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https://github.com/rvandewater/yaib
🧪Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109
https://github.com/rvandewater/yaib
amsterdamumcdb benchmark clinical-data clinical-ml deep-learning ehr eicu-crd framework hirid-dataset icu machine-learning mimic-iii mimic-iv patient-monitoring time-series
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🧪Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109
- Host: GitHub
- URL: https://github.com/rvandewater/yaib
- Owner: rvandewater
- License: mit
- Created: 2022-08-15T09:13:56.000Z (over 2 years ago)
- Default Branch: development
- Last Pushed: 2024-10-18T08:31:46.000Z (4 months ago)
- Last Synced: 2024-10-19T11:10:51.042Z (4 months ago)
- Topics: amsterdamumcdb, benchmark, clinical-data, clinical-ml, deep-learning, ehr, eicu-crd, framework, hirid-dataset, icu, machine-learning, mimic-iii, mimic-iv, patient-monitoring, time-series
- Language: Python
- Homepage: https://github.com/rvandewater/YAIB/wiki
- Size: 10.3 MB
- Stars: 50
- Watchers: 5
- Forks: 9
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.MD
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# 🧪 Yet Another ICU Benchmark
[](https://github.com/rvandewater/YAIB/actions/workflows/ci.yml)
[](https://github.com/psf/black)
[](http://arxiv.org/abs/2306.05109)
[](https://pypi.python.org/pypi/yaib/)
[](https://www.python.org/downloads/release/python-3100/)
[](https://pytorch.org/get-started/locally/)
[](https://pytorchlightning.ai/)
[](LICENSE)
[//]: # (TODO: add coverage once we have some tests )
Yet another ICU benchmark (YAIB) provides a framework for doing clinical machine learning experiments on Intensive Care Unit
(ICU) EHR data.
We support the following datasets out of the box:
| **Dataset** | [MIMIC-III](https://physionet.org/content/mimiciii/) / [IV](https://physionet.org/content/mimiciv/) | [eICU-CRD](https://physionet.org/content/eicu-crd/) | [HiRID](https://physionet.org/content/hirid/1.1.1/) | [AUMCdb](https://doi.org/10.17026/dans-22u-f8vd) |
|-----------------------------|-----------------------------------------------------------------------------------------------------|-----------------------------------------------------|-----------------------------------------------------|--------------------------------------------------|
| **Admissions** | 40k / 73k | 200k | 33k | 23k |
| **Version** | v1.4 / v2.2 | v2.0 | v1.1.1 | v1.0.2 |
| **Frequency** (time-series) | 1 hour | 5 minutes | 2 / 5 minutes | up to 1 minute |
| **Originally published** | 2015 / 2020 | 2017 | 2020 | 2019 |
| **Origin** | USA | USA | Switzerland | Netherlands |
New datasets can also be added. We are currently working on a package to make this process as smooth as possible.
The benchmark is designed for operating on preprocessed parquet files.
We provide five common tasks for clinical prediction by default:
| No | Task | Frequency | Type |
|-----|---------------------------|---------------------------|-----------------------|
| 1 | ICU Mortality | Once per Stay (after 24H) | Binary Classification |
| 2 | Acute Kidney Injury (AKI) | Hourly (within 6H) | Binary Classification |
| 3 | Sepsis | Hourly (within 6H) | Binary Classification |
| 4 | Kidney Function(KF) | Once per stay | Regression |
| 5 | Length of Stay (LoS) | Hourly (within 7D) | Regression |
New tasks can be easily added.
To get started right away, we include the eICU and MIMIC-III demo datasets in our repository.
The following repositories may be relevant as well:
- [YAIB-cohorts](https://github.com/rvandewater/YAIB-cohorts): Cohort generation for YAIB.
- [YAIB-models](https://github.com/rvandewater/YAIB-models): Pretrained models for YAIB.
- [ReciPys](https://github.com/rvandewater/ReciPys): Preprocessing package for YAIB pipelines.
For all YAIB-related repositories, please see: https://github.com/stars/rvandewater/lists/yaib.
# 📄Paper
To reproduce the benchmarks in our paper, we refer to the [ML reproducibility document](PAPER.md).
If you use this code in your research, please cite the following publication:
```
@inproceedings{vandewaterYetAnotherICUBenchmark2024,
title = {Yet Another ICU Benchmark: A Flexible Multi-Center Framework for Clinical ML},
shorttitle = {Yet Another ICU Benchmark},
booktitle = {The Twelfth International Conference on Learning Representations},
author = {van de Water, Robin and Schmidt, Hendrik Nils Aurel and Elbers, Paul and Thoral, Patrick and Arnrich, Bert and Rockenschaub, Patrick},
year = {2024},
month = oct,
urldate = {2024-02-19},
langid = {english},
}
```
This paper can also be found on arxiv [2306.05109](https://arxiv.org/abs/2306.05109)
# 💿Installation
YAIB is currently ideally installed from source, however we also offer it an early PyPi release.
## Installation from source
First, we clone this repository using git:
````
git clone https://github.com/rvandewater/YAIB.git
````
Please note the branch. The newest features and fixes are available at the development branch:
````
git checkout development
````
YAIB can be installed using a conda environment (preferred) or pip. Below are the three CLI commands to install YAIB
using **conda**.
The first command will install an environment based on Python 3.10.
```
conda env update -f environment.yml
```
> Use `environment.yml` on x86 hardware. Please note that this installs Pytorch as well.
> For mps, one needs to comment out _pytorch-cuda_, see the [PyTorch install guide](https://pytorch.org/get-started/locally/).
We then activate the environment and install a package called `icu-benchmarks`, after which YAIB should be operational.
```
conda activate yaib
pip install -e .
```
[//]: # (If you want to install the icu-benchmarks package with **pip**, execute the command below:)
[//]: # ()
[//]: # (```)
[//]: # (pip install torch numpy && pip install -e .)
[//]: # (```)
After installation, please check if your Pytorch version works with CUDA (in case available) to ensure the best performance.
YAIB will automatically list available processors at initialization in its log files.
# 👩💻Usage
Please refer to [our wiki](https://github.com/rvandewater/YAIB/wiki) for detailed information on how to use YAIB.
## Quickstart 🚀 (demo data)
The authors of MIMIC-III and eICU have made a small demo dataset available to demonstrate their use. They can be found on Physionet: [MIMIC-III Clinical Database Demo](https://physionet.org/content/mimiciii-demo/1.4/) and [eICU Collaborative Research Database Demo](https://physionet.org/content/eicu-crd-demo/2.0.1/). These datasets are published under the [Open Data Commons Open Database License v1.0](https://opendatacommons.org/licenses/odbl/1-0/) and can be used without credentialing procedure. We have created demo cohorts processed **solely from these datasets** for each of our currently supported task endpoints. To the best of our knowledge, this complies with the license and the respective dataset author's instructions. Usage of the task cohorts and the dataset is only permitted with the above license.
We **strongly recommend** completing a human subject research training to ensure you properly handle human subject research data.
In the folder `demo_data` we provide processed publicly available demo datasets from eICU and MIMIC with the necessary labels
for `Mortality at 24h`,`Sepsis`, `Akute Kidney Injury`, `Kidney Function`, and `Length of Stay`.
If you do not yet have access to the ICU datasets, you can run the following command to train models for the included demo
cohorts:
```
wandb sweep --verbose experiments/demo_benchmark_classification.yml
wandb sweep --verbose experiments/demo_benchmark_regression.yml
```
```train
wandb agent
```
> Tip: You can choose to run each of the configurations on a SLURM cluster instance by `wandb agent --count 1 `
> Note: You will need to have a wandb account and be logged in to run the above commands.
## Getting the datasets
HiRID, eICU, and MIMIC IV can be accessed through [PhysioNet](https://physionet.org/). A guide to this process can be
found [here](https://eicu-crd.mit.edu/gettingstarted/access/).
AUMCdb can be accessed through a separate access [procedure](https://github.com/AmsterdamUMC/AmsterdamUMCdb). We do not have
involvement in the access procedure and can not answer to any requests for data access.
## Cohort creation
Since the datasets were created independently of each other, they do not share the same data structure or data identifiers. In
order to make them interoperable, use the preprocessing utilities
provided by the [ricu package](https://github.com/eth-mds/ricu).
Ricu pre-defines a large number of clinical concepts and how to load them from a given dataset, providing a common interface to
the data, that is used in this
benchmark. Please refer to our [cohort definition](https://github.com/rvandewater/YAIB-cohorts) code for generating the cohorts
using our python interface for ricu.
After this, you can run the benchmark once you have gained access to the datasets.
# 👟 Running YAIB
## Preprocessing and Training
The following command will run training and evaluation on the MIMIC demo dataset for (Binary) mortality prediction at 24h with
the
LGBMClassifier. Child samples are reduced due to the small amount of training data. We load available cache and, if available,
load
existing cache files.
```
icu-benchmarks \
-d demo_data/mortality24/mimic_demo \
-n mimic_demo \
-t BinaryClassification \
-tn Mortality24 \
-m LGBMClassifier \
-hp LGBMClassifier.min_child_samples=10 \
--generate_cache \
--load_cache \
--seed 2222 \
-l ../yaib_logs/ \
--tune
```
> For a list of available flags, run `icu-benchmarks train -h`.
> Run with `PYTORCH_ENABLE_MPS_FALLBACK=1` on Macs with Metal Performance Shaders.
[//]: # (> Please note that, for Windows based systems, paths need to be formatted differently, e.g: ` r"\..\data\mortality_seq\hirid"`.)
> For Windows based systems, the next line character (\\) needs to be replaced by (^) (Command Prompt) or (`) (Powershell)
> respectively.
Alternatively, the easiest method to train all the models in the paper is to run these commands from the directory root:
```train
wandb sweep --verbose experiments/benchmark_classification.yml
wandb sweep --verbose experiments/benchmark_regression.yml
```
This will create two hyperparameter sweeps for WandB for the classification and regression tasks.
This configuration will train all the models in the paper. You can then run the following command to train the models:
```train
wandb agent
```
> Tip: You can choose to run each of the configurations on a SLURM cluster instance by `wandb agent --count 1 `
> Note: You will need to have a wandb account and be logged in to run the above commands.
## Evaluate or Finetune
It is possible to evaluate a model trained on another dataset and no additional training is done.
In this case, the source dataset is the demo data from MIMIC and the target is the eICU demo:
```
icu-benchmarks \
--eval \
-d demo_data/mortality24/eicu_demo \
-n eicu_demo \
-t BinaryClassification \
-tn Mortality24 \
-m LGBMClassifier \
--generate_cache \
--load_cache \
-s 2222 \
-l ../yaib_logs \
-sn mimic \
--source-dir ../yaib_logs/mimic_demo/Mortality24/LGBMClassifier/2022-12-12T15-24-46/repetition_0/fold_0
```
> A similar syntax is used for finetuning, where a model is loaded and then retrained. To run finetuning, replace `--eval` with `-ft`.
## Models
We provide several existing machine learning models that are commonly used for multivariate time-series data.
`pytorch` is used for the deep learning models, `lightgbm` for the boosted tree approaches, and `sklearn` for other classical
machine learning models.
The benchmark provides (among others) the following built-in models:
- [Logistic Regression](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html?highlight=logistic+regression):
Standard regression approach.
- [Elastic Net](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.ElasticNet.html): Linear regression with
combined L1 and L2 priors as regularizer.
- [LightGBM](https://proceedings.neurips.cc/paper/2017/file/6449f44a102fde848669bdd9eb6b76fa-Paper.pdf): Efficient gradient
boosting trees.
- [Long Short-term Memory (LSTM)](https://ieeexplore.ieee.org/document/818041): The most commonly used type of Recurrent Neural
Networks for long sequences.
- [Gated Recurrent Unit (GRU)](https://arxiv.org/abs/1406.1078) : A extension to LSTM which showed
improvements ([paper](https://arxiv.org/abs/1412.3555)).
- [Temporal Convolutional Networks (TCN)](https://arxiv.org/pdf/1803.01271 ): 1D convolution approach to sequence data. By
using dilated convolution to extend the receptive field of the network it has shown great performance on long-term
dependencies.
- [Transformers](https://papers.nips.cc/paper/2017/file/3f5ee243547dee91fbd053c1c4a845aa-Paper.pdf): The most common Attention
based approach.
# 🛠️ Development
To adapt YAIB to your own use case, you can use
the [development information](https://github.com/rvandewater/YAIB/wiki/Contribution-and-development) page as a reference.
We appreciate contributions to the project. Please read the [contribution guidelines](CONTRIBUTING.MD) before submitting a pull
request.
# Acknowledgements
This project has been developed partially under the funding of “Gemeinsamer Bundesausschuss (G-BA) Innovationsausschuss” in the framework of “CASSANDRA - Clinical ASSist AND aleRt Algorithms”.
(project number 01VSF20015). We would like to acknowledge the work of Alisher Turubayev, Anna Shopova, Fabian Lange, Mahmut Kamalak, Paul Mattes, and Victoria Ayvasky for adding Pytorch Lightning, Weights and Biases compatibility, and several optional imputation methods to a later version of the benchmark repository.
We do not own any of the datasets used in this benchmark. This project uses heavily adapted components of
the [HiRID benchmark](https://github.com/ratschlab/HIRID-ICU-Benchmark/). We thank the authors for providing this codebase and
encourage further development to benefit the scientific community. The demo datasets have been released under
an [Open Data Commons Open Database License (ODbL)](https://opendatacommons.org/licenses/odbl/1-0/).
# License
This source code is released under the MIT license, included [here](LICENSE). We do not own any of the datasets used or
included in this repository.