Regulator wiring: set-pool modes, inert-drug and conserved-participant switches (all default-neutral), specs/032-038 - #76
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…s MP-BioPath 93.9% traced to MAP2K/MAPK-inhibitor drug complexes collapsing a loop) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… bundle's drugs.csv held at baseline like cofactors; default propagate is byte-identical. Network carries drug_stids (nothing = no table, reported as 'inert: no drug table'); parse/solve/CLI round-trip it; solve reports drug_rule and drugs_held; bench refuses an inert arm that held nothing. test_drugs.jl: 47 assertions. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…-drop arm under inert had no drug table); ARM.json records the Drugs line; a confidence-0 observation no longer unpins a drug; Pinned line counts pins on drug nodes; tests for both parse return paths, the silo-bridge path and the confidence gate (59 assertions, mutation-checked; the rebuild pass-through is defensive and noted as unread); API.md and CLAUDE.md document DS_DRUG_MODE, drug_stids, drug_rule, drugs_held. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… worse; held-out +30. RAF collapse traced to a positive loop closed by catalyst + dissociation recycling (p-MAP2K catalyses Phosphorylation of RAF), not the drug complexes Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…or (1,881 catalyst groups x AND in 63 pathways; RAF self-requiring loop); mode chosen on tuning, judged on held-out Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…se inputs are all set_member edges is a set pool; its member folds combine by the mode (product = the AND it replaces; extreme = the member furthest from 1 in log space; geomean). No effect on networks without set_member edges. test_set_pool.jl: 36 assertions. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ool nodes so readouts/pins are unchanged; pooled depletion specified and self-depletion fixed (LNG 81499ef); cycle gate restated excluding pools; product-mode approximations stated Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ut +6, tuning +10, exp +3); mode chosen on tuning; RAF only partly fixed (14->17/49), second cause = inputs wired to recycled downstream copies Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…shape; generator folds Requirement and gene-expression regulation into positive; 32% of catalyst edges fed by a downstream (recycled) copy; low-accuracy configuration cells; mismatch list M1-M7. Tool: bench/analysis/regulator_inventory.py Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…-2 N:M:PDPK1, ERBB2:trastuzumab, Inhibin:ACVR2A), exogenous = 202 drug + 66 pathogen entities; M4 counted: 7,989 input edges (9%) supplied only by their own downstream, 87% with no other copy; design candidates D1-D4. regulator_inventory --cell Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…(D1): 1,722 loop-only inputs released unchanged by their loop (RAF: RAS GAPs, scaffold partners, F-actin, CNKSR) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ed by their own loop held at baseline like cofactors; label-independent SCC detection via containment; solve reports conserved_rule/held; bench refuses an inert arm that held nothing. test_conserved.jl: 15 assertions. RAF: 29 entities; catalog 535 nodes. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…-122, TGF-b -30, MHC -18; PIP3 -308 traced: PIP3 itself met 'released unchanged' (second messenger bound/released) -- the criterion cannot tell scaffold from signal Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… loss is PIP3; next is an iteration trace of the RAF solve, not another rule Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…old binding reaction: PEBP1 self-contained inhibitor pushes, a 27-input AND of ~20 recycled set alternatives amplifies (gain ~20); input sets not expanded: 194 copies / 16 pathways (the 3,709 loose count withdrawn); variant-cap hypothesis under test Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… component (96 cap hits / 21 pathways; RAF binding reaction 28 inputs from a 12000-combination cap) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…e; compounding amplifiers: capped bundles, drug complexes, catalyst=substrate squaring; with all three addressed (mean) KO reads 0.016x correctly, UP 0.83x (4th damper open) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…uites registered; CLAUDE.md keeps both config entries) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ace (cap pools + set pools + inert drugs + dedup, mean pools) against base; attribution arms reported Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… experimental gate excludes RAF (the traced case); concentration gate; no pathway (incl. tuning) below -10; 033 +6/+3 was product-mode; limitations stated Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…edup is the damage (IFN a/b -112, TP53 -80); pools+drugs neutral; RAF 14->23/49 but nothing generalises Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…e per set with OR over curated alternatives, no member fan-out, no catalyst duplication, no scaffold release on dissociation; loops 12/6 vs 138/128; same solver scores it 100% vs 29% Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…hways; cyclic 1,007->413; loop cutting = reaction->output deletions (84 of 148 in loops) and reaction->set-node (38 of 63); 607 set-to-member/same-id deletions; 218 negative edges added that Reactome lacks Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…le) + specs/038 pre-registration: set pools for regulators/catalysts only, max vs product vs fresh control Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…acts; our cyclic nodes are mostly curated input/output reaction cycles (derived edges: depletion 18%, regulator 13%, catalyst 6%); candidate = ratio-based math for interconversion cycles Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… (phosphatase, demethylase, GAP, DUB) against the modified form; 187 absent from ours, 7 present as depletion; the automatic equivalent is the backward arm of interconversion cycles Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…; product passes all gates (held-out -2, exp +8 concentrated in 4 perturbations) -- set pools adoptable on faithfulness under product Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ipants (035), regulator-wiring record (034), cap pools / combined (036/037); CLAUDE.md indexes 032-038; 16 asserting suites Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…lf-inhibitor flags measured (1,215->1,192, 4 pathways); specs/033 pool->complex assembly note; CLAUDE.md wording (concentrated; mean does not gain) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
adamjohnwright
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September 27, 2026 22:51
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Solver side of the regulator-wiring work (specs/032–038). Every new switch defaults to today's behaviour.
DS_SET_POOL_MODE(productdefault;extreme,geomean,mean,max): how a set-pool node combines its members. The generator'sLNG_SET_POOL(Regulator wiring: set-pool nodes (default on), cap pools (off), drugs.csv logic-network-generator#99) emits the pools.productthe pool is adoptable on faithfulness: held-out +6 / −2, experimental +3 / +8 (the +8 is concentrated).maxis refuted (held-out −120, experimental −57), andmeandoes not gain.DS_DRUG_MODE(propagatedefault): not adopted (specs/032).DS_CONSERVED_MODE(offdefault): not adopted (specs/035).regulator_inventory.py.test_drugs.jl(59),test_set_pool.jl(43) andtest_conserved.jl(15).🤖 Generated with Claude Code