Add Supplementary Data 7 (ProtTale without Stage 1) and update README

data/Supplementary_Data/README.md

@@ -1,7 +1,7 @@
 # Supplementary Data — ProtTale
 
 Source data for the figures and tables in the main text and Extended Data:
-five CSV files (UTF-8, comma-separated, first row is the header), one Excel
+six CSV files (UTF-8, comma-separated, first row is the header), one Excel
 workbook and one JSON metadata file.
 
 The reliability score is written `p_JAY` throughout, the predicted probability
@@ -20,6 +20,7 @@ Swiss-Prot, so the two map one to one.
 | `Supplementary_Data_4_shuffled_baseline.csv` | 1,031 | Reliability scores for real versus residue-shuffled sequences |
 | `Supplementary_Data_5_mips_validation.xlsx` | 1,000 | Sequence, structure and EC agreement within MIPS clusters |
 | `Supplementary_Data_6_training_curves.csv` | 8,904 | Training and validation curves for both stages and the reliability head |
+| `Supplementary_Data_7_ablation_no_stage1.csv` | 1,031 | ProtTale retrained without Stage 1, scored on the unseen set |
 
 ---
 
@@ -203,6 +204,38 @@ Regenerates the Extended Data training-dynamics figure.
 
 ---
 
+## Supplementary Data 7 — ProtTale without Stage 1
+
+One row per unseen protein, 1,031 in total, in the same order and with the same
+identifiers as the `ProtTale` rows of Supplementary Data 2, so the two files can
+be joined row by row or on `UniProt_ID`.
+
+ProtTale w/o Stage 1 was trained with Stage 2 only: its frozen encoder was
+initialized from the original ESM-C weights rather than from the Stage 1
+student, and every other setting was unchanged.
+
+| Column | Meaning |
+|---|---|
+| `UniProt_ID`, `UniProt_accession` | Protein identifiers |
+| `Method` | `ProtTale w/o Stage 1` on every row |
+| `Kingdom` | Taxonomic group, as in Supplementary Data 2 |
+| `Length_aa` | Sequence length. The short subset is `<= 1024`, the long subset `> 1024` |
+| `judge_run1` … `judge_run5` | LLM-as-judge label from each of five runs: `Yes`, `No`, `Maybe`, or `Vague`. A blank cell means the judge returned no label in that run, which happened for 21 runs across 5 proteins |
+| `judge_majority` | `Yes` when at least three of the five runs said `Yes`, otherwise `not-Yes`. Blank runs count as not-`Yes` |
+| `p_JAY` | ProtTale's reliability score for the protein, identical to Supplementary Data 2. The ablated model has no reliability head of its own, so the filter applied to it uses ProtTale's |
+| `Retained` | Whether `p_JAY > 0.537` |
+| `SwissProt_description` | Curated reference text given to the judge |
+| `Prediction` | Description generated by ProtTale w/o Stage 1 |
+
+By five-run majority, the *Yes* rate is 15.8% over all 1,031 proteins, 12.7% on
+the short subset and 30.7% on the long subset, against 25.7%, 25.2% and 27.9% for
+ProtTale.
+
+Regenerates the Extended Data figure comparing ProtTale with ProtTale w/o
+Stage 1, and the McNemar tests reported with it in the main text.
+
+---
+
 ## Not covered here
 
 Two display items have no tabular source data: the model architecture figure is