8. Scaling study

The scaling study is the manuscript’s main empirical result. Same architecture, same hyperparameters, same evaluation — only the training-set size varies.

Tiers

Experiment	Tier	n samples	Manifest
(Phase 1 baseline)	545	545	(legacy)
exp 32	5K	5,000	assets/kpsc_expansion_subset_5k.tsv
exp 33	10K	10,000	assets/kpsc_expansion_subset_10k.tsv
exp 34	20K	20,000	assets/kpsc_expansion_subset_20k.tsv
exp 36	40K	40,000	assets/kpsc_expansion_subset_40k.tsv

Each manifest is a strict superset of the previous one — see 4. Subset selection.

Headline results

Note

Results table populates as experiments complete. Currently scheduled: exp 32–34 will retrain at MQ=20 once the 20K download finishes (~3 days from 2026-05-17). Exp 36 follows after.

Chromosomal blaSHV (extra-copy)

Tier	MCC	FNR	PPV	call_rate	n_eval
545 (Phase 1)	—	—	—	—	—
5K	—	—	—	—	—
10K	—	—	—	—	—
20K	—	—	—	—	—
40K	—	—	—	—	—

Plasmid genes (presence)

For each tier we report per-gene MCC across {blaKPC, blaCTX-M, blaNDM, blaOXA-48, qnrB1, aac6-Ib-cr}.

Tier	blaKPC	blaCTX-M	blaNDM	blaOXA-48	qnrB1	aac6-Ib-cr
5K	—	—	—	—	—	—
10K	—	—	—	—	—	—
20K	—	—	—	—	—	—
40K	—	—	—	—	—	—

Reading the curve

We expect:

• Monotonic improvement in MCC for under-represented genes (rare STs, rare plasmid carriages) as the training set grows.

• Plateau at some n* between 10K and 40K — that’s the per-gene saturation point.

• For genes already at MCC ≈ 0.9+ at 545 samples (e.g. blaKPC in the Phase 1 cohort), expect little to no headroom — diminishing returns from scaling. Scaling matters most for the long tail.

Early observation (MQ=40 baseline, since superseded)

The initial exp 32 / 33 runs were done at MQ=40 — too strict for the multi-mapping plasmid reads in the extended reference (see 9. Methods (parameter choices)). With those broken-plasmid results we already saw a striking jump in chromosomal blaSHV call_rate:

Tier	blaSHV call_rate (MQ=40 baseline)
5K	0.44
10K	0.91

The signal is there — the rerun at MQ=20 should produce comparable chromosomal numbers plus working plasmid detection.

Reproducibility note

Every experiment’s evaluation.txt is committed to data/results/{exp}/. The commit hash that produced each result is recorded in the experiment log. See 10. Reproducibility for the exact recipe to regenerate.