Generalization of vision pre-trained models for histopathology

Milad Sikaroudi, Maryam Hosseini, Ricardo Gonzalez, Shahryar Rahnamayan, H. R. Tizhoosh

Research output: Contribution to journalArticlepeer-review


Out-of-distribution (OOD) generalization, especially for medical setups, is a key challenge in modern machine learning which has only recently received much attention. We investigate how different convolutional pre-trained models perform on OOD test data—that is data from domains that have not been seen during training—on histopathology repositories attributed to different trial sites. Different trial site repositories, pre-trained models, and image transformations are examined as specific aspects of pre-trained models. A comparison is also performed among models trained entirely from scratch (i.e., without pre-training) and models already pre-trained. The OOD performance of pre-trained models on natural images, i.e., (1) vanilla pre-trained ImageNet, (2) semi-supervised learning (SSL), and (3) semi-weakly-supervised learning (SWSL) models pre-trained on IG-1B-Targeted are examined in this study. In addition, the performance of a histopathology model (i.e., KimiaNet) trained on the most comprehensive histopathology dataset, i.e., TCGA, has also been studied. Although the performance of SSL and SWSL pre-trained models are conducive to better OOD performance in comparison to the vanilla ImageNet pre-trained model, the histopathology pre-trained model is still the best in overall. In terms of top-1 accuracy, we demonstrate that diversifying the images in the training using reasonable image transformations is effective to avoid learning shortcuts when the distribution shift is significant. In addition, XAI techniques—which aim to achieve high-quality human-understandable explanations of AI decisions—are leveraged for further investigations.

Original languageEnglish (US)
Article number6065
JournalScientific reports
Issue number1
StatePublished - Dec 2023

ASJC Scopus subject areas

  • General


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