Document the PLS generation assets

README.md

@@ -24,6 +24,11 @@ Checkpoints behind the [CELL-FM CondenSeq demo](https://huggingface.co/spaces/Bo
 | `hpa/vae_512.bin` | Image VAE at 512x512, the one `hpa/cellfm_img2seq.bin` was trained against — a different model from `hpa/vae.bin`, not a rename | `pretrain_hpa/vae_512/checkpoint-50000` |
 | `hpa/anchor_cell.npy` | The fixed cell every NLS-screening image is conditioned on: `(3, 256, 256)` float32 in [-1, 1], channels nucleus, ER, microtubules. HPA gene H3C13, cell crop `1194_B2_2_4` | built |
 | `hpa/anchor_masks.npz` | Two 256x256 boolean masks over that cell, `nucleus` and `cell`; cytoplasm is `cell & ~nucleus` | built |
+| `hpa/pls_anchor_nls.npz` | The cell PLS generation conditions on for nuclear signals: `cell` `(3, 512, 512)` nucleus/ER/microtubules and `protein` `(1, 512, 512)`, float32 in [-1, 1]. HPA gene PPM1G (Nucleoplasm), crop `392_B9_1_11` | built |
+| `hpa/pls_anchor_nes.npz` | The same for export signals. HPA gene DIAPH1 (Cytosol, Plasma membrane), crop `1608_B3_1_1` | built |
+| `hpa/proteome_aa_counts.json` | Residue counts over the 12,894 HPA proteins (7,940,784 residues), the proteome baseline the frequency analysis compares against | built |
+| `hpa/pls_reference_nls.csv` | The 315 published NLS signals, 10-25 aa, for comparison against a short run | `output/hpa/pls_generation/nls` |
+| `hpa/pls_reference_nes.csv` | The 320 published NES signals | `output/hpa/pls_generation/nes` |
 
 Hyperparameters for the CondenSeq models are set in `pipeline.py` in the Space and mirror
 `scripts/cell_fm_cs/evaluate_seq2img.sh` and