Add model card (AlphaGenome Derivative; non-commercial terms)
Browse files
README.md
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Four benchmarks, in both JAX (Haiku) and PyTorch where available:
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- **lentiMPRA** (Agarwal et al.) — K562, HepG2, WTC11
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- **Drosophila STARR-seq** (DeepSTARR; de Almeida et al.) — developmental + housekeeping
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- **Plant STARR-seq** (Jores et al. 2021) — tobacco leaf and maize protoplast, 3 data modes
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Plus `jax/{mpra-K562,mpra-HepG2,mpra-WTC11,deepstarr}-optimal` (see the paper for
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their metrics).
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## Notes
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- **Plant `stage1` is a ridge probe, not a model.** It carries no encoder weights — the
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Four benchmarks, in both JAX (Haiku) and PyTorch where available:
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- **lentiMPRA** (Agarwal et al.) — K562, HepG2, WTC11
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- **lentiMPRA** (Gosai et al.) — K562, HepG2, SKNSH
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- **Drosophila STARR-seq** (DeepSTARR; de Almeida et al.) — developmental + housekeeping
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- **Plant STARR-seq** (Jores et al. 2021) — tobacco leaf and maize protoplast, 3 data modes
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Plus `jax/{mpra-K562,mpra-HepG2,mpra-WTC11,deepstarr}-optimal` (see the paper for
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their metrics).
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### `jax/` — Gosai et al. lentiMPRA (`Gosai-<cell>-optimal`)
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Cell-averaged Pearson r (from the paper's 4-panel figure):
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| Panel | Probing (S1) | Fine-tuned (S2) |
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| Genomic Reference | 0.877 | 0.910 |
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| High-Activity Designed | 0.709 | 0.776 |
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| SNV Effects (Ref−Alt) | 0.364 | 0.400 |
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Reproduced here: loading `Gosai-K562-optimal/stage2` and scoring the held-out chr7+13
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K562 set gives Pearson 0.9195.
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## Notes
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- **Plant `stage1` is a ridge probe, not a model.** It carries no encoder weights — the
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