Using Artificial Neural Networks to Model Errors in Biochemical Manipulation of DNA Molecules

In recent years, the non-biological applications of DNA molecules have made considerable progress; most of these applications were performed in vitro, involving biochemical operations such as synthesis, amplification and sequencing. Because errors may occur with specific sequence patterns or experimental instruments, these biochemical operations are not completely reliable. Modeling errors in these biochemical procedures is an interesting research topic. For example, researchers have proposed several methods to avoid the known vulnerable sequence patterns in the study of storing binary information in DNA molecules. However, there are few end-to-end methods to evaluate these biochemical errors with regard to the DNA sequences. In this article, based on the data generated by a DNA storage research, we use artificial neural networks to predict whether a DNA sequence tends to cause errors in biochemical operations. Through comparative experiments and hyperparameter optimization, we analyze the known and potential problems in the research process. As a result, an end-to-end method to model the biochemical errors of DNA molecules in vitro through a computer system is proposed.