Write the model's name as ESMC, as biohub does
Browse files
README.md
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@@ -125,7 +125,7 @@ The qualitative arm's training config names `dataset/full_bal/`, a directory sin
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Training: AdamW, lr 1e-5, betas (0.9, 0.999), eps 1e-8, weight decay 0.01, five-fold CV, best epoch
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by validation loss (20, 27, 28, 28 for the four files above — the epoch each file stores, and the
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corrected argmin of its run). Both sides were fed from precomputed
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-
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store.
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## Architecture
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- 1 joint self-attention block over the two concatenated token sequences
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- masked mean pool, then `Linear(960, 480) -> GELU -> Dropout -> Linear(480, 1)`, one logit
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Inputs are per-residue
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never sees a raw sequence: the epitope is encoded at run time by
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chains are read from a precomputed store.
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## Input format
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hf download daylight-00/prepibind-embeddings emb_hla_esmc_small_0430.h5 --repo-type dataset --local-dir emb
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```
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The
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`huggingface_hub` are the only runtime dependencies for inference — no `pip install esm`.
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```python
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test_path="my_input.csv",
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out_path="outputs",
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)
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cfg["Test"]["precision"] = "as-trained" # bfloat16
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# config is "fp16", which is the demo's setting.
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df = main(cfg) # writes outputs/prediction.csv, returns the DataFrame
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```
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**MIT** for these weights and for the PREpiBind code, same as the repository.
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The backbone is not ours, but it is also MIT.
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[`biohub/esmc-300m-2024-12`](https://huggingface.co/biohub/esmc-300m-2024-12) is ungated and its card
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is tagged `mit` + `other`, and `esm` 3.4.0 — the release the vendored `prepibind/esmc/` source is
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copied from — ships a plain MIT licence, "Copyright 2026 Chan Zuckerberg Biohub, Inc.". These
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checkpoints were produced by training on
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`THIRD_PARTY_NOTICES.md` records the evidence and every other dependency.
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Training data derives from the IEDB Export v3 (free to use, asks to be cited) and allele sequences
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Training: AdamW, lr 1e-5, betas (0.9, 0.999), eps 1e-8, weight decay 0.01, five-fold CV, best epoch
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by validation loss (20, 27, 28, 28 for the four files above — the epoch each file stores, and the
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corrected argmin of its run). Both sides were fed from precomputed
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ESMC 300M embeddings, `emb_hla_esmc_small_0430.h5` for the HLA chains and the matching epitope
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store.
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## Architecture
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- 1 joint self-attention block over the two concatenated token sequences
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- masked mean pool, then `Linear(960, 480) -> GELU -> Dropout -> Linear(480, 1)`, one logit
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Inputs are per-residue ESMC 300M embeddings, 960-dimensional. The head is not a language model and
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never sees a raw sequence: the epitope is encoded at run time by ESMC 300M, the HLA alpha and beta
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chains are read from a precomputed store.
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## Input format
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hf download daylight-00/prepibind-embeddings emb_hla_esmc_small_0430.h5 --repo-type dataset --local-dir emb
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```
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The ESMC encoder is vendored into the package (`prepibind/esmc/`), so `torch` and
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`huggingface_hub` are the only runtime dependencies for inference — no `pip install esm`.
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```python
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test_path="my_input.csv",
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out_path="outputs",
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)
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cfg["Test"]["precision"] = "as-trained" # bfloat16 ESMC, float32 head. The default in that
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# config is "fp16", which is the demo's setting.
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df = main(cfg) # writes outputs/prediction.csv, returns the DataFrame
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```
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**MIT** for these weights and for the PREpiBind code, same as the repository.
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The backbone is not ours, but it is also MIT. ESMC 300M moved to Chan Zuckerberg Biohub:
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[`biohub/esmc-300m-2024-12`](https://huggingface.co/biohub/esmc-300m-2024-12) is ungated and its card
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is tagged `mit` + `other`, and `esm` 3.4.0 — the release the vendored `prepibind/esmc/` source is
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copied from — ships a plain MIT licence, "Copyright 2026 Chan Zuckerberg Biohub, Inc.". These
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checkpoints were produced by training on ESMC 300M embeddings. Checked 2026-09-10; the repository's
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`THIRD_PARTY_NOTICES.md` records the evidence and every other dependency.
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Training data derives from the IEDB Export v3 (free to use, asks to be cited) and allele sequences
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