Removal of Batch Effects using Generative Adversarial Networks

Abstract: Many biological data analysis processes like Cytometry or Next Generation Sequencing (NGS) produce massive amounts of data which needs to be processed in batches for down-stream analysis. Such datasets are prone to technical variations due to difference in handling the batches possibly at different times, by different experimenters or under other different conditions. This adds variation to the batches coming from the same source sample. These variations are known as Batch Effects. It is possible that these variations and natural variations due to biology confound but such situations can be avoided by performing experiments in a carefully planned manner. Batch effects can hamper downstream analysis and may also cause results to be inconclusive. Thus, it is essential to correct for these effects. This can be solved using a novel Generative Adversarial Networks (GANs) based framework that is proposed here, advantage of using this framework over other prior approaches is that here it is not required to choose a reproducing kernel and define its parameters. Results of the framework on a mass cytometry dataset are reported.