Feature Extraction
Transformers
Safetensors
fast_esmfold
protein-language-model
fastplms
custom_code
Instructions to use Synthyra/FastESMFold with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use Synthyra/FastESMFold with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("feature-extraction", model="Synthyra/FastESMFold", trust_remote_code=True)# pip install -U transformers accelerate # Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("Synthyra/FastESMFold", trust_remote_code=True, device_map="auto") - Notebooks
- Google Colab
- Kaggle
File size: 22,541 Bytes
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from __future__ import annotations
import hashlib
import platform
import torch
from collections.abc import Iterable, Mapping, Sequence
from pathlib import Path
from typing import Any
from torch import Tensor
from .pooling import POOLING_SEMANTICS
from .storage import tensor_sha256
from .types import EmbeddingInput
from ..digests import json_sha256
from ..json_files import compact_json
_RUN_FINGERPRINT_SCHEMA_VERSION = 5
_MODEL_STATE_HASH_CHUNK_BYTES = 16 * 1024**2
def _model_device(model: Any) -> torch.device:
try:
return torch.device(next(model.parameters()).device)
except (AttributeError, StopIteration):
return torch.device("cpu")
def _attention_backend(model: Any) -> str | None:
config = getattr(model, "config", None)
for name in ("_attn_implementation", "attn_implementation", "attn_backend"):
value = getattr(config, name, None)
if value:
return str(value)
return None
def _attention_kernel_metadata(backend: str | None) -> dict[str, Any] | None:
if backend not in {"flash_attention_2", "flash_attention_3"}:
return None
from fastplms.registry import get_model_registry
spec = get_model_registry().attention_kernels[backend]
return {
"repository": spec.repository,
"revision": spec.revision,
"version": spec.version,
"expected_variant": spec.expected_variant,
"dtypes": list(spec.dtypes),
}
def _fingerprint_jsonable(value: Any) -> Any:
if isinstance(value, Mapping):
return {str(key): _fingerprint_jsonable(item) for key, item in value.items()}
if isinstance(value, (list, tuple)):
return [_fingerprint_jsonable(item) for item in value]
if isinstance(value, (set, frozenset)):
return sorted((_fingerprint_jsonable(item) for item in value), key=repr)
if isinstance(value, Path):
return str(value)
if isinstance(value, Tensor):
return {
"dtype": str(value.dtype).removeprefix("torch."),
"shape": list(value.shape),
"sha256": tensor_sha256(value),
}
if isinstance(value, torch.dtype):
return str(value).removeprefix("torch.")
if isinstance(value, torch.device):
return str(value)
if value is None or isinstance(value, (str, int, float, bool)):
return value
return {
"class": f"{value.__class__.__module__}.{value.__class__.__qualname__}",
"value": str(value),
}
def _backend_tokenizer_content(backend: Any) -> str | None:
"""The backend tokenizer's serialization, without the padding and truncation of its last call.
Transformers sets padding and truncation on the Rust tokenizer at the start of every encode
call, from that call's own arguments, and leaves them set. What the backend holds is
therefore the previous call's settings, which never change the next encoding. Hashing them
gave the first run in a process a different fingerprint from every identical run after it.
This run's own padding and truncation are fingerprinted through ``max_length``,
``truncate``, and the batching policy.
The settings are cleared on a copy, so the caller's tokenizer keeps its state. A tokenizer
that was never called already serializes without them, so this normalization itself
does not change its identity. The enclosing run schema also versions pooling semantics.
"""
to_str = getattr(backend, "to_str", None)
if not callable(to_str):
return None
serialized = to_str()
from_str = getattr(type(backend), "from_str", None)
if not callable(from_str):
return serialized
call_free = from_str(serialized)
call_free.no_truncation()
call_free.no_padding()
return call_free.to_str()
def _tokenizer_content_sha256(tokenizer: Any) -> str:
content: dict[str, Any] = {
"init_kwargs": getattr(tokenizer, "init_kwargs", None),
"special_tokens_map": getattr(tokenizer, "special_tokens_map", None),
"model_max_length": getattr(tokenizer, "model_max_length", None),
"padding_side": getattr(tokenizer, "padding_side", None),
"truncation_side": getattr(tokenizer, "truncation_side", None),
}
get_vocab = getattr(tokenizer, "get_vocab", None)
if callable(get_vocab):
content["vocabulary"] = get_vocab()
get_added_vocab = getattr(tokenizer, "get_added_vocab", None)
if callable(get_added_vocab):
content["added_vocabulary"] = get_added_vocab()
backend_content = _backend_tokenizer_content(getattr(tokenizer, "backend_tokenizer", None))
if backend_content is not None:
content["backend"] = backend_content
return json_sha256(_fingerprint_jsonable(content), ensure_ascii=False)
def _tokenizer_metadata(model: Any, tokenizer: Any | None) -> dict[str, Any]:
resolved = tokenizer if tokenizer is not None else getattr(model, "tokenizer", None)
if resolved is None:
# Raw-sequence families such as E1 retain their loader context on the
# model/encoder rather than exposing a Transformers tokenizer. Bind the
# non-secret source policy to resume identity without serializing a Hub
# token or forcing lazy tokenizer initialization.
for candidate in (model, getattr(model, "model", None)):
settings = getattr(candidate, "__dict__", {}).get("_fastplms_tokenizer_kwargs")
if isinstance(settings, Mapping):
token_value = settings.get("token")
return {
"mode": "native-sequence",
"source": (
str(settings.get("tokenizer_source"))
if settings.get("tokenizer_source") is not None
else None
),
"revision": settings.get("revision"),
"cache_dir": (
str(settings.get("cache_dir"))
if settings.get("cache_dir") is not None
else None
),
"local_files_only": bool(settings.get("local_files_only", False)),
"token_policy": (
"disabled"
if token_value is False
else "provided"
if token_value is not None
else "default"
),
}
return {"mode": "native-sequence"}
return {
"mode": "tokenizer",
"class": f"{resolved.__class__.__module__}.{resolved.__class__.__qualname__}",
"name_or_path": getattr(resolved, "name_or_path", None),
"vocab_size": getattr(resolved, "vocab_size", None),
"special_token_ids": list(getattr(resolved, "all_special_ids", ())),
"content_sha256": _tokenizer_content_sha256(resolved),
}
def _software_versions() -> dict[str, str | None]:
try:
import fastplms
fastplms_version = fastplms.__version__
except (AttributeError, ImportError):
fastplms_version = None
try:
import safetensors
safetensors_version = safetensors.__version__
except ImportError:
safetensors_version = None
try:
import transformers
transformers_version = transformers.__version__
except ImportError:
transformers_version = None
return {
"fastplms": fastplms_version,
"python": platform.python_version(),
"safetensors": safetensors_version,
"torch": torch.__version__,
"torch_cuda": torch.version.cuda,
"transformers": transformers_version,
}
def _adapter_identity_metadata(model: Any) -> dict[str, Any] | None:
"""Return deterministic PEFT/adapter identity without tensor payloads."""
peft_config = getattr(model, "peft_config", None)
if not isinstance(peft_config, Mapping) or not peft_config:
return None
configurations: dict[str, Any] = {}
for name, config in sorted(peft_config.items(), key=lambda item: str(item[0])):
to_dict = getattr(config, "to_dict", None)
if callable(to_dict):
value = to_dict()
else:
try:
value = vars(config)
except TypeError:
value = config
configurations[str(name)] = _fingerprint_jsonable(value)
active_adapters = getattr(model, "active_adapters", None)
if callable(active_adapters):
active_adapters = active_adapters()
return {
"active": _fingerprint_jsonable(active_adapters),
"configurations": configurations,
}
def _execution_identity_metadata(model: Any) -> dict[str, Any]:
"""Capture runtime policy that can change persisted numerical results."""
parameter_dtypes = sorted(
{
str(parameter.dtype).removeprefix("torch.")
for parameter in getattr(model, "parameters", lambda: ())()
}
)
return {
"device": _model_device(model).type,
"hf_device_map": _fingerprint_jsonable(getattr(model, "hf_device_map", None)),
"parameter_dtypes": parameter_dtypes,
"software": _software_versions(),
}
def _first_metadata_value(*values: Any) -> Any:
for value in values:
if isinstance(value, str):
if value.strip():
return value
elif value is not None:
return value
return None
def _model_identity_metadata(model: Any) -> dict[str, Any]:
"""Resolve model and checkpoint identity, including local artifact fallbacks."""
config = getattr(model, "config", None)
checkpoint_revision = _first_metadata_value(
getattr(config, "fastplms_checkpoint_revision", None),
getattr(config, "_commit_hash", None),
)
return {
"model_id": _first_metadata_value(
getattr(config, "fastplms_model_id", None),
getattr(config, "_name_or_path", None),
),
"model_revision": _first_metadata_value(
getattr(config, "_commit_hash", None),
checkpoint_revision,
),
"checkpoint_repo_id": getattr(config, "fastplms_checkpoint_repo_id", None),
"checkpoint_revision": checkpoint_revision,
"checkpoint_hash": _first_metadata_value(
getattr(model, "checkpoint_hash", None),
getattr(config, "checkpoint_hash", None),
getattr(config, "fastplms_checkpoint_hash", None),
),
"weights_revision": getattr(config, "fastplms_weights_revision", None),
"runtime_revision": getattr(config, "fastplms_runtime_revision", None),
"source_tree_sha256": getattr(config, "fastplms_source_tree_sha256", None),
"runtime_bundle_sha256": getattr(config, "fastplms_runtime_bundle_sha256", None),
}
def _bounded_tensor_chunks(X: Tensor, max_elements: int) -> Iterable[Tensor]:
"""Yield X in logical row-major order without materializing a full copy."""
# X: (...)
if X.numel() == 0:
return
if X.ndim == 0:
yield X
return
trailing_elements = 1
for size in X.shape[1:]:
trailing_elements *= int(size)
if trailing_elements <= max_elements:
rows_per_chunk = max(1, max_elements // trailing_elements)
for start in range(0, X.shape[0], rows_per_chunk):
yield X[start : start + rows_per_chunk] # (chunk_rows, ...)
return
for row in X:
yield from _bounded_tensor_chunks(row, max_elements)
def _model_state_sha256(model: Any) -> str:
"""Hash named parameters and persistent buffers using bounded CPU copies."""
# Never cache this digest from tensor identity or ``Tensor._version``.
# ``Parameter.data`` and independent tensor aliases can mutate shared storage
# without changing either signal, while persisted resume identity must bind
# the authoritative bytes visible at the start of this run.
state = model.state_dict(keep_vars=True)
digest = hashlib.sha256()
for name, value in sorted(state.items()):
if not isinstance(value, Tensor):
raise TypeError(f"Model state entry {name!r} is not a tensor.")
if value.is_meta:
raise ValueError(
f"Cannot fingerprint meta-device model state entry {name!r}; pass "
"model_state_fingerprint with a caller-owned state identity."
)
header = compact_json(
{
"name": name,
"dtype": str(value.dtype).removeprefix("torch."),
"shape": list(value.shape),
}
).encode()
digest.update(len(header).to_bytes(8, "big"))
digest.update(header)
max_elements = max(1, _MODEL_STATE_HASH_CHUNK_BYTES // value.element_size())
for chunk in _bounded_tensor_chunks(value.detach(), max_elements):
cpu_chunk = chunk.to(device="cpu").contiguous() # chunk.shape
digest.update(cpu_chunk.reshape(-1).view(torch.uint8).numpy().tobytes())
return digest.hexdigest()
def _input_sha256(records: Iterable[EmbeddingInput]) -> str:
"""Hash an ordered input stream without constructing a duplicate JSON payload."""
precomputed = getattr(records, "input_fingerprint", None)
if isinstance(precomputed, str):
return precomputed
digest = hashlib.sha256()
count = 0
for record in records:
count += 1
for value in (record.id, record.sequence):
encoded = value.encode("utf-8")
digest.update(len(encoded).to_bytes(8, "big"))
digest.update(encoded)
digest.update(count.to_bytes(8, "big"))
return digest.hexdigest()
def _run_fingerprint(
model: Any,
records: Sequence[EmbeddingInput],
*,
pooling: Sequence[str],
full_embeddings: bool,
max_length: int | None,
truncate: bool,
dtype: torch.dtype | None,
model_kwargs: dict[str, Any],
tokenizer_metadata: dict[str, Any],
model_state_fingerprint: str | None,
persist_output: bool,
embedding_context: Mapping[str, Any],
batch_size: int,
batch_window_size: int,
max_tokens_per_batch: int | None,
taps: Sequence[Mapping[str, Any]] | None = None,
) -> tuple[str, str, str | None, str]:
input_fingerprint = _input_sha256(records)
attention_backend = _attention_backend(model)
model_identity = _model_identity_metadata(model)
if model_state_fingerprint is None and persist_output:
resolved_model_state_fingerprint = _model_state_sha256(model)
model_state_fingerprint_source = "computed"
elif model_state_fingerprint is not None:
resolved_model_state_fingerprint = model_state_fingerprint.strip()
if not resolved_model_state_fingerprint:
raise ValueError("model_state_fingerprint must not be empty.")
model_state_fingerprint_source = "caller"
else:
resolved_model_state_fingerprint = None
model_state_fingerprint_source = "not-computed"
payload = {
"fingerprint_schema_version": _RUN_FINGERPRINT_SCHEMA_VERSION,
"input_fingerprint": input_fingerprint,
"model_state_fingerprint": resolved_model_state_fingerprint,
"model_state_fingerprint_source": model_state_fingerprint_source,
"model_class": f"{model.__class__.__module__}.{model.__class__.__qualname__}",
**model_identity,
"attention_backend": attention_backend,
"attention_kernel": _attention_kernel_metadata(attention_backend),
"layer": repr(
getattr(model, "embedding_layer", model_kwargs.get("hidden_state_index", -1))
),
"projection": getattr(model, "embedding_projection", None),
"esmc_source": getattr(model, "_esmc_source", None),
"esmc_revision": getattr(model, "_esmc_source_revision", None),
"esmc_files": getattr(model, "_esmc_source_files", None),
"token_policy": getattr(model, "embedding_token_policy", None),
"tokenizer": tokenizer_metadata,
"adapter": _adapter_identity_metadata(model),
"execution": _execution_identity_metadata(model),
"embedding_context": _fingerprint_jsonable(embedding_context),
"pooling": list(pooling),
"pooling_semantics": dict(POOLING_SEMANTICS),
"full_embeddings": full_embeddings,
"max_length": max_length,
"truncate": truncate,
"dtype": str(dtype) if dtype is not None else None,
"batching": {
"batch_size": batch_size,
"batch_window_size": batch_window_size,
"max_tokens_per_batch": max_tokens_per_batch,
},
"model_kwargs": {
key: _fingerprint_jsonable(value) for key, value in sorted(model_kwargs.items())
},
"residue_mask_policy": "attention-mask-minus-special-tokens",
}
if taps is not None:
# Each hidden tap binds its requested dtype; each reduced tap binds its own contract.
payload["taps"] = _fingerprint_jsonable(taps)
run_fingerprint = json_sha256(payload)
return (
input_fingerprint,
run_fingerprint,
resolved_model_state_fingerprint,
model_state_fingerprint_source,
)
def _ordered_string_sha256(values: Sequence[str]) -> str:
digest = hashlib.sha256()
for value in values:
encoded = value.encode("utf-8")
digest.update(len(encoded).to_bytes(8, "big"))
digest.update(encoded)
digest.update(len(values).to_bytes(8, "big"))
return digest.hexdigest()
def _embedding_context(
model: Any,
records: Sequence[EmbeddingInput],
*,
hidden_state_source: str,
decoder_inputs: Sequence[str] | None,
decoder_input_ids: Tensor | None,
decoder_attention_mask: Tensor | None,
model_kwargs: Mapping[str, Any],
) -> tuple[dict[str, Any], tuple[str, ...] | None]:
# decoder_input_ids, decoder_attention_mask: (n_records, l_decoder), aligned with records
if hidden_state_source not in {"encoder", "decoder"}:
raise ValueError("hidden_state_source must be 'encoder' or 'decoder'.")
hidden_state_index = model_kwargs.get("hidden_state_index", -1)
if not isinstance(hidden_state_index, int) or isinstance(hidden_state_index, bool):
raise TypeError("hidden_state_index must be an integer.")
store_all_hidden_states = model_kwargs.get("store_all_hidden_states", False)
if not isinstance(store_all_hidden_states, bool):
raise TypeError("store_all_hidden_states must be a boolean.")
normalized_decoder_inputs: tuple[str, ...] | None = None
has_decoder_inputs = decoder_inputs is not None
has_decoder_ids = decoder_input_ids is not None
if hidden_state_source == "encoder":
if has_decoder_inputs or has_decoder_ids or decoder_attention_mask is not None:
raise ValueError("Decoder inputs are only valid when hidden_state_source='decoder'.")
else:
if has_decoder_inputs == has_decoder_ids:
raise ValueError(
"Decoder embedding requires exactly one of decoder_inputs or decoder_input_ids."
)
decoder_input_fingerprint: str | None = None
if decoder_inputs is not None:
if isinstance(decoder_inputs, (str, bytes)) or not isinstance(decoder_inputs, Sequence):
raise TypeError("decoder_inputs must be an aligned sequence of strings.")
normalized_decoder_inputs = tuple(decoder_inputs)
if not all(isinstance(value, str) and value for value in normalized_decoder_inputs):
raise ValueError("decoder_inputs must contain non-empty strings.")
if len(normalized_decoder_inputs) != len(records):
raise ValueError("decoder_inputs must align one-to-one with embedding inputs.")
decoder_input_fingerprint = _ordered_string_sha256(normalized_decoder_inputs)
if decoder_attention_mask is not None:
raise ValueError("decoder_attention_mask requires decoder_input_ids.")
if decoder_input_ids is not None:
if not isinstance(decoder_input_ids, Tensor) or decoder_input_ids.ndim != 2:
raise ValueError("decoder_input_ids must have shape (batch, sequence).")
if decoder_input_ids.shape[0] != len(records):
raise ValueError("decoder_input_ids must align one-to-one with embedding inputs.")
if decoder_input_ids.dtype == torch.bool or decoder_input_ids.is_floating_point():
raise TypeError("decoder_input_ids must use an integer token dtype.")
decoder_input_fingerprint = tensor_sha256(decoder_input_ids)
decoder_mask_fingerprint: str | None = None
if decoder_attention_mask is not None:
if not isinstance(decoder_attention_mask, Tensor):
raise TypeError("decoder_attention_mask must be a tensor.")
if decoder_input_ids is None or decoder_attention_mask.shape != decoder_input_ids.shape:
raise ValueError("decoder_attention_mask must match decoder_input_ids shape.")
decoder_mask_fingerprint = tensor_sha256(decoder_attention_mask)
context: dict[str, Any] = {
"hidden_state_source": hidden_state_source,
"hidden_state_index": hidden_state_index,
"store_all_hidden_states": store_all_hidden_states,
"decoder_input_fingerprint": decoder_input_fingerprint,
"decoder_attention_mask_fingerprint": decoder_mask_fingerprint,
"decoder_alignment": "input-position" if hidden_state_source == "decoder" else None,
}
metadata_hook = getattr(model, "_embedding_metadata", None)
model_metadata: Mapping[str, Any] | None = None
if callable(metadata_hook):
model_metadata = metadata_hook(**context)
if not isinstance(model_metadata, Mapping):
raise TypeError("_embedding_metadata must return a mapping.")
context["model_embedding"] = _fingerprint_jsonable(model_metadata)
if hidden_state_source == "decoder":
has_decoder_batch = callable(getattr(model, "_embedding_batch", None))
declares_decoder_stack = (
model_metadata is not None and model_metadata.get("hidden_state_stack") == "decoder"
)
if not has_decoder_batch or not declares_decoder_stack:
raise ValueError(
f"{model.__class__.__name__} does not declare decoder embedding support."
)
return context, normalized_decoder_inputs
|