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Heterogeneous Domain Adaptation for IHC Classification of Breast Cancer Subtypes

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Abstract

Increasingly, multiple parallel omics datasets are collected from biological samples. Integrating these datasets for classification is an open area of research. Additionally, whilst multiple datasets may be available for the training samples, future samples may only be measured by a single technology requiring methods which do not rely on the presence of all datasets for sample prediction. This enables us to directly compare the protein and the gene profiles. New samples with just one set of measurements (e.g. just protein) can then be mapped to this latent common space where classification is performed. Using this approach, we achieved an improvement of up to 12% in accuracy when classifying samples based on their protein measurements compared with baseline methods which were trained on the protein data alone. We illustrate that the additional inclusion of the gene expression or protein expression in the training process enabled the separation between the classes to become clearer.

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Details

Original languageEnglish
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
DOIs
Publication statusE-pub ahead of print - 24 Oct 2018