fix(graph): propagation fill bit-parity to main (PROTEA pin)#21
Merged
Conversation
…ges metrics, needs review) (#20) ## Summary (CORRECTNESS-CRITICAL: changes metric numbers , please review) The `CAFAEVAL_SPARSE` env switched not only the confusion-matrix kernel but also the **propagation algorithm**. Under `prop="fill"` (PROTEA's production default), the sparse path (`_propagate_sparse_pushup`) and the dense serial sweep produced **different propagated prediction matrices** on real DAG inputs, shifting Fmax: | Setting | sparse (before) | dense (before) | |, -|, -|, -| | NK Fmax | 0.58859 | 0.58914 | | LK Fmax | 0.61612 | 0.61391 | | PK Fmax | 0.40195 | 0.40195 | ## Which impl was canonical The **dense serial sweep is canonical**: it is bit-identical to upstream cafaeval `prop="fill"` (BioComputingUP/CAFA-evaluator and claradepaolis/CAFA-evaluator-PK, the fork's ancestors). Verified on 5 hand-worked DAGs plus a 200-trial randomized stress; the dense path matched the upstream oracle in 100% of cases. The **sparse pushup was the buggy one**. `fill` is a stepwise leaves-to-roots recurrence where a non-zero intermediate term *blocks* deeper descendants (it keeps its own value, and that value, not the descendant's, flows up to the parent). The pushup scattered every input non-zero straight into every ancestor and group-maxed, ignoring those blockers and overshooting. Worked counter-example (chain leaf->mid->root, leaf=1.0, mid=0.5, root=0): - upstream / dense fill: root = **0.5** (mid blocks the leaf) - sparse pushup: root = **1.0** (leaf scattered straight to root), WRONG This matches the observed "sparse=1.0 where dense=0.86" divergence, concentrated at high tau on biological_process multi-term shared-ancestor rows. ## The fix (which impl was fixed) The **sparse** path is fixed. `mode="fill"` is now routed to a new `_propagate_sparse_fill` that reproduces the recurrence sparsely (walk `ont.order`, per-row max over each term's children's *current* values, never overwrite originally-non-zero cells). The fast scatter pushup is retained for `mode="max"`, where it is proven correct. Minimal, localized change to the propagation path only. ## After: bit-identical - **Propagated prediction matrices: bit-identical** between sparse and dense, `max|diff| = 0.000e+00` across BPO/CCO/MFO (including the BPO rows where the bug lived). - NK/LK/PK Fmax now identical between both paths and equal to the dense (canonical) values: | Setting | sparse (after) | dense (after) | |, -|, -|, -| | NK Fmax | 0.5891445 | 0.5891445 | | LK Fmax | 0.6139093 | 0.6139093 | | PK Fmax | 0.4019451 | 0.4019451 | (Residual ~1e-16 / 1 ULP in some weighted count columns is float reduction-order noise in the counting kernel, downstream of the now-identical propagated matrices, below any metric significance.) - Sparse stays ~5x faster than dense on the fill path (no perf regression). ## Test added `tests/test_propagation_fill_parity.py`: the worked blocked-chain counter-example, shared-ancestor and high-tau BPO-shaped rows, plus a 200-trial randomized DAG stress, all asserting `sparse == dense == upstream-oracle` bit-for-bit. Closes the coverage gap left by the existing self-parity test, which only exercises `prop="max"`. ## Local CI ruff clean; mypy clean (py3.12 target, matching the CI runner); full `tests/` + `tests/diff` (Phase B) green. ## Deploy note PROTEA pins `cafaeval @ git+main`. A redeploy will pick this up once it lands on `main`. I did NOT bump the pin.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Cherry-picks the propagation correctness fix (#20, bdbb103) onto main so PROTEA's git+main pin picks it up. main already has the CSR/sparse-DAG perf (#19); this adds ONLY the prop=fill correctness fix (sparse pushup overshot fill blockers; now bit-identical to dense + upstream, property test included). Metric-changing (tiny, ~0.002 Fmax) but strictly more correct.