dnabert2 / README.md

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datasets:
  - multimolecule/genbank
library_name: multimolecule
license: agpl-3.0
mask_token: <mask>
pipeline_tag: fill-mask
tags:
  - Biology
  - DNA
  - dna
widget:
  - example_title: tumor protein p53
    mask_index: 14
    mask_index_1based: 15
    masked_char: A
    output:
      - label: GCC
        score: 0.046856
      - label: TCC
        score: 0.034778
      - label: CACC
        score: 0.034686
      - label: TGCC
        score: 0.034373
      - label: TC
        score: 0.020678
    pipeline_tag: fill-mask
    sequence_type: DNA
    task: fill-mask
    text: >-
      ACTCCCCTGCCCTC<mask>ACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGG
  - example_title: BRCA1 DNA repair associated
    mask_index: 10
    mask_index_1based: 11
    masked_char: A
    output:
      - label: GAAATG
        score: 0.384974
      - label: GAAAAAAA
        score: 0.185107
      - label: GAAAATT
        score: 0.091941
      - label: GCAATT
        score: 0.076877
      - label: GAAAATG
        score: 0.07223
    pipeline_tag: fill-mask
    sequence_type: DNA
    task: fill-mask
    text: >-
      TCATTGGAAC<mask>GAAAGAAATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGG
  - example_title: hemoglobin subunit beta
    mask_index: 12
    mask_index_1based: 13
    masked_char: A
    output:
      - label: TGTT
        score: 0.025346
      - label: TGA
        score: 0.02065
      - label: CAA
        score: 0.017773
      - label: CTT
        score: 0.016384
      - label: GTT
        score: 0.015401
    pipeline_tag: fill-mask
    sequence_type: DNA
    task: fill-mask
    text: >-
      CATTTGCTTCTG<mask>CACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG
  - example_title: CF transmembrane conductance regulator
    mask_index: 11
    mask_index_1based: 12
    masked_char: A
    output:
      - label: CTA
        score: 0.023278
      - label: TGA
        score: 0.017978
      - label: GTGA
        score: 0.015395
      - label: GAA
        score: 0.015331
      - label: GAAGA
        score: 0.012243
    pipeline_tag: fill-mask
    sequence_type: DNA
    task: fill-mask
    text: >-
      ACTTCACTTCT<mask>ATGGTGATTATGGGAGAACTGGAGCCTTCAGAGGGTAAAATTAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGGCACCATTAAAGAAAATATCATCTTTGGTGTTTCCTATGATGAATATAGATACAGAAGCGTCATCAAAGCATGCCAACTAGAAGAG
  - example_title: telomerase reverse transcriptase
    mask_index: 19
    mask_index_1based: 20
    masked_char: A
    output:
      - label: GGAGCC
        score: 0.060274
      - label: CGAGG
        score: 0.055727
      - label: GGGAA
        score: 0.054949
      - label: GAGC
        score: 0.044957
      - label: CGGAA
        score: 0.038146
    pipeline_tag: fill-mask
    sequence_type: DNA
    task: fill-mask
    text: >-
      CGCGGGGGTGGCCGGGGCC<mask>GGGCTTCCCACGTGCGCAGCAGGACGCAGCGCTGCCTGAAACTCGCGCCGCGAGGAGAGGGCGGGGCCGCGGAAAGGAAGGGGAGGGGCTGGGAGGGCCCGGAGGGGGCTGGGCCGGGGACCCGGGAGGGGTCGGGACGGGGCGGGGTCCGCGCGGAGGAGGCGGAGCTGGAAGGTGAAGGGGCAGGACGGGTGCCCGGGTCCCCAGTCCCTCCGCCACGTGGGAAGCGCGGTCCTGGGCGTCTGTGCCCGCGAATCCACTGGGAGCCCGGCCTGGCCCCGACAGCGCAGCTGCTCCGGGCGGACCCGGGG
  - example_title: KRAS proto-oncogene
    mask_index: 10
    mask_index_1based: 11
    masked_char: A
    output:
      - label: TATA
        score: 0.039074
      - label: TATAAA
        score: 0.036387
      - label: TA
        score: 0.029847
      - label: TATAA
        score: 0.028697
      - label: TGA
        score: 0.018409
    pipeline_tag: fill-mask
    sequence_type: DNA
    task: fill-mask
    text: >-
      GCCTGCTGAA<mask>ATGACTGAATATAAACTTGTGGTAGTTGGAGCTGGTGGCGTAGGCAAGAGTGCCTTGACGATACAGCTAATTCAGAATCATTTTGTGGACGAATATGATCCAACAATAGAG
  - example_title: prion protein (Kanno blood group)
    mask_index: 21
    mask_index_1based: 22
    masked_char: A
    output:
      - label: CGG
        score: 0.092979
      - label: CTCC
        score: 0.049605
      - label: GTCC
        score: 0.034976
      - label: CAGG
        score: 0.027379
      - label: CGCC
        score: 0.025038
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: ATGGCGAACCTTGGCTGCTGG<mask>TGCTGGTTCTCTTTGTGGCCACATGGAGTGACCTGGGCCTCTGC
  - example_title: interleukin 10
    mask_index: 11
    mask_index_1based: 12
    masked_char: A
    output:
      - label: CACA
        score: 0.089619
      - label: TCTT
        score: 0.058608
      - label: TGAA
        score: 0.039673
      - label: CAGA
        score: 0.039484
      - label: TCAA
        score: 0.034905
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: ATGCACAGCTC<mask>GCACTGCTCTGTTGCCTGGTCCTCCTGACTGGGGTGAGGGCC
  - example_title: Zaire ebolavirus
    mask_index: 11
    mask_index_1based: 12
    masked_char: A
    output:
      - label: GCAATT
        score: 0.245573
      - label: GAAATG
        score: 0.23112
      - label: GTCCTT
        score: 0.125824
      - label: GTCCAA
        score: 0.109987
      - label: GAAAATT
        score: 0.070866
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: >-
      AATGTTCAAAC<mask>CTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTCACAGAGCGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATAGAATATTGTAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTAT
  - example_title: SARS coronavirus
    mask_index: 14
    mask_index_1based: 15
    masked_char: A
    output:
      - label: TCTTTT
        score: 0.029207
      - label: TATC
        score: 0.027219
      - label: CATC
        score: 0.014813
      - label: CCTTTT
        score: 0.012734
      - label: CATTTT
        score: 0.011283
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: >-
      ATGTTTATTTTCTT<mask>TTATTTCTTACTCTCACTAGTGGTAGTGACCTTGACCGGTGCACCACTTTTGATGATGTTCAAGCTCCTAATTACACTCAACATACTTCATCTATGAGGGGGGTTTACTATCCTGATGAAATTTTTAGATCAGACACTCTTTATTTAACTCAGGATTTATTTCTTCCATTTTATTCTAATGTTACAGGGTTTCATACTATTAATCATACGTTTGACAACCCTGTCATACCTTTTAAGGATGGTATTTATTTTGCTGCCACAGAGAAATCAAATGTTGTCCGTGGTTGGGTTTTTGGTTCTACCATGAACAACAAGTCACAGTCGGTGATTATTATTAACAATTCTACTAATGTTGTTATACGAGCATGTAACTTTGAATTGTGTGACAACCCTTTCTTTGCTGTTTCTAAACCCATGGGTACACAGACACATACTATGATATTCGATAATGCATTTAAATGCACTTTCGAGTACATATCT
  - example_title: insulin
    mask_index: 12
    mask_index_1based: 13
    masked_char: A
    output:
      - label: CGTCC
        score: 0.573751
      - label: CGAGG
        score: 0.135812
      - label: GCCAGG
        score: 0.060897
      - label: CGTCA
        score: 0.032261
      - label: GCCACA
        score: 0.025581
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: >-
      ATGGCCCTGTGG<mask>TGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG
  - example_title: cyclin dependent kinase inhibitor 2A
    mask_index: 18
    mask_index_1based: 19
    masked_char: A
    output:
      - label: GCGG
        score: 0.469999
      - label: CGCC
        score: 0.130437
      - label: CGCA
        score: 0.092787
      - label: GCGGCGG
        score: 0.084631
      - label: TCGG
        score: 0.063294
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: >-
      ATGGAGCCGGCGGCGGGG<mask>GCAGCATGGAGCCTTCGGCTGACTGGCTGGCCACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTGCGGGCGCTGCTGGAGGCGGGGGCGCTGCCCAACGCACCGAATAGTTACGGTCGGAGGCCGATCCAGGTCATGATGATGGGCAGCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCGGAGCCCAACTGCGCCGACCCCGCCACTCTCACCCGACCCGTGCACGACGCTGCCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCACCGGGCCGGGGCGCGGCTGGACGTGCGCGATGCCTGGGGCCGTCTGCCCGTGGACCTGGCTGAGGAGCTGGGCCATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGCACCAGAGGCAGTAACCATGCCCGCATAGATGCCGCGGAAGGTCCCTCAGACATCCCCGATTGA
  - example_title: human papillomavirus type 16 E6
    mask_index: 10
    mask_index_1based: 11
    masked_char: A
    output:
      - label: GAGA
        score: 0.026885
      - label: CACA
        score: 0.023989
      - label: GAAA
        score: 0.019737
      - label: CAA
        score: 0.018905
      - label: CAAA
        score: 0.015072
    pipeline_tag: fill-mask
    sequence_type: cDNA
    task: fill-mask
    text: >-
      ATGCACCAAA<mask>GAGAACTGCAATGTTTCAGGACCCACAGGAGCGACCCAGAAAGTTACCACAGTTATGCACAGAGCTGCAAACAACTATACATGATATAATATTAGAATGTGTGTACTGCAAGCAACAGTTACTGCGACGTGAGGTATATGACTTTGCTTTTCGGGATTTATGCATAGTATATAGAGATGGGAATCCATATGCTGTATGTGATAAATGTTTAAAGTTTTATTCTAAAATTAGTGAGTATAGACATTATTGTTATAGTTTGTATGGAACAACATTAGAACAGCAATACAACAAACCGTTGTGTGATTTGTTAATTAGGTGTATTAACTGTCAAAAGCCACTGTGTCCTGAAGAAAAGCAAAGACATCTGGACAAAAAGCAAAGATTCCATAATATAAGGGGTCGGTGGACCGGTCGATGTATGTCTTGTTGCAGATCATCAAGAACACGTAGAGAAACCCAGCTGTAA

DNABERT-2

Pre-trained model on multi-species genome using a masked language modeling (MLM) objective.

Disclaimer

This is an UNOFFICIAL implementation of the DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes by Zhihan Zhou, et al.

The OFFICIAL repository of DNABERT-2 is at MAGICS-LAB/DNABERT_2.

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

The team releasing DNABERT-2 did not write this model card for this model so this model card has been written by the MultiMolecule team.

Model Details

DNABERT-2 is a bert-style model pre-trained on a large corpus of multi-species genome sequences in a self-supervised fashion. This means that the model was trained on the raw nucleotides of DNA 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
12	768	12	3072	117.07	125.83	62.92	512

Usage

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

pip install multimolecule

Direct Use

Masked Language Modeling

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

import multimolecule  # you must import multimolecule to register models
from transformers import pipeline

predictor = pipeline("fill-mask", model="multimolecule/dnabert2")
output = predictor("ATCG<mask>TGCA")

Downstream Use

Extract Features

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

from multimolecule import DnaBert2Model
from transformers import AutoTokenizer


tokenizer = AutoTokenizer.from_pretrained("multimolecule/dnabert2")
model = DnaBert2Model.from_pretrained("multimolecule/dnabert2")

text = "ATCGATCGATCGATCG"
input = tokenizer(text, return_tensors="pt")

output = model(**input)

Sequence Classification / Regression

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:

import torch
from multimolecule import DnaBert2ForSequencePrediction
from transformers import AutoTokenizer


tokenizer = AutoTokenizer.from_pretrained("multimolecule/dnabert2")
model = DnaBert2ForSequencePrediction.from_pretrained("multimolecule/dnabert2")

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

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

Token Classification / Regression

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 token classification or regression.

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

import torch
from multimolecule import DnaBert2ForTokenPrediction
from transformers import AutoTokenizer


tokenizer = AutoTokenizer.from_pretrained("multimolecule/dnabert2")
model = DnaBert2ForTokenPrediction.from_pretrained("multimolecule/dnabert2")

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

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

Contact Classification / Regression

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:

import torch
from multimolecule import DnaBert2ForContactPrediction
from transformers import AutoTokenizer


tokenizer = AutoTokenizer.from_pretrained("multimolecule/dnabert2")
model = DnaBert2ForContactPrediction.from_pretrained("multimolecule/dnabert2")

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

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

Training Details

DNABERT-2 used Masked Language Modeling (MLM) as the pre-training objective: 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.

Training Data

The DNABERT-2 model was pre-trained on multi-species genome sequences from GenBank. The dataset encompasses genomes from 135 species, spread across 6 categories. In total, the dataset includes 32.49 billion nucleotide bases, nearly 12 times the volume of the human genome dataset. All sequences with N are excluded, retaining only sequences that consist of A, T, C, and G.

DNABERT-2 uses Byte Pair Encoding (BPE) tokenization with a vocabulary size of 4096. This replaces the k-mer tokenization used in the original DNABERT, providing improved computational and sample efficiency.

Training Procedure

Preprocessing

DNABERT-2 used masked language modeling (MLM) as the pre-training objective. The masking procedure is similar to the one used in BERT:

Mask rate: 15%
Replacement: <mask> for 80% of masked tokens
Replacement: random token for 10% of masked tokens
Replacement: unchanged token for 10% of masked tokens

Pre-training

The model was trained on 8 NVIDIA RTX 2080Ti GPUs.

Batch size: 4,096
Steps: 500,000
Optimizer: AdamW(β1=0.9, β2=0.98, ε=1e-6)
Learning rate: 5e-4
Learning rate warm-up: 30,000 steps
Learning rate scheduler: Linear
Minimum learning rate: 0
Weight decay: 1e-5

Citation

@inproceedings{zhou2024dnabert,
  title={{DNABERT}-2: Efficient Foundation Model and Benchmark For Multi-Species Genomes},
  author={Zhihan Zhou and Yanrong Ji and Weijian Li and Pratik Dutta and Ramana V Davuluri and Han Liu},
  booktitle={The Twelfth International Conference on Learning Representations},
  year={2024},
  url={https://openreview.net/forum?id=oMLQB4EZE1}
}

The artifacts distributed in this repository are part of the MultiMolecule project. If MultiMolecule supports your research, please cite the MultiMolecule project as follows:

@software{chen_2024_12638419,
  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
  title     = {MultiMolecule},
  doi       = {10.5281/zenodo.12638419},
  publisher = {Zenodo},
  url       = {https://doi.org/10.5281/zenodo.12638419},
  year      = 2024,
  month     = may,
  day       = 4
}

Contact

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

Please contact the authors of the DNABERT-2 paper for questions or comments on the paper/model.

License

This model implementation is licensed under the GNU Affero General Public License.

For additional terms and clarifications, please refer to our License FAQ.

SPDX-License-Identifier: AGPL-3.0-or-later

multimolecule
/

dnabert2

DNABERT-2

Disclaimer

Model Details

Model Specification

Links

Usage

Direct Use

Masked Language Modeling

Downstream Use

Extract Features

Sequence Classification / Regression

Token Classification / Regression

Contact Classification / Regression

Training Details

Training Data

Training Procedure

Preprocessing

Pre-training

Citation

Contact

License