Ankh ☥: Optimized Protein Language Model Unlocks General-Purpose Modelling

Ankh is the first general-purpose protein language model trained on Google's TPU-V4 surpassing the state-of-the-art performance with dramatically less parameters, promoting accessibility to research innovation via attainable resources.

This repository will be updated regulary with new pre-trained models for proteins in part of supporting the biotech community in revolutinizing protein engineering using AI.

Table of Contents

•   Installation
•   Models Availability
•   Dataset Availability
•   Usage
•   Original downstream Predictions
•   Followup use-cases
•   Comparisons to other tools
•   Community and Contributions
•   Have a question?
•   Found a bug?
•   Requirements
•   Sponsors
•   Team
•   License
•   Citation

  Installation

python -m pip install ankh

  Models Availability

  Datasets Availability

  Usage

• Loading pre-trained models:

  import ankh

  # Load Ankh base.
  model, tokenizer = ankh.load_ankh_base()
  model.eval()

  # Load Ankh large.
  model, tokenizer = ankh.load_ankh_large()
  model.eval()

  # Load Ankh3 Large
  model, tokenizer = ankh.load_ankh3_large()
  model.eval()

  # Load Ankh3 XL
  model, tokenizer = ankh.load_ankh3_xl()
  model.eval()

• Feature extraction using ankh large example:

  model, tokenizer = ankh.load_ankh_large()
  model.eval()

  protein_sequences = [
    'MKALCLLLLPVLGLLVSSKTLCSMEEAINERIQEVAGSLIFRAISSIGLECQSVTSRGDLATCPRGFAVTGCTCGSACGSWDVRAETTCHCQCAGMDWTGARCCRVQPLEHHHHHH', 
    'GSHMSLFDFFKNKGSAATATDRLKLILAKERTLNLPYMEEMRKEIIAVIQKYTKSSDIHFKTLDSNQSVETIEVEIILPR',
  ]

  protein_sequences = [list(seq) for seq in protein_sequences]

  outputs = tokenizer(
    protein_sequences, 
    add_special_tokens=True, 
    padding=True, 
    is_split_into_words=True, 
    return_tensors="pt",
  )
  with torch.no_grad():
    embeddings = model(input_ids=outputs['input_ids'], attention_mask=outputs['attention_mask'])

• Loading downstream models example:

  # To use downstream model for binary classification:
  binary_classification_model = ankh.ConvBERTForBinaryClassification(
    input_dim=768, 
    nhead=4, 
    hidden_dim=384, 
    num_hidden_layers=1, 
    num_layers=1, 
    kernel_size=7, 
    dropout=0.2, 
    pooling='max',
  )

  # To use downstream model for multiclass classification:
  multiclass_classification_model = ankh.ConvBERTForMultiClassClassification(
    num_tokens=2, 
    input_dim=768, 
    nhead=4, 
    hidden_dim=384, 
    num_hidden_layers=1, 
    num_layers=1, 
    kernel_size=7, 
    dropout=0.2,
  )

  # To use downstream model for regression:
  # training_labels_mean is optional parameter and it's used to fill the output layer's bias with it, 
  # it's useful for faster convergence.
  regression_model = ankh.ConvBERTForRegression(
    input_dim=768, 
    nhead=4, 
    hidden_dim=384, 
    num_hidden_layers=1, 
    num_layers=1, 
    kernel_size=7, 
    dropout=0, 
    pooling='max', 
    training_labels_mean=0.38145,
  )

• Calculating Likelihood

import ankh

seq = "MDDADPEERNYDNMLKMLSDLNKDLEKLLEEMEKISVQATWMAYDMVVMRTNPTLAESMRRLEDAFVNCKEEMEKNWQELLHETKQRL"
likelihood = ankh.compute_pseudo_likelihood(
  "ankh_base",
  sequence,
  device="cpu",
  shard_input=True,
  shard_batch_size=32,
  verbose=True,
)

  Original downstream Predictions

•   Secondary Structure Prediction (Q3):
  

•   Secondary Structure Prediction (Q8):
  

•   Contact Prediction Long Precision Using Embeddings:
  

•   Contact Prediction Long Precision Using attention scores:
  

•   Localization (Q10):
  

•   Remote Homology:
  

•   Solubility:
  

•   Fluorescence (Spearman Correlation):
  

•   Nearest Neighbor Search using Global Pooling:
  

  Team

• Technical University of Munich:
  

• Proteinea:
  

• University of Columbia:
  

  Sponsors

  License

Ankh pretrained models are released under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International.

  Community and Contributions

The Ankh project is a open source project supported by various partner companies and research institutions. We are committed to share all our pre-trained models and knowledge. We are more than happy if you could help us on sharing new ptrained models, fixing bugs, proposing new feature, improving our documentation, spreading the word, or support our project.

  Have a question?

We are happy to hear your question in our issues page Ankh! Obviously if you have a private question or want to cooperate with us, you can always reach out to us directly via Hello.

  Found a bug?

Feel free to file a new issue with a respective title and description on the Ankh repository. If you already found a solution to your problem, we would love to review your pull request!.

✏️  Citation

If you use this code or our pretrained models for your publication, please cite the original paper:

@article{elnaggar2023ankh,
  title={Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling},
  author={Elnaggar, Ahmed and Essam, Hazem and Salah-Eldin, Wafaa and Moustafa, Walid and Elkerdawy, Mohamed and Rochereau, Charlotte and Rost, Burkhard},
  journal={arXiv preprint arXiv:2301.06568},
  year={2023}
}