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specs/048: pathogen-derived nodes inert (DS_PATHOGEN_MODE); pre-registration and amendment - #101
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…; cycles closed through a pooled set) Re-traced on canonical 20261009-2307_132d4b8: PDPK1 KO still reads 100x through the SARS-CoV-2 N:M:PDPK1 inhibitor (7 cases); the RAF scaffold loop of specs/047 trace 3 is gone, replaced by the MAPK <-> p-MAPK cycle closing through R-HSA-169291::pool, which pool detection cannot see (12 of 21 RAF failures). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…nding bug B3; shared-intermediate pools unresolved); arms path/pathctl and bind registered Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…, as drugs are Reads the generator's pathogens.csv into ReactionNetwork.pathogen_stids (default-nothing 8th field, so existing constructors are unchanged), carries it through the CLI and API parse -> solve round trip, and pins the listed nodes at baseline under DS_PATHOGEN_MODE=inert with the drug rule's observation precedence. The solve reports pathogen_rule / pathogens_held; the bench refuses an inert arm on a build without the table or that held nothing, and run_arm.sh records the Pathogens line. Default propagate is byte-identical (asserted). test_drugs.jl 59 -> 121. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…xp, DDX58/IFIH1 -11 held-out); bind changes no prediction, adopt on faithfulness Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…; bind default on in LNG #110 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…athp) before implementation Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…prediction (exp +7, held-out +1, nothing broken) - adopt; combination with bind still to measure Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… +7, held-out +1, 0 broken); combo arm registered; API.md documents pathogen_stids/pathogen_rule Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ered prediction exactly (exp +7, held-out +1, tuning +14, nothing else moves) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…thogens match nothing; API round-trip test for pathogen_stids; numbers and wording fixed; old builds documented as needing propagate; review record in research.md Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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specs/048: two experimental levers from specs/047, pre-registered and measured. The full record is in
specs/048-experimental-levers/research.md.Adopted
DS_PATHOGEN_MODE=inert, now the default. Nodes listed in the generator'spathogens.csvare held at baseline, as drugs are. Combined with the generator's protein-only list (combo, against canonical):LNG_BIND_STOICH, LNG #110). It moves no prediction and is adopted on faithfulness.Negative results recorded
wip/048-mapk-pools.Review: an adversarial review found no propagation defect. Fixed:
One finding is not fixed: the silo-bridge test cannot fail. See the table in research.md.
Merge after LNG #110 and a canonical rebuild. Under the new default, the bench refuses builds without
pathogens.csv, which includes the currentcurrent.🤖 Generated with Claude Code