Source code for immuneML.encodings.word2vec.model_creator.KmerPairModelCreator

# quality: gold

from pathlib import Path

from gensim.models import Word2Vec

from immuneML.data_model.dataset.RepertoireDataset import RepertoireDataset
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 KmerPairModelCreator(ModelCreatorStrategy):
[docs] def create_model(self, dataset: RepertoireDataset, k: int, vector_size: int, batch_size: int, model_path: Path, sequence_type: SequenceType): model = Word2Vec(size=vector_size, min_count=1, window=5) # 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) for kmer in all_kmers: sentences = KmerHelper.create_kmers_within_HD(kmer=kmer[0], alphabet=EnvironmentSettings.get_sequence_alphabet(), distance=1) model.train(sentences=sentences, total_words=len(all_kmers), epochs=model.epochs) model.save(str(model_path)) return model