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README.md

@@ -23,9 +23,10 @@ Code: https://github.com/GainGod-Xu/OccupancyFlow
 | `affinity/test_s90.csv` | 89 | S90 benchmark |
 | `interactome/edges_RSW_20231018_filtered.csv` | 328,433 | human interaction network (Entrez gene IDs + symbols) after removing proteins without a reference sequence |
 | `interactome/proteins_RSW_20231018_clean.csv` | 17,219 | protein table: sequence, PaxDb abundance (ppm), identifiers |
-| `interactome/predictions_esm2_650M_nM.csv` | 328,389 | predicted ΔG and Kd per interaction, plus abundances converted to nM |
-| `weights/interactome_weights_0708.csv` | 328,378 | competition-adjusted weights `w_ij` with complex and free concentrations |
-| `weights/interactome_weights_0630.xlsx` | 328,378 | the weight file used by the disease-module analyses |
+| `interactome/predictions_esmc_300M_nM.csv` | 328,433 | predicted ΔG and Kd per interaction (`esmc_300M`, current), plus abundances |
+| `weights/interactome_weights_esmc_300M.csv` | 328,422 | competition-adjusted weights `w_ij`, complex and free concentrations - current selected encoder (`esmc_300M`); the weight file the manuscript and disease-module analyses use |
+| `interactome/predictions_esm2_650M_nM.csv` | 328,389 | **superseded** — ESM-2 650M predictions, retired with the encoder swap (paper/sn-article.tex, Encoder selection). Pending removal from the Hub. |
+| `weights/interactome_weights_0708.csv` | 328,378 | **superseded** — ESM-2 650M-based weights `w_ij`. Pending removal from the Hub. |
 | `negatome_check/predictions_negatome_random.csv` | 6,352 | predictions for Negatome human non-interactions, Negatome pairs that are also reported interactions, and random pairs of the same proteins |
 | `negatome_check/per_protein_comparison.csv` | 283 | per-protein median ΔG for reported partners vs Negatome partners |
 | `fixed_test_sets/test_s79_fixed.csv` | 111 | S79 with the 1E96 label restored — all 111 chain pairs labelled |