lantern

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#+TITLE: LANTERN: an interpretable genotype-phenotype landscape model

DISCLAIMER: LANTERN is currently in alpha and the primary interface is subject to change

• Documentation The official documentation with usage is available at: [[https://lantern-gpl.readthedocs.io/en/latest/index.html][https://lantern-gpl.readthedocs.io]]. Documentation covers instructions for running ~lantern~ on GPL data, including a demonstration on an example dataset. On a typical desktop, examples should run in under ten minutes.

• System Requirements

** Hardware requirements ~lantern~ requires only a standard computer with enough RAM to support the in-memory operations. Runtime of model training on large-scale GPL datasets ($n \geq 10,000$) will benefit from GPU hardware but is not strictly necessary.

** Software requirements This package is supported for macOS and Linux. The package has been tested on the following systems:

• macOS: Catalina (10.15)
• Linux: Ubuntu 18.04

** Python Dependencies ~lantern~ depends primarily on ~pytorch~ and ~gpytorch~, as well as the components of the Python scientific stack:

• ~pandas~
• ~numpy~

• Installation guide Installation time for ~lantern~ is typically less than one minute.

** Install from github ~LANTERN~ currently must be installed from this repository directly, either through pip: #+begin_src bash python -m pip install git+https://github.com/usnistgov/lantern.git #+end_src of by cloning this repository: #+begin_src bash git clone https://github.com/usnistgov/lantern.git cd lantern python setup.py install #+end_src In either case, it is recommended to install inside a [[https://docs.python.org/3/tutorial/venv.html][virtual environment]].

• Manuscript reproduction Source code to reproduce the analysis of the LANTERN manuscript are available at [[https://github.com/usnistgov/lantern/tree/master/manuscript][github.com/usnistgov/lantern/tree/master/manuscript]].

• License This project is covered under the NIST Software License