Add Pooling Strategy Option for embedding creation (#491)

* Add pooling stratedgy Signed-off-by: Vibhu Jawa <[email protected]> * Ensure pytest is importable in a CPU only environment Signed-off-by: Vibhu Jawa <[email protected]> * Fix last token based on Avinash's feedback Signed-off-by: Vibhu Jawa <[email protected]> * Fix indexing issues Signed-off-by: Vibhu Jawa <[email protected]> * Merge in main Signed-off-by: Vibhu Jawa <[email protected]> * Fix Doc-string Signed-off-by: Vibhu Jawa <[email protected]> * Address Sarah's reviews Signed-off-by: Vibhu Jawa <[email protected]> --------- Signed-off-by: Vibhu Jawa <[email protected]>
NVIDIA · Feb 6, 2025 · 97aa372 · 97aa372
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Showing 4 changed files with 123 additions and 2 deletions.
diff --git a/nemo_curator/modules/config.py b/nemo_curator/modules/config.py
@@ -145,6 +145,7 @@ class SemDedupConfig(BaseConfig):
         embeddings_save_loc (str): Location to save embeddings.
         embedding_model_name_or_path (str): Model name or path for embeddings.
         embedding_batch_size (int): Inital Batch size for processing embeddings.
+        embedding_pooling_strategy (str): Strategy for pooling embeddings, either "mean_pooling" or "last_token". Defaults to "mean_pooling".
         write_embeddings_to_disk (bool): If True, saves the embeddings to disk, defaults to True.
             We recommend setting this to False when you have a delayed pipeline.
             Setting it to False can lead to more memory overhead.
@@ -168,6 +169,8 @@ class SemDedupConfig(BaseConfig):
     embeddings_save_loc: str = "embeddings"
     embedding_model_name_or_path: str = "sentence-transformers/all-MiniLM-L6-v2"
     embedding_batch_size: int = 128
+    # Options: "mean_pooling", "last_token"
+    embedding_pooling_strategy: str = "mean_pooling"
     write_embeddings_to_disk: bool = True
 
     # Clustering config

diff --git a/nemo_curator/modules/semantic_dedup/embeddings.py b/nemo_curator/modules/semantic_dedup/embeddings.py
@@ -41,6 +41,7 @@
 class EmbeddingConfig:
     model_name_or_path: str
     max_seq_length: int = None
+    pooling_strategy: str = "mean_pooling"  # Options: "mean_pooling" or "last_token"
 
     def __post_init__(self):
         self.max_seq_length = AutoTokenizer.from_pretrained(
@@ -52,6 +53,10 @@ def __post_init__(self):
             self.max_seq_length = AutoConfig.from_pretrained(
                 self.model_name_or_path
             ).max_position_embeddings
+        if self.pooling_strategy not in ["mean_pooling", "last_token"]:
+            raise ValueError(
+                "pooling_strategy must be either 'mean_pooling' or 'last_token'"
+            )
 
 
 class EmbeddingPytorchModel(nn.Module):
@@ -70,7 +75,10 @@ def feature(self, input_ids, attention_mask):
     @torch.no_grad()
     def forward(self, batch):
         feature = self.feature(batch["input_ids"], batch["attention_mask"])
-        return self._mean_pooling(feature, batch["attention_mask"])
+        if self.config.pooling_strategy == "mean_pooling":
+            return self._mean_pooling(feature, batch["attention_mask"])
+        else:
+            return self._get_last_token(feature, batch["attention_mask"])
 
     def _mean_pooling(self, model_output, attention_mask):
         token_embeddings = model_output[0]
@@ -81,6 +89,19 @@ def _mean_pooling(self, model_output, attention_mask):
         sum_mask = torch.clamp(input_mask_expanded.sum(dim=1), min=1e-9)
         return F.normalize(sum_embeddings / sum_mask, dim=1)
 
+    def _get_last_token(self, model_output, attention_mask):
+        token_embeddings = model_output[0]
+        # Get indices of last non-padded tokens for each sequence in batch
+        last_token_indices = attention_mask.sum(dim=1) - 1  # -1 for 0-based indexing
+        last_token_indices = last_token_indices.to(
+            torch.long
+        )  # Ensure indices are of type long
+        batch_size = attention_mask.size(0)
+        batch_indices = torch.arange(batch_size, device=attention_mask.device)
+        # Get embeddings of last non-padded tokens
+        last_token_embeddings = token_embeddings[batch_indices, last_token_indices]
+        return F.normalize(last_token_embeddings, dim=1)
+
 
 class EmbeddingCrossFitModel(HFModel):
     def __init__(
@@ -116,6 +137,7 @@ def __init__(
         embedding_batch_size: int,
         embedding_output_dir: str,
         embedding_max_mem_gb: Optional[int] = None,
+        embedding_pooling_strategy: str = "mean_pooling",
         input_column: str = "text",
         embedding_column: str = "embeddings",
         write_embeddings_to_disk: bool = True,
@@ -132,6 +154,7 @@ def __init__(
             embedding_output_dir (str): Directory path where embeddings will be saved.
             embedding_max_mem_gb (int): Maximum memory usage in GB for the embedding process.
                                 If None, it defaults to the available GPU memory minus 4 GB.
+            embedding_pooling_strategy (str): Strategy for pooling embeddings, either "mean_pooling" or "last_token". Defaults to "mean_pooling".
             input_column (str): Column name from the data to be used for embedding generation, defaults to "text".
             write_embeddings_to_disk (bool, optional): If True, saves the embeddings to disk, defaults to True.
                                 We recommend setting this to False when you have a delayed pipeline.
@@ -152,6 +175,7 @@ def __init__(
 
         self.embeddings_config = EmbeddingConfig(
             model_name_or_path=embedding_model_name_or_path,
+            pooling_strategy=embedding_pooling_strategy,
         )
         self.batch_size = embedding_batch_size
         self.logger = self._setup_logger(logger)
@@ -184,7 +208,7 @@ def create_embeddings(
             op.Tokenizer(
                 self.model,
                 cols=[input_column],
-                tokenizer_type="sentencepiece",
+                tokenizer_type="default",
                 max_length=self.embeddings_config.max_seq_length,
             ),
             op.Predictor(

diff --git a/nemo_curator/modules/semantic_dedup/semdedup.py b/nemo_curator/modules/semantic_dedup/semdedup.py
@@ -50,6 +50,7 @@ def __init__(
         self.embedding_creator = EmbeddingCreator(
             embedding_model_name_or_path=config.embedding_model_name_or_path,
             embedding_batch_size=config.embedding_batch_size,
+            embedding_pooling_strategy=config.embedding_pooling_strategy,
             input_column=input_column,
             embedding_output_dir=os.path.join(cache_dir, config.embeddings_save_loc),
             write_embeddings_to_disk=config.write_embeddings_to_disk,

diff --git a/tests/test_semdedup.py b/tests/test_semdedup.py
@@ -13,9 +13,13 @@
 # limitations under the License.
 import os
 
+import numpy as np
 import pytest
+import torch
+import torch.nn.functional as F
 from dask.dataframe.utils import assert_eq
 from distributed import Client
+from transformers import AutoConfig, AutoModel, AutoTokenizer
 
 from nemo_curator import SemDedup, SemDedupConfig
 from nemo_curator.datasets import DocumentDataset
@@ -24,6 +28,9 @@
 cudf = gpu_only_import("cudf")
 dask_cudf = gpu_only_import("dask_cudf")
 LocalCUDACluster = gpu_only_import_from("dask_cuda", "LocalCUDACluster")
+EmbeddingCreator = gpu_only_import_from(
+    "nemo_curator.modules.semantic_dedup.embeddings", "EmbeddingCreator"
+)
 
 
 @pytest.fixture
@@ -80,3 +87,89 @@ def test_sem_dedup(
         duplicate_docs = [2, 3, 4, 200, 300]
         expected_df = cudf.Series(duplicate_docs, name="id")
         assert_eq(result_df["id"].sort_values(), expected_df, check_index=False)
+
+    @pytest.mark.parametrize("pooling_strategy", ["last_token", "mean_pooling"])
+    def test_embedding_creator_pooling_strategies(self, tmpdir, pooling_strategy):
+        test_text_1 = "The quick brown fox jumps over the lazy dog"
+        test_text_2 = "The brown fox jumps over the dog"
+        test_texts = [test_text_1, test_text_2] * 32
+        df = cudf.DataFrame({"text": test_texts})
+        ddf = dask_cudf.from_cudf(df, 1)
+        cache_dir = os.path.join(tmpdir, "test_embeddings_cache")
+
+        embedding_creator = EmbeddingCreator(
+            embedding_model_name_or_path="sentence-transformers/all-MiniLM-L6-v2",
+            embedding_batch_size=32,
+            embedding_pooling_strategy=pooling_strategy,
+            input_column="text",
+            embedding_output_dir=os.path.join(cache_dir, "mean_embeddings"),
+        )
+        embeddings = embedding_creator.create_embeddings(ddf).compute()
+        embeddings = embeddings["embeddings"].to_arrow().to_pylist()
+        embeddings = np.array(embeddings)
+        reference_embeddings = get_reference_embeddings(
+            test_texts, pooling_strategy=pooling_strategy
+        )
+        assert np.allclose(
+            embeddings, reference_embeddings, atol=1e-3
+        ), "Embeddings should match reference embeddings"
+
+
+def get_reference_embeddings(
+    texts,
+    model_name="sentence-transformers/all-MiniLM-L6-v2",
+    pooling_strategy="last_token",
+):
+    """
+    Get embeddings using either last token or mean pooling strategy.
+
+    Args:
+        texts: List of input texts
+        model_name: Name or path of the model to use
+        pooling_strategy: Either "last_token" for last token or "mean" for mean pooling
+    """
+    tokenizer = AutoTokenizer.from_pretrained(model_name)
+    model = AutoModel.from_pretrained(model_name)
+    model = model.to("cuda")
+    model.eval()
+    max_len_to_use = tokenizer.model_max_length
+    if max_len_to_use > 1e5:
+        max_len_to_use = AutoConfig.from_pretrained(model_name).max_position_embeddings
+    max_seq_length: int = max_len_to_use
+
+    embs = []
+    for text in texts:
+        inputs = tokenizer(
+            text,
+            return_tensors="pt",
+            padding=True,
+            truncation=True,
+            max_length=max_seq_length,
+        )
+        inputs = {k: v.to("cuda") for k, v in inputs.items()}
+
+        with torch.no_grad():
+            with torch.autocast(device_type="cuda"):
+                outputs = model(**inputs)
+
+        if pooling_strategy == "last_token":
+            embeddings = outputs.last_hidden_state[:, -1, :]
+        elif pooling_strategy == "mean_pooling":
+            token_embeddings = outputs.last_hidden_state
+            attention_mask = inputs["attention_mask"]
+            input_mask_expanded = (
+                attention_mask.unsqueeze(-1).expand(token_embeddings.size()).float()
+            )
+            sum_embeddings = torch.sum(token_embeddings * input_mask_expanded, dim=1)
+            sum_mask = torch.clamp(input_mask_expanded.sum(dim=1), min=1e-9)
+            embeddings = sum_embeddings / sum_mask
+        else:
+            raise ValueError(
+                "pooling_strategy must be either 'last_token' or 'mean_pooling'"
+            )
+
+        normed_emb = F.normalize(embeddings, dim=1).cpu()
+        normed_emb = normed_emb.squeeze(0)
+        embs.append(normed_emb)
+
+    return np.array(embs)