Biological measurements often contain systematic errors, also known as "batch effects", which may invalidate downstream analysis when not handled correctly. The problem of removing batch effects is of major importance in the biological community. Despite recent advances in this direction via deep learning techniques, most current methods may not fully preserve the true biological patterns the data contains. In this work we propose a deep learning approach for batch effect removal. The crux of

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... r approach is learning a batch-free encoding of the data, representing its intrinsic biological properties, but not batch effects. In addition, we also encode the systematic factors through a decoding mechanism and require accurate reconstruction of the data. Altogether, this allows us to fully preserve the true biological patterns represented in the data. Experimental results are reported on data obtained from two high throughput technologies, mass cytometry and single-cell RNA-seq. Beyond good performance on training data, we also observe that our system performs well on test data obtained from new patients, which was not available at training time. Our method is easy to handle, a publicly available code can be found at https://github.com/ushaham/BatchEffectRemoval2018.