In theory, reproducing this paper should only require a clone of a public Git repository, and the execution of a Makefile (detailed in the README of the paper repository at https://github.com/psychoinformatics-de/paper-remodnav). We've set up our paper to be dynamically generated, retrieving and installing the relevant data and software automatically, and we've even created a tutorial about it, so that others can reuse the same setup for their work. Nevertheless, we've for example never tried it out across different operating systems - who knows whether it works on Windows? We'd love to share the tips and tricks we found to work, and even more love feedback on how to improve this further.
Because: - Two fellow PhDs working on different topics have been able to reproduce some figures by following the README instructions and I hope this extends to other people - I've tried to incorporate as many of the best practices as possible to make my code and data open and accessible - I've tried to make sure that my data is exactly reproducible with the specified random seed strategy - the paper suggests a method that should be useful to other researchers in my field, which is not useful unless my results are reproducible
The current code is written in Torch, which is no longer actively maintained. Since deep learning in nanophotonics is an area of active interest (e.g. for the design of new metamaterials), it is important to update the code to use a more modern deep learning library such as tensorflow/keras
I tried hard to make this paper as reproducible as possible, but as techniques and dependencies become more complex, it is hard to make it 100% clear. Any form of feedback is more than welcome.
The original data took quite a while to produce for a previous paper, but for this paper, all tables and figures should be exactly reproducible by simply running the jupyter notebook.