FastESM

FastESM is a Huggingface compatible plug in version of ESM2 rewritten with a newer PyTorch attention implementation.

Load any ESM2 models into a FastEsm model to dramatically speed up training and inference without ANY cost in performance.

Outputting attention maps (or the contact prediction head) is not natively possible with SDPA. You can still pass output_attentions to have attention calculated manually and returned. Various other optimizations also make the base implementation slightly different than the one in transformers.

Use with 🤗 transformers

Supported models

model_dict = {
    # Synthyra/ESM2-8M
    'ESM2-8M': 'facebook/esm2_t6_8M_UR50D',
    # Synthyra/ESM2-35M
    'ESM2-35M': 'facebook/esm2_t12_35M_UR50D',
    # Synthyra/ESM2-150M
    'ESM2-150M': 'facebook/esm2_t30_150M_UR50D',
    # Synthyra/ESM2-650M
    'ESM2-650M': 'facebook/esm2_t33_650M_UR50D',
    # Synthyra/ESM2-3B
    'ESM2-3B': 'facebook/esm2_t36_3B_UR50D',
}

For working with embeddings

import torch
from transformers import AutoModel, AutoTokenizer

model_path = 'Synthyra/ESM2-8M'
model = AutoModel.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
tokenizer = model.tokenizer

sequences = ['MPRTEIN', 'MSEQWENCE']
tokenized = tokenizer(sequences, padding=True, return_tensors='pt')
with torch.no_grad():
    embeddings = model(**tokenized).last_hidden_state

print(embeddings.shape) # (2, 11, 1280)

For working with sequence logits

import torch
from transformers import AutoModelForMaskedLM, AutoTokenizer

model = AutoModelForMaskedLM.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
with torch.no_grad():
    logits = model(**tokenized).logits

print(logits.shape) # (2, 11, 33)

For working with attention maps

import torch
from transformers import AutoModel, AutoTokenizer

model = AutoModel.from_pretrained(model_path, torch_dtype=torch.float16, trust_remote_code=True).eval()
with torch.no_grad():
    attentions = model(**tokenized, output_attentions).attentions # tuples of (batch_size, num_heads, seq_len, seq_len)

print(attentions[-1].shape) # (2, 20, 11, 11)

Embed entire datasets with no new code

To embed a list of protein sequences fast, just call embed_dataset. Sequences are sorted to reduce padding tokens, so the initial progress bar estimation is usually much longer than the actual time.

embeddings = model.embed_dataset(
    sequences=sequences, # list of protein strings
    batch_size=16, # embedding batch size
    max_len=2048, # truncate to max_len
    full_embeddings=True, # return residue-wise embeddings
    full_precision=False, # store as float32
    pooling_type='mean', # use mean pooling if protein-wise embeddings
    num_workers=0, # data loading num workers
    sql=False, # return dictionary of sequences and embeddings
)

_ = model.embed_dataset(
    sequences=sequences, # list of protein strings
    batch_size=16, # embedding batch size
    max_len=2048, # truncate to max_len
    full_embeddings=True, # return residue-wise embeddings
    full_precision=False, # store as float32
    pooling_type='mean', # use mean pooling if protein-wise embeddings
    num_workers=0, # data loading num workers
    sql=True, # store sequences in local SQL database
    sql_db_path='embeddings.db', # path to .db file of choice
)

Citation

If you use any of this implementation or work please cite it (as well as the ESM2 paper).

@misc {FastESM2,
    author       = { Hallee, L. and Bichara, D. and Gleghorn, J, P. },
    title        = { FastESM2 },
    year         = 2024,
    url          = { https://huggingface.co/Synthyra/FastESM2_650 },
    doi          = { 10.57967/hf/3729 },
    publisher    = { Hugging Face }
}

Synthyra
/

FastESM2_650