├── .gitignore ├── LICENSE.md ├── README.md ├── conda_environment.yml ├── config_dataset ├── dataset_utils.py ├── main_config │ ├── testmode.csv │ ├── train.csv │ └── val.csv └── make_dataset_setting_file.py ├── data ├── bpe_simple_vocab_16e6.txt.gz ├── dummy_dataframes │ ├── df_clinicobiological_data.csv │ └── gpt_augs.txt └── dummy_mri_dataset │ ├── 001-0001-A-A │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ ├── D30 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ │ └── .placeholder │ ├── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M3 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ └── .placeholder │ ├── 001-0002-B-B │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ └── .placeholder │ ├── 001-0003-C-C │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ ├── D30 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ │ └── .placeholder │ ├── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M3 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ └── .placeholder │ ├── 001-0004-D-D │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ ├── D30 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ │ └── .placeholder │ ├── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M3 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ └── .placeholder │ ├── 001-0005-E-E │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ └── .placeholder │ ├── 001-0006-F-F │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ └── .placeholder │ ├── 001-0007-G-G │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ ├── D30 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ │ └── .placeholder │ ├── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M3 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ └── .placeholder │ ├── 001-0008-H-H │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ └── .placeholder │ ├── 001-0009-I-I │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ ├── D30 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ │ └── .placeholder │ ├── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M3 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_TUB │ │ └── .placeholder │ ├── 001-0010-J-J │ ├── D15 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_iv │ │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_art │ │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ │ └── .placeholder │ └── M12 │ │ ├── 1_WATER_AX_LAVA-Flex_ss_IV │ │ └── .placeholder │ │ ├── 2_WATER_AX_LAVA-Flex_ART │ │ └── .placeholder │ │ └── 3_WATER_AX_LAVA-Flex_tub │ │ └── .placeholder │ └── dummy_mri.nii.gz ├── figures └── overview_final.jpg ├── main_train.py ├── models ├── model.py ├── model_config.yaml └── model_pretrained.py ├── slurm_main_train.py └── utils ├── dataset.py ├── scheduler.py ├── simple_tokenizer.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leomlck/MEDIMP/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leomlck/MEDIMP/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leomlck/MEDIMP/HEAD/README.md -------------------------------------------------------------------------------- /conda_environment.yml: 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