OpenProblems2022Analysis

Analysis of OpenProblems 2022 Kaggle competition on modality prediction in longitudinal single-cell data

Re-implmentation of the top 3 methods for modality prediction

Please find the description on how to install the top three methods (top solutions according to overall rank) at:

• Rank 1: code/rank1/open-problems-multimodal
• Rank 2: separate repository for easier installation: https://github.com/lueckenlab/senkin-tmp-cite-pred/
• Rank 3: code/open-problems-multimodal-3rd-solution

With example notebooks to run the best models of the Multiome and CITE-Seq tasks:

• Rank 1 (Best on Multiome task): code/Run_rank_1_model_with_open_problems_data.ipynb & code/Run_rank_1_model_with_new_data.ipynb
• Rank 2 (Best on Cite-Seq task): example.ipynb

Downstream analysis

See reproducibility notebooks for figures in code/