# Baselines

This directory contains the baselines for our various tasks.

## Differential expression and direction of change

- `sanity_check` contains the MLP and GAT baselines.
- GEARS was run with the [authors' original
  codebase](https://github.com/snap-stanford/GEARS/tree/master/gears)
  without pre-filtering for highly variables genes.
- GenePT was run with the [published
  embeddings](https://github.com/yiqunchen/GenePT)
  using `LogisticRegression` from `scikit-learn` on default settings (as
  published).

## Gene set enrichment
- `gene_set.py` contains the gene set over-representation analysis
code. This requires package `gseapy`.

