glucosedao-glucobench 0.4.0

GlucoseDao's fork of GlucoBench by IrinaStatsLab

GlucoBench

The official implementation of the paper "GlucoBench: Curated List of Continuous Glucose Monitoring Datasets with Prediction Benchmarks." If you found our work interesting and plan to re-use the code, please cite us as:

@article{
  author  = {Renat Sergazinov and Valeriya Rogovchenko and Elizabeth Chun and Nathaniel Fernandes and Irina Gaynanova},
  title   = {GlucoBench: Curated List of Continuous Glucose Monitoring Datasets with Prediction Benchmarks},
  journal = {arXiv}
  year    = {2023},
}

Dependencies

We recommend to setup clean Python environment with conda by running conda create -n glucobench python=3.10. Then we can install all dependenices by running pip install -r requirments.txt.

To run Latent ODE model, install torchdiffeq.

Code organization

The code is organized as follows:

• bin/: training commands for all models
• config/: configuration files for all datasets
• data_formatter/
  • base.py: performs all pre-processing for all CGM datasets
• exploratory_analysis/: notebooks with processing steps for pulling the data and converting to .csv files
• lib/
  • gluformer/: model implementation
  • latent_ode/: model implementation
  • *.py: hyper-paraemter tuning, training, validation, and testing scripts
• output/: hyper-parameter optimization and testing logs
• paper_results/: code for producing tables and plots, found in the paper
• utils/: helper functions for model training and testing
• raw_data.zip: web-pulled CGM data (processed using exploratory_analysis)
• environment.yml: conda environment file

Data

The datasets are distributed according to the following licences and can be downloaded from the following links outlined in the table below.

Dataset	License	Number of patients	CGM Frequency
Colas	Creative Commons 4.0	208	5 minutes
Dubosson	Creative Commons 4.0	9	5 minutes
Hall	Creative Commons 4.0	57	5 minutes
Broll	GPL-2	5	5 minutes
Weinstock	Creative Commons 4.0	200	5 minutes

To process the data, follow the instructions in the exploratory_analysis/ folder. Processed datasets should be saved in the raw_data/ folder. We provide examples in the raw_data.zip file.

How to reproduce results?

Setting up the enviroment

We recommend setting up a clean Python environment using Conda. Follow these steps:

1. Create a new environment named glucobench with Python 3.10 by running:

   conda env create -n glucobench python=3.10
   

2. Activate the environment with:

   conda activate glucobench
   

3. Install all required dependencies by running:

   pip install -r requirements.txt
   

4. (Optional) To confirm that you're installing in the correct environment, run:

   which pip
   

   This should display the path to the pip executable within the glucobench environment."

Changing the configs

The config/ folder stores the best hyper-parameters (selected by Optuna) for each dataset and model. The config/ also stores the dataset-specific parameters for interpolation, dropping, splitting, and scaling. To train and evaluate the models with these defaults, we can simply run:

python ./lib/model.py --dataset dataset --use_covs False --optuna False

Changing the hyper-parameters

To change the search grid for hyper-parameters, we need to modify the ./lib/model.py file. Specifically, we look at the objective() function and modify the trial.suggest_* parameters to set the desired ranges. Once we are done, we can run the following command to re-run the hyper-parameter optimization:

python ./lib/model.py --dataset dataset --use_covs False --optuna True

How to work with the repository?

We provide a detailed example of the workflow in the example.ipynb notebook. For clarification, we provide some general suggestions below in order of increasing complexity.

Just the data

To start experimenting with the data, we can run the following command:

import yaml
from data_formatter.base import DataFormatter

with open(f'./config/{dataset}.yaml', 'r') as f:
    config = yaml.safe_load(f)
formatter = DataFormatter(config)

The command exposes an object of class DataFormatter which automatically pre-processes the data upon initialization. The pre-processing steps can be controlled via the config/ files. The DataFormatter object exposes the following attributes:

1. formatter.train_data: training data (as pandas.DataFrame)
2. formatter.val_data: validation data
3. formatter.test_data: testing (in-distribution and out-of-distribution) data i. formatter.test_data.loc[~formatter.test_data.index.isin(formatter.test_idx_ood)]: in-distribution testing data ii. formatter.test_data.loc[formatter.test_data.index.isin(formatter.test_idx_ood)]: out-of-distribution testing data
4. formatter.data: unscaled full data

Integration with PyTorch

Training models with PyTorch typically boils down to (1) defining a Dataset class with __getitem__() method, (2) wrapping it into a DataLoader, (3) defining a torch.nn.Module class with forward() method that implements the model, and (4) optimizing the model with torch.optim in a training loop.

Parts (1) and (2) crucically depend on the definition of the Dataset class. Essentially, having the data in the table format (e.g. formatter.train_data), how do we sample input-output pairs and pass the covariate information? The various Dataset classes conveniently adopted from the Darts library (see here) offer one way to wrap the data into a Dataset class. Different Dataset classes differ in what information is provided to the model:

1. SamplingDatasetPast: supports only past covariates
2. SamplingDatasetDual: supports only future-known covariates
3. SamplingDatasetMixed: supports both past and future-known covariates

Below we give an example of loading the data and wrapping it into a Dataset:

from utils.darts_processing import load_data
from utils.darts_dataset import SamplingDatasetDual

formatter, series, scalers = load_data(seed=0,
                                       dataset=dataset,
                                       use_covs=True, 
                                       cov_type='dual',
                                       use_static_covs=True)
dataset_train = SamplingDatasetDual(series['train']['target'],
                                    series['train']['future'],
                                    output_chunk_length=out_len,
                                    input_chunk_length=in_len,
                                    use_static_covariates=True,
                                    max_samples_per_ts=max_samples_per_ts,)

Parts (3) and (4) are model-specific, so we omit their discussion. For inspiration, we suggest to take a look at the lib/gluformer/model.py and lib/latent_ode/trainer_glunet.py files.