DrEvalPy: Python Cancer Cell Line Drug Response Prediction Suite

Focus on Innovating Your Models — DrEval Handles the Rest!

• DrEval is a toolkit that ensures drug response prediction evaluations are statistically sound, biologically meaningful, and reproducible.
• Focus on model innovation while using our automated standardized evaluation protocols and preprocessing workflows.
• A flexible model interface supports all model types (e.g. Machine Learning, Stats, Network-based analyses)

By contributing your model to the DrEval catalog, you can increase your work's exposure, reusability, and transferability.

Use DrEval to Build Drug Response Models That Have an Impact

1. Maintained, up-to-date baseline catalog, no need to re-implement literature models

2. Gold standard datasets for benchmarking

3. Consistent application-driven evaluation

4. Ablation studies with permutation tests

5. Cross-study evaluation for generalization analysis

6. Optimized nextflow pipeline for fast experiments

7. Easy-to-use hyperparameter tuning

8. Paper-ready visualizations to display performance

This project is a collaboration of the Technical University of Munich (TUM, Germany) and the Freie Universität Berlin (FU, Germany).

Installation

Using pip:

pip install drevalpy

Using docker:

docker pull ghcr.io/daisybio/drevalpy:main

From source:

git clone https://github.com/daisybio/drevalpy.git
cd drevalpy
pip install poetry
poetry install

Quickstart

To run models from the catalog, you can run:

python run_suite.py --run_id my_first_run --models ElasticNet SimpleNeuralNetwork --dataset GDSC2 --test_mode LCO

This will train and tune a neural network and an elastic net model on gene expression features and drug fingerprint features to predict IC50 values of the GDSC2 database. It will evaluate in "LCO" which is the leave-cell-line-out splitting strategy using 5 fold cross validation. The results will be stored in

results/my_first_run/LCO

You can visualize them using

python create_report.py --run_id my_first_run

This will create an index.html file which you can open in your webbrowser.

You can also run a drug response experiment using Python:

from drevalpy import drug_response_experiment

drug_response_experiment(
            models=["MultiOmicsNeuralNetwork"],
            baselines=["RandomForest"],
            response_data="GDSC1",
            metric="mse",
            n_cv_splits=5,
            test_mode="LPO",
            run_id="my_second_run",
        )

We recommend the use of our nextflow pipeline for computational demanding runs and for improved reproducibility. No knowledge of nextflow is required to run it. The nextflow pipeline is available here: nf-core-drugresponseeval.

Contact

Main developers:

• Judith Bernett, Data Science in Systems Biology, TUM
• Pascal Iversen, Data Integration in the Life Sciences, FU Berlin, Hasso Plattner Institute