Test Time Transform Prediction for Open Set Histopathological Image Recognition

arXiv (Cornell University)

Abstract

Tissue typology annotation in Whole Slide histological images is a complex and tedious, yet necessary task for the development of computational pathology models. We propose to address this problem by applying Open Set Recognition techniques to the task of jointly classifying tissue that belongs to a set of annotated classes, e.g. clinically relevant tissue categories, while rejecting in test time Open Set samples, i.e. images that belong to categories not present in the training set. To this end, we introduce a new approach for Open Set histopathological image recognition based on training a model to accurately identify image categories and simultaneously predict which data augmentation transform has been applied. In test time, we measure model confidence in predicting this transform, which we expect to be lower for images in the Open Set. We carry out comprehensive experiments in the context of colorectal cancer assessment from histological images, which provide evidence on the strengths of our approach to automatically identify samples from unknown categories. Code is released at https://github.com/agaldran/t3po .

Authors 6

1. Adrián Galdrán

   The University of Adelaide · Universitat Pompeu Fabra

   Affiliation as printed

   BCN Medtech , Dept. of Information and Communication Technologies , Universitat Pompeu Fabra , Barcelona , Spain ,

   University of Adelaide , Adelaide , Australia ,

2. Katherine Jane Hewitt Aachen Department of Medicine III

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Department of Medicine III , University Hospital RWTH Aachen , Germany ,

3. Narmin L. Ghaffari Aachen Department of Medicine III

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Department of Medicine III , University Hospital RWTH Aachen , Germany ,

4. Jakob Nikolas Kather
5. Gustavo Carneiro Aachen Department of Medicine III

   RWTH Aachen University · Universitätsklinikum Aachen · The University of Adelaide

   Affiliation as printed

   Department of Medicine III , University Hospital RWTH Aachen , Germany ,

   University of Adelaide , Adelaide , Australia ,

6. Miguel Á. González Ballester

   Institució Catalana de Recerca i Estudis Avançats · Universitat Pompeu Fabra

   Affiliation as printed

   BCN Medtech , Dept. of Information and Communication Technologies , Universitat Pompeu Fabra , Barcelona , Spain ,

   Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona , Spain