# coding=utf-8 # Copyright 2025 Mariusz Kurman, MedIT Solutions Sp. z o.o, Poland. All rights reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """PyTorch NeuroBLAST model.""" import math from typing import List, Optional, Tuple, Union import torch import torch.nn.functional as F import torch.utils.checkpoint from torch import nn from torch.nn import CrossEntropyLoss from transformers.activations import ACT2FN from transformers.cache_utils import Cache, DynamicCache from transformers.modeling_outputs import ( BaseModelOutputWithPast, CausalLMOutputWithPast, ) from transformers.modeling_utils import PreTrainedModel from transformers import GenerationMixin from transformers.utils import ( add_start_docstrings, add_start_docstrings_to_model_forward, logging, replace_return_docstrings, ) from .configuration_neuroblast import NeuroBLASTConfig logger = logging.get_logger(__name__) _CONFIG_FOR_DOC = "NeuroBLASTConfig" class NeuroBLASTRMSNorm(nn.Module): def __init__(self, hidden_size, eps=1e-6): super().__init__() self.weight = nn.Parameter(torch.ones(hidden_size)) self.variance_epsilon = eps def forward(self, hidden_states): input_dtype = hidden_states.dtype hidden_states = hidden_states.to(torch.float32) variance = hidden_states.pow(2).mean(-1, keepdim=True) hidden_states = hidden_states * torch.rsqrt(variance + self.variance_epsilon) return self.weight * hidden_states.to(input_dtype) class NeuroBLASTMLP(nn.Module): def __init__(self, config): super().__init__() self.config = config self.hidden_size = config.hidden_size self.intermediate_size = config.intermediate_size self.gate_proj = nn.Linear(self.hidden_size, self.intermediate_size, bias=False) self.up_proj = nn.Linear(self.hidden_size, self.intermediate_size, bias=False) self.down_proj = nn.Linear(self.intermediate_size, self.hidden_size, bias=False) self.act_fn = ACT2FN[config.hidden_act] def forward(self, x): return self.down_proj(self.act_fn(self.gate_proj(x)) * self.up_proj(x)) def rotate_half(x): x1 = x[..., : x.shape[-1] // 2] x2 = x[..., x.shape[-1] // 2 :] return torch.cat((-x2, x1), dim=-1) def apply_rotary_pos_emb(q, k, cos, sin, position_ids=None, unsqueeze_dim=1): cos = cos.unsqueeze(unsqueeze_dim) sin = sin.unsqueeze(unsqueeze_dim) q_embed = (q * cos) + (rotate_half(q) * sin) k_embed = (k * cos) + (rotate_half(k) * sin) return q_embed.to(q.dtype), k_embed.to(q.dtype) class NeuroBLASTAttention(nn.Module): def __init__(self, config: NeuroBLASTConfig, layer_idx: Optional[int] = None, use_rope: bool = True): super().__init__() self.config = config self.layer_idx = layer_idx self.use_rope = use_rope if layer_idx is None: logger.warning_once( f"Instantiating {self.__class__.__name__} without passing a `layer_idx` is not recommended and will " "lead to errors during the forward call if caching is used. Please make sure to provide a `layer_idx` " "when creating this class." ) self.hidden_size = config.hidden_size self.num_heads = config.num_attention_heads self.head_dim = getattr(config, "head_dim", self.hidden_size // self.num_heads) self.num_key_value_heads = config.num_key_value_heads self.num_key_value_groups = self.num_heads // self.num_key_value_heads self.max_position_embeddings = config.max_position_embeddings self.rope_theta = config.rope_theta self.is_causal = True self.q_proj = nn.Linear(self.hidden_size, self.num_heads * self.head_dim, bias=config.attention_bias) self.k_proj = nn.Linear(self.hidden_size, self.num_key_value_heads * self.head_dim, bias=config.attention_bias) self.v_proj = nn.Linear(self.hidden_size, self.num_key_value_heads * self.head_dim, bias=config.attention_bias) self.o_proj = nn.Linear(self.num_heads * self.head_dim, self.hidden_size, bias=config.attention_bias) self.q_norm = NeuroBLASTRMSNorm(self.head_dim, eps=config.rms_norm_eps) self.k_norm = NeuroBLASTRMSNorm(self.head_dim, eps=config.rms_norm_eps) def forward( self, hidden_states: torch.Tensor, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.LongTensor] = None, past_key_value: Optional[Cache] = None, output_attentions: bool = False, use_cache: bool = False, position_embeddings: Optional[Tuple[torch.Tensor, torch.Tensor]] = None, ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]: bsz, q_len, _ = hidden_states.size() query_states = self.q_proj(hidden_states) key_states = self.k_proj(hidden_states) value_states = self.v_proj(hidden_states) query_states = query_states.view(bsz, q_len, self.num_heads, self.head_dim) key_states = key_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim) value_states = value_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim) # Norm query_states = self.q_norm(query_states) key_states = self.k_norm(key_states) query_states = query_states.transpose(1, 2) key_states = key_states.transpose(1, 2) value_states = value_states.transpose(1, 2) kv_seq_len = key_states.shape[-2] if past_key_value is not None: if self.layer_idx is None: raise ValueError( f"The `layer_idx` should be defined when calling the forward function of {self.__class__.__name__}. " "Please make sure to pass a `layer_idx` when creating this class." ) kv_seq_len += past_key_value.get_seq_length(self.layer_idx) if self.use_rope and position_embeddings is not None: cos, sin = position_embeddings cos = cos.squeeze(2) sin = sin.squeeze(2) query_states, key_states = apply_rotary_pos_emb(query_states, key_states, cos, sin, unsqueeze_dim=1) else: cos = None sin = None if past_key_value is not None: key_states, value_states = past_key_value.update(key_states, value_states, self.layer_idx, cache_kwargs={"cos": cos, "sin": sin}) # repeat k/v heads if n_kv_heads < n_heads key_states = repeat_kv(key_states, self.num_key_value_groups) value_states = repeat_kv(value_states, self.num_key_value_groups) attn_weights = torch.matmul(query_states, key_states.transpose(2, 3)) / math.sqrt(self.head_dim) if attention_mask is not None: attn_weights = attn_weights + attention_mask # upcast attention to fp32 attn_weights = nn.functional.softmax(attn_weights, dim=-1, dtype=torch.float32).to(query_states.dtype) attn_weights = nn.functional.dropout(attn_weights, p=self.config.attention_dropout, training=self.training) attn_output = torch.matmul(attn_weights, value_states) if attn_output.size() != (bsz, self.num_heads, q_len, self.head_dim): raise ValueError( f"`attn_output` should be of size {(bsz, self.num_heads, q_len, self.head_dim)}, but is" f" {attn_output.size()}" ) attn_output = attn_output.transpose(1, 2).contiguous() attn_output = attn_output.reshape(bsz, q_len, self.num_heads * self.head_dim) attn_output = self.o_proj(attn_output) if not output_attentions: attn_weights = None return attn_output, attn_weights, past_key_value def repeat_kv(hidden_states: torch.Tensor, n_rep: int) -> torch.Tensor: 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) class NeuroBLASTRMSNorm2d(nn.Module): def __init__(self, dim, eps=1e-6): super().__init__() self.weight = nn.Parameter(torch.ones(dim)) self.variance_epsilon = eps def forward(self, x): # x: (B, C, H, W) input_dtype = x.dtype x = x.to(torch.float32) variance = x.pow(2).mean(dim=1, keepdim=True) x_norm = x * torch.rsqrt(variance + self.variance_epsilon) return self.weight.view(1, -1, 1, 1) * x_norm.to(input_dtype) class NeuroBLASTCausalConv2DBlock(nn.Module): def __init__(self, config, dilation=1, layer_idx=0): super().__init__() self.config = config self.dilation = dilation self.layer_idx = layer_idx k = config.kernel_size d = config.hidden_size s = config.scale self.conv_padding = (k // 2, 0) if s == 1: self.conv = nn.Conv2d( d, d, kernel_size=(k, k), dilation=(1, dilation), padding=self.conv_padding, bias=False ) self.use_gating = False self.use_projection = False elif s > 1: internal_dim = int(d * s) self.conv = nn.Conv2d( d, internal_dim, kernel_size=(k, k), dilation=(1, dilation), padding=self.conv_padding, bias=False ) self.use_gating = True self.use_projection = False else: internal_dim = max(int(d * s), d // 4) self.conv = nn.Conv2d( d, internal_dim, kernel_size=(k, k), dilation=(1, dilation), padding=self.conv_padding, bias=False ) self.use_gating = False self.use_projection = True self.proj_back = nn.Conv2d(internal_dim, d, kernel_size=(1, 1), bias=False) self.norm_in = NeuroBLASTRMSNorm2d(d, eps=config.rms_norm_eps) self.norm_out = NeuroBLASTRMSNorm2d(d, eps=config.rms_norm_eps) self.dropout = nn.Dropout(config.dropout) def forward(self, x): # x: (B, C, H, W) B, C, H, W = x.shape residual = x y = self.norm_in(x) k = self.config.kernel_size pad_w = (k - 1) * self.dilation # Pad W on the left y_pad = F.pad(y, (pad_w, 0, 0, 0)) y = self.conv(y_pad) if self.use_gating: gate, val = torch.chunk(y, 2, dim=1) y = val * F.softmax(gate, dim=1) elif self.use_projection: y = self.proj_back(y) y = self.norm_out(y) x = residual + self.dropout(y) return x class NeuroBLASTDecoderLayer(nn.Module): def __init__(self, config: NeuroBLASTConfig, layer_idx: int, attention_type: str = "full_attention"): super().__init__() self.hidden_size = config.hidden_size self.self_attn = NeuroBLASTAttention( config=config, layer_idx=layer_idx, use_rope=(attention_type != "no_rope"), ) self.mlp = NeuroBLASTMLP(config) self.input_layernorm = NeuroBLASTRMSNorm(config.hidden_size, eps=config.rms_norm_eps) self.post_attention_layernorm = NeuroBLASTRMSNorm(config.hidden_size, eps=config.rms_norm_eps) def forward( self, hidden_states: torch.Tensor, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.LongTensor] = None, past_key_value: Optional[Tuple[torch.Tensor]] = None, output_attentions: Optional[bool] = False, use_cache: Optional[bool] = False, position_embeddings: Optional[Tuple[torch.Tensor, torch.Tensor]] = None, ) -> Tuple[torch.Tensor, Optional[Tuple[torch.Tensor, torch.Tensor]]]: residual = hidden_states hidden_states = self.input_layernorm(hidden_states) # Self Attention hidden_states, self_attn_weights, present_key_value = self.self_attn( hidden_states=hidden_states, attention_mask=attention_mask, position_ids=position_ids, past_key_value=past_key_value, output_attentions=output_attentions, use_cache=use_cache, position_embeddings=position_embeddings, ) hidden_states = residual + hidden_states # MLP residual = hidden_states hidden_states = self.post_attention_layernorm(hidden_states) hidden_states = self.mlp(hidden_states) hidden_states = residual + hidden_states outputs = (hidden_states,) if output_attentions: outputs += (self_attn_weights,) if use_cache: outputs += (present_key_value,) return outputs class NeuroBLASTToken2D(nn.Module): def forward(self, x, mode="seq_to_2d"): if mode == "seq_to_2d": return x.permute(0, 2, 1).unsqueeze(2) else: return x.squeeze(2).permute(0, 2, 1) class NeuroBLASTRotaryEmbedding(nn.Module): def __init__(self, config): super().__init__() self.dim = config.head_dim self.max_position_embeddings = config.max_position_embeddings self.base = config.rope_theta inv_freq = 1.0 / (self.base ** (torch.arange(0, self.dim, 2).float() / self.dim)) self.register_buffer("inv_freq", inv_freq, persistent=False) def forward(self, x, position_ids): # x: (B, L, H, D) or similar. Not used for shape here. # position_ids: (B, L) inv_freq_expanded = self.inv_freq[None, :, None] position_ids_expanded = position_ids[:, :, None].float() freqs = torch.matmul(position_ids_expanded, self.inv_freq[None, None, :]) emb = torch.cat((freqs, freqs), dim=-1) cos = emb.cos() sin = emb.sin() # Output: (B, L, 1, D) return cos[:, :, None, :], sin[:, :, None, :] class NeuroBLASTPreTrainedModel(PreTrainedModel): config_class = NeuroBLASTConfig base_model_prefix = "model" supports_gradient_checkpointing = True _no_split_modules = ["NeuroBLASTDecoderLayer", "NeuroBLASTCausalConv2DBlock"] _skip_keys_device_placement = "past_key_values" def _init_weights(self, module): std = self.config.initializer_range if isinstance(module, nn.Linear): module.weight.data.normal_(mean=0.0, std=std) if module.bias is not None: module.bias.data.zero_() elif isinstance(module, nn.Embedding): module.weight.data.normal_(mean=0.0, std=std) if module.padding_idx is not None: module.weight.data[module.padding_idx].zero_() class NeuroBLASTModel(NeuroBLASTPreTrainedModel): def __init__(self, config: NeuroBLASTConfig): super().__init__(config) self.padding_idx = config.pad_token_id self.vocab_size = config.vocab_size self.embed_tokens = nn.Embedding(config.vocab_size, config.hidden_size, self.padding_idx) self.token2d = NeuroBLASTToken2D() self.sensory_layers = nn.ModuleList() dilatation_step = 1 for i in range(config.num_sensory_layers): if i % 2 == 0: layer = NeuroBLASTDecoderLayer(config, layer_idx=i, attention_type="full_attention") else: dilation = min(2 ** ((i - 1) // dilatation_step), 8) layer = NeuroBLASTCausalConv2DBlock(config, dilation=dilation, layer_idx=i) self.sensory_layers.append(layer) self.sensory_to_associative = NeuroBLASTRMSNorm(config.hidden_size, eps=config.rms_norm_eps) self.associative_layers = nn.ModuleList() next_layer_type = "full_attention" for i in range(config.num_associative_layers): idx = i + config.num_sensory_layers if i % 2 == 0: layer = NeuroBLASTDecoderLayer(config, layer_idx=idx, attention_type=next_layer_type) if next_layer_type == "full_attention": next_layer_type = "no_rope" else: next_layer_type = "full_attention" else: dilation = min(2 ** ((i - 1) // dilatation_step), 8) layer = NeuroBLASTCausalConv2DBlock(config, dilation=dilation, layer_idx=idx) self.associative_layers.append(layer) self.sensory_to_motor = NeuroBLASTRMSNorm(config.hidden_size, eps=config.rms_norm_eps) self.motor_layers = nn.ModuleList() next_layer_type = "full_attention" for i in range(config.num_motor_layers): idx = i + config.num_sensory_layers + config.num_associative_layers layer = NeuroBLASTDecoderLayer(config, layer_idx=idx, attention_type=next_layer_type) if next_layer_type == "full_attention": next_layer_type = "no_rope" else: next_layer_type = "full_attention" self.motor_layers.append(layer) self.norm = NeuroBLASTRMSNorm(config.hidden_size, eps=config.rms_norm_eps) self.rotary_emb = NeuroBLASTRotaryEmbedding(config) self.gradient_checkpointing = False self.post_init() def forward( self, input_ids: torch.LongTensor = None, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.LongTensor] = None, past_key_values: Optional[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, cache_position: Optional[torch.LongTensor] = None, return_dict: Optional[bool] = None, ) -> Union[Tuple, 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 return_dict = return_dict if return_dict is not None else self.config.use_return_dict if input_ids is not None and inputs_embeds is not None: raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time") elif input_ids is not None: batch_size, seq_length = input_ids.shape elif inputs_embeds is not None: batch_size, seq_length, _ = inputs_embeds.shape else: raise ValueError("You have to specify either input_ids or inputs_embeds") if position_ids is None: device = input_ids.device if input_ids is not None else inputs_embeds.device past_length = 0 if past_key_values is not None: if isinstance(past_key_values, DynamicCache): past_length = past_key_values.get_seq_length() elif isinstance(past_key_values, (tuple, list)): past_length = past_key_values[0][0].shape[-2] position_ids = torch.arange(past_length, past_length + seq_length, dtype=torch.long, device=device) position_ids = position_ids.unsqueeze(0).view(-1, seq_length) else: position_ids = position_ids.view(-1, seq_length).long() if inputs_embeds is None: inputs_embeds = self.embed_tokens(input_ids) if attention_mask is None: attention_mask = torch.ones( (batch_size, seq_length), dtype=torch.bool, device=inputs_embeds.device ) # Create causal mask min_dtype = torch.finfo(inputs_embeds.dtype).min causal_mask = torch.full((seq_length, seq_length), min_dtype, device=inputs_embeds.device) causal_mask = torch.triu(causal_mask, diagonal=1) causal_mask = causal_mask[None, None, :, :] # (1, 1, L, L) # Expand attention_mask # attention_mask: (B, L) -> (B, 1, 1, L) padding_mask = attention_mask[:, None, None, :].to(inputs_embeds.dtype) padding_mask = (1.0 - padding_mask) * min_dtype combined_mask = causal_mask + padding_mask # Initialize cache if needed if use_cache and past_key_values is None: past_key_values = DynamicCache() hidden_states = inputs_embeds # RoPE position_embeddings = self.rotary_emb(hidden_states, position_ids) all_hidden_states = () if output_hidden_states else None all_self_attns = () if output_attentions else None residual = hidden_states # Sensory for i, layer in enumerate(self.sensory_layers): if output_hidden_states: all_hidden_states += (hidden_states,) if i % 2 == 1: # Conv layer hidden_states = self.token2d(hidden_states, mode="seq_to_2d") hidden_states = layer(hidden_states) hidden_states = self.token2d(hidden_states, mode="d2_to_seq") else: # Attention layer layer_outputs = layer( hidden_states, attention_mask=combined_mask, position_ids=position_ids, past_key_value=past_key_values, output_attentions=output_attentions, use_cache=use_cache, position_embeddings=position_embeddings, ) hidden_states = layer_outputs[0] if output_attentions: all_self_attns += (layer_outputs[1],) hidden_states = hidden_states + self.sensory_to_associative(F.silu(residual)) # Associative for i, layer in enumerate(self.associative_layers): if output_hidden_states: all_hidden_states += (hidden_states,) if i % 2 == 1: hidden_states = self.token2d(hidden_states, mode="seq_to_2d") hidden_states = layer(hidden_states) hidden_states = self.token2d(hidden_states, mode="d2_to_seq") else: layer_outputs = layer( hidden_states, attention_mask=combined_mask, position_ids=position_ids, past_key_value=past_key_values, output_attentions=output_attentions, use_cache=use_cache, position_embeddings=position_embeddings, ) hidden_states = layer_outputs[0] if output_attentions: all_self_attns += (layer_outputs[1],) hidden_states = hidden_states + self.sensory_to_motor(F.silu(-residual)) # Motor for i, layer in enumerate(self.motor_layers): if output_hidden_states: all_hidden_states += (hidden_states,) layer_outputs = layer( hidden_states, attention_mask=combined_mask, position_ids=position_ids, past_key_value=past_key_values, output_attentions=output_attentions, use_cache=use_cache, position_embeddings=position_embeddings, ) hidden_states = layer_outputs[0] if output_attentions: all_self_attns += (layer_outputs[1],) hidden_states = self.norm(hidden_states) if output_hidden_states: all_hidden_states += (hidden_states,) if not return_dict: return tuple(v for v in [hidden_states, past_key_values, all_hidden_states, all_self_attns] if v is not None) return BaseModelOutputWithPast( last_hidden_state=hidden_states, past_key_values=past_key_values, hidden_states=all_hidden_states, attentions=all_self_attns, ) class NeuroBLASTPreTrainedModel(PreTrainedModel): config_class = NeuroBLASTConfig base_model_prefix = "model" supports_gradient_checkpointing = True _no_split_modules = ["NeuroBLASTBlock"] _skip_keys_device_placement = "past_key_values" def _init_weights(self, module): std = self.config.initializer_range if isinstance(module, nn.Linear): module.weight.data.normal_(mean=0.0, std=std) if module.bias is not None: module.bias.data.zero_() elif isinstance(module, nn.Embedding): module.weight.data.normal_(mean=0.0, std=std) if module.padding_idx is not None: module.weight.data[module.padding_idx].zero_() class NeuroBLASTForCausalLM(NeuroBLASTPreTrainedModel, GenerationMixin): _tied_weights_keys = ["lm_head.weight"] def __init__(self, config): super().__init__(config) self.model = NeuroBLASTModel(config) self.vocab_size = config.vocab_size self.lm_head = nn.Linear(config.hidden_size, config.vocab_size, bias=False) # Initialize weights and apply final processing self.post_init() def get_input_embeddings(self): return self.model.embed_tokens def set_input_embeddings(self, value): self.model.embed_tokens = value def get_output_embeddings(self): return self.lm_head def set_output_embeddings(self, new_embeddings): self.lm_head = new_embeddings def set_decoder(self, decoder): self.model = decoder def get_decoder(self): return self.model 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[Cache] = None, inputs_embeds: Optional[torch.FloatTensor] = None, labels: Optional[torch.LongTensor] = None, use_cache: Optional[bool] = None, output_attentions: Optional[bool] = None, output_hidden_states: Optional[bool] = None, cache_position: Optional[torch.LongTensor] = None, logits_to_keep: Union[int, torch.Tensor] = 0, return_dict: Optional[bool] = None, **kwargs, ) -> Union[Tuple, CausalLMOutputWithPast]: 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 ) return_dict = return_dict if return_dict is not None else self.config.use_return_dict # decoder outputs consists of (dec_features, layer_state, dec_hidden, dec_attn) outputs = self.model( input_ids=input_ids, attention_mask=attention_mask, position_ids=position_ids, past_key_values=past_key_values, inputs_embeds=inputs_embeds, use_cache=use_cache, output_attentions=output_attentions, output_hidden_states=output_hidden_states, cache_position=cache_position, return_dict=return_dict, ) hidden_states = outputs[0] slice_indices = ( slice(-logits_to_keep, None) if isinstance(logits_to_keep, int) else logits_to_keep ) logits = self.lm_head(hidden_states[:, slice_indices, :]) loss = None if labels is not None: loss = self.loss_function( logits=logits, labels=labels, vocab_size=self.config.vocab_size, **kwargs, ) if not return_dict: output = (logits,) + outputs[1:] return ((loss,) + output) if loss is not None else output return CausalLMOutputWithPast( loss=loss, logits=logits, past_key_values=outputs.past_key_values, hidden_states=outputs.hidden_states, attentions=outputs.attentions, )