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1 Parent(s): 2e831b9

Write the model's name as ESMC, as biohub does

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  1. README.md +7 -7
README.md CHANGED
@@ -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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- ESM C 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
@@ -137,8 +137,8 @@ store.
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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 ESM C 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 ESM C 300M, the HLA alpha and beta
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  chains are read from a precomputed store.
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  ## Input format
@@ -178,7 +178,7 @@ hf download daylight-00/esmc-300m-2024-12 esmc_300m_2024_12_v0_fp16.pth --l
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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 ESM C 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
@@ -192,7 +192,7 @@ cfg = load_config(
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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 ESM C, 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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  ```
@@ -233,11 +233,11 @@ back to float32 and says so.
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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. ESM C 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 ESM C 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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  Training: AdamW, lr 1e-5, betas (0.9, 0.999), eps 1e-8, weight decay 0.01, five-fold CV, best epoch
126
  by validation loss (20, 27, 28, 28 for the four files above — the epoch each file stores, and the
127
  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
129
  store.
130
 
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  ## Architecture
 
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  - 1 joint self-attention block over the two concatenated token sequences
138
  - masked mean pool, then `Linear(960, 480) -> GELU -> Dropout -> Linear(480, 1)`, one logit
139
 
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+ Inputs are per-residue ESMC 300M embeddings, 960-dimensional. The head is not a language model and
141
+ never sees a raw sequence: the epitope is encoded at run time by ESMC 300M, the HLA alpha and beta
142
  chains are read from a precomputed store.
143
 
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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
182
  `huggingface_hub` are the only runtime dependencies for inference — no `pip install esm`.
183
 
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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
196
  # 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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  ```
 
233
 
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  **MIT** for these weights and for the PREpiBind code, same as the repository.
235
 
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+ The backbone is not ours, but it is also MIT. ESMC 300M moved to Chan Zuckerberg Biohub:
237
  [`biohub/esmc-300m-2024-12`](https://huggingface.co/biohub/esmc-300m-2024-12) is ungated and its card
238
  is tagged `mit` + `other`, and `esm` 3.4.0 — the release the vendored `prepibind/esmc/` source is
239
  copied from — ships a plain MIT licence, "Copyright 2026 Chan Zuckerberg Biohub, Inc.". These
240
+ checkpoints were produced by training on ESMC 300M embeddings. Checked 2026-09-10; the repository's
241
  `THIRD_PARTY_NOTICES.md` records the evidence and every other dependency.
242
 
243
  Training data derives from the IEDB Export v3 (free to use, asks to be cited) and allele sequences