README.md

---
library_name: transformers
license: "mit"
tags:
  - protein-language-model
  - fastplms
---

<!-- Generated from src/fastplms/models.toml. Do not edit. -->

# ESMFold2-Experimental-Cutoff2025

## Model overview

`Synthyra/ESMFold2-Experimental-Cutoff2025` packages the
`biohub/ESMFold2-Experimental-Cutoff2025` checkpoint with the FastPLMs runtime
for Hugging Face Transformers. It accepts raw amino-acid sequences or typed
molecular-complex specifications; low-level forward accepts prepared feature
tensors.

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/ESMFold2-Experimental-Cutoff2025/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 structure dependencies.

The release contract requires a CUDA device. The current validated target is
the exact NVIDIA GH200 on Linux aarch64. Linux x86-64, CPU-only, Windows, and
macOS structure runs are not release evidence.

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/ESMFold2-Experimental-Cutoff2025"
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/ESMFold2-Experimental-Cutoff2025` path. Pass `local_files_only=True`.

## Attention backends

The quick start uses `sdpa`.

Available backends are `eager`, `sdpa`, `flex_attention`. 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.

## 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.
The folding trunk is skipped. The classifier uses the checkpoint's learned pLM
state mixture and projection, followed by one trainable transformer probe.

```python
import torch
from transformers import (
    AutoModelForSequenceClassification,
    AutoModelForTokenClassification,
)

model_id = "Synthyra/ESMFold2-Experimental-Cutoff2025"
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()
sequences = ["MSTNPKPQRKTKRNT", "MKTIIALSYIFCLVFA"]
batch = sequence_model.prepare_classifier_inputs(sequences)
biological = batch["attention_mask"].bool()

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:

```bash
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.

## Alignment-conditioning contract

This is a full 48-block ESMFold2 checkpoint. It supports single-sequence
inference and optional MSA-conditioned inference. Typed multichain and
multimolecule inputs can attach an MSA to each applicable protein chain.


## Protein folding

The single-protein helper returns typed structure and confidence outputs:

```python
result = model.fold_protein(
    "MSTNPKPQRKTKRNT",
    num_loops=1,
    num_sampling_steps=200,
    num_diffusion_samples=1,
    seed=7,
)
pdb_text = model.result_to_pdb(result)
cif_text = model.result_to_cif(result)
print(result.ptm, result.plddt.mean().item())
```

No target structure is required. For complexes, construct the input from the
types exposed by the loaded artifact:

```python
types = model.input_types
complex_input = types.StructurePredictionInput(
    sequences=[
        types.ProteinInput(id="A", sequence="MSTNPKPQRKTKRNT"),
        types.ProteinInput(id="B", sequence="MKTIIALSYIFCLVFA"),
        types.DNAInput(id="C", sequence="ATGC"),
        types.LigandInput(id="L", smiles="O"),
    ]
)
complex_result = model.fold(
    complex_input,
    num_loops=1,
    num_sampling_steps=200,
    seed=7,
)
print(complex_result.ptm, complex_result.plddt.mean().item())
```

The typed interface also supports RNA, protein MSAs, modifications, and covalent
bonds. The public schema recognizes `PocketConditioning` and
`DistogramConditioning`, but the pinned official forward consumes neither. Its
feature builder hard-codes a zero pocket feature and constructs distogram tensors
that the released model ignores. FastPLMs therefore rejects non-null pocket and
distogram conditioning instead of silently ignoring scientific inputs. Prepared
`ref_pos` values are component reference geometries created during featurization,
not target coordinates.
Predicted coordinates and confidence scores are outputs and do not establish
biochemical activity.

## Learned representation and ESMC precision

ESMFold2 applies its learned state mixture and projection as
`H: (b, l, 81, 2560) -> Z: (b, l, 256)`. Retrieve `Z` through the public
embedding API:

```python
representations = model.embed_dataset(
    ["MSTNPKPQRKTKRNT", "MKTIIALSYIFCLVFA"],
    batch_size=2,
    full_embeddings=True,
)
print(representations[0].tensor.shape)  # (sequence_length, 256)
```

`model.embed_dataset(..., full_embeddings=True)` returns one `(l, 256)` residue
tensor per single-chain input. It rejects complexes, ligands, MSAs,
chain-separated inputs, `cls`, and `parti` in the embedding path.

Set `esmc_precision` to `auto`, `bf16`, `fp32`, or `fp8` when loading.
`auto` always resolves to BF16. Explicit FP8 is experimental, inference-only,
and strict:

```python
model.reload_esmc(precision="fp8", device="cuda:0")
print(model.esmc_precision_status)
```

FP8 raises when the validated CUDA and Transformer Engine path is unavailable.
Canonical BF16 weights are retained, and transient quantization state is never
serialized.

The ESMC backbone uses SDPA as the recommended highest-fidelity path. Flex
Attention is supported and non-experimental but can be numerically divergent;
ESMFold2 does not advertise FlashAttention for the folding interface.

| Backend | Support | Measurement status |
| --- | --- | --- |
| `sdpa` | Recommended fidelity path | Pending release measurement |
| `eager` | Supported | Pending release measurement |
| `flex_attention` | Supported, numerically divergent | Pending release measurement |

Detailed backend measurements, release guardrails, and the GH200 package
compatibility exception are maintained in the
[attention backend guide](https://github.com/Synthyra/FastPLMs/blob/main/docs/attention_backends.md)
and
[release evidence manifest](https://github.com/Synthyra/FastPLMs/blob/main/docs/generated/capability_evidence.md).


## Verified CCD runtime asset

Structure preparation requires `ccd.pkl` from
`biohub/ESMFold2`. The manifest pins its repository, revision, size, content
identity, and MIT terms. This is a trusted-deserialization boundary. FastPLMs
accepts only the pinned snapshot link inside the repository blob directory.
User-supplied asset and `cache_dir` symlinks are rejected. The loader verifies a
private temporary snapshot before deserialization, protecting against
path-replacement and in-place source-write races. Offline execution requires the
exact cached object and never downloads a replacement.

## Test-time training

This experimental checkpoint does not expose folding TTT. Use the corresponding
standard or Fast checkpoint when you need opt-in ESMC-backbone adaptation.

## Binder-design research example

The FastPLMs binder-design workflow uses the experimental Fast Cutoff2025
checkpoint for differentiable inversion, both experimental Cutoff2025
checkpoints as critics, and ESM++ as the sequence prior:

![FastPLMs EGFR minibinder design](https://raw.githubusercontent.com/Synthyra/FastPLMs/main/docs/assets/egfr_fastplms_binder_design.png)

```bash
python examples/binder_design_fastplms.py \
  --target-name pd-l1 \
  --binder-name minibinder \
  --batch-size 4 \
  --steps 150 \
  --output-dir artifacts/binder-design
```

The workflow ranks candidates by mean iPTM across the approved critics after
the minibinder isoelectric-point filter. These are model-based prioritization
signals, not experimental evidence of affinity or specificity. See the
[complete workflow](https://github.com/Synthyra/FastPLMs/blob/main/docs/binder_design.md).

## Technical details

- Inputs: Raw amino-acid sequences or typed molecular-complex specifications; low-level forward accepts prepared feature tensors
- Transformers classes: `AutoConfig`, `AutoModel`, `AutoModelForSequenceClassification`, `AutoModelForTokenClassification`
- Checkpoint weights: `AutoConfig` = `FastPLMs extension`, `AutoModel` = `pretrained`, `AutoModelForSequenceClassification` = `base weights + untrained task head`, `AutoModelForTokenClassification` = `base weights + untrained task head`
- Attention backends: `eager`, `sdpa`, `flex_attention`
- Precision: `auto`, `fp32`, `bf16`, `fp8` (experimental)
- BF16 execution: `fp32_parameters_autocast`
- Generation contract: `not_applicable`
- Dependencies: `core + structure`
- 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/ESMFold2-Experimental-Cutoff2025`
- Runtime revision: recorded separately in the built artifact and published commit
- Runtime source identities: recorded in `source-record.json`
- Official checkpoint: `biohub/ESMFold2-Experimental-Cutoff2025`
- Artifact source: `fast`
- State transform: `identity`
- Pinned upstreams: `biohub-esm`, `biohub-transformers`, `protein-ttt`
- Release tiers: `check`, `compliance`, `structure`, `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.