluation-agents.md (§Phase-4 benchmark).

"Fast" is part of the deliverable, so apply the speed gate (within ≈2-3x of the reference on realistic-density inputs, or justify the gap). If it is missed, a performance-optimization iteration is a normal sub-phase, not a failure — optimize and re-benchmark before shipping; the first cut being slow is expected. To amortize the multi-minute --release build + venv, fold related checks into one agent (e.g. run the live-reference real-corpus parity inside the benchmark agent).

Re-verify any fix yourself (rebuild, re-run the parity check). Carry the parity table, determinism result, and speed table into Gate B — the reviewers work from these.

Phase 5 — Gate B: dual review before the PR

Goal: the same two-reviewer fidelity check as Gate A, now against the finished artifact, before the PR is opened.

Hand the implementation diff, the spec, and the Phase-4 benchmark/parity results to the same two fixed reviewers, in the same roles as Gate A:

1. Reviewer A (faithful / full parity — Codex) via the codex skill: does the diff faithfully and completely reproduce the method, and do the measured parity numbers actually support the "faithful" claim (no overclaim past the noise floor)?
2. Reviewer B (adversarial — Gemini) via the antigravity skill: silent deviations, correctness bugs, determinism holes, overclaimed parity/speed, untested edge cases.
3. Reviewer C (comparative — Claude subagent, opus, isolated worktree): how the finished model stacks up against its same-family topica siblings on accuracy, speed, and memory, and whether the PR's comparative claims are honest. Gate B only (needs the built artifact to benchmark). Prompt in references/evaluation-agents.md (§Reviewer C).
4. Reviewer D (sample-user on real data — Claude general-purpose subagent): a first-time computational social scientist ("a random sociologist") who takes the model through the whole paper workflow on a real bundled dataset, docs-only, and reports ranked friction (Tier-1 analytical traps first). Gate B only. Uses the sample-user skill; prompt in references/evaluation-agents.md (§Reviewer D).

Gate B is thus four reviewers (A+B+C+D); Gate A is two (A+B).

Fall back per-slot to a Claude subagent (model opus, isolated worktree, background) only if the external model is unavailable — same role, do not swap. Then synthesize both reports into one findings list. Genuine fidelity gaps, broken determinism, failing gates, and overclaims are blockers — fix and re-verify yourself before the PR. Defensible design choices (a topica-canonical name, a shared optimizer) are documented, not "fixed." Use the exact prompts and synthesis rule in references/evaluation-agents.md (§Gate B, §Synthesis).

Phase 5.5 — Post-fix reference sanity check

Goal: confirm the Gate-B fixes didn't regress the model, by running the finished artifact head-to-head against the live reference one more time.

The Phase-4 benchmark measured the model before the Gate-B fixes, and those fixes change code — so re-verify against the reference after they land, on a real dataset (not just the synthetic parity fixture — e.g. a 20 Newsgroups subset). Fit both topica and the reference implementation on the same corpus and compare, side by side:

• Accuracy / fidelity — the metric Phase 4 used (topic-aligned cosine, or a discovered-K-appropriate metric like cross-NMI / document-clustering agreement where the two land on different K), against the noise floor.
• Speed — wall-clock for both at a realistic corpus size, so the speed claim in the PR reflects the shipped code, not the pre-fix version.

A regression here — accuracy below the Phase-4 number, or a speed cliff — is a blocker: the fixes broke something; diagnose and re-verify before the PR. If both hold, record the head-to-head accuracy-and-speed numbers in the PR body next to the parity result. This is the same comparison benchmarks/full_model_run.py runs across the roster (reference-ceiling accuracy + timing ratio); add or refresh the model's row there if it belongs on the table, capping the corpus where a fit is otherwise intractable (as HDP/HLDA do at ~2k docs).

Phase 6 — Ship: issue, PR, README, docs

Goal: a merged PR that follows GitHub best practices and leaves the docs current.

Read references/pr-and-docs.md for the checklist. In short:

1. Create or reference a tracking issue describing the model, the reference, and the validation result (one often already exists — reuse it, e.g. #178 for NMF).
2. Open a PR from the feature branch (squash-merge, delete branch on merge, per CLAUDE.md). The PR body summarizes the method, the parity result, and the synthesized verdicts from both dual-review gates (Gate A on the plan, Gate B on the diff) — naming the reviewer models used and any documented deviations.
3. Update the docs as part of the same PR. Both generated tables come from the registry (python/topica/registry.py), enforced by test_registry.py: add a ModelInfo to REGISTRY (drives the README/docs roster) and an ImplInfo to IMPL (drives the contributor docs/contributing/model-map.md — source file, binding, feature, parity tests; its paths are existence-checked in CI). Then run scripts/gen_model_tables.py (or just gen-tables) to regenerate both; do NOT hand-edit a generated table (it fights the generator). Your hand-written work is the per-model prose section (in docs/guides/models.md), a validation/replication note where the existing models keep theirs, and the README acknowledgement. (Updating the paper is out of scope — that is the maintainer's, not a contributor's, job.)
4. Confirm all gates green (just test, mkdocs build --strict) before requesting merge.

Bundled references

• references/conventions.md — fitted-model surface, naming + alias rules, the determinism guarantee, build/test gates, file layout.
• references/reference-and-gold-standard.md — finding/running the reference, license rules, capturing the gold-standard fixture, the parity/ pattern.
• references/evaluation-agents.md — the dual-review mechanism: the two fixed reviewers (faithful-parity Codex + adversarial Gemini, Claude fallback), the two gates (plan and pre-PR), ready-to-use prompts, the synthesis rule, and the Phase-4 benchmark rubric.
• references/pr-and-docs.md — the issue/PR template and the README + docs update checklist.

Bundled scripts

• scripts/compare_to_reference.py — align a topica model's topic-word matrix to a saved reference matrix (Hungarian assignment) and report per-topic cosine, the mean, and doc-topic correlation. Use it in Phase 2/4 to score parity objectively. Run python scripts/compare_to_reference.py --help.