An image representation based convolutional network for DNA classification
This work addresses the challenge of understanding DNA-chromatin interactions for researchers in genomics and computational biology, though it appears incremental as it applies a known neural network approach to a specific domain problem.
The authors tackled the problem of predicting chromatin structure determinants from DNA sequences by developing a convolutional neural network that uses an image representation of DNA as input, and their method outperformed existing approaches in both prediction accuracy and training time.
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary DNA sequence, though the interaction is not yet fully understood. In this paper we develop a convolutional neural network that takes an image-representation of primary DNA sequence as its input, and predicts key determinants of chromatin structure. The method is developed such that it is capable of detecting interactions between distal elements in the DNA sequence, which are known to be highly relevant. Our experiments show that the method outperforms several existing methods both in terms of prediction accuracy and training time.