immunogenicity: legacy arms, and species keyed on the restricting allele

The Calis deposit's Species column is the host, not the restriction, and they disagree on 31% of its
rows -- HLA-transgenic mice. Keyed on the allele its human arm is 1,619 immunogenic against 272, not
1,113 against one.

immunogenicity/SOURCES.md

@@ -261,3 +261,31 @@ Arm counts, the filter cascade and the selection tree are `bench/results/corpus_
 tested is assumed non-immunogenic. 38,322 rows in the rebuild have a measured negative T-cell assay
 instead, held under evidence `tcell_negative` and deliberately **not** merged into the arm: swapping
 the negative definition changes what every AUROC recorded on these corpora means.
+
+### `immunogenicity_legacy_arms.tsv.gz` (2026-08-19)
+
+The published deposits and the legacy Kešmir arms in one table, keyed `corpus` ∈ {`chowell_vanilla`,
+`kesmir_S1`, `kesmir_S2`, `kesmir_S3`}, so a held-out evaluation can be reproduced without the
+copyrighted spreadsheets. 15,991 rows.
+
+**Species is keyed on the restricting allele, not on the deposit's own `Species` column.** The two
+disagree on 777 of the 2,508 Calis rows (31%), which carry `Species = Mus` with an HLA restriction —
+HLA-transgenic mice, murine host and human restricting molecule. Both readings describe the
+experiment; they build different corpora. Keyed on the host, the Calis human arm is 1,113
+immunogenic against **one** non-immunogenic; keyed on the allele it is **1,619 against 272** and the
+mouse arm is H-2 throughout. The reported host is retained as `host_reported`.
+
+Regenerate with `bench/neoag/corpus_legacy.py` then `deposit_arms.py`.
+
+### What the recognition model is fitted on
+
+`chowell_iedb_full` is the training arm for `mhcmatch.recognition` (0.15.0). Two choices were made
+by measurement and are recorded in `bench/results/recognition_model.md` and
+`feature_importance.md`:
+
+- **The unmatched arm ships.** Resampling negatives to match population HLA usage costs 0.019
+  (human) and 0.058 (mouse) AUROC on held-out published deposits.
+- **ESM2 and the physicochemical features are both kept.** ESM2 adds +0.022/+0.042 over physchem
+  alone; physchem adds +0.009/+0.019 over ESM2 alone. Permutation importance on held-out data ranks
+  the two ESM face-pools first (0.19–0.27), then `kf_tcr`; the whole-peptide Kidera aggregate is
+  worth 0.0165/0.0012 and is not shipped, being exactly the sum of the two role columns.

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immunogenicity/immunogenicity_legacy_arms.tsv.gz

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