Enable training strategy for Indexer

src/maxtext/configs/base.yml

@@ -356,15 +356,15 @@ moba_topk: 8
 
 # DeepSeek Sparse Attention (DSA)
 # deepseek3.2 introduces indexer in MLA
-use_sparse_indexer: False
-index_head_dim: 128
-index_n_heads: 64
-index_topk: 2048
-# Determines the token selection strategy for indexer loss: 
-# - False: Uses all tokens (Dense Warm-up).
-# - True: Uses only top-k tokens (Sparse Training).
+use_indexer: False
+indexer_head_dim: 128
+indexer_n_heads: 64
+indexer_topk: 2048
+# Determines the training strategy for the indexer:
+# - False (Dense Warm-up): Computes indexer loss over all tokens. Used with `trainable_parameters_mask` to freeze other model parameters.
+# - True (Sparse Training): Computes indexer loss over top-k tokens only and detaches the indexer input for independent optimization.
 # Note: This is only active when `indexer_loss_scaling_factor` > 0.
-sparse_indexer_loss: False
+indexer_sparse_training: False
 # Multiplier for the indexer KL divergence loss
 indexer_loss_scaling_factor: 0.0
 
@@ -789,6 +789,10 @@ gradient_clipping_threshold: 1.0
 gradient_accumulation_steps: 1
 
 opt_type: "adamw"  # one of "adamw", "adam_pax", "sgd", or "muon"
+# List of parameter names/patterns to train.
+# If non-empty, all other parameters will be frozen. Example: ['.*indexer.*'].
+# If empty (default), all parameters are trained.
+trainable_parameters_mask: []
 
 # AdamW optimizer parameters
 # We use AdamW following Llama2's training details, see https://arxiv.org/pdf/2307.09288.pdf section 2.2

src/maxtext/configs/models/deepseek-custom.yml

@@ -56,10 +56,10 @@ rope_interleave: True
 rope_truncate: True
 rope_attention_scaling: False
 # Indexer for DeepSeek Sparse Attention
-use_sparse_indexer: True
-index_n_heads: 16              # Reduced from 64
-index_head_dim: 64             # Reduced from 128
-index_topk: 256                # Reduced from 2048
+use_indexer: True
+indexer_n_heads: 16              # Reduced from 64
+indexer_head_dim: 64             # Reduced from 128
+indexer_topk: 256                # Reduced from 2048
 # Hyper-connections: mHC enabled
 mhc_expansion_rate: 4
 sinkhorn_iterations: 20

src/maxtext/configs/models/deepseek3.2-671b.yml

@@ -53,7 +53,7 @@ rope_interleave: True
 rope_truncate: True
 rope_attention_scaling: False
 # Indexer for DeepSeek Sparse Attention
-use_sparse_indexer: True
-index_n_heads: 64
-index_head_dim: 128
-index_topk: 2048
+use_indexer: True
+indexer_n_heads: 64
+indexer_head_dim: 128
+indexer_topk: 2048

src/maxtext/configs/types.py

@@ -542,11 +542,14 @@ class MlaAttention(BaseModel):
 class AttentionIndexer(BaseModel):
   """Configuration for DeepSeek Sparse Attention (DSA): DeepSeek3.2-style MLA with indexer."""
 
-  use_sparse_indexer: bool = Field(False, description="Whether to use sparse indexer for MLA.")
-  index_head_dim: NonNegativeInt = Field(128, description="Head dim for indexer query and key.")
-  index_n_heads: NonNegativeInt = Field(64, description="Number of query heads in indexer.")
-  index_topk: NonNegativeInt = Field(2048, description="Number of tokens selected by the query token in indexer.")
-  sparse_indexer_loss: bool = Field(False, description="Determines the token selection strategy for indexer loss.")
+  use_indexer: bool = Field(False, description="Whether to use sparse indexer for MLA.")
+  indexer_head_dim: NonNegativeInt = Field(128, description="Head dim for indexer query and key.")
+  indexer_n_heads: NonNegativeInt = Field(64, description="Number of query heads in indexer.")
+  indexer_topk: NonNegativeInt = Field(2048, description="Number of tokens selected by the query token in indexer.")
+  indexer_sparse_training: bool = Field(
+      False,
+      description="Determines the training strategy for the indexer: Dense Warm-up or Sparse Training stage.",
+  )
   indexer_loss_scaling_factor: float = Field(0.0, description="Multiplier for the indexer KL divergence loss.")
 
 
@@ -1185,6 +1188,13 @@ class Optimizer(BaseModel):
       ge=-1,
       description="Total steps for the LR schedule. -1 defaults to `steps`.",
   )
+  trainable_parameters_mask: list[str] = Field(
+      default_factory=list,
+      description=(
+          "List of parameter names/patterns to train. If non-empty, all other parameters will be frozen, "
+          "example: ['.*indexer.*']. If empty (default), all parameters are trained."
+      ),
+  )
 
 
 class AdamW(BaseModel):
@@ -2388,7 +2398,7 @@ def calculate_global_batch_sizes(per_device_batch_size, expansion_factor, num_de
         raise ValueError("`local_checkpoint_period` must be > 0 for emergency checkpointing.")
     if self.moba and self.attention not in ("dot_product"):
       raise ValueError("MoBA is only supported with dot_product attention.")
-    if self.use_sparse_indexer:
+    if self.use_indexer:
       if self.q_lora_rank == 0:
         raise NotImplementedError("Sparse indexer has not implemented for q_lora_rank = 0.")
       supports_dot_product = self.attention == "dot_product"

src/maxtext/layers/attention_mla.py

@@ -110,9 +110,9 @@ def __init__(
     self.dtype = config.dtype
     self.weight_dtype = config.weight_dtype
 
-    self.n_heads = config.index_n_heads
-    self.head_dim = config.index_head_dim
-    self.index_topk = config.index_topk
+    self.n_heads = config.indexer_n_heads
+    self.head_dim = config.indexer_head_dim
+    self.indexer_topk = config.indexer_topk
     self.emb_dim = config.emb_dim
     self.rope_head_dim = config.qk_rope_head_dim
     self.q_lora_rank = config.q_lora_rank
@@ -180,13 +180,13 @@ def apply_partial_rope(
     2. Input Layout: Indexer uses concatenated layout (interleave=False), whereas MLA uses interleaved (interleave=True).
 
     Args:
-      inputs: Input array of shape [batch, seqlen, index_n_heads, index_head_dim].
+      inputs: Input array of shape [batch, seqlen, indexer_n_heads, indexer_head_dim].
       positions: Position array of shape [batch, seqlen].
 
     Returns:
-      Array with partial RoPE applied, with shape [batch, seqlen, index_n_heads, index_head_dim]
+      Array with partial RoPE applied, with shape [batch, seqlen, indexer_n_heads, indexer_head_dim]
     """
-    # index_head_dim -> [rope_head_dim, index_head_dim - rope_head_dim]
+    # indexer_head_dim -> [rope_head_dim, indexer_head_dim - rope_head_dim]
     x_pe, x_nope = jnp.split(inputs, [self.rope_head_dim], axis=-1)
     # x_pe [B, S, H, rope_head_dim], positions [B, S]
     x_pe = self.rotary_embedding(x_pe, position=inputs_positions)
@@ -256,14 +256,37 @@ def __call__(
       b: Batch size
       t: Query Sequence Length (Target), note t = s here
       s: Key/Value Sequence Length (Source)
-      h: Number of Indexer Heads (index_n_heads)
-      d: Indexer Head Dimension (index_head_dim)
+      h: Number of Indexer Heads (indexer_n_heads)
+      d: Indexer Head Dimension (indexer_head_dim)
     """
     # NOTE: If sequence length <= topk, indexer always selects all tokens.
-    if self.config.max_target_length <= self.index_topk:
+    if self.config.max_target_length <= self.indexer_topk:
       return None, None, None
 
     bsz, seqlen, _ = inputs_q.shape  # s = t = seqlen
+    # ==============================================================================
+    # Gradient Isolation Strategy: Main Model vs. Indexer
+    # ==============================================================================
+    # This creates a barrier to train both components independently, and applies
+    # for both Dense Warm-up and Sparse Training stages:
+    #
+    # Forward Pass:
+    # - The Indexer receives a detached copy of the inputs (via `stop_gradient`)
+    #   to independently calculate its scores and `indexer_loss`.
+    #
+    # Backward Pass (Main Model):
+    # - The main model optimizes its weights based solely on the LM loss.
+    # - The `indexer_mask` in the Attention layer prevents gradients from the main
+    #   loss from flowing into the Indexer's weights.
+    #
+    # Backward Pass (Indexer):
+    # - Gradients from the `indexer_loss` flow back to update the Indexer's weights.
+    # - The `stop_gradient` applied to the inputs acts as a mathematical wall, dropping
+    #   gradients to 0.0 and preventing the Indexer loss from altering the main model's
+    #   earlier layers.
+    inputs_q = jax.lax.stop_gradient(inputs_q)
+    low_rank_q = jax.lax.stop_gradient(low_rank_q)
+    inputs_kv = jax.lax.stop_gradient(inputs_kv)
 
     # Query Processing: Project from Latent low_rank_q
     q = self.wq_b(low_rank_q)  # [b, t, q_lora_rank] -> [b, t, h * d]
@@ -295,7 +318,7 @@ def __call__(
       indexer_score += attention_mask
 
     # TopK selection based on index score
-    _, topk_indices = jax.lax.top_k(indexer_score, k=self.index_topk)  # topk_indices [b, t, k]
+    _, topk_indices = jax.lax.top_k(indexer_score, k=self.indexer_topk)  # topk_indices [b, t, k]
 
     # Create Sparse Index Mask: 0 and large negatives
     indexer_mask = self.generate_mask(topk_indices, seqlen)  # [b, t, s]
@@ -607,8 +630,8 @@ def __init__(
     )
 
     # Initialize Indexer
-    self.use_sparse_indexer = config.use_sparse_indexer
-    if self.use_sparse_indexer:
+    self.use_indexer = config.use_indexer
+    if self.use_indexer:
       # Need two versions of rope.
       # MLA applies yarn with interleave layout.
       # Indexer applies yarn with concatenate layout.
@@ -989,6 +1012,13 @@ def calculate_indexer_loss(
     Returns:
       The computed KL divergence loss.
     """
+    # Detach main model components from the computational graph.
+    # The indexer should match the main model, but the main model should not be influenced
+    # by the indexer's learning progress via this loss in sparse training stage.
+    # We also apply this during the Dense Warm-up stage to save compute and memory.
+    query = jax.lax.stop_gradient(query)
+    key = jax.lax.stop_gradient(key)
+
     # Compute attention scores: [b, t, h, d] @ [b, s, h, d] -> [b, h, t, s]
     attention_scores = jnp.einsum("bthd, bshd -> bhts", query, key, precision=self.config.matmul_precision)
 
@@ -1080,7 +1110,7 @@ def __call__(
 
     # Indexer Logic
     indexer_mask = None
-    if self.use_sparse_indexer:
+    if self.use_indexer:
       if model_mode != MODEL_MODE_TRAIN:
         raise NotImplementedError("Sparse indexer has not implemented for inference yet.")
       # generate mask: with 0 and large negative, [b, 1, 1, q_len, kv_len] -> [b, q_len, kv_len]
@@ -1098,14 +1128,14 @@ def __call__(
           attention_mask=attention_mask,
       )
 
-      if self.config.indexer_loss_scaling_factor > 0.0:
+      if indexer_mask is not None and self.config.indexer_loss_scaling_factor > 0.0:
         indexer_loss = self.calculate_indexer_loss(
             indexer_score=indexer_score,
             query=query,
             key=key,
             attention_mask=attention_mask,
             indexer_mask=indexer_mask,
-            sparse_loss=self.config.sparse_indexer_loss,
+            sparse_loss=self.config.indexer_sparse_training,
             scaling_factor=self.config.indexer_loss_scaling_factor,
         )
         self.sow(nnx.Intermediate, "indexer_loss", indexer_loss)

src/maxtext/layers/attention_op.py

@@ -1415,7 +1415,7 @@ def wrap_flash_attention(
         decoder_segment_ids_tuple = None
 
       if self.config.use_tokamax_splash:
-        if self.config.use_sparse_indexer and indexer_mask is not None:
+        if self.config.use_indexer and indexer_mask is not None:
           # Construct the splash kernel call with dynamic mask
           def dynamic_mask_splash_kernel(q, k, v, segment, sinks, indexer_mask):
             splash_kernel = tokamax_splash_kernel.make_dynamic_splash_mha(

src/maxtext/layers/decoders.py

@@ -1081,7 +1081,10 @@ def __call__(
     # When invoking from vLLM with RPA attention, logit computation is deferred to a later stage.
     if cfg.attention == "vllm_rpa":
       logits = None
-
+    # When in the Indexer Dense Warm-up stage, skip the expensive output head projection
+    # for efficiency, as the main model is frozen and the LM loss is not needed.
+    elif (cfg.use_indexer and not cfg.indexer_sparse_training) and self.model_mode == MODEL_MODE_TRAIN:
+      logits = None
     # When vocab tiling is enabled in training mode, full logits won't generate to reduce memory
     # Instead, we keep track on the hidden states, which has smaller size compared to full logits
     elif cfg.num_vocab_tiling > 1 and self.model_mode == MODEL_MODE_TRAIN:

src/maxtext/optimizers/optimizers.py

@@ -24,31 +24,35 @@
 from maxtext.utils.muon_utils import get_muon_weight_dimension_numbers
 
 
-def get_adamw_mask(config):
-  """Create a mask function for AdamW optimizer to exclude certain parameters from weight decay."""
-  if not getattr(config, "adamw_mask", None):
+def _get_path_mask_fn(patterns, match_returns_true=True):
+  """Helper to create a mask function from a list of regex patterns."""
+  if not patterns:
     return None
 
-  compiled_patterns = [re.compile(pattern) for pattern in config.adamw_mask]
+  compiled_patterns = [re.compile(pattern) for pattern in patterns]
 
   def mask_fn(params):
-    def _is_decayed(path, _):
+    def _is_masked(path, _):
       # Join path keys into a single string for pattern matching (e.g., "layer1/bias")
-      path_str = "/".join(str(getattr(p, "key", getattr(p, "idx", getattr(p, "name", p)))) for p in path)
-      # If any pattern in adamw_mask matches the path, exclude from weight decay (return False).
-      # Otherwise, apply weight decay (return True).
-      return not any(pattern.search(path_str) for pattern in compiled_patterns)
+      path_str = jax.tree_util.keystr(path, simple=True, separator="/")
+      matched = any(pattern.search(path_str) for pattern in compiled_patterns)
+      return matched if match_returns_true else not matched
 
-    return jax.tree_util.tree_map_with_path(_is_decayed, params)
+    return jax.tree_util.tree_map_with_path(_is_masked, params)
 
   return mask_fn
 
 
+def get_adamw_mask(config):
+  """Create a mask function for AdamW optimizer to exclude certain parameters from weight decay."""
+  return _get_path_mask_fn(getattr(config, "adamw_mask", None), match_returns_true=False)
+
+
 def get_optimizer(config, learning_rate_schedule, model=None):
   """Create optimizer."""
   if config.opt_type == "adamw":
     # Create AdamW Optimizer following Llama2's training details, see https://arxiv.org/pdf/2307.09288.pdf section 2.2
-    return optax.adamw(
+    base_opt = optax.adamw(
         learning_rate_schedule,
         b1=config.adam_b1,
         b2=config.adam_b2,
@@ -59,7 +63,7 @@ def get_optimizer(config, learning_rate_schedule, model=None):
         mask=get_adamw_mask(config),
     )
   elif config.opt_type == "adam_pax":
-    return adam_pax(
+    base_opt = adam_pax(
         learning_rate_schedule,
         beta1=config.adam_b1,
         beta2=config.adam_b2,
@@ -69,7 +73,7 @@ def get_optimizer(config, learning_rate_schedule, model=None):
         mask=get_adamw_mask(config),
     )
   elif config.opt_type == "sgd":
-    return optax.sgd(learning_rate_schedule)
+    base_opt = optax.sgd(learning_rate_schedule)
   elif config.opt_type == "muon":
     # extract muon dimension number from model structure
     if model is not None:
@@ -92,10 +96,26 @@ def get_optimizer(config, learning_rate_schedule, model=None):
         "adam_eps_root": config.adam_eps_root,
         "adam_weight_decay": config.adam_weight_decay,
     }
-    return muon(**muon_kwargs)
+    base_opt = muon(**muon_kwargs)
   else:
     raise ValueError(f"{config.opt_type=} is not a supported.")
 
+  # If a whitelist of trainable parameters is provided, freeze everything else.
+  # When trainable_parameters_mask is empty, freeze_mask_fn is None and all parameters are trained.
+  trainable_patterns = getattr(config, "trainable_parameters_mask", None)
+  freeze_mask_fn = _get_path_mask_fn(trainable_patterns, match_returns_true=False)
+  if freeze_mask_fn is not None:
+    # Use optax.multi_transform to explicitly map frozen parameters to a stateless set_to_zero() optimizer.
+    # If we simply wrapped base_opt in optax.masked() or chained it, Optax would still allocate
+    # massive states (momentum, variance) for the entire model before zeroing the updates.
+    # By using multi_transform, only the trainable parameters get states allocated.
+    return optax.multi_transform(
+        {"trainable": base_opt, "frozen": optax.set_to_zero()},
+        lambda params: jax.tree_util.tree_map(lambda x: "frozen" if x else "trainable", freeze_mask_fn(params)),
+    )
+
+  return base_opt
+
 
 def adam_pax(
     learning_rate_fn: optax.Schedule,