Statistical Genomics Foundry
Instance #2. The second Foundry — the one whose diff from instance #1 earns the pattern its abstraction.
Read the instance’s own repo: https://github.com/jmchilton/statistical-genomics-foundry
Domain
Keep an LLM agent doing statistical genomics both productive and statistically honest. Left alone, such an agent is the only judge in its own loop: it produces plausible-but-invalid work — at worst inventing a method with a convincing name and no validity — and self-certifies it. The work splits into two families: Family A does the analysis (frame the question, review the design, pick an established method, run it reproducibly); Family B referees it (audit validity; construct the empirical checks the field trusts).
Corpus
Grounded in a deliberately bipolar corpus: established-good methods and cautionary-bad exemplars. The bad exemplars matter as much as the good ones — they are what the referee learns to recognize (double-dipping, confounding, naive correction, invented methods).
The gate — an empirical referee (“doing never self-certifies”)
This instance’s external check — which it calls the gate — is its defining extension. No CLI can decide “is this statistical method valid,” so the gate is itself authored knowledge cast into a skill: an analyze → referee → revise loop. A Family-A protocol may not terminate in self-certification — it must hand off to a Family-B referee whose verdict gates certification (the gate obligation). The referee does two things: critique (reason about known invalidity patterns — fast, but still model reasoning) and calibrate (construct and run an empirical check — permutation under the null, simulation-under-truth, calibration). The strong gate requires at least one calibrate pass, because critique is reasoning and reasoning is what failed. The gate becomes a deliverable, not infrastructure.
This is the far end of the external check‘s range: where validity can’t be parsed, the check is a Mold that constructs its own external verdict.
Targets
Casts to portable skill artifacts, inheriting the Mold → Cast → provenance architecture, the human-navigable KB, and the validator from instance #1 — adapting the domain and adding the referee.
Status
Early — be honest about it. Mostly design and positioning so far: problem statement, a four-lens SOTA survey, verified positioning against five neighboring systems, a three-pillar narrative, and an architecture expressed as an explicit diff from the parent. The defining REFEREE_LOOP.md is a design sketch with open decisions flagged; nothing is implemented, the repo is freshly stood up, and the flagship Mold (audit-method-validity) is yet to be prototyped.
Compare against instance #1 in the-diff — this instance inherits the substrate and brings a different domain’s extensions to it. For the shared substrate beneath both, see anatomy-of-an-instance.