adding support for NJTs

README.md

@@ -60,9 +60,10 @@ model_name = "facebook/drama-base"
 device = "cuda" if torch.cuda.is_available() else "cpu"
 tokenizer = AutoTokenizer.from_pretrained(model_name)
 model = AutoModel.from_pretrained(model_name, trust_remote_code=True).to(device)
+use_nested = False
+query_embs = model.encode_queries(tokenizer, queries, use_nested=use_nested)
+doc_embs = model.encode_documents(tokenizer, documents, use_nested=use_nested)
 
-query_embs = model.encode_queries(tokenizer, queries)
-doc_embs = model.encode_documents(tokenizer, documents)
 
 scores = query_embs @ doc_embs.T
 print(scores.tolist())
@@ -77,8 +78,8 @@ print(scores.tolist())
 DRAMA models are trained using Matryoshka Representation Learning ([MRL](https://github.com/RAIVNLab/MRL)) to support flexible dimensionality. Both queries and documents can be encoded into smaller dimensions, such as 256, using the following:
 
 ```python
-query_embs = model.encode_queries(tokenizer, queries, dim=256)
-doc_embs = model.encode_documents(tokenizer, documents, dim=256)
+query_embs = model.encode_queries(tokenizer, queries, dim=256, use_nested=use_nested)
+doc_embs = model.encode_documents(tokenizer, documents, dim=256, use_nested=use_nested)
 
 scores = query_embs @ doc_embs.T
 print(scores.tolist())
@@ -101,8 +102,8 @@ documents = [
 
 model = SentenceTransformer("facebook/drama-base", trust_remote_code=True)
 
-query_embs = model.encode(queries, prompt_name="query")
-doc_embs = model.encode(documents)
+query_embs = model.encode(queries, prompt_name="query",  use_nested=use_nested)
+doc_embs = model.encode(documents,  use_nested=use_nested)
 
 scores = model.similarity(query_embs, doc_embs)
 print(scores.tolist())
@@ -128,8 +129,8 @@ documents = [
 
 model = SentenceTransformer("facebook/drama-base", truncate_dim=256, trust_remote_code=True)
 
-query_embs = model.encode(queries, prompt_name="query")
-doc_embs = model.encode(documents)
+query_embs = model.encode(queries, prompt_name="query",  use_nested=use_nested)
+doc_embs = model.encode(documents,  use_nested=use_nested)
 
 scores = model.similarity(query_embs, doc_embs)
 print(scores.tolist())

modeling_drama.py

@@ -1,30 +1,302 @@
 from __future__ import annotations
 
 import torch
+import torch.nn as nn
 import torch.nn.functional as F
+from torch.nested._internal.nested_tensor import nested_from_padded
 
-from transformers import LlamaModel, LlamaConfig, PreTrainedTokenizer
+from transformers import (
+    LlamaConfig,
+    LlamaModel,
+    LlamaPreTrainedModel,
+    PreTrainedTokenizer,
+)
+from transformers.cache_utils import Cache, DynamicCache
 from transformers.modeling_attn_mask_utils import AttentionMaskConverter
+from transformers.modeling_flash_attention_utils import FlashAttentionKwargs
+from transformers.modeling_outputs import BaseModelOutputWithPast
+from transformers.models.llama.modeling_llama import (
+    LlamaAttention,
+    LlamaDecoderLayer,
+    LlamaMLP,
+    LlamaRMSNorm,
+    LlamaRotaryEmbedding,
+    rotate_half,
+)
+from transformers.processing_utils import Unpack
 
 
-class DramaModel(LlamaModel):
+class ModifiedLlamaAttention(LlamaAttention):
+    def __init__(self, *args: Any, **kwargs: Any) -> None:
+        super().__init__(*args, **kwargs)
+        self.is_causal = False
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        position_embeddings: Tuple[torch.Tensor, torch.Tensor],
+        attention_mask: Optional[torch.Tensor],
+        past_key_value: Optional[Cache] = None,
+        cache_position: Optional[torch.LongTensor] = None,
+        **kwargs: Unpack[FlashAttentionKwargs],
+    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
+        input_shape = hidden_states.shape[:-1]
+        hidden_shape = (*input_shape, -1, self.head_dim)
+
+        query_states = self.q_proj(hidden_states).view(hidden_shape).transpose(1, 2)
+        key_states = self.k_proj(hidden_states).view(hidden_shape).transpose(1, 2)
+        value_states = self.v_proj(hidden_states).view(hidden_shape).transpose(1, 2)
+
+        cos, sin = position_embeddings
+        query_states, key_states = apply_rotary_pos_emb(
+            query_states, key_states, cos, sin
+        )
+
+        if past_key_value is not None:
+            # sin and cos are specific to RoPE models; cache_position needed for the static cache
+            cache_kwargs = {"sin": sin, "cos": cos, "cache_position": cache_position}
+            key_states, value_states = past_key_value.update(
+                key_states, value_states, self.layer_idx, cache_kwargs
+            )
+
+        if self.config._attn_implementation != "eager":
+            if self.config._attn_implementation == "sdpa" and kwargs.get(
+                "output_attentions", False
+            ):
+                warnings.warn(
+                    "`torch.nn.functional.scaled_dot_product_attention` does not support `output_attentions=True`. Falling back to "
+                    'eager attention. This warning can be removed using the argument `attn_implementation="eager"` when loading the model.'
+                )
+
+        attn_output, attn_weights = sdpa_attention_forward(
+            self,
+            query_states,
+            key_states,
+            value_states,
+            attention_mask,
+            dropout=0.0,
+            scaling=self.scaling,
+            is_causal=False,
+            **kwargs,
+        )
+
+        attn_output = attn_output.reshape(*input_shape, -1).contiguous()
+        attn_output = self.o_proj(attn_output)
+        return attn_output, attn_weights
+
+
+def sdpa_attention_forward(
+    module: torch.nn.Module,
+    query: torch.Tensor,
+    key: torch.Tensor,
+    value: torch.Tensor,
+    attention_mask: torch.Tensor,
+    dropout: float = 0.0,
+    scaling: Optional[float] = None,
+    is_causal: Optional[bool] = None,
+    **kwargs: Any,
+) -> Tuple[torch.Tensor, None]:
+    if hasattr(module, "num_key_value_groups"):
+        if key.is_nested:
+            key = repeat_jagged_kv(key, module.num_key_value_groups)
+            value = repeat_jagged_kv(value, module.num_key_value_groups)
+        else:
+            key = repeat_dense_kv(key, module.num_key_value_groups)
+            value = repeat_dense_kv(value, module.num_key_value_groups)
+
+    causal_mask = attention_mask
+    if attention_mask is not None and causal_mask.ndim == 4:
+        causal_mask = causal_mask[:, :, :, : key.shape[-2]]
+
+    # SDPA with memory-efficient backend is bugged with non-contiguous inputs and custom attn_mask for some torch versions
+    # Reference: https://github.com/pytorch/pytorch/issues/112577.
+    query = query.contiguous()
+    key = key.contiguous()
+    value = value.contiguous()
+
+    # We dispatch to SDPA's Flash Attention or Efficient kernels via this `is_causal` if statement instead of an inline conditional assignment
+    # in SDPA to support both torch.compile's dynamic shapes and full graph options. An inline conditional prevents dynamic shapes from compiling.
+    # Note that it is important to check first for the shape, otherwise compile will fail with `argument 'is_causal' must be bool, not SymBool`
+    if is_causal is None:
+        is_causal = query.shape[2] > 1 and causal_mask is None
+
+    # Shapes (e.g. query.shape[2]) are tensors during jit tracing, resulting in `is_causal` being a tensor.
+    # We convert it to a bool for the SDPA kernel that only accepts bools.
+    if torch.jit.is_tracing() and isinstance(is_causal, torch.Tensor):
+        is_causal = is_causal.item()
+
+    attn_output = torch.nn.functional.scaled_dot_product_attention(
+        query,
+        key,
+        value,
+        attn_mask=causal_mask,
+        dropout_p=dropout,
+        scale=scaling,
+        is_causal=is_causal,
+    )
+    attn_output = attn_output.transpose(1, 2).contiguous()
+
+    return attn_output, None
+
+
+def repeat_jagged_kv(hidden_states: torch.Tensor, n_rep: int) -> torch.Tensor:
     """
-    DramaModel is a modified version of the LlamaModel that supports bi-directional attention
-    and provides query and document encoding functionalities.
+    This is the equivalent of torch.repeat_interleave(x, dim=1, repeats=n_rep). The hidden states go from (batch,
+    num_key_value_heads, seqlen, head_dim) to (batch, num_attention_heads, seqlen, head_dim)
     """
+    batch, num_key_value_heads, slen, head_dim = hidden_states.shape
+    expand_shape = (batch, num_key_value_heads, -1, n_rep, head_dim)
+    if n_rep == 1:
+        return hidden_states
+    hidden_states = (
+        hidden_states.unsqueeze(3)
+        .expand(expand_shape)
+        .transpose(1, 2)
+        .flatten(2, 3)
+        .transpose(1, 2)
+    )
+    return hidden_states
+
+
+def repeat_dense_kv(hidden_states: torch.Tensor, n_rep: int) -> torch.Tensor:
+    """
+    This is the equivalent of torch.repeat_interleave(x, dim=1, repeats=n_rep). The hidden states go from (batch,
+    num_key_value_heads, seqlen, head_dim) to (batch, num_attention_heads, seqlen, head_dim)
+    """
+    batch, num_key_value_heads, slen, head_dim = hidden_states.shape
+    if n_rep == 1:
+        return hidden_states
+    hidden_states = hidden_states[:, :, None, :, :].expand(
+        batch, num_key_value_heads, n_rep, slen, head_dim
+    )
+    return hidden_states.reshape(batch, num_key_value_heads * n_rep, slen, head_dim)
+
+
+def apply_rotary_pos_emb(
+    q: torch.Tensor,
+    k: torch.Tensor,
+    cos: torch.Tensor,
+    sin: torch.Tensor,
+    unsqueeze_dim: int = 1,
+) -> Tuple[torch.Tensor, torch.Tensor]:
+    """Applies Rotary Position Embedding to the query and key tensors.
+
+    Args:
+        q (`torch.Tensor`): The query tensor.
+        k (`torch.Tensor`): The key tensor.
+        cos (`torch.Tensor`): The cosine part of the rotary embedding.
+        sin (`torch.Tensor`): The sine part of the rotary embedding.
+        position_ids (`torch.Tensor`, *optional*):
+            Deprecated and unused.
+        unsqueeze_dim (`int`, *optional*, defaults to 1):
+            The 'unsqueeze_dim' argument specifies the dimension along which to unsqueeze cos[position_ids] and
+            sin[position_ids] so that they can be properly broadcasted to the dimensions of q and k. For example, note
+            that cos[position_ids] and sin[position_ids] have the shape [batch_size, seq_len, head_dim]. Then, if q and
+            k have the shape [batch_size, heads, seq_len, head_dim], then setting unsqueeze_dim=1 makes
+            cos[position_ids] and sin[position_ids] broadcastable to the shapes of q and k. Similarly, if q and k have
+            the shape [batch_size, seq_len, heads, head_dim], then set unsqueeze_dim=2.
+    Returns:
+        `tuple(torch.Tensor)` comprising of the query and key tensors rotated using the Rotary Position Embedding.
+    """
+    cos = cos.unsqueeze(unsqueeze_dim)
+    sin = sin.unsqueeze(unsqueeze_dim)
+    if q.is_nested and k.is_nested:
+        if q.layout != torch.jagged:
+            raise NotImplementedError(f"Unsupported layout: {q.layout}")
+        if k.layout != torch.jagged:
+            raise NotImplementedError(f"Unsupported layout: {k.layout}")
+        return _jagged_tensor_forward(q, k, cos, sin)
+    else:
+        return _padded_tensor_forward(q, k, cos, sin)
+
+
+def _jagged_tensor_forward(
+    q: torch.Tensor,
+    k: torch.Tensor,
+    cos: torch.Tensor,
+    sin: torch.Tensor,
+) -> Tuple[torch.Tensor, torch.Tensor]:
+    q_dense = q.to_padded_tensor(0.0)
+    k_dense = k.to_padded_tensor(0.0)
+    q_dense_embed = (q_dense * cos) + (rotate_half(q_dense) * sin)
+    k_dense_embed = (k_dense * cos) + (rotate_half(k_dense) * sin)
+    q_jagged_embed = convert_dense_to_jagged(q, q_dense_embed)
+    k_jagged_embed = convert_dense_to_jagged(k, k_dense_embed)
+    return q_jagged_embed, k_jagged_embed
+
+
+def _padded_tensor_forward(
+    q: torch.Tensor,
+    k: torch.Tensor,
+    cos: torch.Tensor,
+    sin: torch.Tensor,
+) -> Tuple[torch.Tensor, torch.Tensor]:
+    q_embed = (q * cos) + (rotate_half(q) * sin)
+    k_embed = (k * cos) + (rotate_half(k) * sin)
+    return q_embed, k_embed
+
+
+def convert_dense_to_jagged(nested_q: torch.Tensor, q: torch.Tensor) -> torch.Tensor:
+    padded_max_S = nested_q._get_max_seqlen()
+    total_L = nested_q._values.shape[nested_q._ragged_idx - 1]
+    if padded_max_S is None:
+        # use upper bound on max seqlen if it's not present
+        padded_max_S = total_L
+
+    # convert dense tensor -> jagged
+    q = q.expand(
+        [
+            x if i != nested_q._ragged_idx else padded_max_S
+            for i, x in enumerate(q.shape)
+        ]
+    )
+    nested_result = nested_from_padded(
+        q,
+        offsets=nested_q._offsets,
+        ragged_idx=nested_q._ragged_idx,
+        sum_S=total_L,
+        min_seqlen=nested_q._get_min_seqlen(),
+        max_seqlen=padded_max_S,
+    )
+    return nested_result
+
+
+class ModifiedLlamaDecoderLayer(LlamaDecoderLayer):
+    def __init__(self, config: LlamaConfig, layer_idx: int) -> None:
+        nn.Module.__init__(self)
+        self.hidden_size: int = config.hidden_size
+
+        self.self_attn = ModifiedLlamaAttention(config=config, layer_idx=layer_idx)
+
+        self.mlp = LlamaMLP(config)
+        self.input_layernorm = LlamaRMSNorm(config.hidden_size, eps=config.rms_norm_eps)
+        self.post_attention_layernorm = LlamaRMSNorm(
+            config.hidden_size, eps=config.rms_norm_eps
+        )
+
+
+class LlamaBiModel(LlamaModel):
+    def __init__(self, config: LlamaConfig) -> None:
+        LlamaPreTrainedModel.__init__(self, config)
+        self.padding_idx: int = config.pad_token_id
+        self.vocab_size: int = config.vocab_size
+
+        self.embed_tokens = nn.Embedding(
+            config.vocab_size, config.hidden_size, self.padding_idx
+        )
+        self.layers = nn.ModuleList(
+            [
+                ModifiedLlamaDecoderLayer(config, layer_idx)
+                for layer_idx in range(config.num_hidden_layers)
+            ]
+        )
+        self.norm = LlamaRMSNorm(config.hidden_size, eps=config.rms_norm_eps)
+        self.rotary_emb = LlamaRotaryEmbedding(config=config)
+        self.gradient_checkpointing = False
+
+        # Initialize weights and apply final processing
+        self.post_init()
 
-    def __init__(self, config: LlamaConfig):
-        """
-        Initializes the DramaModel by disabling causal masking in self-attention layers.
-        """
-        super().__init__(config)
-        for layer in self.layers:
-            layer.self_attn.is_causal = False
-        # query prefix
-        self.query_prefix = "Query: "
-        self.max_seq_len = 8192
-        self.hidden_size = config.hidden_size
-    
     def _update_causal_mask(
         self,
         attention_mask: torch.Tensor,
@@ -42,12 +314,182 @@ class DramaModel(LlamaModel):
             return None
         if attention_mask is None or attention_mask.dim() == 4:
             return attention_mask
-        
+
         return AttentionMaskConverter._expand_mask(
             mask=attention_mask,
             dtype=input_tensor.dtype,
         )
 
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[Union[Cache, List[torch.FloatTensor]]] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+        cache_position: Optional[torch.LongTensor] = None,
+    ) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPast]:
+        output_attentions = (
+            output_attentions
+            if output_attentions is not None
+            else self.config.output_attentions
+        )
+        output_hidden_states = (
+            output_hidden_states
+            if output_hidden_states is not None
+            else self.config.output_hidden_states
+        )
+        # use_cache = use_cache if use_cache is not None else self.config.use_cache
+        use_cache = False
+        return_dict = (
+            return_dict if return_dict is not None else self.config.use_return_dict
+        )
+
+        if (input_ids is None) ^ (inputs_embeds is not None):
+            raise ValueError(
+                "You cannot specify both input_ids and inputs_embeds at the same time, and must specify either one"
+            )
+        if self.gradient_checkpointing and self.training and use_cache:
+            warnings.warn(
+                "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            use_cache = False
+
+        if inputs_embeds is None:
+            inputs_embeds = self.embed_tokens(input_ids)
+
+        return_legacy_cache = False
+        if (
+            use_cache and not isinstance(past_key_values, Cache) and not self.training
+        ):  # kept for BC (non `Cache` `past_key_values` inputs)
+            return_legacy_cache = True
+            past_key_values = DynamicCache.from_legacy_cache(past_key_values)
+            warnings.warn(
+                "We detected that you are passing `past_key_values` as a tuple and this is deprecated and will be removed in v4.43. "
+                "Please use an appropriate `Cache` class (https://huggingface.co/docs/transformers/v4.41.3/en/internal/generation_utils#transformers.Cache)",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+
+        if cache_position is None:
+            past_seen_tokens = (
+                past_key_values.get_seq_length() if past_key_values is not None else 0
+            )
+            if inputs_embeds.is_nested:
+                seq_len = inputs_embeds._get_max_seqlen()
+            else:
+                seq_len = inputs_embeds.shape[1]
+            cache_position = torch.arange(
+                past_seen_tokens,
+                past_seen_tokens + seq_len,
+                device=inputs_embeds.device,
+            )
+        if position_ids is None:
+            position_ids = cache_position.unsqueeze(0)
+        if not inputs_embeds.is_nested:
+            causal_mask = self._update_causal_mask(
+                attention_mask,
+                inputs_embeds,
+                cache_position,
+                past_key_values,
+            )
+
+        else:
+            causal_mask = None
+        hidden_states = inputs_embeds
+
+        # create position embeddings to be shared across the decoder layers
+        position_embeddings = self.rotary_emb(hidden_states, position_ids)
+
+        # decoder layers
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attns = () if output_attentions else None
+        next_decoder_cache = None
+
+        for decoder_layer in self.layers:
+            if output_hidden_states:
+                all_hidden_states += (hidden_states,)
+
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    decoder_layer.__call__,
+                    hidden_states,
+                    causal_mask,
+                    position_ids,
+                    past_key_values,
+                    output_attentions,
+                    use_cache,
+                    cache_position,
+                    position_embeddings,
+                )
+            else:
+                layer_outputs = decoder_layer(
+                    hidden_states,
+                    attention_mask=causal_mask,
+                    position_ids=position_ids,
+                    past_key_value=past_key_values,
+                    output_attentions=output_attentions,
+                    use_cache=use_cache,
+                    cache_position=cache_position,
+                    position_embeddings=position_embeddings,
+                )
+
+            hidden_states = layer_outputs[0]
+
+            if use_cache:
+                next_decoder_cache = layer_outputs[2 if output_attentions else 1]
+
+            if output_attentions:
+                all_self_attns += (layer_outputs[1],)
+
+        hidden_states = self.norm(hidden_states)
+
+        # add hidden states from the last decoder layer
+        if output_hidden_states:
+            all_hidden_states += (hidden_states,)
+
+        next_cache = next_decoder_cache if use_cache else None
+        if return_legacy_cache:
+            next_cache = next_cache.to_legacy_cache()
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [hidden_states, next_cache, all_hidden_states, all_self_attns]
+                if v is not None
+            )
+        return BaseModelOutputWithPast(
+            last_hidden_state=hidden_states,
+            past_key_values=next_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attns,
+        )
+
+
+class DramaModel(LlamaBiModel):
+    """
+    DramaModel is a modified version of the LlamaModel that supports bi-directional attention
+    and provides query and document encoding functionalities.
+    """
+
+    def __init__(self, config: LlamaConfig):
+        """
+        Initializes the DramaModel by disabling causal masking in self-attention layers.
+        """
+        super().__init__(config)
+        for layer in self.layers:
+            layer.self_attn.is_causal = False
+        # query prefix
+        self.query_prefix = "Query: "
+        self.max_seq_len = 8192
+        self.hidden_size = config.hidden_size
+
     def _average_pool(
         self, last_hidden_states: torch.Tensor, attention_mask: torch.Tensor
     ) -> torch.Tensor:
@@ -60,107 +502,138 @@ class DramaModel(LlamaModel):
         return last_hidden.sum(dim=1) / attention_mask.sum(dim=1)[..., None]
 
     def _tokenize(
-            self,
-            tokenizer: PreTrainedTokenizer,
-            texts: list[str],
-            max_seq_len: int = None,
-        ):
+        self,
+        tokenizer: PreTrainedTokenizer,
+        texts: list[str],
+        max_seq_len: int = None,
+        use_nested: bool = False,
+    ):
         """
         Tokenizes input text sequences with optional sequence length restriction.
         """
         if max_seq_len is None:
             max_seq_len = self.max_seq_len
-        tokenized = tokenizer(
-            texts,
-            padding=True,
-            truncation=True,
-            max_length=max_seq_len,
-            return_tensors='pt',
-        ).to(self.device)
-        return tokenized
+        if use_nested:
+            tokenized = tokenizer(
+                texts,
+                truncation=True,
+                max_length=max_seq_len,
+                return_length=True,
+            )
+            tokenized.input_ids = torch.nested.nested_tensor(
+                tokenized.input_ids, layout=torch.jagged
+            ).to(self.device)
+            tokenized.attention_mask = None
+        else:
+            tokenized = tokenizer(
+                texts,
+                padding=True,
+                truncation=True,
+                max_length=max_seq_len,
+                return_tensors="pt",
+            ).to(self.device)
+        tokenizer_ouput = {}
+        tokenizer_ouput["input_ids"] = tokenized.input_ids
+        tokenizer_ouput["attention_mask"] = tokenized.attention_mask
+        return tokenizer_ouput
 
     def encode(self, input_ids, attention_mask, dim, *args, **kwargs):
         """
         Pass through the model and compute normalized embeddings.
-        
+
         Args:
             input_ids (torch.Tensor): Input token IDs.
             attention_mask (torch.Tensor): Attention mask tensor.
             dim (int): Dimensionality for output embeddings.
-        
+
         Returns:
             torch.Tensor: Normalized output embeddings.
         """
+
         outputs = self.forward(
             input_ids, attention_mask, *args, **kwargs
-        )
-        embeddings = self._average_pool(
-            outputs.last_hidden_state[:, :, :dim], attention_mask
-        )
+        ).last_hidden_state
+        if not outputs.is_nested:
+            if dim is not None:
+                outputs = outputs[:, :, :dim]
+            embeddings = self._average_pool(outputs, attention_mask)
+        else:
+            if dim is not None:
+                outputs, _ = outputs.split_with_sizes(
+                    split_sizes=[dim, outputs.shape[-1] - dim], dim=-1
+                )
+            embeddings = outputs.sum(dim=-2)
         # normalize embeddings
         embeddings = F.normalize(embeddings, p=2, dim=1)
         return embeddings
 
     def encode_queries(
-            self,
-            tokenizer: PreTrainedTokenizer,
-            queries: list[str],
-            max_seq_len: int = None,
-            dim: int = None,
-        ):
+        self,
+        tokenizer: PreTrainedTokenizer,
+        queries: list[str],
+        max_seq_len: int = None,
+        dim: int = None,
+        use_nested: bool = False,
+    ):
         """
         Encodes a list of queries into embeddings.
-        
+
         Args:
             tokenizer (PreTrainedTokenizer): Tokenizer for text processing.
             queries (list[str]): List of query texts.
             max_seq_len (int, optional): Maximum sequence length.
             dim (int, optional): Dimensionality for output embeddings.
-        
+
         Returns:
             torch.Tensor: Encoded query embeddings in shape (num_queries, dim).
         """
         if not queries:
             raise ValueError("queries must not be empty.")
-        if not isinstance(queries, list) or not all(isinstance(q, str) for q in queries):
+        if not isinstance(queries, list) or not all(
+            isinstance(q, str) for q in queries
+        ):
             raise ValueError("queries must be a list of strings.")
         if tokenizer is None:
             raise ValueError("tokenizer must not be None.")
         if dim is not None and (dim < 1 or dim > self.hidden_size):
             raise ValueError(f"dim must be in range [1, {self.hidden_size}].")
         queries = [self.query_prefix + query for query in queries]
-        tokenized_queries = self._tokenize(tokenizer, queries, max_seq_len)
+        tokenized_queries = self._tokenize(tokenizer, queries, max_seq_len, use_nested)
         embeddings = self.encode(**tokenized_queries, dim=dim)
         return embeddings
 
     def encode_documents(
-            self,
-            tokenizer: PreTrainedTokenizer,
-            documents: list[str],
-            max_seq_len: int = None,
-            dim: int = None,
-        ):
+        self,
+        tokenizer: PreTrainedTokenizer,
+        documents: list[str],
+        max_seq_len: int = None,
+        dim: int = None,
+        use_nested: bool = False,
+    ):
         """
         Encodes a list of documents into embeddings.
-        
+
         Args:
             tokenizer (PreTrainedTokenizer): Tokenizer for text processing.
             documents (list[str]): List of document texts.
             max_seq_len (int, optional): Maximum sequence length.
             dim (int, optional): Dimensionality for output embeddings.
-        
+
         Returns:
             torch.Tensor: Encoded document embeddings in shape (num_documents, dim).
         """
         if not documents:
             raise ValueError("documents must not be empty.")
-        if not isinstance(documents, list) or not all(isinstance(d, str) for d in documents):
+        if not isinstance(documents, list) or not all(
+            isinstance(d, str) for d in documents
+        ):
             raise ValueError("documents must be a list of strings.")
         if tokenizer is None:
             raise ValueError("tokenizer must not be None.")
         if dim is not None and (dim < 1 or dim > self.hidden_size):
             raise ValueError(f"dim must be in range [1, {self.hidden_size}].")
-        tokenized_documents = self._tokenize(tokenizer, documents, max_seq_len)
+        tokenized_documents = self._tokenize(
+            tokenizer, documents, max_seq_len, use_nested
+        )
         embeddings = self.encode(**tokenized_documents, dim=dim)
         return embeddings
-