dnabert2-H3K27ac / configuration_bert.py
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Add DNABERT-2 model for H3K27ac prediction
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# Copyright 2022 MosaicML Examples authors
# SPDX-License-Identifier: Apache-2.0
from transformers import BertConfig as TransformersBertConfig
class BertConfig(TransformersBertConfig):
def __init__(
self,
alibi_starting_size: int = 512,
attention_probs_dropout_prob: float = 0.0,
**kwargs,
):
"""Configuration class for MosaicBert.
Args:
alibi_starting_size (int): Use `alibi_starting_size` to determine how large of an alibi tensor to
create when initializing the model. You should be able to ignore this parameter in most cases.
Defaults to 512.
attention_probs_dropout_prob (float): By default, turn off attention dropout in Mosaic BERT
(otherwise, Flash Attention will be off by default). Defaults to 0.0.
"""
super().__init__(
attention_probs_dropout_prob=attention_probs_dropout_prob, **kwargs)
self.alibi_starting_size = alibi_starting_size