/DeepVent

Primary LanguagePythonMIT LicenseMIT

DeepVent

Official code for "Towards Safe Mechanical Ventilation Treatment Using Deep Offline Reinforcement Learning" https://arxiv.org/abs/2210.02552

Table of Contents

Note: M1 chip is still not supported in many packages so there might be compatibility issues if you are running using M1 chip.

About the Project

Mechanical ventilation is a key form of life support for patients with pulmonary impairment. Healthcare workers are required to continuously adjust ventilator settings for each patient, a challenging and time consuming task. Hence, it would be beneficial to develop an automated decision support tool to optimize ventilation treatment. We present DeepVent, a Conservative Q-Learning (CQL) based offline Deep Reinforcement Learning (DRL) agent that learns to predict the optimal ventilator parameters for a patient to promote 90 day survival. We design a clinically relevant intermediate reward that encourages continuous improvement of the patient vitals as well as addresses the challenge of sparse reward in RL. We find that DeepVent recommends ventilation parameters within safe ranges, as outlined in recent clinical trials. The CQL algorithm offers additional safety by mitigating the overestimation of the value estimates of out-of-distribution states/actions. We evaluate our agent using Fitted Q Evaluation (FQE) and demonstrate that it outperforms physicians from the MIMIC-III dataset.

Installation

  1. Go to the parent directory
cd DeepVent
  1. Create and activate virtual environment

Linux:

python -m venv env
source env/bin/activate

Windows (run this from the command prompt NOT powershell):

python -m venv env
.\env\Scripts\activate.bat
  1. install the required libraries
pip install -r requirements.txt
  1. install the root package (Run this from the ROOT directory of the repository, i.e. the directory which contains "data_preprocessing", "evaluation", etc.)
pip install -e .
  1. install pytorch with CUDA capabilities

(Only do this if you want to train your own policies, if you are using the provided pre-trained policies then you can skip this step, if you do not have a CUDA-compatible GPU then you cannot train your own policies) Go to https://pytorch.org/get-started/locally/ and follow the instructions to install PyTorch with CUDA capabilities (using pip) on your OS and with your CUDA version.

Processing Data

  1. Data Extraction
  2. Data Imputation
  3. Compute Trajectories
  4. Modify elements
  5. Split the data and create OOD

To run the data preprocessing:

  1. Obtain the raw data following the instructions in data_preprocessing/data_extraction folder. You will need to insert your path in the scripts.
  2. within the parent directory, run data preprocessing
python3 data_preprocessing/run.py

Note: A more detailed description for each section of data preprocessing is provided in the data preprocessing folder.

Training policies

  1. To find the optimal hyperparameters, grid search can be conducted using:
python3 training/find_cql.py 
python3 training/find_dqn.py
  1. Train the policy. Edit the values for the other hyperparameters such as LEARNING_RATE, N_EPOCHS, etc. within the script. The given values are the optimal values that was found in this given problem. The path to the policy weights for each epoch will be output in the console. In the same folder as the policy weights you can find the csv files for all the metrics for the policy at each epoch.
python3 training/train_eval_loop.py

Note: Each run was done with a different train-test split and took around 14 hours to complete.

Running the above scripts will generate ouputs in d3rlpy_logs folder.

  1. Then run python3 training/get_all_final_policies.py to get all policies in the correct format for evaluation (modifying run_num and model_num and fqe_model_num to match the parameters you set in step 3 in training/train_eval_loop.py).

Evaluation

Evaluation directory contains all code necessary to generate graphs and results from DeepVent paper. Requires having 5 runs of both CQL without intermediate reward (DeepVent-), CQL with intermediate reward (DeepVent) and DDQN in the final policies directory defined in constants.py

To simplify things for you, we have provided the trained policies for this problem. These policies are within d3rlpy_logs folder.

If you encounter any bugs while running any files in the evaluation directory, try running train_test_split.py in the data_preprocessing folder

To run evalutaion script, simply do:

cd evaluation
python3 compare_policies.py
python3 percent_each_setting_close_to_physician.py
python3 grouped_action_bar_plot.py
python3 make_u_curves.py
python3 compare_ood_id.py

Citation

@misc{https://doi.org/10.48550/arxiv.2210.02552,

doi = {10.48550/ARXIV.2210.02552},

url = {https://arxiv.org/abs/2210.02552},

author = {Kondrup, Flemming and Jiralerspong, Thomas and Lau, Elaine and de Lara, Nathan and Shkrob, Jacob and Tran, My Duc and Precup, Doina and Basu, Sumana},

keywords = {Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences},

title = {Towards Safe Mechanical Ventilation Treatment Using Deep Offline Reinforcement Learning},

publisher = {arXiv},

year = {2022},

copyright = {arXiv.org perpetual, non-exclusive license}

}