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Transformer Model for Genome Sequence Analysis
Noah Hurmer · Xiao-Yin To · Martin Binder · Hüseyin Anil Gündüz · Philipp Münch · René Mreches · Alice McHardy · Bernd Bischl · Mina Rezaei
Event URL: https://openreview.net/forum?id=xwn3ywFknri »

One major challenge of applying machine learning in genomics is the scarcity of labeled data, which often requires expensive and time-consuming physical experiments under laboratory conditions to obtain. However, the advent of high throughput sequencing has made large quantities of unlabeled genome data available. This can be used to apply semi-supervised learning methods through representation learning. In this paper, we investigate the impact of a popular and well-established language model, namely \emph{BERT}, for sequence genome datasets. Specifically, we develop \emph{GenomeNet-BERT} to produce useful representations for downstream classification tasks.We compare its performance to strictly supervised training and baselines on different training set size setups. The conducted experiments show that this architecture provides an increase in performance compared to existing methods at the cost of more resource-intensive training.

Author Information

Noah Hurmer (University of Munich, Ludwig-Maximilians-Universität München)
Xiao-Yin To (Ludwig-Maximilians-Universität München)
Martin Binder (Department of Statistics)
Hüseyin Anil Gündüz (LMU Munich)
Philipp Münch (Harvard University)
René Mreches (Helmholtz Centre for Infection Research)
Alice McHardy (HZI)
Bernd Bischl (LMU)
Mina Rezaei (Ludwig-Maximilian University)

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