Attention
ESM2DotProductAttention
Bases: DotProductAttention
ESM2-Specific core attention.
Region where selective activation recomputation is applied. This region is memory intensive but less compute intensive which makes activation checkpointing more efficient for LLMs (20B+). See Reducing Activation Recomputation in Large Transformer Models: https://arxiv.org/abs/2205.05198 for more details.
We use the following notation
h: hidden size n: number of attention heads p: number of tensor model parallel partitions b: batch size s: sequence length
Source code in bionemo/esm2/model/attention.py
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__init__(config, layer_number, attn_mask_type, attention_type, attention_dropout=None)
Initializes the Attention class.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
config
|
TransformerConfig
|
The configuration object for the transformer. |
required |
layer_number
|
int
|
The layer number of the attention module. |
required |
attn_mask_type
|
AttnMaskType
|
The type of attention mask to be used. |
required |
attention_type
|
str
|
The type of attention mechanism. |
required |
attention_dropout
|
Optional[float]
|
The dropout rate for attention weights. Defaults to None. |
None
|
Source code in bionemo/esm2/model/attention.py
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esm2_scale_mask_softmax(input, mask=None, scale=None, mask_func=None)
Scale Mask Softmax function.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
input
|
Tensor
|
Tensor of shape (Batch, NP, SK, SQ). The input may or may not have already had a mask applied to it. |
required |
mask
|
Optional[Tensor]
|
If a mask is to be applied, it will go here. |
None
|
scale
|
Optional[Union[float, int]]
|
A scale factor that will be applied before the softmax. |
None
|
mask_func
|
Optional[Callable]
|
An optional function to apply to the mask. If None, it is assumed that the input already had the mask applied to it. |
None
|
Returns:
Name | Type | Description |
---|---|---|
probs |
Tensor
|
Tensor of normalized probabilities after the softmax has been applied, of shape (Batch, NP, SK, SQ). |
Source code in bionemo/esm2/model/attention.py
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forward(query, key, value, attention_mask, attn_mask_type=None, packed_seq_params=None)
Forward pass of the ESM2DotProductAttention module.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
query
|
Tensor
|
The query tensor of shape [sq, b, np, hn]. |
required |
key
|
Tensor
|
The key tensor of shape [sk, b, ng, hn]. |
required |
value
|
Tensor
|
The value tensor of shape [sk, b, ng, hn]. |
required |
attention_mask
|
Tensor
|
The attention mask tensor of shape [b, np, sq, sk]. |
required |
attn_mask_type
|
Optional[AttnMaskType]
|
The attention mask type, currently unused. Defaults to None. |
None
|
packed_seq_params
|
Optional[PackedSeqParams]
|
The packed sequence parameters. These are used for context parallelism so will be needed to be implemented if we want to support this. Defaults to None. |
None
|
Returns:
Name | Type | Description |
---|---|---|
Tensor |
The context tensor of shape [sq, b, hp]. |
Source code in bionemo/esm2/model/attention.py
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ESM2TEDotProductAttention
Bases: TEDotProductAttention
ESM2-Specific transformer engine core attention.
Override the softmax_scale to 1.0 to match the ESM2 implementation while keeping the rest from the original TEDotProductAttention.
Source code in bionemo/esm2/model/attention.py
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__init__(config, layer_number, attn_mask_type, attention_type, attention_dropout=None, softmax_scale=1.0, k_channels=None, v_channels=None, cp_comm_type='p2p')
Initialize ESM2TEDotProductAttention.
Source code in bionemo/esm2/model/attention.py
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