File size: 1,769 Bytes
78b2584 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | {
"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"
}
} |