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RESULTS: canonical with pathogen proteins held (specs/048): experimental 591/849 #102

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adamjohnwright merged 1 commit into from
Oct 10, 2026
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RESULTS: canonical with pathogen proteins held (specs/048): experimental 591/849 #102

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2 changes: 2 additions & 0 deletions CLAUDE.md
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Expand Up @@ -535,6 +535,8 @@ for the last feature that touched it rather than re-deriving from the code.
cases in DDX58/IFIH1 (net −11).
- **Homodimer binding fix (`LNG_BIND_STOICH`): adopted** on faithfulness;
it moves no prediction.
- Canonical build `20261010-1415_c0e1b2a` (LNG #110, DS #101): experimental
591/849 (+7), held-out +1.
- Pools that share intermediates (the RAF knockout→UP class) are
unresolved; that work is on `wip/048-mapk-pools`.
- `specs/009-solver-defaults/` — the one-variable-at-a-time re-measurement
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42 changes: 42 additions & 0 deletions docs/RESULTS.md
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Expand Up @@ -19,6 +19,48 @@ commit.
---


> **2026-10-10 (later): canonical numbers with pathogen proteins held and
> homodimer-aware binding (specs/048).**
> - Build `20261010-1415_c0e1b2a`: generator c0e1b2a, LNG #110, with
> `LNG_PATHOGEN_PROTEIN` and `LNG_BIND_STOICH` on by default.
> - Solver `575c817`: `DS_PATHOGEN_MODE=inert` by default, DS #101.
> - Results: `results/575c817`.
>
> | | cases | accuracy | macro-F1 |
> |---|---|---|---|
> | **curator held-out, in release** (70 pathways) | 18,573 | **88.63%** | **0.8525** |
> | curator held-out, every case (71 pathways) | 19,000 | 88.03% | 0.8441 |
> | curator, all pathways, in release (81) | 23,625 | 86.04% | 0.8286 |
> | curator, all pathways, every case | 24,100 | 85.48% | 0.8213 |
> | experimental, every case (10 pathways) | 849 | **69.61%** | **0.6164** |
>
> **What moved since the previous box.** Only the 22 cases the arms
> predicted moved, and nothing broke:
> - **Pathogen-derived nodes are held at baseline** for a cell without the
> pathogen. The generator lists only entities carrying a pathogen protein.
> - SARS-CoV-2 N:M:PDPK1 had de-repressed AKT on every PDPK1 knockout.
> Experimental is now +7 (584 → 591, 7 fixed / 0 broken, p 0.016).
> - Curator held-out is +1 (CREBBP knockout), tuning +14 (PIP3).
> - The first rule also held viral RNA, the ligand DDX58/IFIH1 senses. It
> broke 12 cases and was not adopted.
> - **Homodimers bind to homodimers** when a reaction is split into variant
> copies. This moves no prediction.
> - The rebuild reproduces the measured arm (`combo`) exactly.
>
> Converged: 1,654 / 1,725 curator and 215 / 244 experimental solves
> (unchanged).
>
> **Against MP-BioPath's published figures:**
> - Curator: 85.48% / 0.8213 against 83.34% / 0.8063, **+2.14pp**.
> - Experimental: 69.61% (591/849) against 75.74% (643/849), **−6.13pp**.
>
> The rest of the experimental gap is network construction (specs/047).
> The largest remaining class is the RAF knockout→UP cycle (12 of 21 RAF
> failures), which needs pools that share intermediates (specs/048
> amendment 1).
>
> **Previous box**, kept below for the record.

> **2026-10-10: canonical numbers with variant complex nodes (specs/046).**
> Build `20261009-2307_132d4b8` (generator 132d4b8: `LNG_VARIANT_NODES` on by
> default, LNG #109), solver `0f0a11e` (`src/` unchanged since 5979e48),
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