├── .gitignore ├── README.md ├── attia_encoder_256.keras ├── requirements.txt └── src ├── core ├── activations.py ├── hierarchical_moe.py ├── hme.py ├── hme_seq.py ├── interp.py ├── model.py ├── module.py ├── sparse_moe.py └── train.py ├── preprocessing ├── data.py ├── data_mimiciv.py ├── mimiciv_notes.md ├── mimiciv_preprocessing │ ├── MIMIC_IV_HAIM_API.py │ ├── README.md │ ├── create_24_phenotyping_task.ipynb │ ├── create_decompensation_task.ipynb │ ├── create_haim_embeddings.ipynb │ ├── create_ihm_task.ipynb │ ├── create_los_task.ipynb │ ├── create_phenotyping_task.ipynb │ ├── create_shortened_version.ipynb │ ├── cxr_icu_stay.ipynb │ ├── ecg_embeddings.ipynb │ ├── haim_replication.ipynb │ ├── hcup_ccs_2015_definitions.yaml │ ├── icd10cmtoicd9gem.csv │ ├── img_embeddings.ipynb │ ├── missingness.ipynb │ ├── note_embeddings.ipynb │ ├── notes_text.ipynb │ ├── npj_replication.ipynb │ ├── npj_utils.py │ ├── plot_ts copy.ipynb │ ├── prediction_util.py │ ├── ts_imputed.ipynb │ └── ts_irregular.ipynb └── preprocessing.py ├── scripts ├── load_result.py ├── main.py ├── main_mimiciv.py ├── moe_cifar_example.py ├── moe_toy_example.py ├── run.sh ├── run_ll.sh ├── run_ls.sh ├── run_mimiciv.sh ├── run_sim.sh ├── run_sl.sh ├── run_ss.sh ├── sim_plots.py └── simulation.ipynb └── utils ├── checkpoint.py ├── config.py ├── ihm.pdf ├── los.pdf ├── los.png ├── pheno.pdf ├── plot.ipynb ├── text_utils.py └── util.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/README.md -------------------------------------------------------------------------------- /attia_encoder_256.keras: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/attia_encoder_256.keras -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/requirements.txt -------------------------------------------------------------------------------- /src/core/activations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/activations.py -------------------------------------------------------------------------------- /src/core/hierarchical_moe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/hierarchical_moe.py -------------------------------------------------------------------------------- /src/core/hme.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/hme.py -------------------------------------------------------------------------------- /src/core/hme_seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/hme_seq.py -------------------------------------------------------------------------------- /src/core/interp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/interp.py -------------------------------------------------------------------------------- /src/core/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/model.py -------------------------------------------------------------------------------- /src/core/module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/module.py -------------------------------------------------------------------------------- /src/core/sparse_moe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/sparse_moe.py -------------------------------------------------------------------------------- /src/core/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/core/train.py -------------------------------------------------------------------------------- /src/preprocessing/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/data.py -------------------------------------------------------------------------------- /src/preprocessing/data_mimiciv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/data_mimiciv.py -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_notes.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_notes.md -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/MIMIC_IV_HAIM_API.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/MIMIC_IV_HAIM_API.py -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/README.md -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_24_phenotyping_task.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_24_phenotyping_task.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_decompensation_task.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_decompensation_task.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_haim_embeddings.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_haim_embeddings.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_ihm_task.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_ihm_task.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_los_task.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_los_task.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_phenotyping_task.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_phenotyping_task.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/create_shortened_version.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/create_shortened_version.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/cxr_icu_stay.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/cxr_icu_stay.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/ecg_embeddings.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/ecg_embeddings.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/haim_replication.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/haim_replication.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/hcup_ccs_2015_definitions.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/hcup_ccs_2015_definitions.yaml -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/icd10cmtoicd9gem.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/icd10cmtoicd9gem.csv -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/img_embeddings.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/img_embeddings.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/missingness.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/missingness.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/note_embeddings.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/note_embeddings.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/notes_text.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/notes_text.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/npj_replication.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/npj_replication.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/npj_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/npj_utils.py -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/plot_ts copy.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/plot_ts copy.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/prediction_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/prediction_util.py -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/ts_imputed.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/ts_imputed.ipynb -------------------------------------------------------------------------------- /src/preprocessing/mimiciv_preprocessing/ts_irregular.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/mimiciv_preprocessing/ts_irregular.ipynb -------------------------------------------------------------------------------- /src/preprocessing/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/preprocessing/preprocessing.py -------------------------------------------------------------------------------- /src/scripts/load_result.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/load_result.py -------------------------------------------------------------------------------- /src/scripts/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/main.py -------------------------------------------------------------------------------- /src/scripts/main_mimiciv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/main_mimiciv.py -------------------------------------------------------------------------------- /src/scripts/moe_cifar_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/moe_cifar_example.py -------------------------------------------------------------------------------- /src/scripts/moe_toy_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/moe_toy_example.py -------------------------------------------------------------------------------- /src/scripts/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run.sh -------------------------------------------------------------------------------- /src/scripts/run_ll.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run_ll.sh -------------------------------------------------------------------------------- /src/scripts/run_ls.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run_ls.sh -------------------------------------------------------------------------------- /src/scripts/run_mimiciv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run_mimiciv.sh -------------------------------------------------------------------------------- /src/scripts/run_sim.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run_sim.sh -------------------------------------------------------------------------------- /src/scripts/run_sl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run_sl.sh -------------------------------------------------------------------------------- /src/scripts/run_ss.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/run_ss.sh -------------------------------------------------------------------------------- /src/scripts/sim_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/sim_plots.py -------------------------------------------------------------------------------- /src/scripts/simulation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/scripts/simulation.ipynb -------------------------------------------------------------------------------- /src/utils/checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/checkpoint.py -------------------------------------------------------------------------------- /src/utils/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/config.py -------------------------------------------------------------------------------- /src/utils/ihm.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/ihm.pdf -------------------------------------------------------------------------------- /src/utils/los.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/los.pdf -------------------------------------------------------------------------------- /src/utils/los.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/los.png -------------------------------------------------------------------------------- /src/utils/pheno.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/pheno.pdf -------------------------------------------------------------------------------- /src/utils/plot.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/plot.ipynb -------------------------------------------------------------------------------- /src/utils/text_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/text_utils.py -------------------------------------------------------------------------------- /src/utils/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronhan223/FuseMoE/HEAD/src/utils/util.py --------------------------------------------------------------------------------