Semi-Supervised Approach for EGFR Mutation Prediction on CT Images

Cláudia Pinheiro, Francisco Silva, Tania Pereira () and Hélder P. Oliveira
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Cláudia Pinheiro: INESC TEC—Institute for Systems and Computer Engineering, Technology and Science, 4200-465 Porto, Portugal
Francisco Silva: INESC TEC—Institute for Systems and Computer Engineering, Technology and Science, 4200-465 Porto, Portugal
Tania Pereira: INESC TEC—Institute for Systems and Computer Engineering, Technology and Science, 4200-465 Porto, Portugal
Hélder P. Oliveira: INESC TEC—Institute for Systems and Computer Engineering, Technology and Science, 4200-465 Porto, Portugal

Mathematics, 2022, vol. 10, issue 22, 1-18

Abstract: The use of deep learning methods in medical imaging has been able to deliver promising results; however, the success of such models highly relies on large, properly annotated datasets. The annotation of medical images is a laborious, expensive, and time-consuming process. This difficulty is increased for the mutations status label since these require additional exams (usually biopsies) to be obtained. On the other hand, raw images, without annotations, are extensively collected as part of the clinical routine. This work investigated methods that could mitigate the labelled data scarcity problem by using both labelled and unlabelled data to improve the efficiency of predictive models. A semi-supervised learning (SSL) approach was developed to predict epidermal growth factor receptor ( EGFR ) mutation status in lung cancer in a less invasive manner using 3D CT scans.The proposed approach consists of combining a variational autoencoder (VAE) and exploiting the power of adversarial training, intending that the features extracted from unlabelled data to discriminate images can help in the classification task. To incorporate labelled and unlabelled images, adversarial training was used, extending a traditional variational autoencoder. With the developed method, a mean AUC of 0.701 was achieved with the best-performing model, with only 14 % of the training data being labelled. This SSL approach improved the discrimination ability by nearly 7 percentage points over a fully supervised model developed with the same amount of labelled data, confirming the advantage of using such methods when few annotated examples are available.

Keywords: semi-supervised learning; adversarial training; generative adversarial networks; medical image analysis; genotype prediction (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2022
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