Fix methods - Githubissues

openproblems-bio / task_perturbation_prediction

A benchmark on predicting how small molecules change gene expression in different cell types.

https://openproblems.bio/results/perturbation_prediction/

MIT License

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Fix methods #40

Closed rcannood closed 6 months ago

rcannood commented 6 months ago

Describe your changes

Fixes to methods based on the last benchmarking run:

lstm_gru_cnn_ensemble: More shared mem
nn_retraining_with_pseudolabels: Use nvcr tensorflow image to ensure tensorflow is already installed with the proper cuda libraries.
scape: Use nvcr tensorflow image to ensure tensorflow is already installed with the proper cuda libraries.
transformer_ensemble: Increase memory size, and fix device passing to several helper functions.

Checklist before requesting a review

[x] I have performed a self-review of my code
Check the correct box. Does this PR contain:
- [ ] Breaking changes
- [ ] New functionality (new method, new metric, ...)
- [ ] Major changes
- [ ] Minor changes
- [x] Bug fixes
[ ] Proposed changes are described in the CHANGELOG.md
[x] CI Tests succeed and look good!