Add MED4 epoch-8 checkpoint used for low-confidence Y2H screening, with sidecar note

checkpoints/ppiDCE_epoch8.md

@@ -0,0 +1,35 @@
+# ppiDCE_epoch8.pth
+
+**Checkpoint used for screening low-confidence Y2H pairs in the *Prochlorococcus marinus* MED4 interactome.**
+
+## Provenance
+
+| | |
+|---|---|
+| Model | ppiDCE (dual cross-encoder, ESM-1b-inspired transformer, trained from scratch) |
+| Architecture | 12 transformer layers |
+| Epoch | 8 |
+| File size | ~913 MB |
+| Training run | `out_MED4_12L` |
+| Training set | `train_MED4_ppiBTEPM-pseudo_Int_combo1-2-3.csv` (≈13,008 pairs, pre-clean — see note below) |
+| Validation set | `val_MED4_100_Y2H-RND_ppiBRTPM.csv` |
+
+## Intended use
+
+Inference / screening of candidate MED4 protein–protein interactions that
+were originally flagged as **low-confidence Y2H hits**. The model is run on
+each candidate pair (sequences encoded jointly as
+`[CLS] Seq_A [SEP] Seq_B [EOS]`) and its softmax probability is used (in
+concert with the other tri-model components, ppiBTEP and ppiGPLM) to retain
+or discard the pair.
+
+## Notes
+
+- This checkpoint was produced **before** the PRS/RRS de-overlapping pass on
+  `train.csv` (see [`MED4-PPIs-low-confidence_ppiTEPM_prompts.csv`](../MED4-PPIs-low-confidence_ppiTEPM_prompts.csv) and the cleaned
+  `train.clean.csv` / `train.clean2x.csv` companions). Approximately 608 of
+  the 13,008 training rows (4.67 %) overlap with the PRS+RRS evaluation pairs
+  in either orientation. Treat metrics on those pairs accordingly.
+- Loading: use `train_ppiDCE.py` / `inference_ppiDCE.py` from the parent repo
+  with `--model_config facebook/esm1b_t33_650M_UR50S` (config-only — weights
+  are loaded from this checkpoint, not from the HF ESM-1b release).