shu65 / open-problems-multimodal

1st place solution of Kaggle Open Problems - Multimodal Single-Cell Integration

open-problems-multimodal

1st place solution of Kaggle Open Problems - Multimodal Single-Cell Integration

Preparation

Install the solution code.

pip3 install -e .

In addtion, download the following data

1. Open Problems - Multimodal Single-Cell Integration data set from Kaggle
2. tab separated hgnc_complete_set file from https://www.genenames.org/download/archive/
3. Reactome Pathways Gene Set from https://reactome.org/download-data

Compress data and make addtitional data

compress kaggle dataset and make addtional data to use in training

export DATA_DIR=/path/to/kaggle/dataset/Directory
python3 script/make_compressed_dataset.py --data_dir ${DATA_DIR}
python3 script/make_additional_files.py --data_dir ${DATA_DIR}
python3 script/make_cite_input_mask.py --data_dir ${DATA_DIR} --hgnc_complete_set_path /path/to/hgnc_complete_set --reactome_pathways_path /path/to/reactome_pathways

Training

Multi

python3 scripts/train_mode.py --data_dir ${DATA_DIR} --task_type multi 

Cite

python3 scripts/train_mode.py --data_dir ${DATA_DIR} --task_type cite