genomeNLP: Case study of deep learning
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.. raw:: html

  Copyright (c) 2023 <a href="https://orcid.org/0000-0002-9207-0385">Tyrone Chen <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-8797-3168">Navya Tyagi <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, and <a href="https://orcid.org/0000-0003-0181-6258">Sonika Tyagi <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>.


Code in this repository is provided under a `MIT license`_. 
Documentation for this specific case study is provided with © all rights reserved (temporary until publication).
All other documentation not on this page is provided under a `CC-BY-3.0 AU license`_.

.. _MIT license: https://opensource.org/licenses/MIT

.. _CC-BY-3.0 AU license: https://creativecommons.org/licenses/by/3.0/au/

Workshops and tutorials landing page
====================================

- `INCOB 2023`_
- `K-CAP 2023`_

.. - AJCAI 2023 (coming soon)
.. _INCOB 2023: https://genomenlp-tutorials.readthedocs.io/en/latest/incob_2023.html
.. _AJCAI 2023
.. _K-CAP 2023: https://kcap-2023.readthedocs.io/en/latest/ 

Case studies per molecule type
==============================

Please select the case study relevant to your use case:

Introduction
------------

:doc:`case_study_intro`

DNA case study
--------------

:doc:`case_study_dna`

RNA case study
--------------

*coming soon*

Protein case study
------------------

:doc:`case_study_protein`


Citation
========

Cite our manuscript here::

  @article{chen2023genomicbert,
      title={genomicBERT and data-free deep-learning model evaluation},
      author={Chen, Tyrone and Tyagi, Navya and Chauhan, Sarthak and Peleg, Anton Y and Tyagi, Sonika},
      journal={bioRxiv},
      month={jun},
      pages={2023--05},
      year={2023},
      publisher={Cold Spring Harbor Laboratory},
      doi={10.1101/2023.05.31.542682},
      url={https://doi.org/10.1101/2023.05.31.542682}
  }


Cite our software here::

  @software{tyrone_chen_2023_8135591,
    author       = {Tyrone Chen and
                    Navya Tyagi and
                    Sarthak Chauhan and
                    Anton Y. Peleg and
                    Sonika Tyagi},
    title        = {{genomicBERT and data-free deep-learning model 
                    evaluation}},
    month        = jul,
    year         = 2023,
    publisher    = {Zenodo},
    version      = {latest},
    doi          = {10.5281/zenodo.8135590},
    url          = {https://doi.org/10.5281/zenodo.8135590} 
  }