Automatic Labels are as Effective as Manual Labels in Biomedical Images Classification with Deep Learning

Niccolò Marini; Stefano Marchesin; Lluis Borras Ferris; Simon Püttmann; Marek Wodzinski; Riccardo Fratti; Damian Podareanu; Alessandro Caputo; Svetla Boytcheva; Simona Vatrano; Filippo Fraggetta; Iris Nagtegaal; Gianmaria Silvello; Manfredo Atzori; Henning Müller

arXiv · 2406.14351

Automatic Labels are as Effective as Manual Labels in Biomedical Images Classification with Deep Learning

Niccolò Marini·Stefano Marchesin·Lluis Borras Ferris·Simon Püttmann·Marek Wodzinski·Riccardo Fratti·Damian Podareanu·Alessandro Caputo·Svetla Boytcheva·Simona Vatrano·Filippo Fraggetta·Iris Nagtegaal·Gianmaria Silvello·Manfredo Atzori·Henning Müller

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Abstract

The increasing availability of biomedical data is helping to design more robust deep learning (DL) algorithms to analyze biomedical samples. Currently, one of the main limitations to train DL algorithms to perform a specific task is the need for medical experts to label data. Automatic methods to label data exist, however automatic labels can be noisy and it is not completely clear when automatic labels can be adopted to train DL models. This paper aims to investigate under which circumstances automatic labels can be adopted to train a DL model on the classification of Whole Slide Images (WSI). The analysis involves multiple architectures, such as Convolutional Neural Networks (CNN) and Vision Transformer (ViT), and over 10000 WSIs, collected from three use cases: celiac disease, lung cancer and colon cancer, which one including respectively binary, multiclass and multilabel data. The results allow identifying 10% as the percentage of noisy labels that lead to train competitive models for the classification of WSIs. Therefore, an algorithm generating automatic labels needs to fit this criterion to be adopted. The application of the Semantic Knowledge Extractor Tool (SKET) algorithm to generate automatic labels leads to performance comparable to the one obtained with manual labels, since it generates a percentage of noisy labels between 2-5%. Automatic labels are as effective as manual ones, reaching solid performance comparable to the one obtained training models with manual labels.

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Niccolò Marini, Stefano Marchesin, Lluis Borras Ferris, Simon Püttmann, Marek Wodzinski, Riccardo Fratti, Damian Podareanu, Alessandro Caputo, Svetla Boytcheva, Simona Vatrano, Filippo Fraggetta, Iris Nagtegaal, Gianmaria Silvello, Manfredo Atzori, Henning Müller. 2024-06-20. Automatic Labels are as Effective as Manual Labels in Biomedical Images Classification with Deep Learning. https://arxiv.org/abs/2406.14351

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