Hendrik Raetz
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hendraet.bsky.social
Hendrik Raetz
@hendraet.bsky.social
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Reposted by Hendrik Raetz
pascivers.bsky.social
Despite hundreds of published models for cancer drug response prediction, none are used in clinical practice.

Why?

In our preprint, we outline key challenges and introduce a living benchmark to help the field move forward.

Check out the thread by my co–first author @judith-bernett.bsky.social:
judith-bernett.bsky.social Judith Bernett @judith-bernett.bsky.social · Jun 3
🧬🖥️So excited to show you the outcome of @pascivers.bsky.social and my latest project: "From Hype to Health Check: Critical Evaluation of Drug Response Prediction Models with DrEval" doi.org/10.1101/2025.05.26.655288, published with M. Picciani, M. Wilhelm, K. Baum & @itisalist.bsky.social.
🧵1/10
Overview of the DrEval framework. Via input options, implemented state-of-the-art models can be compared against baselines of varying complexity. We address obstacles to progress in the field at each point in our pipeline: Our framework is available on PyPI and nf-core and we follow FAIReR standards for optimal reproducibility. DrEval is easily extendable as demonstrated here with a pseudocode implementation of a proteomics-based random forest. Custom viability data can be preprocessed with CurveCurator, leading to more consistent data and metrics. DrEval supports five widely used datasets with application-aware train/test splits that enable detecting weak generalization. Models are free to use provided or custom cell line– and drug features. The pipeline supports randomization-based ablation studies and performs robust hyperparameter tuning for all models. Evaluation is conducted using meaningful, bias-resistant metrics to avoid inflated results from artifacts such as Simpson’s paradox. All results are compiled into an interactive HTML report. Created in https://BioRender.com.
June 3, 2025 at 2:58 PM
Reposted by Hendrik Raetz
hheyne.bsky.social
Check out this great talk by @franriss.bsky.social (PhD student in my lab) on "Comparing protein language models through embedding space comparison" in the famous MIA meeting. Thanks so much to Sumaiya Iqbal for co-supervising and hosting her at @broadinstitute.org
www.youtube.com/watch?v=y747...
MIA Lightning Talks (2025)
YouTube video by Broad Institute
www.youtube.com
March 20, 2025 at 10:36 AM