Standardize BGC-SetNet naming in model card
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README.md
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@@ -18,10 +18,10 @@ This repository contains the final five-seed model artifacts for the manuscript
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The release includes two model families:
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- **Pfam-augmented SetNet** (`pfam_setnet`): a Set Transformer encoder over frozen ESM-2 gene embeddings, relative gene positions, padding masks, and a BGC-level Pfam inventory embedding.
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- **Weighted Pfam Jaccard** (`weighted_pfam_jaccard`): learned non-negative Pfam-domain weights used in a weighted set-Jaccard retrieval baseline.
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The manuscript's main result is conservative: Pfam-domain content remains the strongest signal for this silver-label retrieval benchmark, while the ESM
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## Repository Contents
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| Method | Recall@50 | MRR | MAP | nDCG@50 |
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| Raw ESM mean | 0.7946 | 0.2550 | 0.7251 | 0.8078 |
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| Pfam Jaccard | 0.8788 | 0.3071 | 0.8480 | 0.9042 |
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| ESM
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| Weighted Pfam Jaccard | 0.8789 | 0.3069 | 0.8477 | 0.9040 |
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The weighted Pfam Recall@50 advantage over unweighted Pfam is numerically tiny (+0.00003) and should not be interpreted as a meaningful improvement.
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The release includes two model families:
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- **Pfam-augmented BGC-SetNet** (`pfam_setnet`): a Set Transformer encoder over frozen ESM-2 gene embeddings, relative gene positions, padding masks, and a BGC-level Pfam inventory embedding.
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- **Weighted Pfam Jaccard** (`weighted_pfam_jaccard`): learned non-negative Pfam-domain weights used in a weighted set-Jaccard retrieval baseline.
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The manuscript's main result is conservative: Pfam-domain content remains the strongest signal for this silver-label retrieval benchmark, while the ESM + BGC-SetNet + Pfam ensemble gives small, statistically unsupported gains on some secondary metrics.
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## Repository Contents
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| Method | Recall@50 | MRR | MAP | nDCG@50 |
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|---|---:|---:|---:|---:|
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| Raw ESM mean | 0.7946 | 0.2550 | 0.7251 | 0.8078 |
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| BGC-SetNet + Pfam | 0.8472 | 0.2786 | 0.7771 | 0.8502 |
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| Pfam Jaccard | 0.8788 | 0.3071 | 0.8480 | 0.9042 |
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| ESM + BGC-SetNet + Pfam | 0.8769 | 0.3096 | 0.8503 | 0.9058 |
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| Weighted Pfam Jaccard | 0.8789 | 0.3069 | 0.8477 | 0.9040 |
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The weighted Pfam Recall@50 advantage over unweighted Pfam is numerically tiny (+0.00003) and should not be interpreted as a meaningful improvement.
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