def __init__(self, model: str, device: Union[None, str, torch.device] = None, **kwargs):
"""
Initialize annotation extractor. Must define non-positional arguments for paths of files.
:param membrane_checkpoint_file: path of the membrane boundness inference model checkpoint file
:param subcellular_location_checkpoint_file: path of the subcellular location inference model checkpoint file
"""
self._options = kwargs
self._device = get_device(device)
# Create un-trained (raw) model
self._subcellular_location_model = LightAttention(output_dim=10).to(self._device)
self._membrane_model = LightAttention(output_dim=2).to(self._device)
self._subcellular_location_checkpoint_file = self._options.get('subcellular_location_checkpoint_file')
self._membrane_checkpoint_file = self._options.get('membrane_checkpoint_file')
self._device = get_device(device)
# Download files if needed
for file in self.necessary_files:
if not self._options.get(file):
self._options[file] = get_model_file(model=model, file=file)
# load pre-trained weights for annotation machines
subcellular_state = torch.load(self._subcellular_location_checkpoint_file, map_location=self._device)
membrane_state = torch.load(self._membrane_checkpoint_file, map_location=self._device)
# load pre-trained weights into raw model
self._subcellular_location_model.load_state_dict(subcellular_state['state_dict'])
self._membrane_model.load_state_dict(membrane_state['state_dict'])
# ensure that model is in evaluation mode (important for batchnorm and dropout)
self._subcellular_location_model.eval()
self._membrane_model.eval()
def __init__(self, device: Union[None, str, torch.device] = None, **kwargs):
"""
Initializer accepts location of a pre-trained model and options
"""
self._options = kwargs
self._device = get_device(device)
# Special case because SeqVec can currently be used with either a model directory or two files
if self.__class__.__name__ == "SeqVecEmbedder":
# No need to download weights_file/options_file if model_directory is given
if "model_directory" in self._options:
return
files_loaded = 0
for file in self.necessary_files:
if not self._options.get(file):
self._options[file] = get_model_file(model=self.name, file=file)
files_loaded += 1
for directory in self.necessary_directories:
if not self._options.get(directory):
self._options[directory] = get_model_directories_from_zip(
model=self.name, directory=directory
)
files_loaded += 1
total_necessary = len(self.necessary_files) + len(self.necessary_directories)
if 0 < files_loaded < total_necessary:
logger.warning(
f"You should pass either all necessary files or directories, or none, "
f"while you provide {files_loaded} of {total_necessary}"
)
def __init__(self,
model_type: str,
device: Union[None, str, torch.device] = None,
**kwargs):
"""
Initialize annotation extractor. Must define non-positional arguments for paths of files.
:param model_file: path of conservation inference model checkpoint file (only CNN-architecture from paper)
"""
self._options = kwargs
self._model_type = model_type
self._device = get_device(device)
# Create un-trained (raw) model and ensure self._model_type is valid
self._conservation_model = ConservationCNN().to(self._device)
# Download the checkpoint files if needed
if not self._options.get("model_file"):
self._options["model_file"] = get_model_file(model=f"prott5cons",
file="model_file")
self.model_file = self._options["model_file"]
# load pre-trained weights for annotation machines
conservation_state = torch.load(self.model_file,
map_location=self._device)
# load pre-trained weights into raw model
self._conservation_model.load_state_dict(
conservation_state["state_dict"])
# ensure that model is in evaluation mode (important for batchnorm and dropout)
self._conservation_model.eval()
def __init__(self, device: Union[None, str, torch.device] = None, **kwargs):
self._options = kwargs
self._device = get_device(device)
# Download the checkpoint files if needed
for file in self.necessary_files:
if not self._options.get(file):
self._options[file] = get_model_file(model='tmbed', file=file)
self._models = []
for model_idx in range(5):
# Create blank model
model = TmbedModel()
# Get model file
model_file = self._options[f'model_{model_idx}_file']
# Load pre-trained weights
model.load_state_dict(torch.load(model_file)['model'])
# Finalize model
model = model.eval().to(self._device)
# Add to model list
self._models.append(model)
self._decoder = Decoder()
def pb_tucker(file_manager: FileManagerInterface,
result_kwargs: Dict[str, Any]) -> Dict[str, Any]:
device = get_device(result_kwargs.get("device"))
if "model_file" not in result_kwargs:
model_file = get_model_file("pb_tucker", "model_file")
else:
model_file = result_kwargs["model_file"]
pb_tucker = PBTucker(model_file, device)
reduced_embeddings_file_path = result_kwargs["reduced_embeddings_file"]
projected_reduced_embeddings_file_path = file_manager.create_file(
result_kwargs.get("prefix"),
result_kwargs.get("stage_name"),
"projected_reduced_embeddings_file",
extension=".csv",
)
result_kwargs[
"projected_reduced_embeddings_file"] = projected_reduced_embeddings_file_path
with h5py.File(reduced_embeddings_file_path,
"r") as input_embeddings, h5py.File(
projected_reduced_embeddings_file_path,
"w") as output_embeddings:
for h5_id, reduced_embedding in input_embeddings.items():
output_embeddings[h5_id] = pb_tucker.project_reduced_embedding(
reduced_embedding)
return result_kwargs
def __init__(self,
device: Union[None, str, torch.device] = None,
**kwargs):
"""
Initialize annotation extractor. Must define non-positional arguments for paths of files.
:param membrane_checkpoint_file: path of the membrane boundness inference model checkpoint file
:param subcellular_location_checkpoint_file: path of the subcellular location inference model checkpoint file
"""
self._options = kwargs
self._device = get_device(device)
# Create un-trained (raw) model
self._subcellular_location_model = LightAttention(output_dim=10).to(
self._device)
self._membrane_model = LightAttention(output_dim=2).to(self._device)
self._subcellular_location_checkpoint_file = self._options.get(
'subcellular_location_checkpoint_file')
self._membrane_checkpoint_file = self._options.get(
'membrane_checkpoint_file')
self._device = get_device(device)
# check that file paths are passed
for file in self.necessary_files:
if file not in self._options:
raise MissingParameterError(
'Please provide subcellular_location_checkpoint_file and membrane_checkpoint_file paths as named '
'parameters to the constructor. Mind that these should match the embeddings used, '
'e.g.: prottrans_bert_bfd should use la_protbert weights')
# load pre-trained weights for annotation machines
subcellular_state = torch.load(
self._subcellular_location_checkpoint_file,
map_location=self._device)
membrane_state = torch.load(self._membrane_checkpoint_file,
map_location=self._device)
# load pre-trained weights into raw model
self._subcellular_location_model.load_state_dict(
subcellular_state['state_dict'])
self._membrane_model.load_state_dict(membrane_state['state_dict'])
# ensure that model is in evaluation mode (important for batchnorm and dropout)
self._subcellular_location_model.eval()
self._membrane_model.eval()
def __init__(self,
model_type: str,
device: Union[None, str, torch.device] = None,
**kwargs):
"""
Initialize annotation extractor. Must define non-positional arguments for paths of files.
:param secondary_structure_checkpoint_file: path of secondary structure inference model checkpoint file
:param subcellular_location_checkpoint_file: path of the subcellular location inference model checkpoint file
"""
self._options = kwargs
self._model_type = model_type
self._device = get_device(device)
# Create un-trained (raw) model and ensure self._model_type is valid
if self._model_type == "seqvec_from_publication":
self._subcellular_location_model = SUBCELL_FNN().to(self._device)
elif self._model_type == "bert_from_publication": # Drop batchNorm for ProtTrans models
self._subcellular_location_model = SUBCELL_FNN(
use_batch_norm=False).to(self._device)
else:
print("You first need to define your custom model architecture.")
raise NotImplementedError
# Download the checkpoint files if needed
for file in self.necessary_files:
if not self._options.get(file):
self._options[file] = get_model_file(
model=f"{self._model_type}_annotations_extractors",
file=file)
self._secondary_structure_checkpoint_file = self._options[
'secondary_structure_checkpoint_file']
self._subcellular_location_checkpoint_file = self._options[
'subcellular_location_checkpoint_file']
# Read in pre-trained model
self._secondary_structure_model = SECSTRUCT_CNN().to(self._device)
# load pre-trained weights for annotation machines
subcellular_state = torch.load(
self._subcellular_location_checkpoint_file,
map_location=self._device)
secondary_structure_state = torch.load(
self._secondary_structure_checkpoint_file,
map_location=self._device)
# load pre-trained weights into raw model
self._subcellular_location_model.load_state_dict(
subcellular_state['state_dict'])
self._secondary_structure_model.load_state_dict(
secondary_structure_state['state_dict'])
# ensure that model is in evaluation mode (important for batchnorm and dropout)
self._subcellular_location_model.eval()
self._secondary_structure_model.eval()
def __init__(
self,
device: Union[None, str, torch.device] = None,
model_directory: Optional[str] = None,
half_precision_model: bool = False,
):
"""Loads the Bert Model for Masked LM"""
self.device = get_device(device)
self._half_precision_model = half_precision_model
if not model_directory:
model_directory = get_model_directories_from_zip(
model=ProtTransBertBFDEmbedder.name,
directory="model_directory")
self.tokenizer = BertTokenizer.from_pretrained(model_directory,
do_lower_case=False)
self.model = BertForMaskedLM.from_pretrained(model_directory)
# Compute in half precision, which is a lot faster and saves us half the memory
if self._half_precision_model:
self.model = self.model.half()
self.model = self.model.eval().to(self.device)
def __init__(self,
device: Union[None, str, torch.device] = None,
**kwargs):
"""
Initialize annotation extractor. Must define non-positional arguments for paths of files.
:param model_file: path of bindEmbed21DL inference model checkpoint file
"""
self._options = kwargs
self._device = get_device(device)
# Create un-trained (raw) models
self._binding_residue_model_1 = BindingResiduesCNN().to(self._device)
self._binding_residue_model_2 = BindingResiduesCNN().to(self._device)
self._binding_residue_model_3 = BindingResiduesCNN().to(self._device)
self._binding_residue_model_4 = BindingResiduesCNN().to(self._device)
self._binding_residue_model_5 = BindingResiduesCNN().to(self._device)
# Download the checkpoint files if needed
for file in self.necessary_files:
if not self._options.get(file):
self._options[file] = get_model_file(model=f"bindembed21dl",
file=file)
self.model_file_1 = self._options['model_1_file']
self.model_file_2 = self._options['model_2_file']
self.model_file_3 = self._options['model_3_file']
self.model_file_4 = self._options['model_4_file']
self.model_file_5 = self._options['model_5_file']
# load pre-trained weights for annotation machines
binding_residue_state_1 = torch.load(self.model_file_1,
map_location=self._device)
binding_residue_state_2 = torch.load(self.model_file_1,
map_location=self._device)
binding_residue_state_3 = torch.load(self.model_file_1,
map_location=self._device)
binding_residue_state_4 = torch.load(self.model_file_1,
map_location=self._device)
binding_residue_state_5 = torch.load(self.model_file_1,
map_location=self._device)
# load pre-trained weights into raw model
self._binding_residue_model_1.load_state_dict(
binding_residue_state_1['state_dict'])
self._binding_residue_model_2.load_state_dict(
binding_residue_state_2['state_dict'])
self._binding_residue_model_3.load_state_dict(
binding_residue_state_3['state_dict'])
self._binding_residue_model_4.load_state_dict(
binding_residue_state_4['state_dict'])
self._binding_residue_model_5.load_state_dict(
binding_residue_state_5['state_dict'])
# ensure that model is in evaluation mode (important for batchnorm and dropout)
self._binding_residue_model_1.eval()
self._binding_residue_model_2.eval()
self._binding_residue_model_3.eval()
self._binding_residue_model_4.eval()
self._binding_residue_model_5.eval()
def run(**kwargs):
"""BETA: in-silico mutagenesis using BertForMaskedLM
optional (see extract stage for details):
* model_directory
* device
* half_precision
* half_precision_model
* temperature: temperature for softmax
"""
required_kwargs = [
"protocol",
"prefix",
"stage_name",
"remapped_sequences_file",
"mapping_file",
]
check_required(kwargs, required_kwargs)
result_kwargs = deepcopy(kwargs)
if result_kwargs["protocol"] not in _PROTOCOLS:
raise RuntimeError(
f"Passed protocol {result_kwargs['protocol']}, but allowed are: {', '.join(_PROTOCOLS)}"
)
temperature = result_kwargs.setdefault("temperature", 1)
device = get_device(result_kwargs.get("device"))
model_class: Type[ProtTransBertBFDMutagenesis] = _PROTOCOLS[
result_kwargs["protocol"]
]
model = model_class(
device,
result_kwargs.get("model_directory"),
result_kwargs.get("half_precision_model"),
)
file_manager = get_file_manager()
file_manager.create_stage(result_kwargs["prefix"], result_kwargs["stage_name"])
# The mapping file contains the corresponding ids in the same order
sequences = [
str(entry.seq)
for entry in SeqIO.parse(result_kwargs["remapped_sequences_file"], "fasta")
]
mapping_file = read_mapping_file(result_kwargs["mapping_file"])
probabilities_all = dict()
with tqdm(total=int(mapping_file["sequence_length"].sum())) as progress_bar:
for sequence_id, original_id, sequence in zip(
mapping_file.index, mapping_file["original_id"], sequences
):
with torch.no_grad():
probabilities = model.get_sequence_probabilities(
sequence, temperature, progress_bar=progress_bar
)
for p in probabilities:
assert math.isclose(
1, (sum(p.values()) - p["position"]), rel_tol=1e-6
), "softmax values should add up to 1"
probabilities_all[sequence_id] = probabilities
residue_probabilities = probabilities_as_dataframe(
mapping_file, probabilities_all, sequences
)
probabilities_file = file_manager.create_file(
result_kwargs.get("prefix"),
result_kwargs.get("stage_name"),
"residue_probabilities_file",
extension=".csv",
)
residue_probabilities.to_csv(probabilities_file, index=False)
result_kwargs["residue_probabilities_file"] = probabilities_file
return result_kwargs