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kemalandClaude Opus 5.5 0cd7eb8aa0

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P3 validated: normalization bit-identical on 2141 vendor GTCs

Normalization 1.1.2 reproduces all 109,191 bins of the 1000 Genomes
Omni2.5 GTCs (AutoCall 1.6.2.2) with 0 ULP difference, reserved fields
included; 1.2.0 and 1.1.2 are bit-identical to the no-FMA gtc2vcf oracle
on 36 GSA samples. AWS run: 33 min, ~$0.15, no resources left.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

2026-09-27 23:41:43 +01:00

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Phase P3 validation report — normalization

Date: 2026-09-27. Development and oracle tests on the Pi; vendor comparison on a self-destructing AWS spot instance (run-20260927T220605Z, 33 min, ≈ $0.15). Summary: P3_omni2141_summary.json.

Delivered

Item	Module
Vendor numerics: percentile, trimmean, IQR, MAD sigma (old/new), bisquare robust fits, sequential sums	`signal/normalization/numerics.py`
Six-parameter fit (outliers, offset, rotation, shear, scale, nn12/rr12) and the two-parameter single-channel model; normalization 1.2.0 and 1.1.2	`signal/normalization/fit.py`
Exact and binned (vendor) nearest-neighbour sweeps, vectorised	`signal/normalization/fit.py`
Transform application and θ/R	`signal/normalization/apply.py`
`simurg normalize` (per-sample transforms + normalized X/Y/θ/R Parquet)	`pipeline/normalize.py`

Acceptance (plan §18 P3: transforms within 2 ULP for ≥ 99.9 % of bins)

Check	Data	Result
Transforms, normalization 1.2.0	36 GSA v4 samples × 48 bins, oracle = gtc2vcf built without FMA	1728/1728 bins, 0 ULP (all 10 fields incl. nn12, rr12, taa, tbb)
Transforms, normalization 1.1.2	same samples, 1.1.2 oracle	1728/1728 bins, 0 ULP
Transforms vs vendor GTCs (AutoCall 1.6.2.2)	2141 Omni2.5 samples × 51 bins	1.1.2: 109 191/109 191 bins, 0 ULP; all 6 reserved fields identical in 2141/2141 samples
Same vendor GTCs with 1.2.0		1/109 191 bins (expected: that software predates 1.2.0)
`ingest` → `normalize` end to end	18 GSA samples	bit-identical transforms

The gate is exceeded: every bin is bit-identical (0 ULP), not just within 2 ULP.

Findings

The public 1000 Genomes GTCs were produced with normalization 1.1.2; simurg normalize --norm-version 1.1.2 reproduces them exactly.
Compilers that fuse a*b+c into FMA instructions (gcc on aarch64 by default) shift the last bits of the reference C implementation by up to 4 ULP; the vendor's .NET code does not fuse. Oracle GTCs are therefore generated with -ffp-contract=off (scripts/make_oracle_gtcs.sh).

Performance

Machine	Normalization fit per sample
Raspberry Pi 5, 1 core, GSA (683 k loci)	1.4 s
AWS m7g.4xlarge, 16 workers, Omni2.5 (2.45 M loci), both versions	2141 samples in 8.5 min (≈ 3.8 s per sample-core for two fits)

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