Evaluation of convolutionary neural networks modeling of DNA sequences using ordinal versus one-hot encoding method

Convolutionary neural network (CNN) is a popular choice for supervised DNA motif prediction due to its excellent performances. To employ CNN, the input DNA sequences are required to be encoded as numerical values and represented as either vectors or multi-dimensional matrices. This paper evaluated a simple and more compact ordinal encoding method versus the popular one-hot encoding for DNA sequences. We compared the performances of both encoding methods using three sets of datasets enriched with DNA motifs. We found that the ordinal encoding performs comparable to the one-hot method but with significant reduction in training time. In addition, the one-hot encoding performances were rather consistent across various datasets but would require suitable CNN configuration to perform well. The ordinal encoding with matrix representation performed best in some of the evaluated datasets. This study implied that the performances of CNN for DNA motif discovery depends on the suitable design of the sequence encoding and representation. The good performances of the ordinal encoding method demonstrates that there are still rooms for improvement for the one-hot encoding method.