Repo of master thesis

Workflow

Intermediary data is not stored on this repo and has to be generated. Run the following files if this is your first time:

checks.ipynb to create folder structure (where the following scripts will save their data)
Eligibility Criteria.ipynb to generate list of eligible patient ids
Generating Dataset Pipeline.ipynb to generate a json dataset of the admissions data
Split dataset.ipynb to generate the train-validation-test splits.
Register best model.ipynb to create, train and save a model's weights and hyperparameters
Create Variational Outputs.ipynb to use the previous model (or any other really) to generate several forward passes on the validation set

Having done this the analysis notebooks can work:

Accuracy as a function of confidence.ipynb for the general uncertainty analysis
TODO

To be able to run and reproduce this repo, create a conda environment:

conda env create -n <env_name> -f environment.yml

Name		Name	Last commit message	Last commit date
Latest commit History 83 Commits
Abstention		Abstention
EDAs		EDAs
Generate model outputs		Generate model outputs
Hyper Parameter Tunning		Hyper Parameter Tunning
Register Models		Register Models
Setup		Setup
grouper_data		grouper_data
icd_mappings		icd_mappings
media		media
mourga_variational		mourga_variational
results		results
utils		utils
.env		.env
.gitignore		.gitignore
CITATION.cff		CITATION.cff
CodesGrouper_Playground.ipynb		CodesGrouper_Playground.ipynb
Describing MIMIC.ipynb		Describing MIMIC.ipynb
ICDCodesGrouper.py		ICDCodesGrouper.py
ICDMappings.py		ICDMappings.py
Improving Metrics.ipynb		Improving Metrics.ipynb
Logits2Predictions.py		Logits2Predictions.py
Metrics.py		Metrics.py
MimicIII.py		MimicIII.py
MimicIV.py		MimicIV.py
MostFrequent.py		MostFrequent.py
MostFrequent_experiment.ipynb		MostFrequent_experiment.ipynb
README.md		README.md
RNN.ipynb		RNN.ipynb
Testing mimic.ipynb		Testing mimic.ipynb
Untitled.ipynb		Untitled.ipynb
Untitled6.ipynb		Untitled6.ipynb
config.py		config.py
environment.yml		environment.yml
icare2021_EDA.ipynb		icare2021_EDA.ipynb
icare2021_eligibility.ipynb		icare2021_eligibility.ipynb
icare21_pytorch.ipynb		icare21_pytorch.ipynb
icare_pytorchV3.ipynb		icare_pytorchV3.ipynb
icare_pytorchV5.ipynb		icare_pytorchV5.ipynb
latest.ipynb		latest.ipynb
mimicIV_ts.1.month		mimicIV_ts.1.month
mimic_iii_pytorchV2.ipynb		mimic_iii_pytorchV2.ipynb
rnn_utils.py		rnn_utils.py
temperature_scaling.py		temperature_scaling.py
test.csv		test.csv
testbed.ipynb		testbed.ipynb
train_variational.ipynb		train_variational.ipynb