config.py

"""Shared configuration — the SINGLE SOURCE OF TRUTH for both build_index.py and app.py.

Keeping these constants in one module guarantees the offline corpus and the live query
are embedded with the *same* model. If they ever diverge, the query vector and the corpus
vectors live in different spaces and every retrieval result is silently wrong.
"""

# --- Embedding models ----------------------------------------------------------------
# We build & ship artifacts for BOTH models so the Space can switch between them live.
# model_key -> (display label, HuggingFace model name). The key is used in artifact
# filenames (embeddings_<key>.npy, umap_<key>.joblib, umap_coords_<key>.npy), so keep it
# filesystem-safe. Add a model here + rebuild to offer it in the UI.
EMBEDDING_MODELS = {
    "general": ("General — MiniLM-L6 (384-dim)", "sentence-transformers/all-MiniLM-L6-v2"),
    "biomedical": ("Biomedical — S-PubMedBert (768-dim)", "pritamdeka/S-PubMedBert-MS-MARCO"),
}
DEFAULT_MODEL_KEY = "general"

# --- Reranker (cross-encoder, runtime only) ------------------------------------------
# A cross-encoder scores (query, document) PAIRS jointly — more accurate than the
# bi-encoder dense retrieval, but it can't be precomputed, so it only runs on a shortlist.
RERANKER_MODEL = "cross-encoder/ms-marco-MiniLM-L-6-v2"
# Biomedical alternative: "ncbi/MedCPT-Cross-Encoder"
RERANK_CANDIDATES = 30  # size of the hybrid shortlist fed to the reranker

# --- Corpus (offline build only) -----------------------------------------------------
# Europe PMC search query. See https://europepmc.org/Help for the query syntax.
EUROPE_PMC_QUERY = (
    "microRNA AND disease AND HAS_ABSTRACT:Y AND LANG:eng "
    "AND (FIRST_PDATE:[2018-01-01 TO 2025-12-31])"
)
TARGET_N = 4000  # number of abstracts to fetch & index

# --- Retrieval -----------------------------------------------------------------------
RRF_K = 60  # Reciprocal Rank Fusion constant (standard default)

# --- Paths ---------------------------------------------------------------------------
DATA_DIR = "./data"