diff --git a/open_instruct/dataset_transformation.py b/open_instruct/dataset_transformation.py
index 0c5d38bc1f..1d703dfb57 100644
--- a/open_instruct/dataset_transformation.py
+++ b/open_instruct/dataset_transformation.py
@@ -1180,24 +1180,38 @@ def sft_span_seach_mask_out(
     max_seq_length: int,
     asst_tag: str = "<|start_of_role|>assistant<|end_of_role|>",
     end_tag: str = "<|end_of_text|>",
+    think_tag: str = "\n<think>\n",
+    mask_think_tag: bool = False,
     ignore_label: int = -100,
 ):
     """This function encodes a single example into a format that
     can be used for sft training (similar to sft_tulu_tokenize_and_truncate_v1).
     Instead of performing label masking iteratively, this function performs
-    masking via span search and can handle complex chat templates with thinking."""
-
-    # Span label masking strategy
-    # - search spans asst_tag ... end_tag
-    # - all such spans are left unmasked
-    # - if an asst_tage is undetected due to tokenization issues
-    #   then a span can be erronously masked
-    # - to avoid this, use tags that are guarded by special tokens
+    masking via span search and can handle complex chat templates with thinking.
+    It dynamically determines the assistant tag based on the presence of a
+    <think> block in the assistant's response.
+    """
+
+    # Dynamically determine the assistant tag based on the conversation content.
+    def has_thinking_content(messages):
+        for message in messages:
+            if message.get("role") == "assistant":
+                # Check for an explicit 'thought' field or a '<think>' tag in the content.
+                if message.get("thought") or (
+                    isinstance(message.get("content"), str) and think_tag.strip() in message["content"]
+                ):
+                    return True
+        return False
+
     def masking_strategy_span_search(input_ids: torch.tensor, tokenizer):
         # some prep
         match = lambda x, y: torch.all(x == y)
-        _asst_tag = tokenizer.encode(asst_tag)
-        _end_tag = tokenizer.encode(end_tag)
+        # `asst_tag` is captured from the outer scope's dynamic variable
+        # By default, tokenizers for models like LLaMA, Mistral, and Phi-2 have add_bos_token=True, which means they # automatically prepend a BOS token. This would shift all token positions by 1 and break any span matching logic.
+        # Other models like Qwen, etc., have add_bos_token=False by default, so they behave differently — leading to # inconsistent behavior across model families if not explicitly handled.
+
+        _asst_tag = tokenizer.encode(asst_tag, add_special_tokens=False)
+        _end_tag = tokenizer.encode(end_tag, add_special_tokens=False)
         _asst_tag = torch.tensor([_asst_tag])
         _end_tag = torch.tensor([_end_tag])
 
@@ -1223,7 +1237,7 @@ def masking_strategy_span_search(input_ids: torch.tensor, tokenizer):
         else:
             raise ValueError(
                 f"asst_tag has {num_tokens_asst} tokens, and end_tag has {num_tokens_end} "
-                "tokens, whereas the example has {num_tokens} tokens. Either "
+                f"tokens, whereas the example has {num_tokens} tokens. Either "
                 "the example is invalid or wrong tags have been passed."
             )
 
@@ -1233,7 +1247,12 @@ def masking_strategy_span_search(input_ids: torch.tensor, tokenizer):
     additional_inputs = {}
     for k in ["tools", "documents"]:
         if k in row:
-            additional_inputs[k] = row[k]
+            row_data = row[k]
+            try:
+                row_data = json.loads(row_data)
+            except (json.JSONDecodeError, TypeError) as e:
+                pass
+            additional_inputs[k] = row_data
 
     if len(messages) == 0:
         raise ValueError("messages field is empty.")
@@ -1248,6 +1267,12 @@ def masking_strategy_span_search(input_ids: torch.tensor, tokenizer):
         **additional_inputs,
     )
 
+    # If the user has set `mask_think_tag=True` and the current sample is a thinking sample,
+    # then the <think> token is appended to the base `asst_tag` used for span matching.
+    # This causes the <think> tag to be masked along with the asst_tag
+    if mask_think_tag and has_thinking_content(messages):
+        asst_tag += think_tag
+
     # Assume truncation if hitting the exact max length (for downstream data filtering)
     was_truncated = input_ids.shape[1] == max_seq_length
     row["was_truncated"] = was_truncated