Synthyra/ESM2-650M

This checkpoint contains the FastPLMs ESM2 implementation.

Accepted inputs are amino-acid sequences tokenized to residue IDs. Supported Transformers entry points are AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification.

Capabilities

Feature	Status
Sequence classification	Supported: base weights with an untrained task head
Token classification	Supported: base weights with an untrained task head
PEFT fine-tuning	Supported pattern: preserve the separately trained classifier
Embeddings	Supported: shared ordered embedding API
Test-time training	Supported: low-rank masked-residue adaptation
Attention variants	Supported: eager, sdpa, flex_attention, flash_attention_2, flash_attention_3
Compliance	Declared: exact release evidence is required

A supported interface is not a pretrained downstream predictor. Classification heads start untrained. Compliance metadata does not show that a local build passed its release gate.

Install and platform requirements

Install the direct dependencies published with this model:

python -m pip install -r \
  "https://huggingface.co/Synthyra/ESM2-650M/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

from transformers import AutoModel

model_id = "Synthyra/ESM2-650M"
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/ESM2-650M path. Pass local_files_only=True.

Attention and compliance

The quick start selects sdpa explicitly. Declared variants are eager, sdpa, flex_attention, flash_attention_2, flash_attention_3. An unavailable requested backend raises. It does not silently change implementation. output_attentions=True can use the documented one-call eager fallback to materialize attention tensors. The configured backend does not change.

This family declares the compliance tier. Release evidence identifies the checkpoint, backend, dtype, hardware, inputs, and reference revision.

Tokenization and forward inference

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

import torch
from transformers import AutoTokenizer

model_id = "Synthyra/ESM2-650M"
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:

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 classification

Both downstream 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:

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

model_id = "Synthyra/ESM2-650M"
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"

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:

from transformers import AutoModelForMaskedLM

ttt_model = AutoModelForMaskedLM.from_pretrained(
    "Synthyra/ESM2-650M",
    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:

import torch
from transformers import AutoModelForMaskedLM, AutoTokenizer

model_id = "Synthyra/ESM2-650M"
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.

Runtime contract

• Public input: Amino-acid sequences tokenized to residue IDs
• Advertised AutoClasses: AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification
• AutoClass weight status: AutoConfig = FastPLMs extension, AutoModel = pretrained, AutoModelForMaskedLM = pretrained, AutoModelForSequenceClassification = base weights + untrained task head, AutoModelForTokenClassification = base weights + untrained task head
• Attention implementations: eager, sdpa, flex_attention, flash_attention_2, flash_attention_3
• Precision policies: default
• BF16 execution: fp32_parameters_autocast
• Generation contract: not_applicable
• Artifact dependency set: core
• Weight publication allowed: true
• Weight license status: resolved
• Redistributable: true
• Complete weight publication required: false

Release record

• FastPLMs weights: Synthyra/ESM2-650M
• Runtime revision: recorded in the built artifact and published commit
• Source-tree and runtime-bundle SHA-256: recorded in the source record
• Official checkpoint: facebook/esm2_t33_650M_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

The source record records exact file identities, conversion, source revisions, legal texts, schema, and attestations. A nonzero unresolved count blocks a release.

Validation boundary

Declared tiers compare configuration, tokenizer behavior, state, and representative inference with the pinned reference. Metadata 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.