Upload folder using huggingface_hub
Browse files- config.json +3 -2
- esm_nv.py +145 -74
- special_tokens_map.json +42 -5
- tokenizer.json +176 -0
- tokenizer_config.json +8 -1
config.json
CHANGED
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@@ -8,7 +8,8 @@
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"auto_map": {
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"AutoConfig": "esm_nv.NVEsmConfig",
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"AutoModel": "esm_nv.NVEsmModel",
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-
"AutoModelForMaskedLM": "esm_nv.NVEsmForMaskedLM"
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},
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"classifier_dropout": null,
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"dtype": "float32",
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@@ -35,7 +36,7 @@
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"position_embedding_type": "rotary",
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"qkv_weight_interleaved": true,
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"token_dropout": true,
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-
"transformers_version": "4.57.
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"use_cache": true,
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"vocab_list": null,
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"vocab_size": 33
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"auto_map": {
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"AutoConfig": "esm_nv.NVEsmConfig",
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"AutoModel": "esm_nv.NVEsmModel",
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+
"AutoModelForMaskedLM": "esm_nv.NVEsmForMaskedLM",
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+
"AutoModelForTokenClassification": "esm_nv.NVEsmForTokenClassification"
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},
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"classifier_dropout": null,
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"dtype": "float32",
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"position_embedding_type": "rotary",
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"qkv_weight_interleaved": true,
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"token_dropout": true,
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+
"transformers_version": "4.57.3",
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"use_cache": true,
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"vocab_list": null,
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"vocab_size": 33
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esm_nv.py
CHANGED
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@@ -23,7 +23,7 @@
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Adapted from `modeling_esm.py` in huggingface/transformers.
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"""
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-
from typing import Literal, Optional
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# TODO: put import guard around transformer_engine here, with an informative error message around
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# installation and the nvidia docker container.
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@@ -36,15 +36,26 @@ from transformers.modeling_outputs import (
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BaseModelOutput,
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BaseModelOutputWithPooling,
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MaskedLMOutput,
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)
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from transformers.modeling_utils import PreTrainedModel
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from transformers.models.esm.configuration_esm import EsmConfig
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from transformers.models.esm.modeling_esm import EsmPooler
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from transformers.utils import logging
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logger = logging.get_logger(__name__)
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class NVEsmConfig(EsmConfig):
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"""NVEsmConfig is a configuration for the NVEsm model."""
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@@ -149,7 +160,9 @@ class NVEsmEncoder(nn.Module):
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for i in range(config.num_hidden_layers)
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]
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)
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self.emb_layer_norm_after = transformer_engine.pytorch.LayerNorm(
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if config.position_embedding_type == "rotary":
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self.rotary_embeddings = RotaryPositionEmbedding(config.hidden_size // config.num_attention_heads)
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self,
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hidden_states: torch.Tensor,
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attention_mask: Optional[torch.Tensor] = None,
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-
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cu_seq_lens_q: torch.IntTensor | None = None,
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cu_seq_lens_k: torch.IntTensor | None = None,
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max_length_q: int | None = None,
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max_length_k: int | None = None,
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):
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"""Forward pass of the NVEsmEncoder.
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Args:
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hidden_states (torch.Tensor): The hidden states.
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attention_mask (torch.Tensor): The attention mask.
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-
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cu_seq_lens_q (torch.IntTensor): The cumulative sequence lengths for the query state, if using THD inputs.
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cu_seq_lens_k (torch.IntTensor): The cumulative sequence lengths for the key state, if using THD inputs.
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max_length_q (int): The maximum length for the query state, if using THD inputs.
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max_length_k (int): The maximum length for the key state, if using THD inputs.
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"""
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all_hidden_states: tuple[torch.Tensor, ...] = ()
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if self.config.attn_input_format == "thd":
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-
if
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raise ValueError(
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"cu_seq_lens_q, cu_seq_lens_k, max_length_q, and max_length_k must be provided when using THD inputs."
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)
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hidden_states = hidden_states.squeeze(0)
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attention_mask = None
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elif self.config.attn_input_format == "bshd":
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-
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-
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-
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)
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# Ensure that rotary embeddings are computed with at a higher precision outside the torch autocast context.
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with torch.autocast(device_type="cuda", enabled=False):
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if self.config.attn_input_format == "bshd":
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te_rope_emb = self.rotary_embeddings(max_seq_len=hidden_states.shape[1])
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elif self.config.attn_input_format == "thd":
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te_rope_emb = self.rotary_embeddings(
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for layer_module in self.layers:
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if output_hidden_states:
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all_hidden_states = (*all_hidden_states, hidden_states)
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hidden_states = layer_module(
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hidden_states,
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attention_mask,
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rotary_pos_emb=te_rope_emb,
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cu_seqlens_q=cu_seq_lens_q,
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cu_seqlens_kv=cu_seq_lens_k,
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)
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hidden_states = self.emb_layer_norm_after(hidden_states)
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if output_hidden_states:
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all_hidden_states = (*all_hidden_states, hidden_states)
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return BaseModelOutput(
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@@ -233,6 +253,7 @@ class NVEsmPreTrainedModel(PreTrainedModel):
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config_class = NVEsmConfig
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base_model_prefix = "esm"
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supports_gradient_checkpointing = False
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_no_split_modules = (
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"TransformerLayer",
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"EsmEmbeddings",
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if module.layer_norm_bias is not None:
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module.layer_norm_bias.data.zero_()
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class NVEsmModel(NVEsmPreTrainedModel):
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"""The ESM Encoder-only protein language model.
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attention_mask: Optional[torch.Tensor] = None,
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position_ids: Optional[torch.Tensor] = None,
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inputs_embeds: Optional[torch.Tensor] = None,
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-
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cu_seq_lens_q: torch.IntTensor | None = None,
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cu_seq_lens_k: torch.IntTensor | None = None,
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max_length_q: int | None = None,
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max_length_k: int | None = None,
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) -> BaseModelOutputWithPooling:
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"""Forward pass of the NVEsmModel.
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attention_mask (torch.Tensor): The attention mask.
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position_ids (torch.Tensor): The position ids.
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inputs_embeds (torch.Tensor): The input embeddings.
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-
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cu_seq_lens_q (torch.IntTensor): The cumulative sequence lengths for the query state, if using THD inputs.
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-
cu_seq_lens_k (torch.IntTensor): The cumulative sequence lengths for the key state, if using THD inputs.
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max_length_q (int): The maximum length for the query state, if using THD inputs.
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max_length_k (int): The maximum length for the key state, if using THD inputs.
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Returns:
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BaseModelOutputWithPooling: The output of the model.
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"""
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-
output_hidden_states = (
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output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
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-
)
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if input_ids is not None and inputs_embeds is not None:
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raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
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elif input_ids is not None:
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input_ids=input_ids,
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attention_mask=attention_mask,
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inputs_embeds=inputs_embeds,
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-
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cu_seq_lens_k=cu_seq_lens_k,
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-
max_length_q=max_length_q,
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max_length_k=max_length_k,
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)
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encoder_outputs = self.encoder(
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embedding_output,
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attention_mask=extended_attention_mask,
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-
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cu_seq_lens_q=cu_seq_lens_q,
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cu_seq_lens_k=cu_seq_lens_k,
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max_length_q=max_length_q,
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max_length_k=max_length_k,
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)
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sequence_output = encoder_outputs[0]
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pooled_output = self.pooler(sequence_output) if self.pooler is not None else None
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position_ids: Optional[torch.LongTensor] = None,
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inputs_embeds: Optional[torch.FloatTensor] = None,
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labels: Optional[torch.LongTensor] = None,
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-
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cu_seq_lens_q: torch.IntTensor | None = None,
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cu_seq_lens_k: torch.IntTensor | None = None,
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max_length_q: int | None = None,
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max_length_k: int | None = None,
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) -> MaskedLMOutput:
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"""Forward pass of the NVEsmForMaskedLM.
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position_ids (torch.LongTensor): The position ids.
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inputs_embeds (torch.FloatTensor): The input embeddings.
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labels (torch.LongTensor): The labels.
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-
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cu_seq_lens_q (torch.IntTensor): The cumulative sequence lengths for the query state, if using THD inputs.
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cu_seq_lens_k (torch.IntTensor): The cumulative sequence lengths for the key state, if using THD inputs.
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max_length_q (int): The maximum length for the query state, if using THD inputs.
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max_length_k (int): The maximum length for the key state, if using THD inputs.
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Returns:
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MaskedLMOutput: The output of the model.
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attention_mask=attention_mask,
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position_ids=position_ids,
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inputs_embeds=inputs_embeds,
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cu_seq_lens_q=cu_seq_lens_q,
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cu_seq_lens_k=cu_seq_lens_k,
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max_length_q=max_length_q,
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max_length_k=max_length_k,
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)
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sequence_output = outputs[0]
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prediction_scores = self.lm_head(sequence_output)
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config (NVEsmConfig): The configuration of the model.
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"""
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super().__init__()
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self.dense = transformer_engine.pytorch.Linear(
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self.decoder = transformer_engine.pytorch.LayerNormLinear(
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config.hidden_size,
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config.padded_vocab_size if config.padded_vocab_size is not None else config.vocab_size,
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bias=True,
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eps=config.layer_norm_eps,
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)
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def forward(self, features, **kwargs):
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"""Initialize a NVEsmEmbeddings."""
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super().__init__()
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self.word_embeddings = nn.Embedding(
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config.padded_vocab_size,
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)
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self.layer_norm = (
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-
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)
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if config.position_embedding_type != "rotary":
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input_ids=None,
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attention_mask=None,
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inputs_embeds=None,
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cu_seq_lens_k: torch.IntTensor | None = None,
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max_length_q: int | None = None,
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max_length_k: int | None = None,
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):
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"""Forward pass of the NVEsmEmbeddings."""
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if inputs_embeds is None:
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# embedding_scale factor here.
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embeddings = inputs_embeds
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if
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using_thd = True
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attention_mask = None
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else:
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embeddings = (embeddings * scale_factor[:, None, None]).to(embeddings.dtype)
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else:
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src_lengths = torch.diff(cu_seq_lens_q)
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# We need to find the number of masked tokens in each sequence in the padded batch.
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is_masked = (input_ids == self.mask_token_id).squeeze(0)
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n_masked_per_seq = torch.nested.nested_tensor_from_jagged(
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mask_ratio_observed = n_masked_per_seq.float() / src_lengths
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scale_factor = (1 - mask_ratio_train) / (1 - mask_ratio_observed)
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reshaped_scale_factor = torch.repeat_interleave(scale_factor, src_lengths, dim=0)
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embeddings = (embeddings * attention_mask.unsqueeze(-1)).to(embeddings.dtype)
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return embeddings
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Adapted from `modeling_esm.py` in huggingface/transformers.
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"""
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+
from typing import Literal, Optional, Unpack
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# TODO: put import guard around transformer_engine here, with an informative error message around
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| 29 |
# installation and the nvidia docker container.
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BaseModelOutput,
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BaseModelOutputWithPooling,
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MaskedLMOutput,
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+
TokenClassifierOutput,
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)
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from transformers.modeling_utils import PreTrainedModel
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from transformers.models.esm.configuration_esm import EsmConfig
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| 43 |
from transformers.models.esm.modeling_esm import EsmPooler
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from transformers.utils import logging
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+
from transformers.utils.generic import TransformersKwargs
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logger = logging.get_logger(__name__)
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+
# Dictionary that gets inserted into config.json to map Auto** classes to our TE-optimized model classes defined below.
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+
# These should be prefixed with esm_nv., since we name the file esm_nv.py in our exported checkpoints.
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+
AUTO_MAP = {
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"AutoConfig": "esm_nv.NVEsmConfig",
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"AutoModel": "esm_nv.NVEsmModel",
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+
"AutoModelForMaskedLM": "esm_nv.NVEsmForMaskedLM",
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+
"AutoModelForTokenClassification": "esm_nv.NVEsmForTokenClassification",
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+
}
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+
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class NVEsmConfig(EsmConfig):
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"""NVEsmConfig is a configuration for the NVEsm model."""
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for i in range(config.num_hidden_layers)
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]
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)
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+
self.emb_layer_norm_after = transformer_engine.pytorch.LayerNorm(
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+
config.hidden_size, eps=config.layer_norm_eps, params_dtype=config.dtype
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+
)
|
| 166 |
if config.position_embedding_type == "rotary":
|
| 167 |
self.rotary_embeddings = RotaryPositionEmbedding(config.hidden_size // config.num_attention_heads)
|
| 168 |
|
|
|
|
| 170 |
self,
|
| 171 |
hidden_states: torch.Tensor,
|
| 172 |
attention_mask: Optional[torch.Tensor] = None,
|
| 173 |
+
**kwargs: Unpack[TransformersKwargs],
|
|
|
|
|
|
|
|
|
|
|
|
|
| 174 |
):
|
| 175 |
"""Forward pass of the NVEsmEncoder.
|
| 176 |
|
| 177 |
Args:
|
| 178 |
hidden_states (torch.Tensor): The hidden states.
|
| 179 |
attention_mask (torch.Tensor): The attention mask.
|
| 180 |
+
**kwargs: Additional arguments, see TransformersKwargs for more details.
|
|
|
|
|
|
|
|
|
|
|
|
|
| 181 |
"""
|
| 182 |
all_hidden_states: tuple[torch.Tensor, ...] = ()
|
| 183 |
+
has_thd_input = [
|
| 184 |
+
x is not None
|
| 185 |
+
for x in [
|
| 186 |
+
kwargs.get("cu_seq_lens_q", None),
|
| 187 |
+
kwargs.get("cu_seq_lens_k", None),
|
| 188 |
+
kwargs.get("max_length_q", None),
|
| 189 |
+
kwargs.get("max_length_k", None),
|
| 190 |
+
]
|
| 191 |
+
]
|
| 192 |
|
| 193 |
if self.config.attn_input_format == "thd":
|
| 194 |
+
if not all(has_thd_input):
|
| 195 |
raise ValueError(
|
| 196 |
"cu_seq_lens_q, cu_seq_lens_k, max_length_q, and max_length_k must be provided when using THD inputs."
|
| 197 |
)
|
|
|
|
| 201 |
hidden_states = hidden_states.squeeze(0)
|
| 202 |
attention_mask = None
|
| 203 |
|
| 204 |
+
elif self.config.attn_input_format == "bshd" and any(has_thd_input):
|
| 205 |
+
raise ValueError(
|
| 206 |
+
"cu_seq_lens_q, cu_seq_lens_k, max_length_q, and max_length_k are not allowed when using BSHD inputs."
|
| 207 |
+
)
|
|
|
|
| 208 |
|
| 209 |
# Ensure that rotary embeddings are computed with at a higher precision outside the torch autocast context.
|
| 210 |
with torch.autocast(device_type="cuda", enabled=False):
|
|
|
|
| 212 |
if self.config.attn_input_format == "bshd":
|
| 213 |
te_rope_emb = self.rotary_embeddings(max_seq_len=hidden_states.shape[1])
|
| 214 |
elif self.config.attn_input_format == "thd":
|
| 215 |
+
te_rope_emb = self.rotary_embeddings(
|
| 216 |
+
max_seq_len=kwargs["cu_seq_lens_q_padded"][-1]
|
| 217 |
+
if "cu_seq_lens_q_padded" in kwargs
|
| 218 |
+
else kwargs["cu_seq_lens_q"][-1]
|
| 219 |
+
)
|
| 220 |
+
te_rope_emb = te_rope_emb.to(hidden_states.device, non_blocking=True)
|
| 221 |
|
| 222 |
for layer_module in self.layers:
|
| 223 |
+
if kwargs.get("output_hidden_states", False):
|
| 224 |
all_hidden_states = (*all_hidden_states, hidden_states)
|
| 225 |
|
| 226 |
hidden_states = layer_module(
|
| 227 |
hidden_states,
|
| 228 |
attention_mask,
|
| 229 |
rotary_pos_emb=te_rope_emb,
|
| 230 |
+
cu_seqlens_q=kwargs.get("cu_seq_lens_q", None),
|
| 231 |
+
cu_seqlens_kv=kwargs.get("cu_seq_lens_k", None),
|
| 232 |
+
cu_seqlens_q_padded=kwargs.get("cu_seq_lens_q_padded", None),
|
| 233 |
+
cu_seqlens_kv_padded=kwargs.get("cu_seq_lens_k_padded", None),
|
| 234 |
+
max_seqlen_q=kwargs.get("max_length_q", None),
|
| 235 |
+
max_seqlen_kv=kwargs.get("max_length_k", None),
|
| 236 |
+
pad_between_seqs=kwargs.get("pad_between_seqs", None),
|
| 237 |
)
|
| 238 |
|
| 239 |
hidden_states = self.emb_layer_norm_after(hidden_states)
|
| 240 |
|
| 241 |
+
if kwargs.get("output_hidden_states", False):
|
| 242 |
all_hidden_states = (*all_hidden_states, hidden_states)
|
| 243 |
|
| 244 |
return BaseModelOutput(
|
|
|
|
| 253 |
config_class = NVEsmConfig
|
| 254 |
base_model_prefix = "esm"
|
| 255 |
supports_gradient_checkpointing = False
|
| 256 |
+
accepts_loss_kwargs = False
|
| 257 |
_no_split_modules = (
|
| 258 |
"TransformerLayer",
|
| 259 |
"EsmEmbeddings",
|
|
|
|
| 286 |
if module.layer_norm_bias is not None:
|
| 287 |
module.layer_norm_bias.data.zero_()
|
| 288 |
|
| 289 |
+
@classmethod
|
| 290 |
+
def get_init_context(cls, is_quantized: bool, _is_ds_init_called: bool):
|
| 291 |
+
"""Override the default get_init_context method to allow for fp8 model initialization."""
|
| 292 |
+
return []
|
| 293 |
+
|
| 294 |
|
| 295 |
class NVEsmModel(NVEsmPreTrainedModel):
|
| 296 |
"""The ESM Encoder-only protein language model.
|
|
|
|
| 336 |
attention_mask: Optional[torch.Tensor] = None,
|
| 337 |
position_ids: Optional[torch.Tensor] = None,
|
| 338 |
inputs_embeds: Optional[torch.Tensor] = None,
|
| 339 |
+
**kwargs: Unpack[TransformersKwargs],
|
|
|
|
|
|
|
|
|
|
|
|
|
| 340 |
) -> BaseModelOutputWithPooling:
|
| 341 |
"""Forward pass of the NVEsmModel.
|
| 342 |
|
|
|
|
| 345 |
attention_mask (torch.Tensor): The attention mask.
|
| 346 |
position_ids (torch.Tensor): The position ids.
|
| 347 |
inputs_embeds (torch.Tensor): The input embeddings.
|
| 348 |
+
**kwargs: Additional arguments, see TransformersKwargs for more details.
|
|
|
|
|
|
|
|
|
|
|
|
|
| 349 |
|
| 350 |
Returns:
|
| 351 |
BaseModelOutputWithPooling: The output of the model.
|
| 352 |
"""
|
|
|
|
|
|
|
|
|
|
|
|
|
| 353 |
if input_ids is not None and inputs_embeds is not None:
|
| 354 |
raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
|
| 355 |
elif input_ids is not None:
|
|
|
|
| 377 |
input_ids=input_ids,
|
| 378 |
attention_mask=attention_mask,
|
| 379 |
inputs_embeds=inputs_embeds,
|
| 380 |
+
**kwargs,
|
|
|
|
|
|
|
|
|
|
| 381 |
)
|
| 382 |
encoder_outputs = self.encoder(
|
| 383 |
embedding_output,
|
| 384 |
attention_mask=extended_attention_mask,
|
| 385 |
+
**kwargs,
|
|
|
|
|
|
|
|
|
|
|
|
|
| 386 |
)
|
| 387 |
sequence_output = encoder_outputs[0]
|
| 388 |
pooled_output = self.pooler(sequence_output) if self.pooler is not None else None
|
|
|
|
| 434 |
position_ids: Optional[torch.LongTensor] = None,
|
| 435 |
inputs_embeds: Optional[torch.FloatTensor] = None,
|
| 436 |
labels: Optional[torch.LongTensor] = None,
|
| 437 |
+
**kwargs: Unpack[TransformersKwargs],
|
|
|
|
|
|
|
|
|
|
|
|
|
| 438 |
) -> MaskedLMOutput:
|
| 439 |
"""Forward pass of the NVEsmForMaskedLM.
|
| 440 |
|
|
|
|
| 444 |
position_ids (torch.LongTensor): The position ids.
|
| 445 |
inputs_embeds (torch.FloatTensor): The input embeddings.
|
| 446 |
labels (torch.LongTensor): The labels.
|
| 447 |
+
**kwargs: Additional arguments, see TransformersKwargs for more details.
|
|
|
|
|
|
|
|
|
|
|
|
|
| 448 |
|
| 449 |
Returns:
|
| 450 |
MaskedLMOutput: The output of the model.
|
|
|
|
| 454 |
attention_mask=attention_mask,
|
| 455 |
position_ids=position_ids,
|
| 456 |
inputs_embeds=inputs_embeds,
|
| 457 |
+
**kwargs,
|
|
|
|
|
|
|
|
|
|
|
|
|
| 458 |
)
|
| 459 |
sequence_output = outputs[0]
|
| 460 |
prediction_scores = self.lm_head(sequence_output)
|
|
|
|
| 488 |
config (NVEsmConfig): The configuration of the model.
|
| 489 |
"""
|
| 490 |
super().__init__()
|
| 491 |
+
self.dense = transformer_engine.pytorch.Linear(
|
| 492 |
+
config.hidden_size,
|
| 493 |
+
config.hidden_size,
|
| 494 |
+
params_dtype=config.dtype,
|
| 495 |
+
)
|
| 496 |
|
| 497 |
self.decoder = transformer_engine.pytorch.LayerNormLinear(
|
| 498 |
config.hidden_size,
|
| 499 |
config.padded_vocab_size if config.padded_vocab_size is not None else config.vocab_size,
|
| 500 |
bias=True,
|
| 501 |
eps=config.layer_norm_eps,
|
| 502 |
+
params_dtype=config.dtype,
|
| 503 |
)
|
| 504 |
|
| 505 |
def forward(self, features, **kwargs):
|
|
|
|
| 522 |
"""Initialize a NVEsmEmbeddings."""
|
| 523 |
super().__init__()
|
| 524 |
self.word_embeddings = nn.Embedding(
|
| 525 |
+
config.padded_vocab_size,
|
| 526 |
+
config.hidden_size,
|
| 527 |
+
padding_idx=config.pad_token_id,
|
| 528 |
+
dtype=config.dtype,
|
| 529 |
)
|
| 530 |
|
| 531 |
self.layer_norm = (
|
| 532 |
+
transformer_engine.pytorch.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
|
| 533 |
+
if config.emb_layer_norm_before
|
| 534 |
+
else None
|
| 535 |
)
|
| 536 |
|
| 537 |
if config.position_embedding_type != "rotary":
|
|
|
|
| 549 |
input_ids=None,
|
| 550 |
attention_mask=None,
|
| 551 |
inputs_embeds=None,
|
| 552 |
+
**kwargs: Unpack[TransformersKwargs],
|
|
|
|
|
|
|
|
|
|
| 553 |
):
|
| 554 |
"""Forward pass of the NVEsmEmbeddings."""
|
| 555 |
if inputs_embeds is None:
|
|
|
|
| 559 |
# embedding_scale factor here.
|
| 560 |
embeddings = inputs_embeds
|
| 561 |
|
| 562 |
+
if (
|
| 563 |
+
kwargs.get("cu_seq_lens_q") is not None
|
| 564 |
+
and kwargs.get("cu_seq_lens_k") is not None
|
| 565 |
+
and kwargs.get("max_length_q") is not None
|
| 566 |
+
and kwargs.get("max_length_k") is not None
|
| 567 |
+
):
|
| 568 |
using_thd = True
|
| 569 |
attention_mask = None
|
| 570 |
else:
|
|
|
|
| 590 |
embeddings = (embeddings * scale_factor[:, None, None]).to(embeddings.dtype)
|
| 591 |
|
| 592 |
else:
|
| 593 |
+
src_lengths = torch.diff(kwargs["cu_seq_lens_q"])
|
| 594 |
# We need to find the number of masked tokens in each sequence in the padded batch.
|
| 595 |
is_masked = (input_ids == self.mask_token_id).squeeze(0)
|
| 596 |
+
n_masked_per_seq = torch.nested.nested_tensor_from_jagged(
|
| 597 |
+
is_masked, offsets=kwargs["cu_seq_lens_q"]
|
| 598 |
+
).sum(1)
|
| 599 |
mask_ratio_observed = n_masked_per_seq.float() / src_lengths
|
| 600 |
scale_factor = (1 - mask_ratio_train) / (1 - mask_ratio_observed)
|
| 601 |
reshaped_scale_factor = torch.repeat_interleave(scale_factor, src_lengths, dim=0)
|
|
|
|
| 608 |
embeddings = (embeddings * attention_mask.unsqueeze(-1)).to(embeddings.dtype)
|
| 609 |
|
| 610 |
return embeddings
|
| 611 |
+
|
| 612 |
+
|
| 613 |
+
class NVEsmForTokenClassification(NVEsmPreTrainedModel):
|
| 614 |
+
"""Adds a token classification head to the model.
|
| 615 |
+
|
| 616 |
+
Adapted from EsmForTokenClassification in Hugging Face Transformers `modeling_esm.py`.
|
| 617 |
+
"""
|
| 618 |
+
|
| 619 |
+
def __init__(self, config):
|
| 620 |
+
"""Initialize NVEsmForTokenClassification."""
|
| 621 |
+
super().__init__(config)
|
| 622 |
+
self.num_labels = config.num_labels
|
| 623 |
+
|
| 624 |
+
self.esm = NVEsmModel(config, add_pooling_layer=False)
|
| 625 |
+
self.dropout = nn.Dropout(config.hidden_dropout_prob)
|
| 626 |
+
self.classifier = transformer_engine.pytorch.Linear(
|
| 627 |
+
config.hidden_size, config.num_labels, params_dtype=config.dtype
|
| 628 |
+
)
|
| 629 |
+
|
| 630 |
+
self.init_weights()
|
| 631 |
+
self.post_init()
|
| 632 |
+
|
| 633 |
+
def forward(
|
| 634 |
+
self,
|
| 635 |
+
input_ids: Optional[torch.LongTensor] = None,
|
| 636 |
+
attention_mask: Optional[torch.Tensor] = None,
|
| 637 |
+
position_ids: Optional[torch.LongTensor] = None,
|
| 638 |
+
inputs_embeds: Optional[torch.FloatTensor] = None,
|
| 639 |
+
labels: Optional[torch.LongTensor] = None,
|
| 640 |
+
**kwargs: Unpack[TransformersKwargs],
|
| 641 |
+
) -> TokenClassifierOutput:
|
| 642 |
+
"""Forward pass for the token classification head.
|
| 643 |
+
|
| 644 |
+
labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
|
| 645 |
+
Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
|
| 646 |
+
"""
|
| 647 |
+
outputs = self.esm(
|
| 648 |
+
input_ids,
|
| 649 |
+
attention_mask=attention_mask,
|
| 650 |
+
position_ids=position_ids,
|
| 651 |
+
inputs_embeds=inputs_embeds,
|
| 652 |
+
**kwargs,
|
| 653 |
+
)
|
| 654 |
+
|
| 655 |
+
sequence_output = outputs[0]
|
| 656 |
+
|
| 657 |
+
sequence_output = self.dropout(sequence_output)
|
| 658 |
+
logits = self.classifier(sequence_output)
|
| 659 |
+
|
| 660 |
+
loss = None
|
| 661 |
+
if labels is not None:
|
| 662 |
+
loss_fct = CrossEntropyLoss()
|
| 663 |
+
|
| 664 |
+
labels = labels.to(logits.device)
|
| 665 |
+
loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
|
| 666 |
+
|
| 667 |
+
return TokenClassifierOutput(
|
| 668 |
+
loss=loss,
|
| 669 |
+
logits=logits,
|
| 670 |
+
hidden_states=outputs.hidden_states,
|
| 671 |
+
attentions=outputs.attentions,
|
| 672 |
+
)
|
special_tokens_map.json
CHANGED
|
@@ -1,7 +1,44 @@
|
|
| 1 |
{
|
| 2 |
-
"
|
| 3 |
-
|
| 4 |
-
|
| 5 |
-
|
| 6 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 7 |
}
|
|
|
|
| 1 |
{
|
| 2 |
+
"bos_token": {
|
| 3 |
+
"content": "<cls>",
|
| 4 |
+
"lstrip": false,
|
| 5 |
+
"normalized": false,
|
| 6 |
+
"rstrip": false,
|
| 7 |
+
"single_word": false
|
| 8 |
+
},
|
| 9 |
+
"cls_token": {
|
| 10 |
+
"content": "<cls>",
|
| 11 |
+
"lstrip": false,
|
| 12 |
+
"normalized": false,
|
| 13 |
+
"rstrip": false,
|
| 14 |
+
"single_word": false
|
| 15 |
+
},
|
| 16 |
+
"eos_token": {
|
| 17 |
+
"content": "<eos>",
|
| 18 |
+
"lstrip": false,
|
| 19 |
+
"normalized": false,
|
| 20 |
+
"rstrip": false,
|
| 21 |
+
"single_word": false
|
| 22 |
+
},
|
| 23 |
+
"mask_token": {
|
| 24 |
+
"content": "<mask>",
|
| 25 |
+
"lstrip": false,
|
| 26 |
+
"normalized": false,
|
| 27 |
+
"rstrip": false,
|
| 28 |
+
"single_word": false
|
| 29 |
+
},
|
| 30 |
+
"pad_token": {
|
| 31 |
+
"content": "<pad>",
|
| 32 |
+
"lstrip": false,
|
| 33 |
+
"normalized": false,
|
| 34 |
+
"rstrip": false,
|
| 35 |
+
"single_word": false
|
| 36 |
+
},
|
| 37 |
+
"unk_token": {
|
| 38 |
+
"content": "<unk>",
|
| 39 |
+
"lstrip": false,
|
| 40 |
+
"normalized": false,
|
| 41 |
+
"rstrip": false,
|
| 42 |
+
"single_word": false
|
| 43 |
+
}
|
| 44 |
}
|
tokenizer.json
ADDED
|
@@ -0,0 +1,176 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
| 1 |
+
{
|
| 2 |
+
"version": "1.0",
|
| 3 |
+
"truncation": null,
|
| 4 |
+
"padding": null,
|
| 5 |
+
"added_tokens": [
|
| 6 |
+
{
|
| 7 |
+
"id": 0,
|
| 8 |
+
"content": "<cls>",
|
| 9 |
+
"single_word": false,
|
| 10 |
+
"lstrip": false,
|
| 11 |
+
"rstrip": false,
|
| 12 |
+
"normalized": false,
|
| 13 |
+
"special": true
|
| 14 |
+
},
|
| 15 |
+
{
|
| 16 |
+
"id": 1,
|
| 17 |
+
"content": "<pad>",
|
| 18 |
+
"single_word": false,
|
| 19 |
+
"lstrip": false,
|
| 20 |
+
"rstrip": false,
|
| 21 |
+
"normalized": false,
|
| 22 |
+
"special": true
|
| 23 |
+
},
|
| 24 |
+
{
|
| 25 |
+
"id": 2,
|
| 26 |
+
"content": "<eos>",
|
| 27 |
+
"single_word": false,
|
| 28 |
+
"lstrip": false,
|
| 29 |
+
"rstrip": false,
|
| 30 |
+
"normalized": false,
|
| 31 |
+
"special": true
|
| 32 |
+
},
|
| 33 |
+
{
|
| 34 |
+
"id": 3,
|
| 35 |
+
"content": "<unk>",
|
| 36 |
+
"single_word": false,
|
| 37 |
+
"lstrip": false,
|
| 38 |
+
"rstrip": false,
|
| 39 |
+
"normalized": false,
|
| 40 |
+
"special": true
|
| 41 |
+
},
|
| 42 |
+
{
|
| 43 |
+
"id": 32,
|
| 44 |
+
"content": "<mask>",
|
| 45 |
+
"single_word": false,
|
| 46 |
+
"lstrip": false,
|
| 47 |
+
"rstrip": false,
|
| 48 |
+
"normalized": false,
|
| 49 |
+
"special": true
|
| 50 |
+
}
|
| 51 |
+
],
|
| 52 |
+
"normalizer": null,
|
| 53 |
+
"pre_tokenizer": {
|
| 54 |
+
"type": "Split",
|
| 55 |
+
"pattern": {
|
| 56 |
+
"String": ""
|
| 57 |
+
},
|
| 58 |
+
"behavior": "Isolated",
|
| 59 |
+
"invert": false
|
| 60 |
+
},
|
| 61 |
+
"post_processor": {
|
| 62 |
+
"type": "TemplateProcessing",
|
| 63 |
+
"single": [
|
| 64 |
+
{
|
| 65 |
+
"SpecialToken": {
|
| 66 |
+
"id": "<cls>",
|
| 67 |
+
"type_id": 0
|
| 68 |
+
}
|
| 69 |
+
},
|
| 70 |
+
{
|
| 71 |
+
"Sequence": {
|
| 72 |
+
"id": "A",
|
| 73 |
+
"type_id": 0
|
| 74 |
+
}
|
| 75 |
+
},
|
| 76 |
+
{
|
| 77 |
+
"SpecialToken": {
|
| 78 |
+
"id": "<eos>",
|
| 79 |
+
"type_id": 0
|
| 80 |
+
}
|
| 81 |
+
}
|
| 82 |
+
],
|
| 83 |
+
"pair": [
|
| 84 |
+
{
|
| 85 |
+
"SpecialToken": {
|
| 86 |
+
"id": "<cls>",
|
| 87 |
+
"type_id": 0
|
| 88 |
+
}
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"Sequence": {
|
| 92 |
+
"id": "A",
|
| 93 |
+
"type_id": 0
|
| 94 |
+
}
|
| 95 |
+
},
|
| 96 |
+
{
|
| 97 |
+
"SpecialToken": {
|
| 98 |
+
"id": "<eos>",
|
| 99 |
+
"type_id": 0
|
| 100 |
+
}
|
| 101 |
+
},
|
| 102 |
+
{
|
| 103 |
+
"Sequence": {
|
| 104 |
+
"id": "B",
|
| 105 |
+
"type_id": 1
|
| 106 |
+
}
|
| 107 |
+
},
|
| 108 |
+
{
|
| 109 |
+
"SpecialToken": {
|
| 110 |
+
"id": "<eos>",
|
| 111 |
+
"type_id": 1
|
| 112 |
+
}
|
| 113 |
+
}
|
| 114 |
+
],
|
| 115 |
+
"special_tokens": {
|
| 116 |
+
"<cls>": {
|
| 117 |
+
"id": "<cls>",
|
| 118 |
+
"ids": [
|
| 119 |
+
0
|
| 120 |
+
],
|
| 121 |
+
"tokens": [
|
| 122 |
+
"<cls>"
|
| 123 |
+
]
|
| 124 |
+
},
|
| 125 |
+
"<eos>": {
|
| 126 |
+
"id": "<eos>",
|
| 127 |
+
"ids": [
|
| 128 |
+
2
|
| 129 |
+
],
|
| 130 |
+
"tokens": [
|
| 131 |
+
"<eos>"
|
| 132 |
+
]
|
| 133 |
+
}
|
| 134 |
+
}
|
| 135 |
+
},
|
| 136 |
+
"decoder": null,
|
| 137 |
+
"model": {
|
| 138 |
+
"type": "WordLevel",
|
| 139 |
+
"vocab": {
|
| 140 |
+
"<cls>": 0,
|
| 141 |
+
"<pad>": 1,
|
| 142 |
+
"<eos>": 2,
|
| 143 |
+
"<unk>": 3,
|
| 144 |
+
"L": 4,
|
| 145 |
+
"A": 5,
|
| 146 |
+
"G": 6,
|
| 147 |
+
"V": 7,
|
| 148 |
+
"S": 8,
|
| 149 |
+
"E": 9,
|
| 150 |
+
"R": 10,
|
| 151 |
+
"T": 11,
|
| 152 |
+
"I": 12,
|
| 153 |
+
"D": 13,
|
| 154 |
+
"P": 14,
|
| 155 |
+
"K": 15,
|
| 156 |
+
"Q": 16,
|
| 157 |
+
"N": 17,
|
| 158 |
+
"F": 18,
|
| 159 |
+
"Y": 19,
|
| 160 |
+
"M": 20,
|
| 161 |
+
"H": 21,
|
| 162 |
+
"W": 22,
|
| 163 |
+
"C": 23,
|
| 164 |
+
"X": 24,
|
| 165 |
+
"B": 25,
|
| 166 |
+
"U": 26,
|
| 167 |
+
"Z": 27,
|
| 168 |
+
"O": 28,
|
| 169 |
+
".": 29,
|
| 170 |
+
"-": 30,
|
| 171 |
+
"<null_1>": 31,
|
| 172 |
+
"<mask>": 32
|
| 173 |
+
},
|
| 174 |
+
"unk_token": "<unk>"
|
| 175 |
+
}
|
| 176 |
+
}
|
tokenizer_config.json
CHANGED
|
@@ -1,4 +1,6 @@
|
|
| 1 |
{
|
|
|
|
|
|
|
| 2 |
"added_tokens_decoder": {
|
| 3 |
"0": {
|
| 4 |
"content": "<cls>",
|
|
@@ -41,13 +43,18 @@
|
|
| 41 |
"special": true
|
| 42 |
}
|
| 43 |
},
|
|
|
|
| 44 |
"clean_up_tokenization_spaces": false,
|
| 45 |
"cls_token": "<cls>",
|
| 46 |
"eos_token": "<eos>",
|
| 47 |
"extra_special_tokens": {},
|
| 48 |
"mask_token": "<mask>",
|
|
|
|
|
|
|
|
|
|
|
|
|
| 49 |
"model_max_length": 1000000000000000019884624838656,
|
| 50 |
"pad_token": "<pad>",
|
| 51 |
-
"tokenizer_class": "
|
| 52 |
"unk_token": "<unk>"
|
| 53 |
}
|
|
|
|
| 1 |
{
|
| 2 |
+
"add_bos_token": true,
|
| 3 |
+
"add_eos_token": true,
|
| 4 |
"added_tokens_decoder": {
|
| 5 |
"0": {
|
| 6 |
"content": "<cls>",
|
|
|
|
| 43 |
"special": true
|
| 44 |
}
|
| 45 |
},
|
| 46 |
+
"bos_token": "<cls>",
|
| 47 |
"clean_up_tokenization_spaces": false,
|
| 48 |
"cls_token": "<cls>",
|
| 49 |
"eos_token": "<eos>",
|
| 50 |
"extra_special_tokens": {},
|
| 51 |
"mask_token": "<mask>",
|
| 52 |
+
"model_input_names": [
|
| 53 |
+
"input_ids",
|
| 54 |
+
"attention_mask"
|
| 55 |
+
],
|
| 56 |
"model_max_length": 1000000000000000019884624838656,
|
| 57 |
"pad_token": "<pad>",
|
| 58 |
+
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 59 |
"unk_token": "<unk>"
|
| 60 |
}
|