Regulator wiring: set-pool nodes (default on), cap pools (off), drugs.csv - #99
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…th any drug component; set whose every member is one) beside cofactors.csv, for a consumer modelling a cell without the drug (deltasignal specs/032). Network output unchanged. Also: stale +228 comment -> +197. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…iled drug query no longer costs containment.csv); class+name from the structure query (the unlabelled MATCH scanned every node, ~30 s a pathway; whole catalog now 0.8 s); list each node's exact id, a set_variant judged by its parent or chosen members; tests: candidate-only set (dropping hasCandidate now caught), the Cypher+cache path, variant ids. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…atalyst/regulator becomes one pool node (the set) fed by set_member edges, feeding each reaction copy once, instead of every member wired onto every copy as a separate AND (catalyst/pos) or OR (neg) term. Reachability unchanged. nodes.csv kind set_pool. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…er (the stId guards compared the SET's id; 4 E3-ligase sets would have closed member->pool-|member cycles); pooling only under complex-as-node; pool->reaction keeps the role flag under LNG_SET_MEMBERS_OR. Tests: depletion self-skip (mutation-checked), complex-as-node guard, SET_MEMBERS_OR, export_nodes set_pool kind. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…xp +3); legacy regulator tests pinned to LNG_SET_POOL=0; test that pooling is the default Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…hat resolves to several nodes in one virtual reaction (alternatives bundled by the variant cap) is emitted as a set pool feeding the reaction once. RAF's scaffold binding reaction: 28 inputs -> its 4 curated components. Tests to follow. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ember not, flag off, no leak between pathways, modifier sets excluded Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…undled (CAPPED_IDS; an uncapped copy's chosen complex alternative resolves to co-required subunits -- miR-93 RISC in PIP3 was averaged); leaves grouped by alternative, a complex alternative is an AND unit (leaves -assembly-> alternative -set_member-> pool); a leaf another input also maps to stays direct; curated set stoichiometry on the pool edge; depletion onto a pool goes to its members. Phase 3 input emission factored into _emit_vr_inputs and tested; gate mutation-checked. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
adamjohnwright
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adamjohnwright
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September 27, 2026 22:51
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Regulator wiring in the generator (deltasignal specs/033, 036, 038, 032).
LNG_SET_POOLnow defaults ON. A set-valued catalyst or regulator becomes one pool node (the set itself). Its members feed the pool byset_memberedges, and the pool feeds each reaction copy once, instead of every member being wired onto every copy.DS_SET_POOL_MODE=product: held-out +6 / −2, experimental +3 / +8. Themaxreading is refuted.nodes.csvgets the node kindset_pool.LNG_CAP_POOLS(default OFF). In a reaction the variant cap bundled, each set input becomes a pool of its alternatives. Each complex alternative is an AND unit, and a leaf shared with another input stays a direct edge. It fixes the structure (RAF's scaffold binding reaction: 28 inputs → its 4 curated components), but it is not adoptable on accuracy (specs/037).drugs.csv: drug-derived entities per pathway (from drugs.csv: drug-derived entities per pathway (deltasignal specs/032) #98, which this includes).test_set_pool.py,test_cap_pools.py(Phase 3 emission included, gates mutation-checked) andtest_provenance_exports.py. The legacy fan-out tests are pinned toLNG_SET_POOL=0. 1,071 pass; the 1 failure is the stale-output test that also fails on main.🤖 Generated with Claude Code