GQA Attention (#59)

protein_lm/modeling/models/apt/model_pytorch.py

@@ -8,6 +8,7 @@
 from transformers.pytorch_utils import Conv1D
 from transformers.activations import ACT2FN
 from transformers.utils import logging
+
 from protein_lm.modeling.utils.rotary_embedding import RotaryEmbedding
 from protein_lm.modeling.utils.rerope_embedding import RectifiedRotaryEmbedding
 from protein_lm.modeling.utils.alibi_embedding import create_alibi_tensor
@@ -34,6 +35,7 @@ def __init__(self, config, is_cross_attention=False, layer_idx=None):
         self.max_sequence_length = config.max_sequence_length
         self.embed_dim = config.hidden_size
         self.num_heads = config.num_attention_heads
+        self.attn_type = config.attn_type
         self.head_dim = self.embed_dim // self.num_heads
         self.split_size = self.embed_dim
         if self.head_dim * self.num_heads != self.embed_dim:
@@ -48,7 +50,15 @@ def __init__(self, config, is_cross_attention=False, layer_idx=None):
         # Layer-wise attention scaling, reordering, and upcasting
         self.scale_attn_by_inverse_layer_idx = config.scale_attn_by_inverse_layer_idx
         self.layer_idx = layer_idx
-        self.reorder_and_upcast_attn = config.reorder_and_upcast_attn
+
+        if self.attn_type == "gqa":
+            self.gqa_attn = True
+        elif self.attn_type == "reorder_and_upcast_attn":
+            self.reorder_and_upcast_attn = True
+        elif self.attn_type == "standard":
+            self.standard_attn = True
+
+        #self.reorder_and_upcast_attn = config.reorder_and_upcast_attn #comment out because config now states attn type
 
         if self.is_cross_attention:
             self.c_attn = Conv1D(2 * self.embed_dim, self.embed_dim)
@@ -116,6 +126,87 @@ def _attn(self, query, key, value, attention_mask=None, head_mask=None,alibi_bia
 
         return attn_output, attn_weights
 
+    def _gqa_attn(self, query, key, value, attention_mask=None, 
+                alibi_bias =None, dropout=0.0):
+        """Group Query Attention implementation."""
+
+        # Check for potential issues before moving on
+        if not query.ndim == key.ndim == value.ndim == 4:
+            raise ValueError(f"Expected query, key, and value to be 4-dimensional, but got shapes "
+                            f"{query.shape}, {key.shape}, and {value.shape}.")
+
+        """
+        Expected shapes: (batch_size, num_heads, query_len, query_dim) similar to _upcast_and_reordered_attn
+        """
+        batch_size, num_heads, query_len, query_dim = query.shape
+
+
+        scale_factor = 1.0
+        if self.scale_attn_weights:
+            scale_factor /= float(value.size(-1)) ** 0.5
+        query = query / scale_factor
+
+        '''
+        Determine the number of groups
+        For example lets say we have 4 queries heads and 2 keys heads, then we have 2 groups
+        Lets say the number of group are 2 and head are 2, 
+        then reshape the query tensor to (batch_size, (2, 2), query_len, query_dim)
+        query shape (batch_size, num_groups, num_heads, query_len, query_dim)
+        attention_weights_grouped shape (batch_size, num_groups, num_heads, query_len, key_len).
+        attention weights shape: (batch_size, num_heads, query_len, key_len)
+        '''
+
+        n_groups = query.size(1) // key.size(1)
+
+        if n_groups > 1:
+            query_shape = query.shape
+            grouped_shape = (query_shape[0], n_groups, query_shape[1]//n_groups, query_shape[2], query_shape[3])
+            query_grouped = query.reshape(grouped_shape)
+            attn_weights_grouped = torch.matmul(query_grouped, key.transpose(-2, -1))
+            attn_weights = attn_weights_grouped.sum(dim=1)
+            #print("attn_weights:", attn_weights.shape)
+
+        else:
+            '''
+            If the number of groups is 1, then we can use the normal attention function
+            '''
+            attn_weights = torch.matmul(query, key.transpose(-2, -1))
+
+        if self.scale_attn_by_inverse_layer_idx:
+                attn_weights = attn_weights / float(self.layer_idx + 1)
+
+        if attention_mask is not None:
+            # Apply the attention mask
+            '''
+            Input attention_mask shape: (batch_size, query_len, key_len)
+            '''
+            attn_weights += attention_mask.unsqueeze(1)  # Unsqueeze to Add head dimension
+
+        # Causal masking ensures that the attention mechanism doesn't attend to "future" tokens in sequences.
+        ## Adapted to work with groups and ensure similarity with vanilla attention
+        if not self.is_cross_attention:
+            query_length, key_length = query.size(-2), key.size(-2)
+            causal_mask = self.bias[:, :, key_length - query_length : key_length, :key_length]
+            mask_value = torch.finfo(attn_weights.dtype).min
+            mask_value = torch.full([], mask_value, dtype=attn_weights.dtype).to(attn_weights.device)
+            attn_weights = torch.where(causal_mask, attn_weights.to(attn_weights.dtype), mask_value)
+
+            # print("attn_weights:", attn_weights)
+        # Softmax normalization to get the attention scores
+        attn_weights = nn.functional.softmax(attn_weights, dim=-1)
+
+        if alibi_bias is not None:
+            attn_weights = attn_weights + alibi_bias[:,:,:attn_weights.size(-1)]
+
+        # Apply dropout if specified
+        attn_weights = attn_weights.type(value.dtype)
+        attn_weights = self.attn_dropout(attn_weights)
+
+        # Compute the output by multiplying the attention scores with the value tensor.
+        attn_output = torch.matmul(attn_weights, value)
+
+        return attn_output, attn_weights
+
     def _upcast_and_reordered_attn(self, query, key, value, attention_mask=None, head_mask=None,alibi_bias=None):
         # Use `torch.baddbmm` (a bit more efficient w/ alpha param for scaling -- from Megatron-LM)
         bsz, num_heads, q_seq_len, dk = query.size()
@@ -233,9 +324,10 @@ def forward(
 
         if self.reorder_and_upcast_attn:
             attn_output, attn_weights = self._upcast_and_reordered_attn(query, key, value, attention_mask, head_mask,alibi_bias=alibi_bias)
-        else:
+        elif self.standard_attn:
             attn_output, attn_weights = self._attn(query, key, value, attention_mask, head_mask,alibi_bias=alibi_bias)
-
+        elif self.gqa_attn:
+            attn_output, attn_weights = self._gqa_attn(query, key, value, attention_mask,alibi_bias=alibi_bias)
         attn_output = self._merge_heads(attn_output, self.num_heads, self.head_dim)
         attn_output = self.c_proj(attn_output)
         attn_output = self.resid_dropout(attn_output)
@@ -244,7 +336,7 @@ def forward(
         if output_attentions:
             outputs += (attn_weights,)
 
-        return outputs  # a, present, (attentions)
+        return outputs # a, present, (attentions)
 
 
 class APTMLP(nn.Module):

protein_lm/tests/test_attention.py

@@ -0,0 +1,89 @@
+import pytest
+import torch
+from torch.nn import functional as F
+
+from model_pytorch import APTAttention
+
+class ParameterConfig:
+    def __init__(self):
+        self.max_position_embeddings = 512
+        self.position_embedding = 'rope'
+        self.max_sequence_length = 512
+        self.hidden_size = 768
+        self.num_attention_heads = 12
+        self.scale_attn_weights = True
+        self.scale_attn_by_inverse_layer_idx = True
+        self.reorder_and_upcast_attn = True
+        self.attn_pdrop = 0.1
+        self.resid_pdrop = 0.1
+        self.rope_scaling_factor = 1
+        self.rope_theta = 1
+        self.attn_type = 'gqa'
+
+
+def test_vanilla_attn():
+    # Initialize with mock config
+    config = ParameterConfig()
+    attention = APTAttention(config, is_cross_attention=False, layer_idx=0)
+
+    # generate random input tensors
+    batch_size = 4
+    seq_length = 100
+    num_heads = config.num_attention_heads 
+    query_dim = config.hidden_size // num_heads
+    query = torch.randn(batch_size, num_heads, seq_length, query_dim)
+    key = torch.randn(batch_size, num_heads, seq_length, query_dim)
+    value = torch.randn(batch_size, num_heads, seq_length, query_dim)
+
+    # Create a random attention mask for testing
+    attention_mask = torch.ones(batch_size,seq_length, seq_length)
+    padding_positions = 10
+    attention_mask[:, -padding_positions:, :] = float('-inf')
+    attention_mask[:, :, -padding_positions:] = float('-inf')
+    attention_mask = attention_mask.unsqueeze(1)
+    # Pass them through the _attn method
+    attn_output, attn_weights = attention._attn(query, key, value, attention_mask=attention_mask)
+
+    # Check the shapes and types of the output
+    assert isinstance(attn_output, torch.Tensor)
+    assert attn_output.shape == (batch_size, num_heads, seq_length, query_dim)
+    assert isinstance(attn_weights, torch.Tensor)
+    assert attn_weights.shape == (batch_size, num_heads, seq_length, seq_length)
+    print("Test passed!")
+
+def test_gqa_attn():
+    # Initialize with mock config
+    config = ParameterConfig()
+    attention = APTAttention(config, is_cross_attention=False, layer_idx=0)
+
+    # generate random input tensors
+    batch_size = 4
+    seq_length = 100
+    num_heads = config.num_attention_heads 
+    query_dim = config.hidden_size // num_heads
+    query = torch.randn(batch_size, num_heads, seq_length, query_dim)
+    key = torch.randn(batch_size, num_heads, seq_length, query_dim)
+    value = torch.randn(batch_size, num_heads, seq_length, query_dim)
+
+    # Create a random attention mask for testing
+    attention_mask = torch.ones(batch_size,seq_length, seq_length)
+    padding_positions = 10
+    attention_mask[:, -padding_positions:, :] = float('-inf')
+    attention_mask[:, :, -padding_positions:] = float('-inf')
+
+    # Pass them through the _gqa_attn method
+    attn_output, attn_weights = attention._gqa_attn(query, key, value, attention_mask=attention_mask)
+
+    # Check the shapes and types of the output
+    assert isinstance(attn_output, torch.Tensor)
+    assert attn_output.shape == (batch_size, num_heads, seq_length, query_dim)
+    assert isinstance(attn_weights, torch.Tensor)
+    assert attn_weights.shape == (batch_size, num_heads, seq_length, seq_length)
+    print("Test passed!")
+
+
+test_gqa_attn()
+test_vanilla_attn()
+
+
+