跳转至

RNABERT

Pre-trained model on non-coding RNA (ncRNA) using masked language modeling (MLM) and structural alignment learning (SAL) objectives.

Disclaimer

This is an UNOFFICIAL implementation of the Informative RNA-base embedding for functional RNA clustering and structural alignment by Manato Akiyama and Yasubumi Sakakibara.

The OFFICIAL repository of RNABERT is at mana438/RNABERT.

Caution

The MultiMolecule team is aware of a potential risk in reproducing the results of RNABERT.

The original implementation of RNABERT does not prepend <cls> and append <eos> tokens to the input sequence. This should not affect the performance of the model in most cases, but it can lead to unexpected behavior in some cases.

Please set cls_token=None and eos_token=None explicitly in the tokenizer if you want the exact behavior of the original implementation.

Tip

The MultiMolecule team has confirmed that the provided model and checkpoints are producing the same intermediate representations as the original implementation.

The team releasing RNABERT did not write this model card for this model so this model card has been written by the MultiMolecule team.

Model Details

RNABERT is a bert-style model pre-trained on a large corpus of non-coding RNA sequences in a self-supervised fashion. This means that the model was trained on the raw nucleotides of RNA sequences only, with an automatic process to generate inputs and labels from those texts. Please refer to the Training Details section for more information on the training process.

Model Specification

Num Layers Hidden Size Num Heads Intermediate Size Num Parameters (M) FLOPs (G) MACs (G) Max Num Tokens
6 120 12 40 0.48 0.15 0.08 440

Usage

The model file depends on the multimolecule library. You can install it using pip:

Bash
1
pip install multimolecule

Direct Use

You can use this model directly with a pipeline for masked language modeling:

Python
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
>>> import multimolecule  # you must import multimolecule to register models
>>> from transformers import pipeline
>>> unmasker = pipeline('fill-mask', model='multimolecule/rnabert')
>>> unmasker("uagc<mask>uaucagacugauguuga")

[{'score': 0.0385337695479393,
  'token': 10,
  'token_str': 'N',
  'sequence': 'U A G C N U A U C A G A C U G A U G U U G A'},
 {'score': 0.03851701319217682,
  'token': 25,
  'token_str': 'I',
  'sequence': 'U A G C I U A U C A G A C U G A U G U U G A'},
 {'score': 0.03850541263818741,
  'token': 3,
  'token_str': '<unk>',
  'sequence': 'U A G C U A U C A G A C U G A U G U U G A'},
 {'score': 0.03850402310490608,
  'token': 5,
  'token_str': '<null>',
  'sequence': 'U A G C U A U C A G A C U G A U G U U G A'},
 {'score': 0.03848475590348244,
  'token': 1,
  'token_str': '<cls>',
  'sequence': 'U A G C U A U C A G A C U G A U G U U G A'}]

Downstream Use

Extract Features

Here is how to use this model to get the features of a given sequence in PyTorch:

Python
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
from multimolecule import RnaTokenizer, RnaBertModel


tokenizer = RnaTokenizer.from_pretrained('multimolecule/rnabert')
model = RnaBertModel.from_pretrained('multimolecule/rnabert')

text = "UAGCUUAUCAGACUGAUGUUGA"
input = tokenizer(text, return_tensors='pt')

output = model(**input)

Sequence Classification / Regression

Note: This model is not fine-tuned for any specific task. You will need to fine-tune the model on a downstream task to use it for sequence classification or regression.

Here is how to use this model as backbone to fine-tune for a sequence-level task in PyTorch:

Python
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
import torch
from multimolecule import RnaTokenizer, RnaBertForSequencePrediction


tokenizer = RnaTokenizer.from_pretrained('multimolecule/rnabert')
model = RnaBertForSequencePrediction.from_pretrained('multimolecule/rnabert')

text = "UAGCUUAUCAGACUGAUGUUGA"
input = tokenizer(text, return_tensors='pt')
label = torch.tensor([1])

output = model(**input, labels=label)

Nucleotide Classification / Regression

Note: This model is not fine-tuned for any specific task. You will need to fine-tune the model on a downstream task to use it for nucleotide classification or regression.

Here is how to use this model as backbone to fine-tune for a nucleotide-level task in PyTorch:

Python
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
import torch
from multimolecule import RnaTokenizer, RnaBertForNucleotidePrediction


tokenizer = RnaTokenizer.from_pretrained('multimolecule/rnabert')
model = RnaBertForNucleotidePrediction.from_pretrained('multimolecule/rnabert')

text = "UAGCUUAUCAGACUGAUGUUGA"
input = tokenizer(text, return_tensors='pt')
label = torch.randint(2, (len(text), ))

output = model(**input, labels=label)

Contact Classification / Regression

Note: This model is not fine-tuned for any specific task. You will need to fine-tune the model on a downstream task to use it for contact classification or regression.

Here is how to use this model as backbone to fine-tune for a contact-level task in PyTorch:

Python
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
import torch
from multimolecule import RnaTokenizer, RnaBertForContactPrediction


tokenizer = RnaTokenizer.from_pretrained('multimolecule/rnabert')
model = RnaBertForContactPrediction.from_pretrained('multimolecule/rnabert')

text = "UAGCUUAUCAGACUGAUGUUGA"
input = tokenizer(text, return_tensors='pt')
label = torch.randint(2, (len(text), len(text)))

output = model(**input, labels=label)

Training Details

RNABERT has two pre-training objectives: masked language modeling (MLM) and structural alignment learning (SAL).

  • Masked Language Modeling (MLM): taking a sequence, the model randomly masks 15% of the tokens in the input then runs the entire masked sentence through the model and has to predict the masked tokens. This is comparable to the Cloze task in language modeling.
  • Structural Alignment Learning (SAL): the model learns to predict the structural alignment of two RNA sequences. The model is trained to predict the alignment score of two RNA sequences using the Needleman-Wunsch algorithm.

Training Data

The RNABERT model was pre-trained on RNAcentral. RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types.

RNABERT used a subset of 76, 237 human ncRNA sequences from RNAcentral for pre-training. RNABERT preprocessed all tokens by replacing “U”s with “T”s.

Note that during model conversions, “T” is replaced with “U”. RnaTokenizer will convert “T”s to “U”s for you, you may disable this behaviour by passing replace_T_with_U=False.

Training Procedure

Preprocessing

RNABERT preprocess the dataset by applying 10 different mask patterns to the 72, 237 human ncRNA sequences. The final dataset contains 722, 370 sequences. The masking procedure is similar to the one used in BERT:

  • 15% of the tokens are masked.
  • In 80% of the cases, the masked tokens are replaced by <mask>.
  • In 10% of the cases, the masked tokens are replaced by a random token (different) from the one they replace.
  • In the 10% remaining cases, the masked tokens are left as is.

PreTraining

The model was trained on 1 NVIDIA V100 GPU.

Citation

BibTeX:

BibTeX
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
@article{akiyama2022informative,
    author = {Akiyama, Manato and Sakakibara, Yasubumi},
    title = "{Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning}",
    journal = {NAR Genomics and Bioinformatics},
    volume = {4},
    number = {1},
    pages = {lqac012},
    year = {2022},
    month = {02},
    abstract = "{Effective embedding is actively conducted by applying deep learning to biomolecular information. Obtaining better embeddings enhances the quality of downstream analyses, such as DNA sequence motif detection and protein function prediction. In this study, we adopt a pre-training algorithm for the effective embedding of RNA bases to acquire semantically rich representations and apply this algorithm to two fundamental RNA sequence problems: structural alignment and clustering. By using the pre-training algorithm to embed the four bases of RNA in a position-dependent manner using a large number of RNA sequences from various RNA families, a context-sensitive embedding representation is obtained. As a result, not only base information but also secondary structure and context information of RNA sequences are embedded for each base. We call this ‘informative base embedding’ and use it to achieve accuracies superior to those of existing state-of-the-art methods on RNA structural alignment and RNA family clustering tasks. Furthermore, upon performing RNA sequence alignment by combining this informative base embedding with a simple Needleman–Wunsch alignment algorithm, we succeed in calculating structural alignments with a time complexity of O(n2) instead of the O(n6) time complexity of the naive implementation of Sankoff-style algorithm for input RNA sequence of length n.}",
    issn = {2631-9268},
    doi = {10.1093/nargab/lqac012},
    url = {https://doi.org/10.1093/nargab/lqac012},
    eprint = {https://academic.oup.com/nargab/article-pdf/4/1/lqac012/42577168/lqac012.pdf},
}

Contact

Please use GitHub issues of MultiMolecule for any questions or comments on the model card.

Please contact the authors of the RNABERT paper for questions or comments on the paper/model.

License

This model is licensed under the AGPL-3.0 License.

Text Only
1
SPDX-License-Identifier: AGPL-3.0-or-later

multimolecule.models.rnabert

RnaTokenizer

Bases: Tokenizer

Tokenizer for RNA sequences.

Parameters:

Name Type Description Default
alphabet Alphabet | str | List[str] | None

alphabet to use for tokenization.

  • If is None, the standard RNA alphabet will be used.
  • If is a string, it should correspond to the name of a predefined alphabet. The options include
    • standard
    • extended
    • streamline
    • nucleobase
  • If is an alphabet or a list of characters, that specific alphabet will be used.
 None
nmers int

Size of kmer to tokenize.

 1
codon bool

Whether to tokenize into codons.

 False
replace_T_with_U bool

Whether to replace T with U.

 True
do_upper_case bool

Whether to convert input to uppercase.

 True

Examples:

Python Console Session
>>> from multimolecule import RnaTokenizer
>>> tokenizer = RnaTokenizer()
>>> tokenizer('<pad><cls><eos><unk><mask><null>ACGUNRYSWKMBDHV.X*-I')["input_ids"]
[1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 2]
>>> tokenizer('acgu')["input_ids"]
[1, 6, 7, 8, 9, 2]
>>> tokenizer('acgt')["input_ids"]
[1, 6, 7, 8, 9, 2]
>>> tokenizer = RnaTokenizer(replace_T_with_U=False)
>>> tokenizer('acgt')["input_ids"]
[1, 6, 7, 8, 3, 2]
>>> tokenizer = RnaTokenizer(nmers=3)
>>> tokenizer('uagcuuauc')["input_ids"]
[1, 83, 17, 64, 49, 96, 84, 22, 2]
>>> tokenizer = RnaTokenizer(codon=True)
>>> tokenizer('uagcuuauc')["input_ids"]
[1, 83, 49, 22, 2]
>>> tokenizer('uagcuuauca')["input_ids"]
Traceback (most recent call last):
ValueError: length of input sequence must be a multiple of 3 for codon tokenization, but got 10
Source code in multimolecule/tokenisers/rna/tokenization_rna.py
Python
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
class RnaTokenizer(Tokenizer):
    """
    Tokenizer for RNA sequences.

    Args:
        alphabet: alphabet to use for tokenization.

            - If is `None`, the standard RNA alphabet will be used.
            - If is a `string`, it should correspond to the name of a predefined alphabet. The options include
                + `standard`
                + `extended`
                + `streamline`
                + `nucleobase`
            - If is an alphabet or a list of characters, that specific alphabet will be used.
        nmers: Size of kmer to tokenize.
        codon: Whether to tokenize into codons.
        replace_T_with_U: Whether to replace T with U.
        do_upper_case: Whether to convert input to uppercase.

    Examples:
        >>> from multimolecule import RnaTokenizer
        >>> tokenizer = RnaTokenizer()
        >>> tokenizer('<pad><cls><eos><unk><mask><null>ACGUNRYSWKMBDHV.X*-I')["input_ids"]
        [1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 2]
        >>> tokenizer('acgu')["input_ids"]
        [1, 6, 7, 8, 9, 2]
        >>> tokenizer('acgt')["input_ids"]
        [1, 6, 7, 8, 9, 2]
        >>> tokenizer = RnaTokenizer(replace_T_with_U=False)
        >>> tokenizer('acgt')["input_ids"]
        [1, 6, 7, 8, 3, 2]
        >>> tokenizer = RnaTokenizer(nmers=3)
        >>> tokenizer('uagcuuauc')["input_ids"]
        [1, 83, 17, 64, 49, 96, 84, 22, 2]
        >>> tokenizer = RnaTokenizer(codon=True)
        >>> tokenizer('uagcuuauc')["input_ids"]
        [1, 83, 49, 22, 2]
        >>> tokenizer('uagcuuauca')["input_ids"]
        Traceback (most recent call last):
        ValueError: length of input sequence must be a multiple of 3 for codon tokenization, but got 10
    """

    model_input_names = ["input_ids", "attention_mask"]

    def __init__(
        self,
        alphabet: Alphabet | str | List[str] | None = None,
        nmers: int = 1,
        codon: bool = False,
        replace_T_with_U: bool = True,
        do_upper_case: bool = True,
        additional_special_tokens: List | Tuple | None = None,
        **kwargs,
    ):
        if codon and (nmers > 1 and nmers != 3):
            raise ValueError("Codon and nmers cannot be used together.")
        if codon:
            nmers = 3  # set to 3 to get correct vocab
        if not isinstance(alphabet, Alphabet):
            alphabet = get_alphabet(alphabet, nmers=nmers)
        super().__init__(
            alphabet=alphabet,
            nmers=nmers,
            codon=codon,
            replace_T_with_U=replace_T_with_U,
            do_upper_case=do_upper_case,
            additional_special_tokens=additional_special_tokens,
            **kwargs,
        )
        self.replace_T_with_U = replace_T_with_U
        self.nmers = nmers
        self.condon = codon

    def _tokenize(self, text: str, **kwargs):
        if self.do_upper_case:
            text = text.upper()
        if self.replace_T_with_U:
            text = text.replace("T", "U")
        if self.condon:
            if len(text) % 3 != 0:
                raise ValueError(
                    f"length of input sequence must be a multiple of 3 for codon tokenization, but got {len(text)}"
                )
            return [text[i : i + 3] for i in range(0, len(text), 3)]
        if self.nmers > 1:
            return [text[i : i + self.nmers] for i in range(len(text) - self.nmers + 1)]  # noqa: E203
        return list(text)

RnaBertConfig

Bases: 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 architecture.

Configuration objects inherit from PreTrainedConfig and can be used to control the model outputs. Read the documentation from PreTrainedConfig for more information.

Parameters:

Name Type Description Default
vocab_size int

Vocabulary size of the RnaBert model. Defines the number of different tokens that can be represented by the inputs_ids passed when calling [RnaBertModel].

 26
hidden_size int | None

Dimensionality of the encoder layers and the pooler layer.

 None
num_hidden_layers int

Number of hidden layers in the Transformer encoder.

 6
num_attention_heads int

Number of attention heads for each attention layer in the Transformer encoder.

 12
intermediate_size int

Dimensionality of the “intermediate” (often named feed-forward) layer in the Transformer encoder.

 40
hidden_dropout float

The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.

 0.0
attention_dropout float

The dropout ratio for the attention probabilities.

 0.0
max_position_embeddings int

The maximum sequence length that this model might ever be used with. Typically set this to something large just in case (e.g., 512 or 1024 or 2048).

 440
initializer_range float

The standard deviation of the truncated_normal_initializer for initializing all weight matrices.

 0.02
layer_norm_eps float

The epsilon used by the layer normalization layers.

 1e-12

Examples:

Python Console Session
>>> from multimolecule import RnaBertModel, RnaBertConfig
Python Console Session
>>> # Initializing a RNABERT multimolecule/rnabert style configuration
>>> configuration = RnaBertConfig()
Python Console Session
>>> # Initializing a model (with random weights) from the multimolecule/rnabert style configuration
>>> model = RnaBertModel(configuration)
Python Console Session
>>> # Accessing the model configuration
>>> configuration = model.config
Source code in multimolecule/models/rnabert/configuration_rnabert.py
Python
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
class RnaBertConfig(PreTrainedConfig):
    r"""
    This is the configuration class to store the configuration of a [`RnaBertModel`][multimolecule.models.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) architecture.

    Configuration objects inherit from [`PreTrainedConfig`][multimolecule.models.PreTrainedConfig] and can be used to
    control the model outputs. Read the documentation from [`PreTrainedConfig`][multimolecule.models.PreTrainedConfig]
    for more information.

    Args:
        vocab_size:
            Vocabulary size of the RnaBert model. Defines the number of different tokens that can be represented by the
            `inputs_ids` passed when calling [`RnaBertModel`].
        hidden_size:
            Dimensionality of the encoder layers and the pooler layer.
        num_hidden_layers:
            Number of hidden layers in the Transformer encoder.
        num_attention_heads:
            Number of attention heads for each attention layer in the Transformer encoder.
        intermediate_size:
            Dimensionality of the "intermediate" (often named feed-forward) layer in the Transformer encoder.
        hidden_dropout:
            The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
        attention_dropout:
            The dropout ratio for the attention probabilities.
        max_position_embeddings:
            The maximum sequence length that this model might ever be used with. Typically set this to something large
            just in case (e.g., 512 or 1024 or 2048).
        initializer_range:
            The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
        layer_norm_eps:
            The epsilon used by the layer normalization layers.

    Examples:
        >>> from multimolecule import RnaBertModel, RnaBertConfig

        >>> # Initializing a RNABERT multimolecule/rnabert style configuration
        >>> configuration = RnaBertConfig()

        >>> # Initializing a model (with random weights) from the multimolecule/rnabert style configuration
        >>> model = RnaBertModel(configuration)

        >>> # Accessing the model configuration
        >>> configuration = model.config
    """

    model_type = "rnabert"

    def __init__(
        self,
        vocab_size: int = 26,
        ss_vocab_size: int = 8,
        hidden_size: int | None = None,
        multiple: int | None = None,
        num_hidden_layers: int = 6,
        num_attention_heads: int = 12,
        intermediate_size: int = 40,
        hidden_act: str = "gelu",
        hidden_dropout: float = 0.0,
        attention_dropout: float = 0.0,
        max_position_embeddings: int = 440,
        initializer_range: float = 0.02,
        layer_norm_eps: float = 1e-12,
        position_embedding_type: str = "absolute",
        is_decoder: bool = False,
        use_cache: bool = True,
        head: HeadConfig | None = None,
        lm_head: MaskedLMHeadConfig | None = None,
        **kwargs,
    ):
        if hidden_size is None:
            hidden_size = num_attention_heads * multiple if multiple is not None else 120
        super().__init__(**kwargs)

        self.vocab_size = vocab_size
        self.ss_vocab_size = ss_vocab_size
        self.type_vocab_size = 2
        self.hidden_size = hidden_size
        self.num_hidden_layers = num_hidden_layers
        self.num_attention_heads = num_attention_heads
        self.intermediate_size = intermediate_size
        self.hidden_act = hidden_act
        self.hidden_dropout = hidden_dropout
        self.attention_dropout = attention_dropout
        self.max_position_embeddings = max_position_embeddings
        self.initializer_range = initializer_range
        self.layer_norm_eps = layer_norm_eps
        self.position_embedding_type = position_embedding_type
        self.is_decoder = is_decoder
        self.use_cache = use_cache
        self.head = HeadConfig(**head if head is not None else {})
        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})

RnaBertForContactPrediction

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertForContactPrediction, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertForContactPrediction(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input, labels=torch.randint(2, (1, 5, 5)))
>>> output["logits"].shape
torch.Size([1, 5, 5, 2])
>>> output["loss"]
tensor(..., grad_fn=<NllLossBackward0>)
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
class RnaBertForContactPrediction(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertForContactPrediction, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertForContactPrediction(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input, labels=torch.randint(2, (1, 5, 5)))
        >>> output["logits"].shape
        torch.Size([1, 5, 5, 2])
        >>> output["loss"]  # doctest:+ELLIPSIS
        tensor(..., grad_fn=<NllLossBackward0>)
    """

    def __init__(self, config: RnaBertConfig):
        super().__init__(config)
        self.rnabert = RnaBertModel(config, add_pooling_layer=True)
        self.contact_head = ContactPredictionHead(config)
        self.head_config = self.contact_head.config

        # Initialize weights and apply final processing
        self.post_init()

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        position_ids: Tensor | None = None,
        head_mask: Tensor | None = None,
        inputs_embeds: Tensor | NestedTensor | None = None,
        labels: Tensor | None = None,
        output_attentions: bool | None = None,
        output_hidden_states: bool | None = None,
        return_dict: bool | None = None,
        **kwargs,
    ) -> Tuple[Tensor, ...] | ContactPredictorOutput:
        if output_attentions is False:
            warn("output_attentions must be True for contact classification and will be ignored.")
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.rnabert(
            input_ids,
            attention_mask=attention_mask,
            position_ids=position_ids,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            output_attentions=True,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
            **kwargs,
        )
        output = self.contact_head(outputs, attention_mask, input_ids, labels)
        logits, loss = output.logits, output.loss

        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return ContactPredictorOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )

RnaBertForMaskedLM

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertForMaskedLM, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertForMaskedLM(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input, labels=input["input_ids"])
>>> output["logits"].shape
torch.Size([1, 7, 26])
>>> output["loss"]
tensor(..., grad_fn=<NllLossBackward0>)
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
class RnaBertForMaskedLM(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertForMaskedLM, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertForMaskedLM(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input, labels=input["input_ids"])
        >>> output["logits"].shape
        torch.Size([1, 7, 26])
        >>> output["loss"]  # doctest:+ELLIPSIS
        tensor(..., grad_fn=<NllLossBackward0>)
    """

    _tied_weights_keys = ["lm_head.decoder.weight", "lm_head.decoder.bias"]

    def __init__(self, config: RnaBertConfig):
        super().__init__(config)
        self.rnabert = RnaBertModel(config, add_pooling_layer=False)
        self.lm_head = MaskedLMHead(config)

        # Initialize weights and apply final processing
        self.post_init()

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        labels: Tensor | None = None,
        output_attentions: bool = False,
        output_hidden_states: bool = False,
        return_dict: bool = True,
        **kwargs,
    ) -> Tuple[Tensor, ...] | MaskedLMOutput:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.rnabert(
            input_ids,
            attention_mask,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
            **kwargs,
        )
        output = self.lm_head(outputs, labels)
        logits, loss = output.logits, output.loss

        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return MaskedLMOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )

RnaBertForNucleotidePrediction

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertForNucleotidePrediction, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertForNucleotidePrediction(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input, labels=torch.randn(1, 5, 2))
>>> output["logits"].shape
torch.Size([1, 5, 2])
>>> output["loss"]
tensor(..., grad_fn=<BinaryCrossEntropyWithLogitsBackward0>)
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
class RnaBertForNucleotidePrediction(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertForNucleotidePrediction, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertForNucleotidePrediction(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input, labels=torch.randn(1, 5, 2))
        >>> output["logits"].shape
        torch.Size([1, 5, 2])
        >>> output["loss"]  # doctest:+ELLIPSIS
        tensor(..., grad_fn=<BinaryCrossEntropyWithLogitsBackward0>)
    """

    def __init__(self, config: RnaBertConfig):
        super().__init__(config)
        self.rnabert = RnaBertModel(config, add_pooling_layer=True)
        self.nucleotide_head = NucleotidePredictionHead(config)
        self.head_config = self.nucleotide_head.config

        # Initialize weights and apply final processing
        self.post_init()

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        position_ids: Tensor | None = None,
        head_mask: Tensor | None = None,
        inputs_embeds: Tensor | NestedTensor | None = None,
        labels: Tensor | None = None,
        output_attentions: bool | None = None,
        output_hidden_states: bool | None = None,
        return_dict: bool | None = None,
        **kwargs,
    ) -> Tuple[Tensor, ...] | NucleotidePredictorOutput:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.rnabert(
            input_ids,
            attention_mask=attention_mask,
            position_ids=position_ids,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
            **kwargs,
        )
        output = self.nucleotide_head(outputs, attention_mask, input_ids, labels)
        logits, loss = output.logits, output.loss

        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return NucleotidePredictorOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )

RnaBertForPreTraining

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertForPreTraining, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertForPreTraining(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input, labels_mlm=input["input_ids"])
>>> output["loss"]
tensor(..., grad_fn=<AddBackward0>)
>>> output["logits_mlm"].shape
torch.Size([1, 7, 26])
>>> output["logits_ss"].shape
torch.Size([1, 7, 8])
>>> output["logits_sal"].shape
torch.Size([1, 2])
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
class RnaBertForPreTraining(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertForPreTraining, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertForPreTraining(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input, labels_mlm=input["input_ids"])
        >>> output["loss"]  # doctest:+ELLIPSIS
        tensor(..., grad_fn=<AddBackward0>)
        >>> output["logits_mlm"].shape
        torch.Size([1, 7, 26])
        >>> output["logits_ss"].shape
        torch.Size([1, 7, 8])
        >>> output["logits_sal"].shape
        torch.Size([1, 2])
    """

    _tied_weights_keys = [
        "lm_head.decoder.weight",
        "lm_head.decoder.bias",
        "pretrain.predictions.decoder.weight",
        "pretrain.predictions.decoder.bias",
        "pretrain.predictions_ss.decoder.weight",
        "pretrain.predictions_ss.decoder.bias",
    ]

    def __init__(self, config: RnaBertConfig):
        super().__init__(config)
        self.rnabert = RnaBertModel(config, add_pooling_layer=True)
        self.pretrain = RnaBertPreTrainingHeads(config)

        # Initialize weights and apply final processing
        self.post_init()

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        labels_mlm: Tensor | None = None,
        labels_ss: Tensor | None = None,
        labels_sal: Tensor | None = None,
        output_attentions: bool = False,
        output_hidden_states: bool = False,
        return_dict: bool = True,
        **kwargs,
    ) -> Tuple[Tensor, ...] | RnaBertForPreTrainingOutput:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.rnabert(
            input_ids,
            attention_mask,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
            **kwargs,
        )
        total_loss, logits_mlm, logits_ss, logits_sal = self.pretrain(
            outputs, labels_mlm=labels_mlm, labels_ss=labels_ss, labels_sal=labels_sal
        )

        if not return_dict:
            output = (logits_mlm, logits_ss, logits_sal) + outputs[2:]
            return ((total_loss,) + output) if total_loss is not None else output

        return RnaBertForPreTrainingOutput(
            loss=total_loss,
            logits_mlm=logits_mlm,
            logits_ss=logits_ss,
            logits_sal=logits_sal,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )

RnaBertForSequencePrediction

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertForSequencePrediction, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertForSequencePrediction(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input, labels=torch.tensor([[1]]))
>>> output["logits"].shape
torch.Size([1, 2])
>>> output["loss"]
tensor(..., grad_fn=<NllLossBackward0>)
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
class RnaBertForSequencePrediction(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertForSequencePrediction, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertForSequencePrediction(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input, labels=torch.tensor([[1]]))
        >>> output["logits"].shape
        torch.Size([1, 2])
        >>> output["loss"]  # doctest:+ELLIPSIS
        tensor(..., grad_fn=<NllLossBackward0>)
    """

    def __init__(self, config: RnaBertConfig):
        super().__init__(config)
        self.rnabert = RnaBertModel(config, add_pooling_layer=True)
        self.sequence_head = SequencePredictionHead(config)
        self.head_config = self.sequence_head.config

        # Initialize weights and apply final processing
        self.post_init()

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        position_ids: Tensor | None = None,
        head_mask: Tensor | None = None,
        inputs_embeds: Tensor | NestedTensor | None = None,
        labels: Tensor | None = None,
        output_attentions: bool | None = None,
        output_hidden_states: bool | None = None,
        return_dict: bool | None = None,
        **kwargs,
    ) -> Tuple[Tensor, ...] | SequencePredictorOutput:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.rnabert(
            input_ids,
            attention_mask=attention_mask,
            position_ids=position_ids,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
            **kwargs,
        )
        output = self.sequence_head(outputs, labels)
        logits, loss = output.logits, output.loss

        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return SequencePredictorOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )

RnaBertForTokenPrediction

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertForTokenPrediction, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertForTokenPrediction(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input, labels=torch.randint(2, (1, 7)))
>>> output["logits"].shape
torch.Size([1, 7, 2])
>>> output["loss"]
tensor(..., grad_fn=<NllLossBackward0>)
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
class RnaBertForTokenPrediction(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertForTokenPrediction, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertForTokenPrediction(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input, labels=torch.randint(2, (1, 7)))
        >>> output["logits"].shape
        torch.Size([1, 7, 2])
        >>> output["loss"]  # doctest:+ELLIPSIS
        tensor(..., grad_fn=<NllLossBackward0>)
    """

    def __init__(self, config: RnaBertConfig):
        super().__init__(config)
        self.rnabert = RnaBertModel(config, add_pooling_layer=True)
        self.token_head = TokenPredictionHead(config)
        self.head_config = self.token_head.config

        # Initialize weights and apply final processing
        self.post_init()

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        position_ids: Tensor | None = None,
        head_mask: Tensor | None = None,
        inputs_embeds: Tensor | NestedTensor | None = None,
        labels: Tensor | None = None,
        output_attentions: bool | None = None,
        output_hidden_states: bool | None = None,
        return_dict: bool | None = None,
        **kwargs,
    ) -> Tuple[Tensor, ...] | TokenPredictorOutput:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.rnabert(
            input_ids,
            attention_mask=attention_mask,
            position_ids=position_ids,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
            **kwargs,
        )
        output = self.token_head(outputs, attention_mask, input_ids, labels)
        logits, loss = output.logits, output.loss

        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return TokenPredictorOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )

RnaBertModel

Bases: RnaBertPreTrainedModel

Examples:

Python Console Session
>>> from multimolecule import RnaBertConfig, RnaBertModel, RnaTokenizer
>>> config = RnaBertConfig()
>>> model = RnaBertModel(config)
>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
>>> input = tokenizer("ACGUN", return_tensors="pt")
>>> output = model(**input)
>>> output["last_hidden_state"].shape
torch.Size([1, 7, 120])
>>> output["pooler_output"].shape
torch.Size([1, 120])
Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
class RnaBertModel(RnaBertPreTrainedModel):
    """
    Examples:
        >>> from multimolecule import RnaBertConfig, RnaBertModel, RnaTokenizer
        >>> config = RnaBertConfig()
        >>> model = RnaBertModel(config)
        >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/rna")
        >>> input = tokenizer("ACGUN", return_tensors="pt")
        >>> output = model(**input)
        >>> output["last_hidden_state"].shape
        torch.Size([1, 7, 120])
        >>> output["pooler_output"].shape
        torch.Size([1, 120])
    """

    def __init__(self, config: RnaBertConfig, add_pooling_layer: bool = True):
        super().__init__(config)
        self.pad_token_id = config.pad_token_id
        self.embeddings = RnaBertEmbeddings(config)
        self.encoder = RnaBertEncoder(config)
        self.pooler = RnaBertPooler(config) if add_pooling_layer else None

        # Initialize weights and apply final processing
        self.post_init()

    def get_input_embeddings(self):
        return self.embeddings.word_embeddings

    def set_input_embeddings(self, value):
        self.embeddings.word_embeddings = value

    def _prune_heads(self, heads_to_prune):
        """
        Prunes heads of the model. heads_to_prune: dict of {layer_num: list of heads to prune in this layer} See base
        class PreTrainedModel
        """
        for layer, heads in heads_to_prune.items():
            self.encoder.layer[layer].attention.prune_heads(heads)

    def forward(
        self,
        input_ids: Tensor | NestedTensor,
        attention_mask: Tensor | None = None,
        position_ids: Tensor | None = None,
        head_mask: Tensor | None = None,
        inputs_embeds: Tensor | NestedTensor | None = None,
        encoder_hidden_states: Tensor | None = None,
        encoder_attention_mask: Tensor | None = None,
        past_key_values: Tuple[Tuple[torch.FloatTensor, torch.FloatTensor], ...] | None = None,
        use_cache: bool | None = None,
        output_attentions: bool | None = None,
        output_hidden_states: bool | None = None,
        return_dict: bool | None = None,
        **kwargs,
    ) -> Tuple[Tensor, ...] | BaseModelOutputWithPoolingAndCrossAttentions:
        r"""
        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
            the model is configured as a decoder.
        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:

            - 1 for tokens that are **not masked**,
            - 0 for tokens that are **masked**.
        past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors
            of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.

            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
        use_cache (`bool`, *optional*):
            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
            `past_key_values`).
        """
        if kwargs:
            warn(
                f"Additional keyword arguments `{', '.join(kwargs)}` are detected in "
                f"`{self.__class__.__name__}.forward`, they will be ignored.\n"
                "This is provided for backward compatibility and may lead to unexpected behavior."
            )
        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

        if self.config.is_decoder:
            use_cache = use_cache if use_cache is not None else self.config.use_cache
        else:
            use_cache = False

        if isinstance(input_ids, NestedTensor):
            input_ids, attention_mask = input_ids.tensor, input_ids.mask
        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")
        if input_ids is not None:
            self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
            input_shape = input_ids.size()
        elif inputs_embeds is not None:
            input_shape = inputs_embeds.size()[:-1]
        else:
            raise ValueError("You have to specify either input_ids or inputs_embeds")

        batch_size, seq_length = input_shape
        device = input_ids.device if input_ids is not None else inputs_embeds.device  # type: ignore[union-attr]

        # past_key_values_length
        past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0

        if attention_mask is None:
            attention_mask = (
                input_ids.ne(self.pad_token_id)
                if self.pad_token_id is not None
                else torch.ones(((batch_size, seq_length + past_key_values_length)), device=device)
            )

        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
        # ourselves in which case we just need to make it broadcastable to all heads.
        extended_attention_mask: Tensor = self.get_extended_attention_mask(attention_mask, input_shape)

        # If a 2D or 3D attention mask is provided for the cross-attention
        # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
        if self.config.is_decoder and encoder_hidden_states is not None:
            encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
            encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
            if encoder_attention_mask is None:
                encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
            encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
        else:
            encoder_extended_attention_mask = None

        # Prepare head mask if needed
        # 1.0 in head_mask indicate we keep the head
        # attention_probs has shape bsz x n_heads x N x N
        # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
        # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
        head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers)

        embedding_output = self.embeddings(
            input_ids=input_ids,
            position_ids=position_ids,
            inputs_embeds=inputs_embeds,
            past_key_values_length=past_key_values_length,
        )
        encoder_outputs = self.encoder(
            embedding_output,
            attention_mask=extended_attention_mask,
            head_mask=head_mask,
            encoder_hidden_states=encoder_hidden_states,
            encoder_attention_mask=encoder_extended_attention_mask,
            past_key_values=past_key_values,
            use_cache=use_cache,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )
        sequence_output = encoder_outputs[0]
        pooled_output = self.pooler(sequence_output) if self.pooler is not None else None

        if not return_dict:
            return (sequence_output, pooled_output) + encoder_outputs[1:]

        return BaseModelOutputWithPoolingAndCrossAttentions(
            last_hidden_state=sequence_output,
            pooler_output=pooled_output,
            past_key_values=encoder_outputs.past_key_values,
            hidden_states=encoder_outputs.hidden_states,
            attentions=encoder_outputs.attentions,
            cross_attentions=encoder_outputs.cross_attentions,
        )

forward

Python
1
forward(input_ids: Tensor | NestedTensor, attention_mask: Tensor | None = None, position_ids: Tensor | None = None, head_mask: Tensor | None = None, inputs_embeds: Tensor | NestedTensor | None = None, encoder_hidden_states: Tensor | None = None, encoder_attention_mask: Tensor | None = None, past_key_values: Tuple[Tuple[FloatTensor, FloatTensor], ...] | None = None, use_cache: bool | None = None, output_attentions: bool | None = None, output_hidden_states: bool | None = None, return_dict: bool | None = None, **kwargs) -> Tuple[Tensor, ...] | BaseModelOutputWithPoolingAndCrossAttentions

encoder_hidden_states (torch.FloatTensor of shape (batch_size, sequence_length, hidden_size), optional): Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if the model is configured as a decoder. encoder_attention_mask (torch.FloatTensor of shape (batch_size, sequence_length), optional): Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in the cross-attention if the model is configured as a decoder. Mask values selected in [0, 1]:

Text Only
1
2
- 1 for tokens that are **not masked**,
- 0 for tokens that are **masked**.

past_key_values (tuple(tuple(torch.FloatTensor)) of length config.n_layers with each tuple having 4 tensors of shape (batch_size, num_heads, sequence_length - 1, embed_size_per_head)): Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.

Text Only
1
2
3
If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
`decoder_input_ids` of shape `(batch_size, sequence_length)`.

use_cache (bool, optional): If set to True, past_key_values key value states are returned and can be used to speed up decoding (see past_key_values).

Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
def forward(
    self,
    input_ids: Tensor | NestedTensor,
    attention_mask: Tensor | None = None,
    position_ids: Tensor | None = None,
    head_mask: Tensor | None = None,
    inputs_embeds: Tensor | NestedTensor | None = None,
    encoder_hidden_states: Tensor | None = None,
    encoder_attention_mask: Tensor | None = None,
    past_key_values: Tuple[Tuple[torch.FloatTensor, torch.FloatTensor], ...] | None = None,
    use_cache: bool | None = None,
    output_attentions: bool | None = None,
    output_hidden_states: bool | None = None,
    return_dict: bool | None = None,
    **kwargs,
) -> Tuple[Tensor, ...] | BaseModelOutputWithPoolingAndCrossAttentions:
    r"""
    encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
        Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
        the model is configured as a decoder.
    encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
        Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
        the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:

        - 1 for tokens that are **not masked**,
        - 0 for tokens that are **masked**.
    past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors
        of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
        Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.

        If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
        don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
        `decoder_input_ids` of shape `(batch_size, sequence_length)`.
    use_cache (`bool`, *optional*):
        If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
        `past_key_values`).
    """
    if kwargs:
        warn(
            f"Additional keyword arguments `{', '.join(kwargs)}` are detected in "
            f"`{self.__class__.__name__}.forward`, they will be ignored.\n"
            "This is provided for backward compatibility and may lead to unexpected behavior."
        )
    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

    if self.config.is_decoder:
        use_cache = use_cache if use_cache is not None else self.config.use_cache
    else:
        use_cache = False

    if isinstance(input_ids, NestedTensor):
        input_ids, attention_mask = input_ids.tensor, input_ids.mask
    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")
    if input_ids is not None:
        self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
        input_shape = input_ids.size()
    elif inputs_embeds is not None:
        input_shape = inputs_embeds.size()[:-1]
    else:
        raise ValueError("You have to specify either input_ids or inputs_embeds")

    batch_size, seq_length = input_shape
    device = input_ids.device if input_ids is not None else inputs_embeds.device  # type: ignore[union-attr]

    # past_key_values_length
    past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0

    if attention_mask is None:
        attention_mask = (
            input_ids.ne(self.pad_token_id)
            if self.pad_token_id is not None
            else torch.ones(((batch_size, seq_length + past_key_values_length)), device=device)
        )

    # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
    # ourselves in which case we just need to make it broadcastable to all heads.
    extended_attention_mask: Tensor = self.get_extended_attention_mask(attention_mask, input_shape)

    # If a 2D or 3D attention mask is provided for the cross-attention
    # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
    if self.config.is_decoder and encoder_hidden_states is not None:
        encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
        encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
        if encoder_attention_mask is None:
            encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
        encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
    else:
        encoder_extended_attention_mask = None

    # Prepare head mask if needed
    # 1.0 in head_mask indicate we keep the head
    # attention_probs has shape bsz x n_heads x N x N
    # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
    # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
    head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers)

    embedding_output = self.embeddings(
        input_ids=input_ids,
        position_ids=position_ids,
        inputs_embeds=inputs_embeds,
        past_key_values_length=past_key_values_length,
    )
    encoder_outputs = self.encoder(
        embedding_output,
        attention_mask=extended_attention_mask,
        head_mask=head_mask,
        encoder_hidden_states=encoder_hidden_states,
        encoder_attention_mask=encoder_extended_attention_mask,
        past_key_values=past_key_values,
        use_cache=use_cache,
        output_attentions=output_attentions,
        output_hidden_states=output_hidden_states,
        return_dict=return_dict,
    )
    sequence_output = encoder_outputs[0]
    pooled_output = self.pooler(sequence_output) if self.pooler is not None else None

    if not return_dict:
        return (sequence_output, pooled_output) + encoder_outputs[1:]

    return BaseModelOutputWithPoolingAndCrossAttentions(
        last_hidden_state=sequence_output,
        pooler_output=pooled_output,
        past_key_values=encoder_outputs.past_key_values,
        hidden_states=encoder_outputs.hidden_states,
        attentions=encoder_outputs.attentions,
        cross_attentions=encoder_outputs.cross_attentions,
    )

RnaBertPreTrainedModel

Bases: PreTrainedModel

An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained models.

Source code in multimolecule/models/rnabert/modeling_rnabert.py
Python
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
class RnaBertPreTrainedModel(PreTrainedModel):
    """
    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
    models.
    """

    config_class = RnaBertConfig
    base_model_prefix = "rnabert"
    supports_gradient_checkpointing = True
    _no_split_modules = ["RnaBertLayer", "RnaBertEmbeddings"]

    # Copied from transformers.models.bert.modeling_bert.BertPreTrainedModel._init_weights
    def _init_weights(self, module: nn.Module):
        """Initialize the weights"""
        if isinstance(module, nn.Linear):
            # Slightly different from the TF version which uses truncated_normal for initialization
            # cf https://github.com/pytorch/pytorch/pull/5617
            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
            if module.bias is not None:
                module.bias.data.zero_()
        elif isinstance(module, nn.Embedding):
            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
            if module.padding_idx is not None:
                module.weight.data[module.padding_idx].zero_()
        elif isinstance(module, nn.LayerNorm):
            module.bias.data.zero_()
            module.weight.data.fill_(1.0)