IgBert
Model pretrained on protein and antibody sequences using a masked language modeling (MLM) objective. It was introduced in the paper Large scale paired antibody language models.
The model is finetuned from IgBert-unpaired using paired antibody sequences from the Observed Antibody Space.
Use
The model and tokeniser can be loaded using the transformers library
from transformers import BertModel, BertTokenizer
tokeniser = BertTokenizer.from_pretrained("Exscientia/IgBert", do_lower_case=False)
model = BertModel.from_pretrained("Exscientia/IgBert", add_pooling_layer=False)
The tokeniser is used to prepare batch inputs
# heavy chain sequences
sequences_heavy = [
"VQLAQSGSELRKPGASVKVSCDTSGHSFTSNAIHWVRQAPGQGLEWMGWINTDTGTPTYAQGFTGRFVFSLDTSARTAYLQISSLKADDTAVFYCARERDYSDYFFDYWGQGTLVTVSS",
"QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYAMYWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCASGSDYGDYLLVYWGQGTLVTVSS"
]
# light chain sequences
sequences_light = [
"EVVMTQSPASLSVSPGERATLSCRARASLGISTDLAWYQQRPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDSAVYYCQQYSNWPLTFGGGTKVEIK",
"ALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQSEDEADYYCNSLTSISTWVFGGGTKLTVL"
]
# The tokeniser expects input of the form ["V Q ... S S [SEP] E V ... I K", ...]
paired_sequences = []
for sequence_heavy, sequence_light in zip(sequences_heavy, sequences_light):
paired_sequences.append(' '.join(sequence_heavy)+' [SEP] '+' '.join(sequence_light))
tokens = tokeniser.batch_encode_plus(
paired_sequences,
add_special_tokens=True,
pad_to_max_length=True,
return_tensors="pt",
return_special_tokens_mask=True
)
Note that the tokeniser adds a [CLS] token at the beginning of each paired sequence, a [SEP] token at the end of each paired sequence and pads using the [PAD] token. For example a batch containing sequences V Q L [SEP] E V V, Q V [SEP] A L will be tokenised to [CLS] V Q L [SEP] E V V [SEP] and [CLS] Q V [SEP] A L [SEP] [PAD] [PAD].
Sequence embeddings are generated by feeding tokens through the model
output = model(
input_ids=tokens['input_ids'],
attention_mask=tokens['attention_mask']
)
residue_embeddings = output.last_hidden_state
To obtain a sequence representation, the residue tokens can be averaged over like so
import torch
# mask special tokens before summing over embeddings
residue_embeddings[tokens["special_tokens_mask"] == 1] = 0
sequence_embeddings_sum = residue_embeddings.sum(1)
# average embedding by dividing sum by sequence lengths
sequence_lengths = torch.sum(tokens["special_tokens_mask"] == 0, dim=1)
sequence_embeddings = sequence_embeddings_sum / sequence_lengths.unsqueeze(1)
For sequence level fine-tuning the model can be loaded with a pooling head by setting add_pooling_layer=True and using output.pooler_output in the down-stream task.