# quality: gold
from pathlib import Path
from gensim.models import Word2Vec
from immuneML.data_model.dataset.Dataset import Dataset
from immuneML.data_model.dataset.RepertoireDataset import RepertoireDataset
from immuneML.data_model.dataset.SequenceDataset import SequenceDataset
from immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy import ModelCreatorStrategy
from immuneML.environment.EnvironmentSettings import EnvironmentSettings
from immuneML.environment.SequenceType import SequenceType
from immuneML.util.KmerHelper import KmerHelper
[docs]
class SequenceModelCreator(ModelCreatorStrategy):
[docs]
def create_model(self, dataset: Dataset, k: int, vector_size: int, batch_size: int, model_path: Path, sequence_type: SequenceType):
model = Word2Vec(vector_size=vector_size, min_count=1, window=self.window) # creates an empty model
all_kmers = KmerHelper.create_all_kmers(k=k, alphabet=EnvironmentSettings.get_sequence_alphabet())
all_kmers = [[kmer] for kmer in all_kmers]
model.build_vocab(all_kmers)
if isinstance(dataset, RepertoireDataset):
model = self._create_for_repertoire(dataset, batch_size, k, model, all_kmers, sequence_type)
elif isinstance(dataset, SequenceDataset):
model = self._create_for_sequences(dataset, batch_size, k, model, all_kmers, sequence_type)
model.save(str(model_path))
return model
def _create_for_repertoire(self, dataset, batch_size, k, model, all_kmers, sequence_type):
for example in dataset.get_data(batch_size=batch_size):
sentences = KmerHelper.create_sentences_from_repertoire(repertoire=example, k=k, sequence_type=sequence_type)
model.train(corpus_iterable=sentences, total_words=len(all_kmers), epochs=self.epochs)
return model
def _create_for_sequences(self, dataset: SequenceDataset, batch_size, k, model, all_kmers, sequence_type):
for sequence_batch in dataset.get_batch(batch_size):
sentences = [KmerHelper.create_kmers_from_sequence(seq, k, sequence_type) for seq in sequence_batch]
model.train(corpus_iterable=sentences, total_words=len(all_kmers), epochs=self.epochs)
return model