src/gemeo/train/txgnn.py

"""TxGNN fine-tune for drug repurposing (Phase 2).

Following Huang et al. *Nature Medicine* 2024. Zero-shot disease–drug link
prediction using a heterogeneous GNN over PrimeKG + our enriched KG.

Approach:
  1. Initialize node features with our raras-app `fused_embeddings.npz`.
  2. Train HGT-style message passing on PrimeKG drug-disease subgraph.
  3. Add Brazilian SUS auxiliary head — bias predictions toward drugs in
     PCDT/CEAF when the patient is in the SUS context.
  4. Save inference module exposing `predict(space, embedding, ckpt) -> DrugSpec`.
"""
from __future__ import annotations
import os
import logging
from typing import Optional

logger = logging.getLogger("gemeo.train.txgnn")

CKPT = os.path.join(os.path.dirname(__file__), "..", "artifacts", "txgnn.pt")


async def predict(space, embedding, ckpt_path: str):
    """Inference path used by `gemeo.repurpose.find`."""
    if not os.path.exists(ckpt_path):
        return None
    try:
        import torch  # noqa: F401
    except ImportError:
        return None

    # Load checkpoint, run forward, return DrugSpec.
    # Stub: defer to bootstrap. Real impl in PR-2.
    return None


def train(epochs: int = 80):
    """Run as `python -m gemeo.train.txgnn`."""
    logger.info("TxGNN scaffold — fill PrimeKG drug-disease loader + link-pred head")
    # TODO: load PrimeKG, freeze HGT base, fine-tune drug-disease head
    # TODO: SUS auxiliary loss using brazilian_context.PCDT mappings
    # TODO: save model with .predict(...) method


if __name__ == "__main__":
    logging.basicConfig(level=logging.INFO)
    train()