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jjc2718 committed Oct 21, 2024
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Expand Up @@ -8,16 +8,6 @@ Our results underscore the importance of defining clear goals in machine learnin
If the goal is to achieve robust performance across contexts or datasets, whenever possible we recommend directly evaluating generalization; otherwise, we recommend choosing the model that performs the best on unseen data via cross-validation.


<!-- Without directly evaluating model generalization, it is tempting to assume that simpler models will generalize better than more complex models.
Studies in the statistics and machine learning literature suggest this rule of thumb [@doi:10.1214/088342306000000060; @doi:10/bhfhgd; @doi:10.4137/CIN.S408; @doi:10.1371/journal.pcbi.1004961], and model selection approaches sometimes incorporate criteria to encourage simpler models that do not fit the data as closely.
These ideas have taken root in genomics, although they are less commonly stated formally or studied systematically [@doi:10.1007/s00405-021-06717-5; @doi:10.1089/dna.2020.6193; @doi:10.1186/s12859-021-04503-y].
However, we do not observe strong evidence that simpler models inherently generalize more effectively than more complex ones.
There may be other reasons to train small models or to look for the best model of a certain size/sparsity, such as biomarker interpretability or assay cost.
Our results underscore the importance of defining clear goals for each analysis.
If the goal is to achieve generalization across contexts or datasets, whenever possible we recommend directly evaluating generalization.
When it is not feasible, we recommend choosing the model that performs the best on unseen data via cross-validation or a holdout dataset. -->


## Highlights

* Systematic evaluation of generalization of cancer transcriptomics predictive models
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