Written by Giulio Isacchini, MPIDS Göttingen - ENS Paris.
The code is written in Python2.7 and not compatible with Python3.
Last updated on 15-03-2020
Reference: On generative models of T cell receptor sequences, Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora, https://arxiv.org/abs/1911.12279
=== Reproduce Plots ===
In order to reproduce the plots you need to unzip the files input.zip and vampire-emerson.zip.
- Sample data.
To sample the data for all figures, run sample_data.py
- Infer the models.
To infer the model for fig1, run fig1_infer.py
To infer the model for fig2, run fig2_infer.py
- Plot the results.
To recreate Fig 1, run fig1_plot.py
To recreate Fig 2a run fig2a_plot.py
To recreate Fig 2b, run fig2b_evaluate.py (in the vampire environment) and then fig2b_plot.py
=== Requisites ===
- olga
- tensorflow
- numpy
- pandas
- scipy
- matplotlib
This directory includes a minimal version of the Sonia package. The full package is available in https://github.com/statbiophys/SONIA/