index.rst

Welcome to 🧬 BEND's documentation!

BEND is a Benchmark collection for evaluating the performance of DNA language models (LMs). The BEND codebase serves three purposes:

• Providing a unified interface for computing embeddings from pretrained DNA LMs.
• Extracting sequences from reference genomes using coordinates listed in bed files, and computing embeddings for these sequences for training and evaluating models.
• Training lightweight supervised CNN models that use DNA LM embeddings as input, and evaluating their performance on a variety of tasks.

The documentation covers the BEND codebase and includes instructions on how to extend it to new LMs and tasks. For a tutorial on how to run BEND on existing tasks, please refer to the README file on GitHub.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   hydra
   bend.utils.embedders
   adding_embedders
   bend.models
   bend.utils
   bend.io

.. automodule:: bend.models
    :members:

.. automodule:: bend.utils
    :members:
    :no-index: embedders

.. automodule:: bend.io
    :members:

Indices and tables

• :ref:`genindex`
• :ref:`modindex`
• :ref:`search`