reorganise rnabert

multimolecule/models/__init__.py

@@ -1,3 +1,17 @@
-from .rnabert import RnaBertConfig, RnaBertModel, RnaTokenizer
+from .rnabert import (
+    RnaBertConfig,
+    RnaBertForMaskedLM,
+    RnaBertForSequenceClassification,
+    RnaBertForTokenClassification,
+    RnaBertModel,
+    RnaTokenizer,
+)
 
-__all__ = ["RnaBertConfig", "RnaBertModel", "RnaTokenizer"]
+__all__ = [
+    "RnaBertConfig",
+    "RnaBertModel",
+    "RnaBertForMaskedLM",
+    "RnaBertForSequenceClassification",
+    "RnaBertForTokenClassification",
+    "RnaTokenizer",
+]

multimolecule/models/modeling_utils.py

@@ -0,0 +1,230 @@
+from typing import Optional, Tuple, Union
+
+import torch
+from chanfig import ConfigRegistry
+from torch import nn
+from torch.nn import functional as F
+from transformers.activations import ACT2FN
+from transformers.modeling_outputs import MaskedLMOutput, SequenceClassifierOutput, TokenClassifierOutput
+
+
+class MaskedLMHead(nn.Module):
+    """Head for masked language modeling."""
+
+    def __init__(self, config):
+        super().__init__()
+        if "proj_head_mode" not in dir(config) or config.proj_head_mode is None:
+            config.proj_head_mode = "none"
+        self.transform = PredictionHeadTransform.build(config)
+        self.decoder = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
+        self.bias = nn.Parameter(torch.zeros(config.vocab_size))
+        self.decoder.bias = self.bias
+
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        encoder_hidden_states: Optional[torch.Tensor] = None,
+        encoder_attention_mask: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], MaskedLMOutput]:
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+        x = self.transform(sequence_output)
+        prediction_scores = self.decoder(x)
+
+        masked_lm_loss = None
+        if labels is not None:
+            masked_lm_loss = F.cross_entropy(prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
+
+        if not return_dict:
+            output = (prediction_scores,) + outputs[2:]
+            return ((masked_lm_loss,) + output) if masked_lm_loss is not None else output
+
+        return MaskedLMOutput(
+            loss=masked_lm_loss,
+            logits=prediction_scores,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+class SequenceClassificationHead(nn.Module):
+    """Head for sequence-level classification tasks."""
+
+    num_labels: int
+
+    def __init__(self, config):
+        super().__init__()
+        if "proj_head_mode" not in dir(config) or config.proj_head_mode is None:
+            config.proj_head_mode = "none"
+        self.num_labels = config.num_labels
+        self.transform = PredictionHeadTransform.build(config)
+        classifier_dropout = (
+            config.classifier_dropout
+            if "classifier_dropout" in dir(config) and config.classifier_dropout is not None
+            else config.hidden_dropout_prob
+        )
+        self.dropout = nn.Dropout(classifier_dropout)
+        self.decoder = nn.Linear(config.hidden_size, self.num_labels, bias=False)
+
+    def forward(
+        self, outputs, labels: Optional[torch.Tensor] = None, return_dict: Optional[bool] = None
+    ) -> Union[Tuple, SequenceClassifierOutput]:
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+        sequence_output = outputs.last_hidden_state if return_dict else outputs[0]
+        x = self.dropout(sequence_output)
+        x = self.transform(x)
+        logits = self.decoder(x)
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+            if self.config.problem_type == "regression":
+                loss = (
+                    F.mse_loss(logits.squeeze(), labels.squeeze())
+                    if self.num_labels == 1
+                    else F.mse_loss(logits, labels)
+                )
+            elif self.config.problem_type == "single_label_classification":
+                loss = F.cross_entropy(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss = F.binary_cross_entropy_with_logits(logits, labels)
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return SequenceClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+class TokenClassificationHead(nn.Module):
+    """Head for token-level classification tasks."""
+
+    num_labels: int
+
+    def __init__(self, config):
+        if "proj_head_mode" not in dir(config) or config.proj_head_mode is None:
+            config.proj_head_mode = "none"
+        super().__init__()
+        self.num_labels = config.num_labels
+        self.transform = PredictionHeadTransform.build(config)
+        classifier_dropout = (
+            config.classifier_dropout
+            if "classifier_dropout" in dir(config) and config.classifier_dropout is not None
+            else config.hidden_dropout_prob
+        )
+        self.dropout = nn.Dropout(classifier_dropout)
+        self.decoder = nn.Linear(config.hidden_size, self.num_labels, bias=False)
+
+    def forward(
+        self, outputs, labels: Optional[torch.Tensor] = None, return_dict: Optional[bool] = None
+    ) -> Union[Tuple, TokenClassifierOutput]:
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+        token_output = outputs.pooled_output if return_dict else outputs[1]
+        x = self.dropout(token_output)
+        x = self.transform(x)
+        logits = self.decoder(x)
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+            if self.config.problem_type == "regression":
+                loss = (
+                    F.mse_loss(logits.squeeze(), labels.squeeze())
+                    if self.num_labels == 1
+                    else F.mse_loss(logits, labels)
+                )
+            elif self.config.problem_type == "single_label_classification":
+                loss = F.cross_entropy(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss = F.binary_cross_entropy_with_logits(logits, labels)
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TokenClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+PredictionHeadTransform = ConfigRegistry(key="proj_head_mode")
+
+
+@PredictionHeadTransform.register("nonlinear")
+class NonLinearTransform(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        if isinstance(config.hidden_act, str):
+            self.transform_act_fn = ACT2FN[config.hidden_act]
+        else:
+            self.transform_act_fn = config.hidden_act
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.transform_act_fn(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states)
+        return hidden_states
+
+
+@PredictionHeadTransform.register("linear")
+class LinearTransform(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size, bias=False)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states)
+        return hidden_states
+
+
+@PredictionHeadTransform.register("none")
+class IdentityTransform(nn.Identity):
+    def __init__(self, config):
+        super().__init__()

multimolecule/models/rnabert/__init__.py

@@ -1,12 +1,36 @@
-from transformers import AutoConfig, AutoModel, AutoTokenizer
+from transformers import (
+    AutoConfig,
+    AutoModel,
+    AutoModelForMaskedLM,
+    AutoModelForSequenceClassification,
+    AutoModelForTokenClassification,
+    AutoModelWithLMHead,
+    AutoTokenizer,
+)
 
 from multimolecule.tokenizers.rna import RnaTokenizer
 
 from .configuration_rnabert import RnaBertConfig
-from .modeling_rnabert import RnaBertModel
+from .modeling_rnabert import (
+    RnaBertForMaskedLM,
+    RnaBertForSequenceClassification,
+    RnaBertForTokenClassification,
+    RnaBertModel,
+)
 
-__all__ = ["RnaBertConfig", "RnaBertModel", "RnaTokenizer"]
+__all__ = [
+    "RnaBertConfig",
+    "RnaBertModel",
+    "RnaTokenizer",
+    "RnaBertForMaskedLM",
+    "RnaBertForSequenceClassification",
+    "RnaBertForTokenClassification",
+]
 
 AutoConfig.register("rnabert", RnaBertConfig)
 AutoModel.register(RnaBertConfig, RnaBertModel)
+AutoModelForMaskedLM.register(RnaBertConfig, RnaBertForMaskedLM)
+AutoModelForSequenceClassification.register(RnaBertConfig, RnaBertForSequenceClassification)
+AutoModelForTokenClassification.register(RnaBertConfig, RnaBertForTokenClassification)
+AutoModelWithLMHead.register(RnaBertConfig, RnaBertForTokenClassification)
 AutoTokenizer.register(RnaBertConfig, RnaTokenizer)

multimolecule/models/rnabert/configuration_rnabert.py

@@ -9,7 +9,7 @@ class RnaBertConfig(PretrainedConfig):
     This is the configuration class to store the configuration of a [`RnaBertModel`]. It is used to instantiate a
     RnaBert model according to the specified arguments, defining the model architecture. Instantiating a configuration
     with the defaults will yield a similar configuration to that of the RnaBert
-    [mana438/RNABERT](https://github.com/mana438/RNABERT/blob/master/RNA_bert_config.json) architecture.
+    [mana438/RNABERT](https://github.com/mana438/RNABERT) architecture.
 
     Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
     documentation from [`PretrainedConfig`] for more information.
@@ -55,7 +55,8 @@ class RnaBertConfig(PretrainedConfig):
     >>> # Initializing a model from the configuration >>> model = RnaBertModel(configuration)
 
     >>> # Accessing the model configuration >>> configuration = model.config
-    ```"""
+    ```
+    """
 
     model_type = "rnabert"
 
@@ -77,6 +78,8 @@ def __init__(
         pad_token_id=0,
         position_embedding_type="absolute",
         use_cache=True,
+        classifier_dropout=None,
+        proj_head_mode="nonlinear",
         **kwargs,
     ):
         super().__init__(pad_token_id=pad_token_id, **kwargs)
@@ -97,3 +100,5 @@ def __init__(
         self.layer_norm_eps = layer_norm_eps
         self.position_embedding_type = position_embedding_type
         self.use_cache = use_cache
+        self.classifier_dropout = classifier_dropout
+        self.proj_head_mode = proj_head_mode

multimolecule/models/rnabert/convert_checkpoint.py

@@ -6,7 +6,7 @@
 import torch
 from torch import nn
 
-from multimolecule.models import RnaBertConfig, RnaBertModel
+from multimolecule.models import RnaBertConfig, RnaBertForMaskedLM
 from multimolecule.tokenizers.rna.config import get_special_tokens_map, get_tokenizer_config, get_vocab_list
 
 CONFIG = {
@@ -19,7 +19,6 @@
     "max_position_embeddings": 440,
     "num_attention_heads": 12,
     "num_hidden_layers": 6,
-    "vocab_size": 25,
     "ss_vocab_size": 8,
     "type_vocab_size": 2,
     "pad_token_id": 0,
@@ -33,27 +32,41 @@ def convert_checkpoint(checkpoint_path: str, output_path: Optional[str] = None):
     if output_path is None:
         output_path = "rnabert"
     config = RnaBertConfig.from_dict(chanfig.FlatDict(CONFIG))
+    config.vocab_size = len(vocab_list)
     ckpt = torch.load(checkpoint_path, map_location=torch.device("cpu"))
     bert_state_dict = ckpt
     state_dict = {}
 
-    model = RnaBertModel(config)
+    model = RnaBertForMaskedLM(config)
 
     for key, value in bert_state_dict.items():
-        if key.startswith("module.cls"):
-            continue
-        key = key[12:]
+        key = key[7:]
         key = key.replace("gamma", "weight")
         key = key.replace("beta", "bias")
-        state_dict[key] = value
+        if key.startswith("bert"):
+            state_dict["rna" + key] = value
+            continue
+        if key.startswith("cls"):
+            # import ipdb; ipdb.set_trace()
+            key = "lm_head." + key[4:]
+            # key = key[4:]
+            state_dict[key] = value
+            continue
 
     word_embed = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
+    word_embed_weight = word_embed.weight.data
+    predictions_bias = torch.zeros(config.vocab_size)
+    predictions_decoder_weight = torch.zeros((config.vocab_size, config.hidden_size))
     # nn.init.normal_(pos_embed.weight, std=0.02)
     for original_token, new_token in zip(original_vocab_list, vocab_list):
         original_index = original_vocab_list.index(original_token)
         new_index = vocab_list.index(new_token)
-        word_embed.weight.data[new_index] = state_dict["embeddings.word_embeddings.weight"][original_index]
-    state_dict["embeddings.word_embeddings.weight"] = word_embed.weight.data
+        word_embed_weight[new_index] = state_dict["rnabert.embeddings.word_embeddings.weight"][original_index]
+        predictions_bias[new_index] = state_dict["lm_head.predictions.bias"][original_index]
+        predictions_decoder_weight[new_index] = state_dict["lm_head.predictions.decoder.weight"][original_index]
+    state_dict["rnabert.embeddings.word_embeddings.weight"] = word_embed_weight
+    state_dict["lm_head.predictions.bias"] = predictions_bias
+    state_dict["lm_head.predictions.decoder.weight"] = predictions_decoder_weight
 
     model.load_state_dict(state_dict)
     model.save_pretrained(output_path, safe_serialization=True)