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Synthyra/
ESM2-3B

Name: ESM2-3B
Rating: 2.5 (175 reviews)

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ESM2-3B

Model overview

Synthyra/ESM2-3B packages the facebook/esm2_t36_3B_UR50D checkpoint with the FastPLMs runtime for Hugging Face Transformers. It accepts amino-acid sequences tokenized to residue IDs.

The repository uses the standard Transformers loading interface with trust_remote_code=True. See Technical details for each registered class and whether its weights come from the checkpoint.

The sequence- and token-classification classes reuse the pretrained backbone, but their task heads are newly initialized. Fine-tune those heads before interpreting their logits as predictions.

Install and platform requirements

Install the direct dependencies published with this model:

bash

python -m pip install -r \
  "https://huggingface.co/Synthyra/ESM2-3B/resolve/main/requirements.txt"

The FastPLMs implementation itself is embedded in the model repository. Transformers loads it through trust_remote_code=True.

This model requires Python 3.11-3.14, PyTorch 2.13, and Transformers 5.13.

The artifact requirements include the FlashAttention loader dependency. FlashAttention also requires compatible CUDA hardware and BF16 execution.

The Hub quick start needs network access for the first download. For an air-gapped run, build the manifest-pinned local artifact first and use the offline example.

Quick start

python

from transformers import AutoModel

model_id = "Synthyra/ESM2-3B"
model = AutoModel.from_pretrained(
    model_id,
    trust_remote_code=True,
    attn_implementation="sdpa",
).eval()

For offline validation, replace model_id with the manifest-built dist/hub/ESM2-3B path. Pass local_files_only=True.

Attention backends

The quick start uses sdpa.

Available backends are eager, sdpa, flex_attention, flash_attention_2, flash_attention_3. Requesting an unavailable backend raises instead of silently changing implementation.

output_attentions=True can use the documented one-call eager fallback to materialize attention tensors. The configured backend does not change.

Tokenization and forward inference

Load the tokenizer from the same artifact as the model. The attention mask shows padding explicitly:

python

import torch
from transformers import AutoTokenizer

model_id = "Synthyra/ESM2-3B"
tokenizer = AutoTokenizer.from_pretrained(
    model_id,
    trust_remote_code=True,
)
batch = tokenizer(
    ["MSTNPKPQRKTKRNT", "MKTIIALSYIFCLVFA"],
    padding=True,
    return_tensors="pt",
)

with torch.inference_mode():
    output = model(**batch)

print(output.last_hidden_state.shape)

Dataset embeddings

The shared embedding mixin keeps input order and biological-position masking. It accepts sequences, identified records, mappings, or a FASTA path:

python

pooled = model.embed_dataset(
    ["MSTNPKPQRKTKRNT", "MKTIIALSYIFCLVFA"],
    batch_size=2,
    pooling=("mean", "std"),
)
residues = model.embed_dataset(
    ["MSTNPKPQRKTKRNT"],
    full_embeddings=True,
)
print(pooled[0].tensor.shape)   # (2 * d,)
print(residues[0].tensor.shape) # (l, d)

Set output and format="safetensors" or "sqlite" for transactional, bounded-memory storage. Resume checks input order, model state, tokenizer policy, backend, dtype, and pooling configuration before it appends data.

Downstream prediction

The sequence and token prediction AutoClasses use the checkpoint backbone and create a new, untrained classifier. Sequence labels have shape (b,). Residue labels have shape (b, l) and use -100 outside biological positions.

python

import torch
from transformers import AutoTokenizer
from transformers import (
    AutoModelForSequenceClassification,
    AutoModelForTokenClassification,
)

model_id = "Synthyra/ESM2-3B"
sequence_model = AutoModelForSequenceClassification.from_pretrained(
    model_id, num_labels=2, trust_remote_code=True
).eval()
token_model = AutoModelForTokenClassification.from_pretrained(
    model_id, num_labels=3, trust_remote_code=True
).eval()
tokenizer = AutoTokenizer.from_pretrained(model_id, trust_remote_code=True)
sequences = ["MSTNPKPQRKTKRNT", "MKTIIALSYIFCLVFA"]
batch = tokenizer(sequences, padding=True, return_tensors="pt")
biological = batch["attention_mask"].bool()
for special_id in tokenizer.all_special_ids:
    biological &= batch["input_ids"].ne(special_id)

sequence_labels = torch.zeros(len(sequences), dtype=torch.long)
token_labels = torch.full_like(batch["input_ids"], -100)
token_labels[biological] = 0

with torch.inference_mode():
    sequence_output = sequence_model(**batch, labels=sequence_labels)
    token_output = token_model(**batch, labels=token_labels)
print(sequence_output.logits.shape)  # (b, 2)
print(token_output.logits.shape)     # (b, l, 3)

PEFT fine-tuning

Install the training dependencies. Then attach LoRA to the loaded checkpoint:

python -m pip install "datasets>=4.8,<5" "peft>=0.19,<0.20"

python

from peft import LoraConfig, TaskType, get_peft_model

peft_model = get_peft_model(
    sequence_model,
    LoraConfig(
        task_type=TaskType.SEQ_CLS,
        r=8,
        lora_alpha=16,
        target_modules="all-linear",
        modules_to_save=["classifier"],
    ),
)

This checkpoint advertises a classification head. Save the separately trained classifier with the adapter. All FastPLMs checkpoints follow the Transformers PreTrainedModel contract and can use PEFT. The ESM2-specific shipped CLI is an example, not a support boundary. Record the target modules, base revision, data identity, and trainable parameter scope.

Test-time training

TTT samples masked views of one protein and updates only injected low-rank adapters. Base checkpoint weights stay frozen:

python

from transformers import AutoModelForMaskedLM

ttt_model = AutoModelForMaskedLM.from_pretrained(
    "Synthyra/ESM2-3B",
    trust_remote_code=True,
)
metrics = ttt_model.ttt(
    seq="MSTNPKPQRKTKRNT",
    ttt_config={"steps": 3, "batch_size": 1, "seed": 7},
)
ttt_model.save_pretrained("adapted", safe_serialization=True)
ttt_model.ttt_reset()
print(metrics)

Saved adapters retain their deterministic reset state. TTT adds latency and memory, can worsen an output, and does not show biological function.

Masked language modeling and contacts

Use the masked-language-model AutoClass when you need logits:

python

import torch
from transformers import AutoModelForMaskedLM, AutoTokenizer

model_id = "Synthyra/ESM2-3B"
tokenizer = AutoTokenizer.from_pretrained(model_id, trust_remote_code=True)
masked_model = AutoModelForMaskedLM.from_pretrained(
    model_id,
    trust_remote_code=True,
).eval()
batch = tokenizer("MSTNPKPQRKTKRNT", return_tensors="pt")

with torch.inference_mode():
    logits = masked_model(**batch).logits
    contacts = masked_model.predict_contacts(
        batch["input_ids"],
        batch["attention_mask"],
    )

print(logits.shape, contacts.shape)

Contact prediction creates attention maps. Do not enable it in a high-throughput embedding path unless you need these maps.

Plain AutoModel omits the optional ESM pooler because this masked-language- model checkpoint has no trained pooler weights. Pass add_pooling_layer=True only when you intend to initialize and train that head.

Notes and limitations

The pinned default SDPA BF16 path uses a checkpoint-specific numeric calibration: relative L2 target/hard limit 0.06/0.07, relative Q99.9 0.15/0.18, first-percentile residue cosine 0.994/0.992, and pooled cosine 0.998/0.997. Exact state identity and the global logits-distribution contract remain required.

Technical details

Inputs: Amino-acid sequences tokenized to residue IDs
Transformers classes: AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification
Checkpoint weights: AutoConfig = FastPLMs extension, AutoModel = pretrained, AutoModelForMaskedLM = pretrained, AutoModelForSequenceClassification = base weights + untrained task head, AutoModelForTokenClassification = base weights + untrained task head
Attention backends: eager, sdpa, flex_attention, flash_attention_2, flash_attention_3
Precision: default
BF16 execution: fp32_parameters_autocast
Generation contract: not_applicable
Dependencies: core
Weight publication allowed: true
Weight license status: resolved
Redistributable: true
Complete weight publication required: false

Validation and provenance

FastPLMs pins the checkpoint, upstream source revisions, state transformation, and required files in models.toml. Built artifacts record exact source identities and conversion details in source-record.json.

FastPLMs checkpoint: Synthyra/ESM2-3B
Runtime revision: recorded separately in the built artifact and published commit
Runtime source identities: recorded in source-record.json
Official checkpoint: facebook/esm2_t36_3B_UR50D
Artifact source: fast
State transform: esm2_hf_to_fastplms_v1
Pinned upstreams: fair-esm
Release tiers: check, compliance, feature, artifact, benchmark
Unresolved required file identities: 0

Release validation includes the compliance tier. Its evidence identifies the checkpoint, backend, dtype, hardware, inputs, and reference revision.

Declared tiers compare configuration, tokenizer behavior, state, and representative inference with the pinned reference. A nonzero unresolved count blocks release. Metadata alone does not show that a build passed, that a backend is faster, or that an output is biologically valid.

License

Checkpoint terms: MIT. The Hub model-card identifier is mit. The local artifact contains applicable source licenses, notices, attribution, and conversion records. Review them before use.