Not again! Data Leakage in Digital Pathology

Nicole Bussola, Alessia Marcolini, Valerio Maggio, Giuseppe Jurman, Cesare Furlanello

Research output: Contribution to journalArticle (Academic Journal)

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Bioinformatics of high throughput omics data (e.g. microarrays and proteomics) has been plagued by uncountable issues with reproducibility at the start of the century. Concerns have motivated international initiatives such as the FDA's led MAQC Consortium, addressing reproducibility of predictive biomarkers by means of appropriate Data Analysis Plans (DAPs). For instance, repreated cross-validation is a standard procedure meant at mitigating the risk that information from held-out validation data may be used during model selection. We prove here that, many years later, Data Leakage can still be a non-negligible overfitting source in deep learning models for digital pathology. In particular, we evaluate the impact of (i) the presence of multiple images for each subject in histology collections; (ii) the systematic adoption of training over collection of subregions (i.e. "tiles" or "patches") extracted for the same subject. We verify that accuracy scores may be inflated up to 41%, even if a well-designed 10x5 iterated cross-validation DAP is applied, unless all images from the same subject are kept together either in the internal training or validation splits. Results are replicated for 4 classification tasks in digital pathology on 3 datasets, for a total of 373 subjects, and 543 total slides (around 27, 000 tiles). Impact of applying transfer learning strategies with models pre-trained on general-purpose or digital pathology datasets is also discussed.
Original languageEnglish
Publication statusPublished - 14 Sep 2019


  • q-bio.QM
  • eess.IV


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