| { |
| "name": "mgxLens-v2", |
| "kind": "proof-of-concept metagenomic taxonomic profiler (retrieval-based)", |
| "status": "POC \u2014 for infrastructure/integration work, NOT production accuracy", |
| "encoder": { |
| "file": "encoder.pt", |
| "arch": "seqLens-89M + attention pooling + 256-d proj", |
| "pooling": "attention", |
| "emb_dim": 256, |
| "window": 150, |
| "max_length": 128, |
| "base_model": "omicseye/seqLens_4096_512_89M-at-base-multi", |
| "trained": "Phase-C contrastive (InfoNCE) + background negatives, genus-selected checkpoint" |
| }, |
| "index": { |
| "faiss": "index.faiss", |
| "type": "IndexFlatIP (cosine via L2-normalized vectors)", |
| "n_vectors": 2322522, |
| "clade_key": "index.clades.npy (SGB ids, row-aligned to faiss)", |
| "leakage": "held-out test markers EXCLUDED (index_bakeoff_mw_notest)" |
| }, |
| "lineage": { |
| "file": "lineage.tsv", |
| "maps": "clade_id (SGB) -> genus, species", |
| "note": "~half of species are SGB placeholder bins (GGBxxxx_SGByyyy), not named species" |
| }, |
| "levels_supported": [ |
| "genus", |
| "species" |
| ], |
| "caveats": [ |
| "POC, not tuned for accuracy", |
| "closed-world: organisms absent from the reference are silently misassigned to nearest reference genus", |
| "novelty rejection UNTESTED and expected weak (abstain ~0%) \u2014 do not deploy on arbitrary open samples", |
| "species = SGB bin; genus-level is the reliable level; species accuracy is limited at 150bp reads" |
| ], |
| "file_sha256_16": { |
| "encoder.pt": "44505362bc52ca24", |
| "index.faiss": "84041c32e5ce6397", |
| "index.clades.npy": "1636e87cdbaa7c29", |
| "index.markers.npy": "b0448b6e2b577071", |
| "index.config.json": "0303c06e90a69973", |
| "mgx_encoder.py": "25d3be65853adaba", |
| "lineage.tsv": "373416a3d4f26f4c" |
| } |
| } |
