{"repo":"nf-core/drugresponseeval","free":true,"listed":false,"github":"https://github.com/nf-core/drugresponseeval","clone":"git clone https://github.com/nf-core/drugresponseeval.git","description":"Pipeline for testing drug response prediction models in a statistically and biologically sound way.","language":"Nextflow","stars":29,"topics":["bioinformatics","cell-lines","cross-validation","deep-learning","drug-response","drug-response-prediction","drugs","fair-principles","generalization","hyperparameter-tuning"],"license":"MIT","category":"machine-learning","readme_excerpt":"Introduction DrEval is a bioinformatics framework that includes a PyPI package (drevalpy) and a Nextflow pipeline (this repo). DrEval ensures that evaluations are statistically sound, biologically meaningful, and reproducible. DrEval simplifies the implementation of drug response prediction models, allowing researchers to focus on advancing their modeling innovations by automating standardized evaluation protocols and preprocessing workflows. With DrEval, hyperparameter tuning is fair and consistent. With its flexible model interface, DrEval supports any model type, ranging from statistical models to complex neural networks. By contributing your model to the DrEval catalog, you can increase your work's exposure, reusability, and transferability. 1. The response data is loaded 2. All models are trained and evaluated in a cross-validation setting 3. For each CV split, the best hyperparameters are determined using a grid search per model 4. The model is trained on the full training set (train & validation) with the best hyperparameters to predict the test set 5. If randomization tests are enabled, the model is trained on the full training set with the best hyperparameters to predict the randomized test set 6. If robustness tests are enabled, the model is trained N times on the full training set with the best hyperparameters 7. Plots are created summarizing the results For baseline models, no randomization or robustness tests are performed. Usage [!NOTE] If you are new to Nextflo","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/drugresponseeval/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}