medical-coding-reproducibility
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Download Latest Version (.zip)- defaults.yaml
- mean_average_precision.yaml
- no_wandb.yaml
- sweep.yaml
- defaults.yaml
- mimiciii_50.yaml
- mimiciii_clean.yaml
- mimiciii_full.yaml
- mimiciv_icd10.yaml
- mimiciv_icd9.yaml
- defaults.yaml
- code_desc.yaml
- defaults.yaml
- huggingface.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- one_hot.yaml
- defaults.yaml
- mimiciii.yaml
- defaults.yaml
- reduce_lr_on_plateau.yaml
- warmup_linear_decay.yaml
- defaults.yaml
- no_auc.yaml
- reproducibility.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- adam.yaml
- adamw.yaml
- sweep-hyperparameters-lr-scheduler.yaml
- sweep-max-len.yaml
- sweep-threshold.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- caml.yaml
- laat.yaml
- multi_res_conv.yaml
- plm_icd.yaml
- vanillaconv.yaml
- vanillagru.yaml
- sweep-best.yaml
- sweep-mimiciv-icd10.yaml
- sweep-mimiciv-icd9.yaml
- sweep-reproducibility.yaml
- sweep-training-data-mimiciv-icd9.yaml
- sweep-training-data.yaml
- defaults.yaml
- word2vec.yaml
- bow.yaml
- huggingface.yaml
- seq_tokens.yaml
- defaults.yaml
- config.yaml
- mimiciii_50_splits.feather
- mimiciii_clean_splits.feather
- mimiciii_clean_subsplit_0.2.feather
- mimiciii_clean_subsplit_0.4.feather
- mimiciii_clean_subsplit_0.6.feather
- mimiciii_clean_subsplit_0.8.feather
- mimiciii_full_splits.feather
- mimiciv_icd10_split.feather
- mimiciv_icd10_train_subset_10k.feather
- mimiciv_icd10_train_subset_25k.feather
- mimiciv_icd10_train_subset_50k.feather
- mimiciv_icd10_train_subset_75k.feather
- mimiciv_icd9_split.feather
- mimiciv_icd9_train_subset_100k.feather
- mimiciv_icd9_train_subset_10k.feather
- mimiciv_icd9_train_subset_125k.feather
- mimiciv_icd9_train_subset_25k.feather
- mimiciv_icd9_train_subset_50k.feather
- mimiciv_icd9_train_subset_75k.feather
- code_count_vs_f1_icd9_diag.png
- code_count_vs_f1_icd9_proc.png
- code_count_vs_f1_mean.png
- code_count_vs_f1_mean_filtered.png
- code_count_vs_f1_std.png
- f1_micro_vs_num_codes.png
- f1_micro_vs_num_words.png
- threshold_tuning_macro_full.png
- threshold_tuning_micro_full.png
- code_count_vs_f1_icd10_diag.png
- code_count_vs_f1_icd10_proc.png
- code_count_vs_f1_mean.png
- code_count_vs_f1_std.png
- f1_micro_vs_num_codes.png
- f1_micro_vs_num_words.png
- mcnemar_all.png
- mcnemar_common.png
- mcnemar_rare.png
- threshold_tuning_macro_full.png
- threshold_tuning_micro_full.png
- code_count_vs_f1_icd9_diag.png
- code_count_vs_f1_icd9_proc.png
- code_count_vs_f1_mean.png
- code_count_vs_f1_std.png
- f1_micro_vs_num_codes.png
- f1_micro_vs_num_words.png
- mcnemar_all.png
- threshold_tuning_macro_full.png
- threshold_tuning_micro_full.png
- train_size_f1.png
- train_size_f1_macro.png
- train_size_f1_micro.png
- chapters.png
- code_count_vs_f1_all_datasets.png
- code_count_vs_f1_all_datasets_filtered.png
- mimiciv_code_freq.png
- code_analysis.ipynb
- __init__.cpython-310.pyc
- __init__.cpython-38.pyc
- __init__.cpython-39.pyc
- utils.cpython-310.pyc
- utils.cpython-38.pyc
- utils.cpython-39.pyc
- __init__.py
- generate_mimiciii_clean_splits.py
- generate_mimiciv_splits.py
- prepare_mimiciii_clean.py
- prepare_mimiciii_mullenbach.py
- prepare_mimiciv.py
- utils.py
- exploritory_data_analysis-checkpoint.ipynb
- mimiciii_data_analysis-checkpoint.ipynb
- Untitled-checkpoint.ipynb
- utils.cpython-39.pyc
- wandb_utils.cpython-310.pyc
- wandb_utils.cpython-39.pyc
- mcnemars_test.cpython-310-pytest-7.2.1.pyc
- db_tuning.py
- mcnemars_test.py
- num_codes_per_case_f1.py
- num_words_f1.py
- training_data_plot.py
- mcnemars_test.cpython-310-pytest-7.2.1.pyc
- db_tuning.py
- mcnemars_test.py
- num_codes_per_case_f1.py
- num_words_f1.py
- training_data_plot.py
- mcnemars_test.cpython-310-pytest-7.2.1.pyc
- db_tuning.py
- mcnemars_test.py
- num_codes_per_case_f1.py
- num_words_f1.py
- training_data_plot.py
- code_freq_f1.py
- mimiciv_code_dist.py
- ablation-study.py
- fair_and_best.py
- mimiciv_icd10.py
- mimiciv_icd9.py
- reproducibility.py
- utils.py
- wandb_utils.py
- __init__.cpython-310.pyc
- __init__.cpython-38.pyc
- __init__.cpython-39.pyc
- factories.cpython-310.pyc
- factories.cpython-38.pyc
- factories.cpython-39.pyc
- lookups.cpython-310.pyc
- lookups.cpython-39.pyc
- metrics.cpython-310.pyc
- metrics.cpython-39.pyc
- optimizer.cpython-39.pyc
- settings.cpython-310.pyc
- settings.cpython-38.pyc
- settings.cpython-39.pyc
- __init__.cpython-310.pyc
- __init__.cpython-38.pyc
- __init__.cpython-39.pyc
- base_dataset.cpython-39.pyc
- batch_sampler.cpython-310.pyc
- batch_sampler.cpython-39.pyc
- data_pipeline.cpython-310.pyc
- data_pipeline.cpython-38.pyc
- data_pipeline.cpython-39.pyc
- data_utils.cpython-38.pyc
- data_utils.cpython-39.pyc
- dataclasses.cpython-39.pyc
- datasets.cpython-310.pyc
- datasets.cpython-39.pyc
- datatypes.cpython-310.pyc
- datatypes.cpython-38.pyc
- datatypes.cpython-39.pyc
- length_sampler.cpython-39.pyc
- mimiciii_data_utils.cpython-39.pyc
- mullenbach_dataset.cpython-39.pyc
- preprocessor.cpython-39.pyc
- tokenizers.cpython-310.pyc
- tokenizers.cpython-38.pyc
- tokenizers.cpython-39.pyc
- transform.cpython-310.pyc
- transform.cpython-39.pyc
- __init__.py
- batch_sampler.py
- data_pipeline.py
- datasets.py
- datatypes.py
- tokenizers.py
- transform.py
- __init__.cpython-310.pyc
- __init__.cpython-38.pyc
- __init__.cpython-39.pyc
- base_model.cpython-310.pyc
- base_model.cpython-38.pyc
- base_model.cpython-39.pyc
- corti_code.cpython-310.pyc
- corti_code.cpython-39.pyc
- get_model.cpython-38.pyc
- get_model.cpython-39.pyc
- laat.cpython-310.pyc
- laat.cpython-39.pyc
- mullenbach.cpython-39.pyc
- mullenbach_models.cpython-310.pyc
- mullenbach_models.cpython-38.pyc
- mullenbach_models.cpython-39.pyc
- multi_res_cnn.cpython-310.pyc
- multi_res_cnn.cpython-39.pyc
- onnx_model.cpython-310.pyc
- onnx_model.cpython-39.pyc
- plm_icd.cpython-310.pyc
- plm_icd.cpython-39.pyc
- attention.cpython-310.pyc
- attention.cpython-39.pyc
- attention.py
- __init__.py
- base_model.py
- laat.py
- mullenbach_models.py
- multi_res_cnn.py
- plm_icd.py
- __init__.cpython-310.pyc
- __init__.cpython-39.pyc
- base_text_encoder.cpython-310.pyc
- base_text_encoder.cpython-39.pyc
- mullenbach.cpython-39.pyc
- word2vec.cpython-310.pyc
- word2vec.cpython-39.pyc
- __init__.py
- base_text_encoder.py
- word2vec.py
- __init__.cpython-310.pyc
- __init__.cpython-39.pyc
- callbacks.cpython-310.pyc
- callbacks.cpython-39.pyc
- trainer.cpython-310.pyc
- trainer.cpython-39.pyc
- __init__.py
- callbacks.py
- trainer.py
- __init__.cpython-310.pyc
- __init__.cpython-39.pyc
- decision_boundary.cpython-310.pyc
- decision_boundary.cpython-39.pyc
- seed.cpython-310.pyc
- seed.cpython-39.pyc
- tensors.cpython-310.pyc
- tensors.cpython-39.pyc
- __init__.cpython-310.pyc
- __init__.cpython-39.pyc
- helper_funcs.cpython-310.pyc
- helper_funcs.cpython-39.pyc
- stratify.cpython-310.pyc
- stratify.cpython-39.pyc
- __init__.py
- helper_funcs.py
- stratify.py
- __init__.py
- decision_boundary.py
- seed.py
- tensors.py
- __init__.py
- factories.py
- lookups.py
- metrics.py
- settings.py
- test_factories.cpython-310-pytest-7.2.1.pyc
- test_factories.cpython-38-pytest-5.4.3.pyc
- test_factories.cpython-39-pytest-7.1.3.pyc
- test_metrics.cpython-310-pytest-7.2.1.pyc
- test_metrics.cpython-39-pytest-7.1.3.pyc
- test_data_utils.cpython-39-pytest-7.1.3.pyc
- test_dataclasses.cpython-39-pytest-7.1.3.pyc
- test_preprocessor.cpython-310-pytest-7.2.1.pyc
- test_preprocessor.cpython-39-pytest-7.1.3.pyc
- test_preprocessor.py
- test_factories.py
- test_metrics.py
- .gitignore
- LICENSE
- main.py
- README.md
- requirements.txt
- setup.py
# Installation Guide
1. Get the code
git clone https://github.com/JoakimEdin/medical-coding-reproducibility
Downloads the entire project code from GitHub to your computer.
cd medical-coding-reproducibility
Moves into the project folder you just downloaded.
2. Python
Easy RecommendedPrerequisites
pip install -r requirements.txt
Installs the Python libraries listed in requirements.txt (or similar).
python main.py
Runs the Python script (or module).
If it runs without errors and prints output in the terminal, it worked.
// repository documentation
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