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README.md
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Multi-Task Learning peptide classifier covering 22 binary peptide-activity tasks. Built on a frozen ESM-2 (650M) backbone with a parallel Transformer + CNN feature extractor and per-task heads, following a PDeepPP-inspired design.
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## Held-out Test Set Performance (Averaged across 22 tasks)
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| Metric | Value |
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| Accuracy | 86.63% |
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| F1 | 84.99% |
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| AUC | 93.47% |
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| MCC | 72.67% |
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Best Val Avg F1 (used for checkpoint selection): 85.56%
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## Per-Task Test Metrics
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| Task | ACC | F1 | AUC | MCC |
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| AntiMRSA | 0.9899 | 0.9667 | 0.9970 | 0.9607 |
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| Anticancer | 0.7035 | 0.7344 | 0.8007 | 0.4184 |
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| ACE_inhibitory | 0.6801 | 0.7392 | 0.8355 | 0.4040 |
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| Antioxidant | 0.7117 | 0.7309 | 0.8173 | 0.4382 |
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| Bitter | 0.8203 | 0.8456 | 0.9591 | 0.6782 |
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| Antimalarial | 0.9736 | 0.7692 | 0.9177 | 0.7579 |
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| Anti_inflammatory | 0.9886 | 0.9887 | 0.9979 | 0.9773 |
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| Antimicrobial | 0.9746 | 0.9552 | 0.9915 | 0.9379 |
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| Signal_peptide | 0.9927 | 0.9927 | 0.9997 | 0.9854 |
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| Antifungal | 0.9465 | 0.9456 | 0.9863 | 0.8935 |
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| Antimalarial_alt | 0.9877 | 0.9630 | 0.9942 | 0.9566 |
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| Anticancer_alt | 0.9330 | 0.9316 | 0.9784 | 0.8667 |
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| Anti_parasitic | 0.7826 | 0.7500 | 0.9216 | 0.5855 |
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| Umami | 0.8427 | 0.7308 | 0.9297 | 0.6243 |
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| Quorum_sensing | 0.9250 | 0.9231 | 0.9850 | 0.8511 |
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| Antibacterial | 0.9431 | 0.9424 | 0.9789 | 0.8863 |
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| NeuroPred | 0.8660 | 0.8543 | 0.9444 | 0.7416 |
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| Toxicity | 0.9086 | 0.8971 | 0.9699 | 0.8178 |
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| Antiviral | 0.8307 | 0.8319 | 0.9098 | 0.6614 |
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| DPPIV_inhibitory | 0.8647 | 0.8732 | 0.9478 | 0.7361 |
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| BBP | 0.6579 | 0.5185 | 0.9141 | 0.3873 |
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| TTCA | 0.7360 | 0.8129 | 0.7858 | 0.4221 |
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## Architecture
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- **Shared encoder**: frozen ESM-2 (`facebook/esm2_t33_650M_UR50D`, 650M params) + learnable base embedding, mixed at `esm_ratio=0.9`
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Multi-Task Learning peptide classifier covering 22 binary peptide-activity tasks. Built on a frozen ESM-2 (650M) backbone with a parallel Transformer + CNN feature extractor and per-task heads, following a PDeepPP-inspired design.
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## Architecture
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- **Shared encoder**: frozen ESM-2 (`facebook/esm2_t33_650M_UR50D`, 650M params) + learnable base embedding, mixed at `esm_ratio=0.9`
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