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.

Additional Metadata
Keywords DNA sequences, Hilbert curves, Convolutional neural networks, Chromatin structure
Project Deep Spiking Vision: Better, Faster, Cheaper
Conference International Conference on Learning Representations (ICLR)
Citation
Yin, B, Balvert, M, Zambrano, D, Schönhuth, A, & Bohte, S.M. (2018). An image representation based convolutional network for DNA classification. In 6th International Conference on Learning Representations.